Ever since the 1953 discovery of DNA's double helix structure researchers wondered how the double strands are separated so that genetic information stored inside the helix can be delivered from generation to generation. A class of proteins known to achieve this separation are DNA helicases (see Sept 2006 highlight), molecular motors that operate at a fork where a double stranded DNA separates into two single stranded DNAs. Helicases translocate along one of the single stranded DNAs, pushing forcefully into the fork to split the double stranded DNA apart further. Helicases seem to work, though, both through force and through persuasion, exposing to the double stranded DNA a surface that is apparently conducive for strand separation. This property suggests itself on account of the fact that many of the amino acid side groups at the relevant surface are highly conserved among species or evolved from species to species through pairwise mutation. But what chemical strategy evolution had in mind in molding the surface was not realized. Recently, however, researchers seeking artificial means of splitting double stranded DNA apart might have found a key clue. They pulled double stranded DNA at one of its single strands by means of an atomic force microscope from DNA's native salt water environment into a so-called non-polar solvent. The force - distance curve measured suggested that the DNA actually split apart, but there existed no direct experimental means of viewing the splitting. The researchers employed instead molecular dynamics simulations, using NAMD, that indeed clearly revealed the splitting of the DNA strands at a water - oil (octane) interface as reported in a recent publication. The study suggests how helicases achieve the splitting of DNA strands, namely by altering the local environment of DNA from water-like (hydrophilic) to oil-like (hydrophobic). More information here.

Globins are oxygen-storing proteins, vital to life. In our blood, hemoglobins carry oxygen from our lungs to every cell in our body. In our muscles, myoglobins keep reserves of oxygen to make sure it is available when needed. In some plants, leghemoglobins capture oxygen molecules that would otherwise be harmful to the production of ammonium necessary for the plant's survival. All these globins possess an iron-containig "heme", that grabs on to oxygen for a short time, and share the same protein architecture, despite large variations in their sequences. Since the heme group is buried inside a globin, scientists wondered how oxygen makes its way inside the protein to reach it. Exploring the motion and energetics of globins using the program NAMD researchers learned to gather data that permitted them to visualize, utilizing the VMD software, all the pathways taken by oxygen migrating inside whale myoglobin (see the Aug 2006 highlight and related publication). However, when the researchers turned their attention to the rest of the globin family to compute their oxygen pathways, they found, on their computational spelunking trip, something surprising. Given the conserved architecture of all globins, they expected to see similar oxygen pathways throughout the globin family, but they saw the opposite! Aside from a conserved pocket right at the heme binding site, the distribution of oxygen pathways showed very little similarity from one globin to the next. This result is described in a recent report, which shows that oxygen-pathways are not conserved by evolution, and that their location is not determined by a protein's overall architecture, but rather by its local amino acids. The researchers also learned which amino acids are found more often than others lining oxygen pathways, recognizing that bulky side groups are not hindering, but favoring oxygen passage. More information can be found here.

Modern computers include a massively parallel graphics processing unit (GPU) designed to perform geometry and lighting calculations at blistering speeds. State of the art GPUs can perform 0.5 teraFLOPS with their hundred cores. The tremendous computational power of GPUs was untapped by scientific computations because it could only be accessed with difficulty until now. As reported in the Journal of Computational Chemistry, recent advances allowing GPUs to be used for general purpose computing have boosted the performance of a number of molecular modeling applications, including NAMD simulations and VMD electrostatic potential calculations. The accelerated versions of these applications run five to one hundred times faster than on the best CPU-based hardware, allowing a single desktop computer equipped with a GPU to provide processing power equivalent to an entire, large computing cluster. More information on GPU acceleration of molecular modeling applications is provided here.

Everyone knows oil and water don't mix. Proteins observe this rule, too, some choosing to stay in the watery cytoplasm and others choosing the oily membrane. But getting into the membrane is not easy, and most newly formed proteins require another protein, the membrane-bound translocon, to help them insert into the membrane. The translocon, surprisingly also serves as a conduit for proteins across the membrane, thus carrying out a unique dual function. The structure of the translocon showed evidence of a likely "lateral gate", i.e., an exit from the channel into the membrane. How the channel opened to the membrane though, and how it closed afterwards, were not clear from the structure alone. Now, molecular dynamics simulations performed with NAMD, covered in a recent publication, have permitted researchers to understand how the channel opens laterally, how it closes, and how the oily lipids are prevented from invading the water-filled pore. Furthermore, the novel simulation technique, residue-based coarse graining, allowed the researchers to simulate the lipid-channel interactions for up to one microsecond, clearly illustrating that the lipids do not want to mix with the channel interior. More information on these results can be found on the Protein Translocation website.

Muscle fibers, in contracting and extending, generate tremendous force that needs to be buffered to protect muscle from damage. This role falls to the protein titin, with about 27,000 amino acids the longest protein in human cells. Titin functions as a molecular rubber band, but unlike uniform rubber bands, titin is made from over 300 different protein domains strung into a chain. While experiments have found that the individual domains of titin feature remarkable resilience against mechanical stretching, little is known about the elasticity of the overall titin chain. Crystallographers teamed up with computational biologists to investigate this elasticity, focusing on two adjacent titin domains. Molecular dynamics simulations using NAMD suggest, as reported recently, that the overall elasticity of the titin chain stems in part from a zigzag, i.e., accordion-like, motion: as titin is contracted and extended, energy is stored and released in the angular tilt of adjacent domains. More on this investigation can be found here.

The cells of higher organisms store their genetic material, the genome, in the so-called nucleus where they organize transcription of DNA into messenger-RNA, the blueprint for proteins. The messenger-RNA leaves the cell to be decoded by ribosomes that synthesize the respective proteins. Transcription factors, also proteins, control in the nucleus which parts of the cells' genomes are transcribed. Naturally, the access to the nucleus as well as exit from it must be restricted to transcription factors and related biomolecules. This is achieved by the nuclear pores, wide channels lined with brushes of polymers. The polymers are disordered proteins and prevent passage for most cellular proteins, except for so-called transport factors which bus transcription factors, messenger RNA, and certain larger biomolecule into and out of the nucleus. How transport factors are permitted to pass the nuclear pores, despite many studies, has been largely unknown. Molecular dynamics simulations, based on relevant crystallographic structures, using NAMD provided a comprehensive picture on the passage mechanism as reported recently. The simulations, analyzed with VMD, revealed that transport factors are dotted rather regularly on their surface with spots that bind to the brushes of nuclear pore proteins. While any protein may accidentally exhibit such a binding spot or two, only transport factors offer a regular pattern of such spots on their surface that apparently is their passport permitting them movement into and out of the nucleus, i.e., helping them to glide through the pores' protein brushes. More on simulations of transport factors can be found here.

Because oxygen gas is very reactive, it is frequently employed by the cell as a reagent by proteins called enzymes, which build the organic compounds that the cell needs. One such enzyme belongs to the copper amine oxidase family. These proteins transform amine-containing compounds into molecules needed by the cell, by reacting the compounds with oxygen. Researchers have long been interested in finding out how the various reagents reach the buried copper active site before the final oxidation reaction can occur. While copper amine oxidases exhibit an obvious channel for capturing the amine compounds to be modified, it had been unclear until now how oxygen molecules make their way through the enzyme. With the help of computer simulations using NAMD, researchers have identified in a recent publication, the routes taken by oxygen inside various copper amine oxidases from different species. In order to accomplish this, they analyzed simulations of the motions of four copper amine oxidases, using the VMD analysis and visualization software, which can predict the probability of finding oxygen molecules anywhere inside the simulated proteins. This analysis found numerous oxygen conduction routes inside each copper amine oxidase, i.e., oxygen can enter the protein through many routes, as it would in a sponge. More information on finding O2 migration pathways in proteins can be found here.

