Aquaporins are membrane water channels that play critical roles in controlling the water contents of cells. These channels are widely distributed in all kingdoms of life, including bacteria, plants, and mammals. More than ten different aquaporins have been found in human body, and several diseases, such as congenital cataracts and nephrogenic diabetes insipidus, are connected to the impaired function of these channels. They form tetramers in the cell membrane, and facilitate the transport of water and, in some cases, other small solutes across the membrane. However, the water pores are completely impermeable to charged species, such as protons, a remarkable property that is critical for the conservation of membrane's electrochemical potential, but paradoxical at the same time, since protons can usually be transfered readily through water molecules. The results of our simulations have now provided new insight into the mechanism underlying this fascinating property. Water molecules passing the channel are forced, by the protein's electrostatic forces, to flip at the center of the channel (see the animation), thereby breaking the alternative donor-acceptor arrangement that is necessary for proton translocation (read the complete story in our Science paper).

High-density lipoproteins (HDL), often called "good cholesterol", are protein-lipid particles which circulate in the blood collecting cholesterol from peripheral tissues and transporting them to the liver for degradation. Native HDL are heterogeneous particles which exhibit a variety of shapes and sizes, thus making structural studies of the major protein component apolipoprotein A-I (apo A-I) difficult. However, nanodiscs which are reconstituted discoidal HDL mimics being developed as platforms in which to embed membrane proteins, can be assembled into homogeneous particles. Thus, we utilized the extensive characterization of nanodiscs in furthering our understanding of the structure of apo A-I as well as the assembly of lipoprotein particles. Whereas, the structure of lipoprotein particles can be studied using all-atom molecular dynamics, the long time scales needed for assembly simulations required the development of a coarse grained protein-lipid model.

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.

Muscle fibers are not rigid structures, but rather, they can both contract and extend in response to physiological demand. As a result, muscle sarcomeres must have a protective mechanism to prevent tearing and damage from overstretching. The giant protein titin fulfills this role by acting as a molecular rubber band, providing a passive resistance force during extension to restore the muscle fiber to its resting length. Conceivably, this rubber band must be anchored to a rigid structure in order to function. Biochemical investigations have speculated that the protein telethonin, located at the sarcomeric Z-disc, may serve this purpose. Genetic diseases related to defects in telethonin have been correlated with dilated cardiomyopathy and a form of muscular dystrophy. To date there have been no studies to determine how strongly bound titin is to telethonin. To explore this issue, we performed molecular dynamics simulations in order to test the strength of the newly resolved titin Z1Z2-telethonin complex. Our results, which have recently been reported (paper), reveal that the force required to dissociate titin from telethonin is significantly higher than that required to unfold isolated titin Ig-domains. This suggests strongly that telethonin is in fact an essential component of the Z-disc titin anchor. In addition, we find that telethonin anchors not just one, but two separate titin molecules, serving as a sort of molecular glue joining both titin molecules together through β-strand crosslinking (a structural motif also seen in fibril pathologies such as Alzheimer's, Parkinson, and Huntington's disease). Thus our simulations reveal also a fundamental architectural element of living cells, namely how cells glues their components together yielding strong mechanical connections. For more information on teletonin and the implications of our findings, see the following webpage here.

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 can 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.

Cells constitute only part of animal tissue, much of tissue is made of the extracellular matrix (ECM), a flexible mesh composed of several classes of macromolecule. Fibronectin (FN) is a component of the ECM that acts as a specific adhesive, forming networks that connect cells to the giant fibrous molecules that make up the majority of the ECM. Proper FN fibril formation is required to maintain prop er cell migration, thus FN plays roles in diseases affecting growth, development, tumors , and wound healing. We have used SMD simulations to examine how the mechanical force s present in the ECM affect FN fibril formation.

