Living cells organize many functions: molecular import and export, signaling, transcription of genes into proteins, movement, building, repair, and more. These functions are realized through a complex architecture of the cell interior reflected in a system of labyrinthine membranes forming manifold cellular organelles from tubes, vesicles and many other shapes. Accordingly, cells need to sculpt their membrane in never ceasing processes and have at their disposal a wide range of mechanisms. A key sculpting mechanism is furnished by proteins, so-called BAR domains, that apparently form lattice-like scaffolds adhering to membrane surfaces. Such scaffolds have been observed through electron microscopy and they are now also being described through molecular dynamics simulations using NAMD. As recently reported, the simulations, carried out at four different levels of resolution (from an atomic to a continuum level), revealed that different arrangements of BAR domains lead to different curvatures. The simulations help to explain why BAR domains working in teams, i.e., in lattice formation, sculpt intra-cellular membranes into different shapes, depending on the exact arrangement. An arrangement of BAR domains that is particularly efficient in bending membranes was identified. More information can be found on our BAR domain web page.

Chromatophores are the photosynthetic machineries of bacteria. Each chromatophore contains, embedded in a membrane, all the photosynthetic proteins needed to absorb sunlight and turn it into chemical fuel. Chromatophores come in different shapes: while some chromatophores are spherical, others are flat or tubular. It has puzzled scientists how all these different geometries arise, and a hypothesis has developed that it is the photosynthetic proteins that render the shape of chromatophore membrane. In a study reported recently, computational biologists using NAMD took an atomistic look at how the chromatophore proteins bend the membrane. Simulations showed that the most numerous photosynthetic proteins dome the membrane, building arched membrane patches that can then be assembled into a spherical chromatophore. These simulations demonstrated that photosynthetic proteins construct their individual membrane environment, and when many of such proteins come together in the bacterial membrane, they can build functional cellular units with unique geometries. For more details, please see our chromatophore website.

Biological cells are surrounded by a highly versatile, yet very feeble cellular membrane and need to balance differences between the cell's interior and exterior that otherwise would burst the membrane. For example, the osmotic pressures inside and outside the cell need to be closely balanced. Thousands of proteins in the membrane act as gatekeepers, opening pores that can also act as safety valves, helping to reduce the interior-exterior difference in pressure rapidly. One such protein, the mechanosensitive channel of small conductance MscS (see the Mar 2008 highlight, "Observation and Simulation Depict Cell's Safety Valve", the Feb 2007 highlight, "Observing and Modeling a Crucial Membrane Channel", the May 2006 highlight, "Electrical Safety Valve", and the Nov 2004 highlight, "Japanese Lantern Protein") opens in response to cellular membrane tension generated due to a drastic imbalance in osmotic pressure as it arises when a bacterial cell suddenly finds itself in fresh water, rather than a highly saline physiological medium. The MscS channel widens then to jettison molecules out of the cell and reduce tension on the cellular membrane quickly. In a recent report, researchers have combined experimental data from electron paramagnetic measurements and computer modeling to reveal in atomic detail how MscS opens and closes its channel. Combining measurement and modeling, the researchers established a highly resolving computational microscope, unmatched by existing microscopes (more on our MscS website).

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.

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.

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.

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.

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 subject 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).

One of the best tools for making the connection between the structure and function of ion channels is molecular dynamics~(MD) simulation, which allows one to foll ow conformational changes in the structure, and movement of K+ ions across the potassium channel. The difficulty in simulating the passing of K+ or Na+ ions through the channel can be overcome by using SMD.

Responding to a great variety of ligands including hormones, neurotransmitters, and peptides, G-protein-coupled receptors (GPCRs) are the most important drug targets. Yet there is still little known about the first step of signal transduction. Rhodopsin is a member of this largest group of transmembrane receptors. The high resolution structure of rhodopsin determined by Palzcewski et al. (2000) gives us the opportunity to take a close look at the activation mechanism. Rhodopsin's ligand, retinal, which is covalently bound to the binding pocket, absorbs light at 500nm and undergoes a cis-trans isomerization triggering conformational changes in the protein. In order to understand the effects of the isomerization on the protein structure, we are performing molecular dynamics of a 40,000 atom model of rhodopsin in membrane.

Adenosine triphosphate (ATP) is the primary energy "currency" in most living organisms. ATP synthase is a large (about 100,000 atoms) protein, which includes a transmembrane F₀ unit coupled to a solvent-exposed F₁ unit via a central stalk gamma. The F₀ unit utilizes a transmembrane electrochemical potential (proton motive force), converting it into the mechanical energy of the stalk rotation. The rotation leads to cyclic conformational changes in the catalytic sites in the F₁ unit, thereby driving ATP synthesis. We seek to identify and explore the chain of the elementary chemical (proton transfer) and mechanical (domain motion) events involved in the process of converting the electrochemical energy of the transmembrane proton gradient into the mechanical energy of the c subunit oligomer rotation.

The purple membrane (PM) of halobacterium salinarium consists of bacteriorhodopsin trimers, lipids and water molecules. Upon light absorption by the chromophore inside bacteriorhodopsin, protons are pumped across the PM to the extra-cellular side of the membrane. With molecular dynamics simulations of the whole PM, we are studying the influence of the native environment on the protein dynamics.

We are applying the steered molecular dynamics method to investigate the action of human synovial protein phospholipase A2 (PLA2) at the lipid water interface. Our hypothesis is that prior to extruding the phospholipid, PLA2 must form the tightly bound complex, while the loosely bound complex should not lead to catalysis.

Formation of bacteriorhodopsin (bR) from the apoprotein and retinal has been studied experimentally, but the actual pathway, including the site of retinal entry, is little understood. Molecular dynamics simulations provide a surprisingly clear prediction.