Like all organisms, bacteria have to eat. However, bringing nutrients in from the outside world is not an easy task for many bacteria that are surrounded by an extra membrane. The second membrane, called the outer membrane, offers additional protection but at a cost: no energy can be generated or stored at the outer fringes of the cell. So, to import large, rare nutrients that cannot cross by diffusion alone, bacteria have evolved a unique transport system which couples the inner, energy-generating membrane to the passive outer membrane, known as the TonB-dependent transport system. TonB, an inner membrane-associated protein, transfers energy across the periplasm to a variety of outer-membrane transporters. These transporters have a large, beta-barrel structure which is blocked in the middle by a plug called the 'luminal domain'. How TonB transfers energy to the transporter and causes the luminal domain to come out is still a mystery though. Now with the help of computer simulations using NAMD and a recent crystal structure of TonB coupled to BtuB, the transporter responsible for vitamin B12 transport, researchers have shown that TonB can mechanically activate the transporter by pulling on the luminal domain, causing it to leave the barrel. Using steered molecular dynamics, it was found that TonB stayed firmly attached to the luminal domain of BtuB, even though the contact between the two is limited to just a handful of residues. Furthermore, this pulling initiated unfolding of the luminal domain, opening a transport pathway for the substrate. These results, the subject of a recent publication and also highlighted in Science, demonstrate how a mechanical coupling can bridge the gap between the two membranes, thus enabling outer membrane transport.

We all know sushi rolls, but just to be sure here is an easy definition: a wrapper encircles rice which holds a precious bit of fish. To make a sushi role is an art and the same holds true for molecular sushi that is made of two lipoproteins as wrapper, lipids as rice, and membrane proteins as filling. Sushi rolls are for eating. Molecular sushi roles are for holding membrane proteins in place for physical analysis; they actually come only in sliced form, one disc at a time. Due to their size, the discs are called nanodiscs. Since membrane proteins are notoriously difficult to study experimentally due to their need to be in a "native" membrane environment, nanodiscs are a great tool, furnishing a membrane environment that has been used to embed a variety of membrane proteins for biochemical assay, including cytochrome P450's, rhodopsin, bacterial chemoreceptors, blood clotting factors, and translocation proteins. Unfortunately, it is difficult to make either real or molecular sushi rolls (nanodiscs). In either case one needs to lay down the ingredients first. In the case of nanodiscs, one starts from the raw ingredients which are solubilized by the detergent cholate. Removing the detergent allows the nanodiscs to self-assemble. However, the assembly process is difficult to quantify experimentally, thus researchers rather studied the disassembly process, i.e., how detergent disassembles preformed nanodiscs. One can watch a sushi chef make rolls, but watching the disassembly and assembly of nanodiscs is harder due the the small size. Fortunately, a computer can image the process. In a recent publication, nanodisc disassembly through the addition of increasing concentrations of cholate was monitored through computer simulations using NAMD and verified through experimental small-angle X-ray scattering. The study showed how cholate molecules insert themselves at the interface between the lipids and lipoproteins towards complete disassembly. The simulations employed a new method called residue-based coarse-graining. For more information, see our webpage on nanodiscs.

Mechanical forces are everywhere in human life. Strong forces power machines and cars, our body's forces let us labor and move, soft forces are sensed through touch, even softer ones through hearing. Forces are also ubiquitous in the living cell, driving its molecular machines and motors as well as signaling ongoing action in its surroundings. Man made, force bearing machines rely on extremely strong materials not found in the cell. How can the cell bear substantial forces? Also, how do cells sense extremely weak forces as in hearing, surpassing most microphones? Single molecule measurements, reviewed in a recent issue of Science, begin to answer these questions offering information on biomolecules' mechanical responses and action. However, the information offered by these measurements is not enough to relate the biomolecular function to the biomolecular architecture. Biomolecules in cells can move in amazing ways, but we did not know why. As one contribution in the Science issue demonstrates, computational modeling comes to the rescue. It can simulate the measurements and, in doing so, can reveal the physical mechanisms underlying cellular mechanics at the atomic level. In as far as observed data are available, the simulations show impressive agreement with actual measurements. While initially only following experiments or, at best, guiding experiments, modeling has advanced now further and through simulated measurements discovered on its own entirely novel mechanical properties that were later verified by experimental measurements. Experimentalists reacted to the new competition and began to do simulations themselves. More here.

PSC News Release: University of Utah chemist Gregory Voth and grad student Phil Blood are using PSC’s Cray XT3 to tackle a basic question of endocytosis—the life-sustaining process by which cells absorb material from outside the cell by bending their membrane to form a “vesicle” and engulf it. All animal cells depend on endocytosis, which involves various steps, but begins with curvature of the membrane.

BAR domains are a family of banana-shaped proteins shown to bind to cellular membrane as it curves. Experiments suggest that BAR domains mold their concave surface to a section of membrane and induce a corresponding curvature. Voth and Blood undertook molecular dynamics simulations to look more closely. With the XT3 they’ve been able to run efficiently, using software called NAMD, with as many as 1,024 processors. “The XT3 has been amazing,” says Blood. “We haven’t found a hard limit on scaling up the number of processors.”

They used TeraGrid systems at SDSC, NCSA and University of Chicago/Argonne to construct a model and to explore how long a stretch of membrane they needed for curvature to occur. Their final simulations used the XT3 to include the protein with a 50-nanometer length of membrane—probably the longest patch of membrane ever simulated—for a total of 738,000 atoms. Their results, reported in Proceedings of the National Academy of Sciences (2006), show that the orientation of the BAR domain as it attaches to the membrane determines the degree of curvature.

SDSC News Release: SDSC and UC San Diego researchers are using NAMD to zero in on the causes of Parkinson's disease, Alzheimer's disease, rheumatoid arthritis and other diseases. The April 2007 FEBS Journal cover story offers—for the first time—a model for the complex process of aggregation of a protein known as alpha-synuclein, which in turn leads to harmful ring-like or pore-like structures in human membranes, the kind of damage found in Parkinson's and Alzheimer's patients. The researchers also found that the destructive properties of alpha-synuclein can be blocked by beta-synuclein—a finding that could lead to treatments for many debilitating diseases.

Lead author Igor Tsigelny, SDSC researcher and project scientist in chemistry and biochemistry at UCSD, said that the team's research helped confirm what researchers had suspected. “The present study—using molecular modeling and molecular dynamics simulations in combination with biochemical and ultrastructural analysis—shows that alpha-synuclein can lead to the formation of pore-like structures on membranes.” In contrast, he said, “beta-synuclein appears to block the propagation of alpha-synucleins into harmful structures.”

“This is one of the first studies to use supercomputers to model how alpha-synuclein complexes damage the cells, and how that could be blocked,” said Eliezer Masliah, professor of neurosciences and pathology at UC San Diego. “We believe that these ring- or pore-like structures might be deleterious to the cells, and we have a unique opportunity to better understand how alpha-synuclein is involved in the pathogenesis of Parkinson's disease, and how to reverse this process.”

Every morning, many people drive to work, while others may bike, take the bus or the metro. Similarly, various biomolecules in the human body also reach their destinations in diverse manners. For example, to cross the cellular membrane, small hydrophobic gas molecules diffuse through the lipid bilayer, while water molecules pass through specialized channel proteins named aquaporins (AQPs). Interestingly, just like one may get to work both by bus and by driving, it has been found recently that some gas molecules may have more than one way to cross the membrane, i.e., besides diffusion through lipids, oxygen and carbon dioxide may also pass through AQPs. However, the pathways that these gas molecules take remained elusive. Using molecular dynamics performed with NAMD, researchers have investigated the gas permeability of AQP1 in a recent study with two complementary methods (explicit gas diffusion simulation and implicit ligand sampling). The simulation results suggest that while the four monomeric pores of AQP1 function as water channels, the central pore of AQP1 may serve as a pathway for gas molecules to cross the membrane. More information on the simulations can be found on the aquaporin web page.

