Research Projects - Other

The nature of modern science is that it is ever-changing, energetically crossing boundaries heretofore defined by traditional areas of inquiry. Research at the Theoretical and Computational Biophysics group reflects this dynamic, with studies employing theoretical perspectives and methodological approaches or addressing topics that don't fall easily into one of the above categories. Included in this broad category are studies of a four-way DNA junction, the nuclear pore complex, gas transport in hydrogenase that may provide a source of renewable fuel, and other topics.

Ion Diffusion on a Grid near MscS

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Traffic flow in a city is affected by large-scale features, like the layout of road networks, as much as it is by small-scale ones, like traffic lights at a road junction. Likewise, the transport of small molecules in cells occur on multiple scales. For example, ions diffusing through the mechanosensitive channel of small conductance (MscS) (see highlights from Jul 2011, "Smart Bacterial Safety Valve", Mar 2008, "Observation and Simulation depict Cell's Safety Valve", Feb 2007, "Observing and Modeling a crucial Membrane Channel", May 2006, "Electrical Safety Valve", and Nov 2004, "Japanese Lantern Protein") must navigate the intricate geometry of the MscS, which varies by the ┼ngstrom. At the same time, the distribution of ions within hundreds of ┼ngstroms of the MscS fluctuate as ions escape through the channel, thus changing the electrostatic landscape seen by other ions as they approach the MscS. In order to model both the fine and bulk aspects of diffusion in systems like that of the MscS, scientists have proposed, in a recent report, a method that marries the high spatial resolution of molecular dynamics to long range diffusion. In the new description, biomolecules "diffuse" by hopping through a grid under the influence of Coulomb and other forces. More on our Kinetic Diffusion web site.

DNA pulling through octane

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Ever since DNA was found with a double-stranded helical structure, people were wondering about how the double strands could be separated apart so that genetic information stored inside the helix could be delivered from generation to generation. A class of protein enzymes known to achieve this function are DNA helicases (see Sept 2006 highlight). Recently, however, researchers have found a novel mechanism that can also serve to split the double strands of DNA apart, namely, by dragging DNA from water to non-polar solvent. This mechanism was demonstrated by means of atomic force microscope-based single molecule force spectroscopy as well as all-atom molecular dynamics simulation, using NAMD, reported in a recent publication. An intriguing idea arising then is that the mechanism may be employed by some DNA helicases, that could achieve the splitting of DNA strands by altering the local-environment from hydrophilic to hydrophobic. More information can be found on our research website.
Light Distribution in the Focus of the 4Pi Microscope

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Since Leeuwenhoek introduced it to biology 300 years ago, the light microscope has brought about multiple discoveries, many achieved through improving over time the instrument's resolution. However, in 1873 Abbe recognized that the resolution has a limit, given by the wave length of light. This limit was considered absolute, until in 1992 Hell suggested a microscope that breaks the limit postulated by Abbe. This is achieved by sending coherent light through two opposing objectives, the resulting interference pattern squeezing the radiation into spots significantly smaller than the light's wavelength. This improvement has already permitted biologists to see a new level of detail in living cells. However, the pattern of light in the Hell microscope is rather complex and certain quantitative measurements require a computational analysis to take advantage of the full benefits of the instrument. Such analysis has been accomplished and validated in a recent study, the validation involving measurements on known systems. The developed numerical algorithms harness the computational power of modern processors, in particular they resort to expoiting the computational power of graphics processors (see also the Oct 2007 highlight). The new methodology combined with the new microscopes opens the avenue to unprecedented measurements in living cells. More information can be found here.
O2 pathways in trematode hemoglobin

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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.
Placement of ions in the ribosome

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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.
Cse1p

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movie: 4.6MB
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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.
Copper amine oxidase

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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.
Spin chemistry in cryptochrome

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The five human senses are based on amazingly sensitive molecular processes: smell and taste are based on molecular recognition, hearing and touch on molecular mechanics, vision on molecular electronic excitation. Some animals have additional sensory capabilities; for example, some possess a magnetic sense used for orientation by means of the geomagnetic field. The magnetic sense has long been poorly understood since the underlying molecular process could not be identified, but recently some progress has been made. Surprisingly, animal vision has been implicated and evidence has been accumulated that animals can see the geomagnetic field. A long-hidden receptor in the eye, a protein aptly called cryptochrome, is likely involved. Unfortunately, cryptochrome exists only in minute amounts in animal eyes, e.g., those of migratory birds, so that only behavioral measurements on animals can be taken, but not physical measurements directly on cryptochromes. Fortunately, cryptochromes exist also in plants where they control hypocotyl growth inhibition in seedlings. Experimentalists have observed that cryptochrome-dependent responses in Arabidopsis thaliana seedlings are magnetic-field-dependent. Researchers have now also computationally demonstrated that light activation of plant cryptochrome is magnetic-field-dependent. A recent report showed that light excitation leads to cascading electron transfer in which electron spins are influenced by weak magnetic fields; the spin dynamics was found to influence the activation of cryptochrome. Arabidopsis thaliana cryptochrome can be produced in quantities large enough for physical measurements so that the door is now wide open for cracking the secret behind the long-mysterious magnetic sense of animals. More on our cryptochrome web site.
NTF2 FG-repeat binding

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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.
Coarse-grained model of the reovirus core

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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.
Motion of the LOV domain

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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.
STMV

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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).