Carbon nanotubes are becoming universal tools and building blocks in nanomedicine, being proposed as nanodevices for drug delivery, DNA transfection, and biosensing. They can also be employed as nanopores that conduct protons, ions, and small molecules (see June 2003 highlight), or as reaction vessels for new types of chemical reactions. Studying carbon nanotubes can assist in designing improved nanodevices. One approach to studying nanotubes is furnished by molecular dynamics simulations. However, such simulations must account for one key property of nanotubes, their large polarizability due to the mobility of -electrons over the tube walls. Until recently this polarizability could only be calculated through expensive quantum chemical calculations that could not be linked to simulations imaging molecular processes around carbon nanotubes. Recent studies ( 1 , 2 ) reports now an empirical model that can be efficiently implemented into molecular dynamics simulations to take into account the polarization effect. The model reproduces results of more expensive quantum chemistry calculations very well. A first application of the new model studied the transport of water molecules through nanotubes. Water has a strong dipole moment that polarizes the nanotube wall and, therefore, provides a stringent test for the new methodology.

Light harvesting complexes provide fascinating challenges to biophysicists. With the availability of atomic structures for protein-pigment complexes such as photosystem I, it is possible to form a comprehensive picture of the light absorption and excitation migration processes based on an atomic level quantum mechanical description. This kind of structural analysis not only forms a rigorous test for our understanding of the physics of these mechanisms through a comparison to spectroscopy and kinetics experiments, but it also provides a framework within which the organizational principles for multi-component pigment-protein assemblies can be investigated.

Molecular motors are efficient nanoscale machines destined to make any human designed engine look clumsy. F1-ATPase is such a machine - so powerful that a spoonful of it could produce as much torque as your car's engine. As part of the enzyme ATP synthase, the protein can work as an engine but also operate in reverse as a generator. In the latter mode it is responsible for the synthesis of the energy-rich molecule ATP that serves as fuel driving many processes in biological cells. It can also convert the energy stored in ATP into mechanical rotation. Our studies suggests that the analogy to a car's engine goes even further! A quantum chemical description of the reaction of ATP combined with a simulation of the protein revealed that an amino acid side group of the protein, called the "arginine finger", controls the progression of the catalytic event, much like a spark plug controls the combustion process in a car engine. The very extensive simulation made use of a powerful computer, the Jonas Cluster at the Pittsburgh Supercomputing Center. The investigation is yet another example for the important role of computational biology unraveling the secret behind the function of the machinery of living cells.

Plants and other photosynthetic organisms convert sunlight into various forms of metabolic energy. To expose themselves optimally to the sun while at the same time avoiding damaging overexposure to light, these organisms employ molecular photosensing systems that control, for example, the orientation of their leaves. Common photosensing systems include photoreceptors of the so-called phot family that are sensitive to blue light and contain Light, Oxygen, and Voltage (LOV) sensitive protein domains as photoactive elements. Light absorbed by a flavin molecule leads to bond formation with the protein (LOV domain), thereby, initiating signaling until the flavin-protein bond breaks spontaneously. Our study of the photosensing events in the LOV domain of the algae C. reinhardtii employs computer simulations that combined quantum mechanical and classical simulation methods to study photoexcitation and subsequent processes. It emerged that formation of the flavin-protein bond is initiated by a unique light-driven transfer of a hydrogen atom between the LOV domain and the flavin molecule.

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.

The nucleus of the cell is centrally important to an organism. It serves to store and organize genetic information, the atomic blueprint for the organism, while separating and protecting this very important information from the host of other cellular components. While the nucleus requires this protective isolation, it also needs to communicate with the rest of the cell, exchanging proteins and RNA, for a variety of nuclear and cytoplasmic processes which act in concert. The nuclear pore complex (NPC), perhaps the largest protein complex in the cell, is responsible for the protected exchange of components between the nucleus and cytoplasm and for preventing the transport of material not destined to cross the nuclear envelope. The large size of the NPC makes it difficult to study experimentally. Computational efforts can go a long way toward revealing properties of the NPC which are inaccessible by experiments. Recent molecular dynamics simulations have revealed interactions between the transport receptor importin-β and key nuclear pore proteins, bringing forth a better understanding of the selectivity of entry and exit from the nucleus.

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.