High-density lipoproteins, otherwise known as the "good cholesterol", are the body's way of naturally removing cholesterol in the blood stream. Since lipid and cholesterol molecules are not soluble in blood, lipoproteins are needed to collect and transport them. The proteins wrap themselves around the hydrophobic portions of lipids and cholesterol, effectively shielding them from the aqueous environment and allowing them to be transported through the bloodstream to the liver for degradation. High-density lipoproteins exhibit a variety of shapes and sizes and presently cannot be imaged through experimental observations. Computational methods, however, can provide detailed images of high-density lipoprotein particles, even showing how these particles form in the body. As recently reported (article 1, article 2), so-called coarse-grained molecular dynamics simulations using NAMD discovered how lipid molecules are corralled by lipoproteins to form disc-like high-density lipoprotein particles. The simulations show in remarkable detail the aggregation of proteins and lipids, starting from a random arrangement of lipids that are mopped-up by two lipoproteins, eventually forcing the lipids into a disc-shape surrounded on its circumference by belt-like lipoproteins. For more information, see our webpages on HDL & nanodiscs and coarse-grained modeling.

Bacteria employ membrane proteins as crucial safety valves that release water and small solutes under challenging osmotic conditions (see the May 2006 highlight, "Electrical Safety Valve" and the Nov 2004 highlight, "Japanese Lantern Protein"). There are valves for balancing small pressure differences between the inside and outside of bacterial cells, that open and close readily, but there are also ones for protection against large pressure differences as a safety measure of last resort. The valves for balancing small pressure differences, like the one shown in the figure, include a filter that presumably keeps the most valuable molecules inside the cell interior, though this is not understood yet in detail. To reveal the function of such channels a combination of X-ray crystallography, physiological measurements, and molecular dynamics simulations using NAMD has been employed. Crystallography, in a prior study, captured the channel in a half-way open state. Now a team of physiologists and modelers reported the details on valve opening and closing. The experiments, using a pipette small enough to measure currents from a single channel, MscS, along with the simulations revealed that the channel conducts both positive and negative ions when subjected to tension and voltage. The unprecedented comparison of experimental and computational results open a new era of quantitative cell biology that borrows successful research strategies from physics (more on our MscS website).

The nucleus is responsible for storing the genome of eukaryotic cells, isolating it from the cellular cytoplasm. Partitioning the genetic material is very important in protecting it from cellular processes or foreign molecules. However, the nucleus also needs to provide access for the rest of the cell to the information stored in the genome. Numerous nuclear pores in the nuclear envelope offer communication pathways between the nucleoplasm and cytoplasm. The pathways are restricted to so-called transport receptors, proteins that taxi molecules into and out of the nucleus. If a molecule wishes to enter or leave the nucleus, it associates with a transport receptor. The complex passes through the pore and then dissociates. The question is why transport receptors can pass the nuclear pores while other proteins cannot. The answer lies in the role of FG-repeat proteins lining the pores and filling much of their free volume. These proteins are disordered peptides, consisting of repeating phenylalanine-glycine (FG) residues separated by a sequence of hydrophilic linker residues. Only proteins that interact favorably with the FG-repeat regions can pass through, while other proteins are excluded. A recent report used molecular dynamics via NAMD to examine the way in which the transport factor NTF2 interacts with the FG-repeats. The study described binding spots for FG-repeat peptides on the surface of NTF2, confirming known binding spots discovered previously via experimental means, and suggesting the existence of further binding spots. The new binding spots may play a role in steering NTF2, upon import or export, along a particular path through the nuclear pore. See also a previous highlight from January 2006, "Gateway to the Nucleus", as well as our webpage on the nuclear pore complex.

The bacterial flagellum is a large biomolecular assembly used by many types of bacteria as a helical propeller for forward swimming and turning. The flagellum is remarkable in that its properties differ greatly depending on the direction in which it is rotated, allowing the bacterium to switch between swimming straight ("running") and turning ("tumbling"). The mechanics of the flagellum are of interest both to biologists and mechanical engineers. The molecular mechanisms of the transition in the flagellum between running and tumbling modes is unknown. Because of the flagellum's size (several micrometers in length) and composition (made up of 30,000 protein subunits) it presents a challenge to computational modeling. Researchers have now achieved an advance describing the flagellum in both its running and tumbling state. For this purpose, the researchers developed a computational model of the system that glosses over atomic level detail, but resolves the shapes of all proteins making up a bacterial flagellum, simulating a simplified version of the system using the program NAMD. The results, reported recently, showed that the flagellum's transition between swimming straight and tumbling is triggered by friction due to the water around the bacterium. More information on the flagellum project can be found here.

Viruses are the cause of many human diseases, from the common cold to AIDS, and medicine is continuously searching for better ways to battle viruses through vaccination or medication. Detailed knowledge of the life cycles of viruses should be useful in the treatment of viral diseases. A key focus of investigations is the virus capsid, a protein coat that protects the viral genome, but also triggers release of the genome and other viral factors upon contact with the body's cells. X-ray crystallography has resolved the average structures of many types of virus capsids, providing the basis for detailed investigations, for example by means of molecular dynamics methods, of capsid dynamical properties, e.g., in assembly and disassembly. Unfortunately, due to their large size most virus capsids are beyond the reach of molecular dynamics simulations, with one notable exception (see the March 2006 highlight "Simulating an Entire Life Form"). This earlier simulation allowed researchers to develop and test a method for coarse-grained molecular dynamics simulations that glosses over atomic detail and, thereby, permits microsecond descriptions of entire viral particles. As reported recently (see also journal cover) such simulations, employing the program NAMD, were applied to the empty capsids of several viruses. These simulations revealed a variety of behaviors, from rapid collapse to high stability, depending on the strength of interactions between the proteins from which capsids are built. The new method offers unprecedented views of capsid dynamics that may assist in battling viral diseases. More information on the simulations can be found on our virus web page.

Bionanotechnology involves a marriage of two different materials: inorganic solids, like silica, and biomolecules, like DNA. The new combinations of materials have to be mastered on the laboratory bench as well as in computer simulations. On the bench, devices are manufactured and tested, in the simulations, they are imaged and designed. So far inorganic solids and biomolecules were simulated successfully, but only separately. To join the materials requires as much effort in simulations as on the bench. Even just the interaction of inorganic solids (like silica) with physiological solutions (water and ions) demands challenging descriptions of silica surface properties. As reported recently, researchers have now succeeded in describing accurately the wetting (by water) of amorphous silica, an essential material for nanoelectronics, clearing a major hurdle to simulating bionanotechnological devices, for example, those suggested for rapid and economical sequencing of DNA (see also Nov 2005 and Oct 2004 highlights). More on silica-water interaction here.

Escherichia coli are bacteria living in the intestines of mammals as part of their healthy gut flora, but also causing disease outside of the gut. The bacteria import from their environment nutriments, for example molecules of lactose, a sugar. For this purpose Escherichia coli employs in its cell membrane a protein channel, lactose permease, that translocates the sugar outside-in. This is the bacterium's "sweet tooth". To establish the unidirectional sugar transport, the bacterium utilizes an electrical potential maintained in the form of a trans-membrane proton gradient (more protons on the outer cellular than on the inner cellular side of the membrane). Protons, very small ions, that enter the channel from the outside one at a time, open the outer channel entrance. This permits access of lactose that gets bound inside the channel. Release of the proton to the cell interior closes the outer channel entrance and opens the inner channel entrance, such that the bound lactose can enter the cell. Despite extensive and elegant biochemical studies, the physical mechanism that couples unidirectional proton and sugar translocation is not yet known in detail. A crystallographic structure of lactose permease permitted now investigations into this mechanism by means of molecular dynamics simulations using NAMD. The simulations, reported in a recent publication, showed one step of the proton - sugar translocation, namely how binding and unbinding of the proton activates a spring-like bond, a so-called salt bridge, that closes and opens the inner channel exit. More information on the lactose permease project can be found here.