FG nucleoporin binding to importin-β

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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.

Holliday Junction

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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.

Nuclear Pore Complex

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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.

O2 gas diffusing to the hydrogenase active site

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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.

Nuclear Hormone Receptor - DNA Complexes

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Nuclear hormone receptors are cellular regulators which activate the transcription of specific genes in response to the binding of nuclear hormones. We studied the specificity of DNA recognition by the estrogen receptor protein. The role of water molecules at the protein-DNA interface and changes in the DNA structure between specific and non-specific binding were monitored and analyzed.

GBP adsorbed onto Au surface

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Through modelling and quantum chemical studies, the group is supporting the design of novel proteins in collaboration with M. Sarikaya, U. Washington, Seattle. It is hypothesized that electrostatic interactions between the polar residues of this genetically engineered polypeptide and the gold surface allow stronger adsorbtion onto the {111} surface than to other Au crystal faces, thus influencing the crystalization of gold in the presence of this polypeptide.

Myoglobin

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movie ( 3.6MB )

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.

Drude water

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movie (YouTube)

Most classical molecular dynamics (MD) simulations employ potential functions that do not account for the effects of induced electronic polarization between atoms, instead treating atoms as simple fixed point charges. Incorporating the influence of polarization in large-scale simulations is a critical challenge in the progress toward computations of increased fidelity, providing a more realistic and accurate representation of microscopic and thermodynamic properties. The Drude oscillator model represents induced electronic polarization by introducing an auxiliary particle attached to each polarizable atom via a harmonic spring. The advantage with the Drude model is that it preserves the simple particle-particle Coulomb electrostatic interaction employed in nonpolarizable force fields, thus its implementation in NAMD is more straightforward than alternative models for polarization. Performance results, reported in a recent paper, show that the implementation of the Drude model maintains good parallel scalability, with an increase in computational cost by not more than twice that of using a nonpolarizable force field. More details are available on the research webpage.
text pending

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movie1: 271KB,
movie2: 1.9MB, movie3: 5.7MB
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Ouch!! You cut your finger with a knife. Blood immediately starts coming out from the wound, and in a panic you search through your drawer for a band-aid. However, well before you can find the band-aid, and even before the "ouch" came out, just about the same time you sensed the pain, your body's self-healing mechanism was turned on. A multistep signaling cascade involving a dozen different proteins in the blood started immediately after the cut, calling for platelet cells to clog arround the wound and form a plug to stop the bleeding. How does our body sense a wound so fast? A possible answer is that the platelet cells carry on their surface a sensitive molecular flow sensor, a protein called GP1b, which senses erroneous blood flow caused by a cut in the blood vessel. It has been hypothesized that a small segment located on the alpha-subunit of GP1b, called the ▀-switch, transforms from a random coil to a ▀-hairpin in the presence of shear flow (see movies). The ▀-switch, in its ▀-hairpin form, is able to bind to a protein called von Willerbrand factor, which will then anchor the platelet to the damage site. To test this hypothesis, researchers resorted to computer simulation using the program NAMD and mimicked blood flow around GP1b. As reported here, researchers discovered that a long suspected part of GP1b indeed changes shape under flow conditions, the likely trigger of the body's self-healing system. For more information see our molecular flow sensor web site.
Integrin-RGD binding under force

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see also movie, 11.5MB
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One of the main unresolved problems in biological science is the time-scale and length-scale gap between computational and experimental methods of studying biological systems. Chemical and mechanical processes on an atomic level form the basis of all phenomena in living systems. The experimental non-invasive observation of such dynamic processes would be greatly beneficial for understanding how life works; however, usually experimental techniques do not achieve a resolution better than ms-&mus in time. On the other hand, there exist theoretical and computational methods, in particular molecular modeling, that enable the description of biological systems with all-atom detail. However up to now these approaches have been practically limited to simulation times and system sizes less than 100 ns and 10 nm, respectively. A possible way to extend molecular modeling and bridge it with experimental techniques is to use coarse-graining: to represent a system by a reduced (in comparison with an all-atom description) number of degrees of freedom. Due to the reduction in the degrees of freedom and elimination of fine interaction details, the simulation of a coarse-grained (CG) system requires less resources and goes faster than that for the same system in all-atom representation. As a result, an increase of orders of magnitude in the simulated time and length scales can be achieved. We have developed two CG approaches to address various scales in biomolecular simulations: the residue-based CG and the shape-based CG.
Integrin-RGD binding under force