Mammalian cells adhere to each other forming tissues. The adhesion is due to a network of proteins, so-called extracellular matrix proteins, "gluing" the cells together. The cell membranes are too soft to provide anchoring points for the extracellular matrix proteins; rather, the cells furnish on their outer surface specialized hooks for anchoring the extracellular matrix proteins. The hooks, in the form of surface proteins, are linked directly through the membranes to the intracellular cytoskeleton that stabilizes and shapes cells. Integrins are an important family of such surface proteins that form hooks specific for certain types of extracellular matrix proteins. The hooks are flexible, they can be open for contacts or closed, the switch being induced by signals from inside or outside the cell through interactions with other proteins. The interactions between integrins and extracellular matrix proteins are rather complex, as the proteins are composed of many subunits; fortunately, their overall structures are presently being solved through crystallography. In a recent report a major component of an integrin and an extracellular matrix protein have been investigated through molecular modeling using NAMD, including steered molecular dynamics. The study described in detail how the extracellular matrix protein induces a transition in integrin, potentially strengthening its adhesion property. See also previous highlights: the May 2006 "Killer's Entry Route", Dec 2004 "Snap Fastener on Biological Cells", Dec 2003 "Body's Glue", and Mar 2002 "Cells Sense Push and Pull". More on modeling of extracellular matrix proteins and integrins can be found here.

Most forms of life need to detect and respond to changes in their environment for survival and optimal growth. For this purpose organisms rely on receptors that are based on sensory proteins. In plants, several sensory proteins detect the ambient light for optimal exposure of their photosynthetic apparatus. One class of plant light sensors, the phototropins, influence photosynthesis and induce the transition between root and stem growth when seedlings emerge out of the ground. Induction is activated through several protein domains, two of which actually absorb light and for their sensitivity to light, oxygen, and voltage, are called LOV1 and LOV2 domains. Understanding the LOV domains' involvement in activation is important for studying the signaling mechanisms of other types of sensory proteins. Strangely, light absorbed by LOV domains is observed to lead to a distinct, but only very minute, structural change that does not explain how activation might come about. NAMD-based molecular dynamics simulations of the LOV domain have now revealed, as reported in a recent publication, that photoactivated LOV domains exhibit altered patterns of motion that can induce a signal for plant cells. More information may be found on our biological photoreceptors website.

Sometimes analogies go a long way, surprisingly long.  Aquaporins are ubiquitous water channels in living cells, known to be tetrameric, each unit contributing one pore.  This much is certain and this is where an analogy begins, namely with a British spy ring that passed information to the Soviet Union during world war II and into the 1950s.  The ring is often referred to as the Cambridge Four since the spies, when recruited, were undergrads at Cambridge Trinity College and there were four of them (cryptonyms Stanley, Homer, Hicks, and Johnson).  But a Fifth Man was long suspected, yet never formally identified. Here the analogy continues: aquaporin was suspected to sport a fifth pore, supposedly at its center, where its four subunits join (hence known as the tetrameric pore).  Strong, but not yet completely conclusive,  evidence has now been put forward in a recent report that the central pore, actually quite plainly visible to the eye when aquaporins are inspected by molecular graphics, e.g., with VMD, is an ion channel gated by a common cellular signaling molecule, cGMP. The evidence stems from a combined computational (molecular dynamics using NAMD) and experimental (verifying computationally suggested mutants) study.  More information on the five pores can be found on our aquaporin website, more on the Cambridge Five here. But the analogy goes further. Today it is suspected that the Cambridge Five actually had more than five members and the same holds for the pores of aquaporin.  An ongoing investigation has lead to evidence that the further pore members conduct gases, for example carbon dioxide.  Hopefully, we will know one day with certainty all members of the Cambridge Five and all pores of aquaporin.

The computer processor is the workhorse of biomolecular modeling, with NAMD the plow to which a single processor or a team of thousands may be hitched. The recent release of NAMD 2.6 has extended the drawbar to harness the power of several thousand processors: 2000 on a Cray XT3 and 8,000 on an IBM Blue Gene/L. This permits the efficient simulation of an entire ribosome, the cell's protein factory, comprising 3,000,000 atoms when solvated. But the features and increased performance of NAMD 2.6 are also available to the scientist with only a laptop, on which a domain of the muscle protein titin (10,000 atoms solvated) can be readily simulated. NAMD has also become more versatile, supporting more force fields (OPLS, CHARMM with CMAP cross terms), calculating free energies, and executing customizable replica exchange simulations. In addition, NAMD can now be called from the structure analysis program VMD to calculate, for example, interaction energies between protein domains. Like increased horsepower in transportation, increased simulation power opens new routes, routes to study entire systems of biopolymers like the ribosome, not just one piece.

DNA with its famous double helix structure stores the genetic information of all life forms known. In order that this information is read, the double helix needs to be first unwound and separated into single helices or strands. This is achieved by cellular motor proteins called helicases that operate on already separated DNA strands. The helicases specialize in unwinding and separating the DNA double helix by scooting along one of DNA's single strands against the point where the two strands merge into the double helix; pushing against this point unwinds and separates the double helix further. The helicases are driven by energy stored in molecules of ATP which bind to the protein and get released in their so-called hydrolyzed, lower energy, form. Based on atomic resolution structures, researchers have studied now one of the smallest helicases known, PcrA, from the electronic to the functional level carrying out quantum mechanical/molecular mechanical simulations (as described in a first publication), as well as a combination of classical molecular dynamics simulation, using NAMD, and stochastic modeling calculations (described in a second publication and a third publication). This resulted in an overall explanation of how ATP's hydrolysis powers helicase activity which has been reported in a fourth publication. The researchers discovered that PcrA moves with two "hands" along single stranded DNA; when ATP binds, one "hand" moves along the DNA; when ADP and Pi (the hydrolysis products of ATP) unbind, the other "hand" moves; through a molecular "trick" both "hands" move in the same direction. Amazingly, the hand movement arises mainly from an increase in random mobility of the hands. i.e., is not enforced. Physicists refer to the underlying mechanism as a ratchet mechanism that was indeed long suspected to drive molecular motors. Interestingly, the helicase motor is very closely related to a wide class of other biological motors, for example the FoF1-ATP synthase (see Mar 2004 and Nov 2004 highlights). For more information visit our helicase research website.

Biological cells, in particular neurons, maintain an inside-outside voltage gradient through active transport of ions (Na⁺, K⁺, Cl^-, and others) across their membranes. The flow of the ions down their gradients through membrane channels is highly selective for each ion. The high selectivity permits nerve cells to signal each other through voltage spikes, which are produced through transient changes of channel conductivities for Na⁺ ions (channels open and close in about a ms) and K⁺ ions (channels open and close in about 10 ms). Crucial for the generation of voltage spikes is the selective, yet quick, conduction of ions, but as one knows from personal experience at border crossings, high selectivity and quick crossing seem to be mutually exclusive. Yet biological ion channels reconcile selectivity and speed. Prior experimental work, primarily that of year 2003 Nobelist MacKinnon, as well as computational work suggested how potassium channels achieve selectivity and speed. But until recently no high resolution atomic structure of a potassium channel was known in the open form and the suggested mechanism could not be tested under natural conditions through atomic level simulations. Last year's solution of the structure of the potassium channel Kv1.2 in its open form made it finally possible to simulate, using NAMD, the conduction of ions through Kv1.2 driven by a voltage gradient. The results reported recently confirmed indeed the high selectivity - high speed mechanism suggested earlier, namely a billiard-type motion of two and three ions, the last ion kicking the first ion out. The simulations revealed for the first time, through movies, the overall permeation process, including the jumps of ions between energetically favorable binding sites and the sequence of multi-ion configurations involved in permeation. More on our potassium channel web site.

How far and how well molecular biologists can look into the living cell depends as much on microscopes and observations, as it depends on computers and their software. The premiere software for looking into the molecular world of the cell, VMD, has made a big leap forward in broadening the molecular horizon of life scientists through its new release, VMD 1.8.5. Researchers are offered now a fresh view through a modern unified bioinformatics environment, MultiSeq, combining sequence and structure analysis for proteins and amino acids. VMD, now literally more colorful, lets scientists quickly exchange VMD views through integration of BioCoRE, calculate APBS electrostatics maps, call on NAMD to calculate energies, build and mutate structures, determine easily force field parameters, and navigate through proteins with a flying camera. VMD 1.8.5, though only a minor version number different from the previous release, includes now many new structure building and analysis tools that make it easier for modelers to set up, run, and analyze computer simulations of biomolecules.

Many proteins interact with gas molecules such as oxygen to perform their functions. In most cases, the gas molecules must reach sites buried deep inside the proteins that bind the molecules, with no obvious way in. Understanding how, for example, oxygen enters the protein, and mapping out which pathways it takes has been a long-standing challenge. As reported recently, computational biologists, inspired by previous work on the hydrogenase enzyme (see the September 2005 highlight), have developed a method, called implicit ligand sampling, that maps the pathways taken by gas molecules inside proteins. The mapping is determined by monitoring fluctuations of the protein, surprisingly, in the absence of the gas molecules. The mapping method is available in the most recent version of the program VMD used for structure and sequence analysis of proteins. The researchers applied the method to myoglobin, an oxygen-storing protein present in muscle cells, and determined detailed three-dimensional maps of oxygen and carbon monoxide pathways inside the protein (for more information see our web page). While some details of these pathways were already known from experiment, the implicit ligand maps revealed a large number of new pathways and suggest that oxygen enters myoglobin using many different entrance doors.

The living state of biological cells manifests itself through mechanical motion on many length scales. Behind this motion are processes that generate and transform mechanical forces of various types. As with other cell functions, the machinery for cellular mechanics involves proteins. Their flexible structures can be deformed and restored, and are often essential for handling, transforming, and using mechanical force. For instance, proteins of muscle and the extracellular matrix exhibit salient elasticity upon stretching, mechanosensory proteins transduce weak mechanical stimuli into electrical signals, and so-called regulatory proteins force DNA into loops controlling, thereby, gene expression. In a recent review, the structure-function relationship of four protein complexes with well defined and representative mechanical functions has been described. The first protein system reviewed is titin, a protein that confers passive elasticity on muscle. The second system reviewed is the elastic extracellular matrix protein fibronectin and its cellular receptor integrin. The third protein system covered are the proteins cadherin and ankyrin involved in the transduction apparatus of mechanical senses and hearing. The last system surveyed is the lac repressor,  a protein which regulates gene expression by looping DNA. In each case, molecular dynamics simulations using NAMD provided insights into the physical mechanisms underlying the associated mechanical functions of living cells. (more on our mechanobiology web site).  

In a recent paper experiences designing and deploying NAMD-G, an infrastructure for executing biomolecular simulations using the parallel molecular dynamics code NAMD within the context of a Computational Grid, are described. The NAMD-G project, and associated paper, is the result of a collaboration between the Theoretical and Computational Biophysics Group (TCBG) and the National Center for Supercomputing Applications (NCSA). James Phillips, Senior Research Programmer for NAMD, and Jordi Cohen, a Ph.D. candidate in Physics at the University of Illinois at Urbana-Champaign, contributed on behalf of the TCBG, while Richard Kufrin, Senior Research Programmer, and Michelle Gower, Research Programmer, led development for NCSA.

NAMD (NAnoscale Molecular Dynamics) can simulate the movement of proteins with millions of atoms, making it the world's fastest parallel molecular dynamics program. The NAMD development team will continue to incorporate the latest parallel-computing advances into NAMD, which already runs efficiently on several thousand parallel processors. Pictured to the right is the current development team for NAMD. James Phillips, a PhD in Physics, is Senior Research Programmer for NAMD at the Theoretical and Computational Biophysics Group (TCBG). Dr. Laxmikant Kale, Professor of Computer Science at UIUC, is a Co-PI at TCBG and leader of the Parallel Programming Laboratory. Kale's computer science graduate students, Chee Wai Lee, Chao Mei, and David Kunzman, also contribute to various aspects of NAMD development.

Many proteins store gases like oxygen, carbon dioxide, and nitric oxide, or react with them. The gases are conducted into the protein through access routes that exist only in passing and as a result of a protein's fluctuations. Accordingly, access routes are difficult to establish, but researchers are now able to image gas access pathways inside proteins computationally. The new method has many implications for biotechnology and science (see our hydrogenase page and Sep 2005 highlight, "Hydrogen Fuel from Protein"). Imaging gas access systematically over whole protein families, e.g., the family of myoglobins, requires a large number of calculations that need to be run and monitored. The traditional means of doing so is very wasteful of the researchers' time. To solve this problem, NAMD-G, a grid-based automation engine for biomolecular simulations running the NAMD software, has been developed in a collaboration with the National Center for Supercomputing Applications (see recent paper). From the researchers' workstations, NAMD-G "farms out" a large number of calculations, in parallel, to supercomputers on the TeraGrid. NAMD-G monitors and manages multiple sequences of calculations at distant sites, and performs the necessary data transfers and backups on an as-needed basis. While the gas transport simulations provide a clear scientific driver for the development, NAMD-G is quite general and will aid any NAMD user with access to the TeraGrid. The result? Less time spent baby-sitting runs and more time for science.

For hard-working scientists, the task of maintaining a single desktop computer is an unwelcome distraction. But what if your work requires the power of ten or a hundred machines? Our recent series of workshops (Sep 2005, Nov 2005, Mar 2006, and Apr 2006) has given nearly one hundred participants hands-on experience installing and using low-cost Linux clusters. Students were taught to eliminate many sources of complexity, such as hard drives, and to automate what remained with cluster management software and a queueing system. Lectures on cluster design stressed the importance of knowing which applications would be run and choosing cost-effective hardware to meet those specific needs, as well as less-obvious aspects of cluster acquisition such as electrical power, cooling, and the purchasing process. After assembling and installing small four-node clusters, students ran both the molecular dynamics program NAMD and a more typical parallel application that they compiled from scratch. Most participants were motivated by concrete plans to build clusters for their own groups in the near future and felt better-equipped to do so following their experience.

Bacterial cells, like those of Escherichia coli, protect themselves against sudden inside-out pressure differences that arise osmotically from changes in a cell's environment and that could burst the cellular envelop. The protection is achieved through so-called mechanosensitive channels in the cell membrane.  One such channel, that dissipates like a safety valve pressure differences across the Escherichia coli cell membrane, is contributed by the protein MscS.  Upon tension in the cell membrane, that can also be applied systematically in the laboratory, the channel opens and permits molecules to pass, as best measured through an ion current leaking through the stretched membrane.  MscS is a channel with a balloon-like filter,  the function of the latter being still a mystery  (see Nov 2004 highlight, "Japanese lantern protein").  Now computational biologists using NAMD teamed up with device engineers using BioMoca to study MscS as reported recently.  The team monitored the mysterious MscS computationally over several microseconds, a record time for protein simulations.  MscS was found to permit water passage, but to also exhibit strong electrostatic forces that focus ions streaming through its filter balloon and channel.  This suggests MscS to be both a hydrostatic and an electrical safety valve.  Even though now better known, MscS' entire function remains shrouded in mystery (more on our MscS web site).

Bacillus anthracis, the cause of anthrax, is one of the most lethal bacteria. In addition to its ability to infect animal and human cells, the bacterium attacks also the cells of the host's immune system, the so-called macrophages. For this purpose the anthrax bacterium releases three types of proteins, or toxins, into the blood stream of the host: protective antigen, lethal factor, and edema factor, referred to as PA, LF, and EF, respectively. LF and EF team up with PA, which transports them into a host macrophage cell. Once inside the cell, LF converts ATP to cyclic AMP, while EF disables MAPKKs, a family of signaling proteins. These attacks disrupt various cellular signaling pathways of macrophages and some other cells, essentially shutting down the host's immune system and often leading to death of the host. To invade macrophages, the toxins take an intricate entry route that involves binding to a cell receptor, capillary morphogenesis protein 2 (CMG2), inducing the cell to internalize the toxins in a bubble like membrane (endosome), the bubble wall being then punctured by seven PAs forming a channel upon a chemical (acidifying) trigger from the host; the channel permits then their lethal cargo, LFs and EFs, to slip into the cell. How exactly the PAs punctured the endosome wall remained a mystery. In a recent report the entry route has been resolved now in greater detail through molecular dynamics simulations using NAMD. The report reveals how acidic conditions in the endosome trigger conformational changes of the PA complex necessary for pore formation, and provides structural insights into the role of unusual interactions between the PAs and its receptor CMG2. Visit also our anthrax toxin webpage.

Computational tools, like the molecular graphics program VMD and molecular dynamics program NAMD, move rapidly from theoretical to experimental biology. To train researchers in the proper use of computational tools, a series of hands-on workshops was organized in the US and Australia in 2003-2005 (see July 2005 highlight). This year the first European hands-on workshop started a new generation of training with three novel features. First, the workshop addressed mainly bench scientists in need of computational methods. Second, the workshop introduced a key expansion of VMD that turned a mainly structurally oriented visualization program into a structure and sequence analysis program. This is achieved through a multiple sequence analysis tool in VMD, called multiseq. Third, all training material has been extended to multiple platforms and participants could bring their own laptops for the training sessions. As in the previous series, participants enjoyed workshop lectures that introduced concepts and good uses of biocomputing software, but were most enthusiastic about practical tutorials that provided opportunities to learn by example and to apply newly mastered tools to their own research. The participants carried all lecture material and software home on a DVD; others can obtain the same material through our web site (workshop lectures, tutorials, case studies, VMD, NAMD).

Anyone who has attempted to fit a long piece of thread through a needle's eye realizes how difficult fitting something so small and flexible into such a small hole can be. Yet this action is carried out every second in every living cell. Flexible polypeptides, proteins, often have to cross a cellular membrane to get to their correct location, whether that location is an organelle within the cell or even outside of it. To accomplish this, they are pushed through a protein pore in an unfolded conformation much like a long string. The channel that accepts the string-like proteins, the protein translocon, allows only certain proteins to pass, while restricting access to molecules even much smaller than the macromolecular proteins. As reported in a recent publication, computer simulations using the molecular dynamics program NAMD helped to answer the question of how such a small channel could achieve this feat, demonstrating how the channel itself can be flexible yet resilient during a protein-crossing event and also elucidating in part how it can maintain such tight control over what is permitted to cross. For more information, see our Protein Translocation website.

Muscle fibers, through their so-called thick and thin filaments, contract and extend in doing their work. To render the fibers elastic and protect them from overstretching, the thick filaments are connected through a long and thin elastic protein, titin, to the base of the fibers. Titin, by far the longest protein in human cells, is a molecular bungee cord and, like such cord, must be affixed firmly to the base. How this is done was a mystery until crystallographers took the first atomic resolution image of the system: it turns out that two titins are spliced together at their ends like ropes. The splicing involves a third small protein, the titin-telethonin-titin system forming a U. The U apparently is thrown over a bollard-like cellular structure to hold the thick filaments much like boats are held by bollards and ropes at their mooring place. The crystallographers teamed up with computational biologists to investigate the mechanical strength of the titin - telethonin - titin cord by means of molecular dynamics simulations using NAMD. As reported recently, the cord has great mechanical strength due to an extended network of hydrogen bonds between beta-strands, common structural features in proteins, that in the present case form a sheet extending through all three proteins. This discovery explains how living cells can splice cellular proteins together through a system of hydrogen-bonded beta-strands that extend through several proteins. Interestingly, such beta-strands were seen previously in cases of diseases like Alzheimers where the feature leads, however, to pathological assembly of proteins. What needs to be understood now is how the telethonin glue is applied only to the right spots in the cell and how the cells prevent telethonin from splicing together the wrong proteins. For more information visit our titin-telethonin web page.

Viruses, the cause of many diseases, are the smallest natural organisms known. They are extremely primitive and parasitic such that biologists refer to them as "particles", rather than organisms. Viruses contain in a protein shell, the capsid, their own building plan, the genome, in the form of DNA or RNA. Viruses hijack a biological cell and make it produce from one virus many new ones. Viruses have evolved elaborate mechanisms to infect host cells, to to produce and assemble their own components, and to leave the host cell when it bursts from viral overcrowding. Because of their simplicity and small size, computational biologists selected a virus for their first attempt to reverse-engineer in a computer program, NAMD, an entire life form, choosing one of the tiniest viruses for this purpose, the satellite tobacco mosaic virus. As described in a recent report, the researchers simulated the virus in a small drop of salt water, altogether involving over a million atoms. This provided an unprecedented view into the dynamics of the virus for a very brief time, revealing nevertheless the key physical properties of the viral particle as well as providing crucial information on its assembly. It may take still a long time to simulate a dog wagging its tail in the computer, but a big first step has been taken to simulate living organisms. Naturally, this step will assist modern medicine (more on our satellite tobacco mosaic virus web page).

Lipoproteins are protein-lipid particles which circulate in the blood collecting cholesterol, fatty acids, and lipids. Low levels of one such lipoprotein particle, called high-density lipoprotein (HDL) or "good cholesterol", has been implicated in the increased risk of coronary heart disease. The ability of lipoproteins to transport lipid and cholesterol through the blood is amazing since these types of particles are not generally soluble in blood plasma. However, when HDLs assemble, proteins wrap themselves around the lipids and cholesterol, shielding the lipid tails from the aqueous environment. Native HDL exhibit a variety of shapes and sizes, for example forming a discoidal particle. Conventional high-resolution imaging techniques, such as NMR and X-ray crystallography, cannot resolve how lipid and cholesterol are being accommodated by HDL, but the assembly and geometry of HDL discs can be captured using computer simulations. Unfortunately, the long time scales required for HDL assembly was a major stumbling block. Now a new simulation method, coarse-grained modeling in conjunction with the molecular dynamics program NAMD, has permitted the simulation of HDL assembly as recently reported. The simulations show that lipids quickly aggregate into a bilayer from their initial spherical "micelle" shape and that the two proteins subsequently attach to either side forming a belt surrounding the lipid core. For more information see HDL & nanodisc and coarse-grained modeling.

Molecular modeling with NAMD (NAnoscale Molecular Dynamics) promises to become a key methodology for research and development in bionanotechnology. Molecular modeling provides nanoscale images at atomic and even electronic resolution, predicts the nanoscale interaction of yet unfamiliar combinations of biological and inorganic materials, and can evaluate strategies for redesigning biopolymers for nanotechnological uses. The methodology's value has been reviewed for three uses in bionanotechnology. The first involves the use of single-walled carbon nanotubes as biomedical sensors where a computationally efficient, yet accurate description of the influence of biomolecules on nanotube electronic properties and a description of nanotube - biomolecule interactions were developed; this development furnishes the ability to test nanotube electronic properties in realistic biological environments (see Dec 2005 highlight). The second case study involves the use of nanopores manufactured into electronic nanodevices based on silicon compounds for single molecule electrical recording, in particular, for DNA sequencing. Here, modeling combining classical molecular dynamics, material science, and device physics, describes the interaction of biopolymers, e.g., DNA, with silicon nitrate and silicon oxide pores, furnishes accurate dynamic images of pore translocation processes, and predicts signals (see Nov 2005 and Oct 2004 highlights). The third case involves the development of nanoscale lipid bilayers for the study of embedded membrane proteins and cholesterol. Molecular modeling tested scaffold proteins, redesigned lipoproteins found in mammalian plasma that hold the discoidal membranes in shape, and predicted the assembly as well as final structure of the nanodiscs (see Feb 2005 highlight). In entirely new technological areas like bionanotechnology qualitative concepts, pictures, and suggestions are sorely needed; the three exemplary applications document that molecular modeling can serve as a critical "imaging" method for bionanotechnology, even though it may still fall short on quantitative precision.

Your favorite flower pot would not survive a weekend in your office without watering, if it wasn't for a sophisticated cellular mechanism evolved in land plants to conserve water under drought conditions. Water exchange between cells and their environment is facilitated by a group of highly specialized membrane proteins called aquaporins. Although present in all life forms, plants are particularly dependent on their function. While in most species these channels function as always-open "cellular pipes" allowing water in and out of the cell, in plants they evolved into "cellular faucets" whose water permeability can be controlled by the cell. Nearly all plant aquaporins can be gated in response to drought or even flooding conditions, through basic biochemical signals, e.g., phosphorylation and change of pH. A recent Nature paper reporting a collaborative study between crystallographers who succeeded in solving the first structure of a plant aquaporin from spinach, and modelers provides the most detailed view of the mechanism of gating for a membrane channel. Molecular dynamics simulations of the channel performed by NAMD reveals a dual gating mechanism in which phosphorylation of certain protein residues unleashes a long cytoplasmic loop that physically blocks water access to the pore. More information on aquaporin research can be found here.

Eukaryotic cells envelop their genetic material in the cell nucleus whose boundary contains numerous pores. Only small molecules can pass through these nuclear pores unhindered. For all larger ones, passage is highly selective and controlled. The control involves import and export proteins (transport receptors) that load and release cargo on the proper side of the nucleus upon interaction with signaling proteins. Researchers are presently solving the structure of the nuclear pore and its transport receptors with increasing resolution, and the first atomic level investigation into the mechanism of nuclear pore selectivity has recently been reported [paper]. The study inspected the interaction between the transport receptor importin-β with key nuclear pore proteins that appear disordered near the center of the pore and contain characteristic phenylalanine-glycine sequence repeats. Molecular dynamics simulations using NAMD and analyzed using VMD revealed a key insight into the selectivity mechanism. The simulations showed that the key sequences of the repeat proteins interact strongly with certain spots on the surface of importin-β. The study confirmed spots that had previously been identified experimentally and, moreover, found numerous binding spots not yet seen in experiment. Further experiments and simulations promise an understanding of the selectivity of entry and exit from the nucleus, a key element of the cell's genetic control. For more information see our nuclear pore complex webpage.

The most celebrated molecule of living cells, DNA, owes its fame to its role as a carrier of genetic information. But DNA is also impressive through other amazing properties, for example its mechanical flexibility. At first sight, it might seem a dull question to ask what is the smallest pore DNA can be squeezed through, as the obvious answer is that the diameter of that pore should be slightly larger than the diameter of a DNA helix. However, recent studies (paper1, paper2) in asking the stated question discovered that double stranded DNA can permeate, without loosing its structural integrity, pores smaller in diameter than a DNA double helix. The discovery was initiated through molecular dynamics simulations, carried out using NAMD and VMD. The simulations demonstrated that if an electrical field, driving negatively charged DNA through a nanopore, exceeds some critical value, the force exerted on DNA stretches DNA to twice its equilibrium length, reducing thereby its diameter and allowing it to squeeze through narrow pores. The simulations predicted precise values of pore radii and associated critical fields. The predictions were validated experimentally by counting the number of DNA copies that passed at different electric fields through synthetic nanopores. Further details about this study can be found here.

It was 1995 when NAMD was introduced (Nelson et al.) as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. In 1999 a major improvement was accomplished in NAMD 2 (Kalé et al.), scaling to 200 processors at the time due to the efforts and software of the Parallel Programming Lab. NAMD has since matured, adding many features and scaling to thousands of processors, garnering accolades and users in the process. This progress is now collected in a NAMD review paper that presents, in a manner accessible to the novice researcher, the concepts and algorithms behind NAMD, features for steered and interactive MD and for free energy calculation, the elements of the NAMD design that enable parallel scaling, performance comparisons of a variety of platforms, and advice for productive use of NAMD on modern research projects. Case studies ranging from the typical to the elaborate demonstrate the capabilities and flexibility of NAMD. This new reference provides an excellent foundation for working through the extensive NAMD tutorials, either on your own or at a hands-on workshop.

For the sequence of DNA, the genetic instructions of cells, to be read, the double helix of DNA is split open, exposing single DNA strands to DNA binding proteins. Once bound to DNA, the proteins, in carrying out their functions, will crawl along the DNA strand in one of two directions, towards DNA's 3' or 5' end. A recent study of DNA discovered a surprising property of single DNA strands that seems to explain how DNA binding proteins recognize the right direction on DNA strands. By measuring the translocation of DNA through alpha-hemolysin, a membrane protein with a narrow pore, researches discovered that directed single stranded DNA moves much faster when entering the pore 3' end first, rather than 5' end first. The underlying mechanism of this directionality was discovered through molecular dynamics simulations using NAMD and VMD. The simulations revealed that, in a narrow pore, DNA bases tilt collectively towards the 5' end, transforming a wide space directionless DNA brush into a tight space DNA ratchet. The 360,000-atom MD simulation did not only reveal how the DNA bases align and move faster in the "smooth" direction, but did also predict how the directional DNA movement can be discerned by means of direction-sensitive ionic currents through the channel blocked by translocating DNA strands. More details about this study can be found here.

In an optimistic future, cars and appliances will be powered by renewable energy produced by burning hydrogen gas, with water being the only waste product. To supply this hydrogen gas, scientists are turning their attention to an enzyme called hydrogenase that is found in certain microorganisms, which produce hydrogen gas from sunlight and water. This enzyme, however, is sensitive to oxygen gas, which irreversibly deactivates its hydrogen-producing active site. Understanding how oxygen reaches the active site will provide insight into how hydrogenase's oxygen tolerance can be increased through protein engineering, and in turn make hydrogenase an economical source of hydrogen fuel. In a recent paper (also described in this webpage), the programs NAMD and VMD are used to analyze the gas diffusion process inside hydrogenase, and how it correlates with the protein's internal fluctuations, thereby creating a map of the oxygen pathways. The calculations revealed two distinct pathways for oxygen to reach the active site. Gases participate in physiological processes of many organisms and the new computational strategy developed promises to image gas diffusion pathways for many relevant proteins. In fact, the researchers are currently inspecting hundreds of proteins for their ability to internally transport gas molecules.

The import of nutriments over their cellular membranes is one of the main tasks of all living cells. Even though a major part of the cell's molecular machinery is devoted to this task, principles of selective membrane transport are not yet well understood, mainly due to the fact that the membrane proteins responsible are notoriously difficult to resolve in their structure, the latter a prerequisite for a full physical description of the function. Recently, cell biology got very lucky in having the structures of two closely related membrane proteins solved. Two highly homologous aquaporins from the same bacterium, Eschericha coli, have become structurally known: one that conducts only water, called AqpZ, and one that conducts water as well as the nutriment glycerol, called GlpF. The discoveries have permitted us through structure analysis with VMD and molecular modeling with NAMD to look over nature's shoulder in the evolutionary design of two similar import channels of different conductivity. As described in a recent paper and on our aquaporin site, in making a water channel also a glycerol channel, nature has turned to a very basic principle, namely adjusting the overall pore size of the channel from a very narrow channel, just wide enough for water, to one wide enough also for glycerol.

To guide cell biology research and explain observation through molecular structures and sequence data, life scientists resort increasingly to computational tools. Sequence and structure viewers (VMD) combined with molecular dynamics modeling software (NAMD) are primary methodologies that revolutionized modern biomedicine. The revolution happened so quickly, though, that traditional university training has not kept up with the pace of developments in computational biology. A series of computational biophysics workshops in Perth (Australia), Urbana, Boston, Lake Tahoe, Chicago, and San Francisco attempted to fill the gap through hands-on training. Theory sessions in the morning introduced the concepts and methods used in molecular modeling today; computer laboratories in the afternoon gave participants, students, postdocs, and faculty, opportunities to work through tutorials at their own pace on provided laptops, as well as work on their own research problems. The workshops funded by NIH, NSF, NCSA, UIUC, and UWA met the needs of novices and experts alike for instruction in a new generation of research methods. All workshop materials are available on the web.

In a biological cell, membrane channels act like miniature valves regulating the flow of ions and other solutes between intracellular compartments and across the cell's boundary. Assembled in complex circuits, they generate, transmit, and amplify signals orchestrating cell function. To investigate how membrane channels work, life scientists, using an extremely fine pipette, isolate a tiny patch of a cell membrane and, in so-called patch clamp measurements, determine electric currents in response to applied electric potentials. Dramatic increase in computational power and its efficient utilization by NAMD allows one today to reproduce such studies computationally, calculating the permeability of a membrane channel to ions and water directly from its atomic structure. In what is one of the largest molecular dynamics simulation to date, described in a recent paper as well as on our web site (here), one copy of the membrane channel alpha-hemolysin, submerged in a lipid membrane and water, was subjected to an external electric field that drove ions and water through the channel. The calculations produced also an image of the electrostatic potential across the channel (see figure).

When Escherichia coli bacteria enjoy lactose and related food molecules in their environment, the cells quickly furnish proteins needed for import and metabolic digestion of the food. A set of genes, called the lac operon, is transcribed into messenger RNA that directs the synthesis of these proteins. When lactose is not available, the protein synthesis would be wasteful and, indeed, is prevented by locking the lac operon. This is achieved by a protein called lac repressor that forces the segment of the lac operon needed to initiate transcription into a loop, but that can be unlocked by a lactose molecule binding to the protein as soon as the food becomes available again. A recent study of the lac repressor combines a 314,000-atom protein simulation using NAMD with a multiscale simulation technique coupling the protein to the DNA loop. The calculations reveal how the lac repressor stretches out two "hands" grabbing the genomic DNA and then keeps a tight grip on the DNA wrestling it into a loop. The discovery is described on our website as well as in a popular article.

The Materials and Processes Simulations (MAPS) platform from Scienomics is a user friendly environment for molecular modeling and simulations. Its plug-in based architecture enables scientists to use the best technology for a given problem. The MAPS platform runs on Linux, IRIX and Windows® XP operating systems. MAPS includes a series of tools enabling the construction of molecular systems, finite and periodic, 3D visualization and other utilities. The NAMD user can quickly create a molecular model, using standard sketching tools or MAPS' polymers builder, and set up calculations using the NAMD graphical user interface which gives access to many of NAMD advanced capabilities. Analysis tools and graphs available in MAPS enable an easy representation of NAMD results. MAPS' native client-server architecture allows to use the best computational resources available and run NAMD simulations on numerous operating systems. Finally, efficient interaction with office productivity software allows to produce quickly presentations and reports.

The ear is a sensitive and robust device, able to perceive the faint sound of flowing water and the thunderous blast of an air plane. Like a microphone, the ear transforms a complex, mechanical stimulus (sound), into an electrical signal, a voltage change in a nerve cell, that can be understood by our brain. This transformation is called "mechanotransduction" and is accomplished by a series of amazingly minute devices that each connect a soft spring to an ion channel, both located in specialized sensory cells, the hair cells of the inner ear. The springs, through their vibrations agitated by particular sound frequencies, control ion currents passing through the channels, thereby, modifying the hair cell internal electrical potential. This leads to neural signaling to the acoustic cortex of the brain. Recently reported molecular dynamics simulations using NAMD, some of the most extensive simulations accomplished to date both in size and duration, showed that the mechanical characteristics of hair cell signaling may be traced to a single protein, ankyrin, that acts as a helical spring. Imagine a soft spring that is extended several inches by the weight of a feather! Ankyrin is such a spring, but a billion times finer (see our ankyrin website).

Biological evolution left its many traces in the form of organisms as well as in "fine print" in the form of gene sequences and associated protein structures. From the "fine print" researchers can draw conclusions about the inner workings of living cells and derive opportunities to battle disease. Researchers enjoy easy access to sequence and to structure information, but so far mainly separately, i.e., either for sequence or for structure. VMD, our widely used structure viewing and analysis program, has already offered a glimpse of the viewed protein's sequence, but with its latest release has taken a key step further, assisting in viewing and aligning multiple structures and sequences with few mouse clicks. Users of VMD 1.8.3 find themselves routinely comparing their protein of interest with analogous ones getting VMD to color the protein by similarity in structure, in sequence, and showing conserved amino acids. VMD 1.8.3 surprises with numerous further features, including a new cartoon representation that follows the actual molecular structure closely and offers superb, publication quality images. VMD continues to work together with the molecular dynamics program NAMD, permitting viewing and analysis of huge trajectory files by supporting 64-bit processors.

Biological cells, the basic units of life, are organized assemblies of nanodevices. Nanobiotechnology can adapt Nature's solutions for its own purposes, using computational biology to redesign Nature's nanodevices. In the case of Nanodiscs, bioengineers thought to construct the smallest possible environment that mimics the native environment of membrane proteins. Researchers borrowed the amino acid sequence of a naturally occurring class of proteins, lipoproteins, which are involved in the transport of lipids and cholesterol. The lipoprotein found in humans, apolipoprotein A-1, was used to synthetically engineer "belts" that surround a discoidal lipid bilayer, shielding the hydrophobic lipid tail groups from water. As recently reported, molecular dynamics simulations using NAMD showed an atomic level image of the structure of such a nanodevice. The predicted discoidal shape, diameter, and thickness of Nanodiscs simulated were experimentally corroborated through so-called small angle X-ray scattering. For more details see the HDL & Nanodisc website.

An important means for generating genetic diversity to provide raw material for evolution and maintain genomic stability is sexual reproduction. At the molecular level, the genes of two individuals are mixed through a process called homologous recombination. This process is found also in many simple life forms, even bacteria. At the beginning of recombination, two DNA duplexes, e.g., from mother and father, are aligned next to one another as the result of homology search, i.e., like strands are brought together with like strands. The four single DNA strands, two in each duplex, cross reciprocally two of the strands between the duplexes. The result is a joint molecule that contains DNA crossovers, named Holliday junctions. The Holliday junction is highly polymorphic in moving along two DNA duplexes, exchanging their DNA. Researchers are now investigating the physical mechanism of Holliday junction migration. The polymorphic, dynamic character of this migration makes observations difficult and the researchers resorted to molecular dynamics simulations using NAMD. The results, reported recently, resolved the dynamics of maternal-paternal DNA exchange through Holliday junction transitions in unprecedented detail providing an atomic level view of sexual reproduction. Check a brief review on our website.

Energy for most of the earth's biosphere is gained when sun light absorbed drives electrons across a membrane through a protein called the photosynthetic reaction center (RC), leaving behind positive electron holes. The electrons join protons to become hydrogen atoms and move, bound pairwise to a quinone molecule, to another protein, the so-called bc1 complex. Here electrons and protons move together back over the membrane and become separated again, thereby establishing an electro-osmotic potential that fuels many cellular processes. However, the electrons need to return to the RC to fill the electron holes left behind. Nature employs for this purpose a kind of bioelectric extension cord in the form of a third protein, cytochrome c2, that shuttles the electrons back from the bc1 complex to the RC. A recent paper reports molecular dynamics simulations using NAMD that investigated how cytochrome c2 plugs into the RC. Landing on a broad face of the RC, interactions steer the protein such that its electron carrying heme group comes close to RC's chlorophylls with electrons missing, a chain of water molecules providing an electrical conduit. The study is yet another example of how simulations provide today complete views of the fundamental processes underlying life.

Biological cells must be capable of attaching themselves to their surroundings. For this purpose they utilize fibrillar proteins, such as fibronectins, that grasp cells through cell surface receptors integrins. The latter act as snap fasteners to the extra-cellular fibrils. The growth, movement, and survival of cells are all dependent on the ability of integrins to fasten cells upon intra-cellular signals or to signal inwards that something has become fastened on the cell surface. The major fastener on integrins are simple divalent ions like Mg⁺⁺ or Ca⁺⁺ that can adhere to specific molecules with amazing strength, even though the interaction at the cell surface is exposed to water. Computer simulations using NAMD, reported recently, revealed a dynamic picture of the interactions used by cells to link themselves to the extra-cellular matrix. They showed that it is actually a brave water molecule that is recruited by integrins as a protective shield for the interaction. The simulations provide for the first time a detailed view of how cell tissues are stabilized through surface ions against mechanical stress.