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see also movie, 11.5MB
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Computer simulations have become an indispensable tool for revealing the molecular mechanism of biological processes. They could provide atomistic details of the processes that are hardly observed through experimental measurements. However, since biological processes, which are normally microsecond or even millisecond long, need to be followed in computer simulations femtosecond by femtosecond, simulating such processes in every atomistic detail is computationally challenging. Despite ever-growing computing power, computer simulations cannot be used for the modeling of large biomolecular systems over time scales long enough to be of biological interest. To overcome the challenge, coarse-grained models, in which multiple atomistic sites are grouped into one site, have been developed for components of biomolecular systems, such as proteins, solvent and membrane. The models significantly reduce computational cost and, thereby, enhance the speed of simulation. However, because of inherent simplification that omits important structural details of proteins, many coarse-grained simulations of proteins rely on information from native protein structures. The coarse-grained models are limited, therefore, in their use in studies of folding, aggregation, large conformational changes of proteins, or conformational features of intrinsically disordered proteins.
HIV-1 Capsid

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see also movie: 15.5MB
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Antiretroviral therapies against human immunodefficiency virus type 1 (HIV-1) have proven to be extremely effective to control viral load and infectivity. However, the virus is increasingly faster acquiring new resistance to antiretroviral drugs used in current treatments. Viral particles of HIV-1 contain conical cores (or ``cones'') formed by a protein shell composed of the viral capsid protein (CA). The capsid protein (CA) plays critical roles in both late and early stages of the infection process and is widely viewed as an important unexploited therapeutic target that could offer the best hope of generating drugs that are active against all HIV-1 variants. The study of the nature of HIV-1 disassembly has been particularly difficult due to the vulnerability of the capsid assembly to experimental manipulation. Although early work suggested that disassembly occurs immediately following viral entry in the cell, thus attributing a trivial role for the capsid in infected cells, recent data suggest that uncoating occurs several hours later and that the capsid has a pivotal role in several stages of the infection process, namely for transport towards the nucleus, reverse transcription and nuclear import. These findings suggest that the viral capsid interacts with the cytoskeleton and other cytoplasmic components of the host cell during its transport to the nucleus and that its stability is crucial for the success of the virus.

lambda folding

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see also movie, 7.8MB
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Proteins, made up of specified sequences of amino acid building blocks, are the workhorses of biological systems, performing most of the tasks necessary to maintain life. One of the greatest challenges in molecular biology today is that of determining how the sequence of a protein -- the exact ordering of amino acids it is composed of -- specifies its structure and function. Protein folding mechanisms have been extensively studied over the past few decades through both experimental and computational means, although the long timescales required for folding processes have meant that simulation of complete folding trajectories in explicit solvent were not possible until very recently. Instead, protein folding simulations have generally made use of coarse models, implicit solvent, or the use of very large ensembles of shorter trajectories to obtain information on the physical folding pathway. Recent advances, however, have made combined experimental and computaitonal studies of protein folding possible through the development and proteins that fold on the microsecond and even sub-microsecond timescale, and through advances in molecular dynamics (MD) simulations allowing simulation of multiple microsecond folding trajectories within a few months on modern supercomputers.

O2 Reactivity in Flavoproteins

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Molecular oxygen participates in numerous cellular processes but in most cases little is known about the mechanisms how oxygen reaches the reaction sites of the related proteins. However, in recent years specific oxygen access channels have been revealed for a number enzymes such as lipoxygenase, copper amine oxidase or glucose oxidase. In guiding oxygen to the catalytic site and by providing specific environmments for oxygen and the according reaction products these channels play significant roles in controlling O2 reactivity. There are many more promising candidates for oxygen access channels, especially among monooxygenases and oxidases from the flavoprotein family. In these enzymes, where O2 (re)oxidizes the reduced flavin cofactor, key questions regarding the control of O2 reactivity with the reduced flavin cofactor are still open.

Tamiflu Binding Pathway

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movie: Windows AVI or Apple MOV

The 2009-2010 outbreak of the H1N1pdm "swine" influenza caught not only its victims by surprise, but also biologists who had assumed that the virulence (and ultimately, lethality) of human flu viruses were generally limited to the elderly and immunocompromised. Most fatal cases of H1N1pdm, however, involved young previously healthy people, raising the possiblity that H1N1pdm may eventually mutate into a strain capable of killing even healthy individuals, such as in the 1918 flu pandemic where an estimated 50 to 100 million people died (approximately 3% of the 1.6 billion world population at the time). Even more alarming however, was that while the intiial strains of H1N1pdm appeared to be susceptible to conventional antiviral therapy, the strain has mutated quickly to become drug-resistant to the front line antiviral drug, oseltamivir (Tamiflu). Oseltamivir normally functions by binding to the flu protein neuraminidase and preventing the virus from budding out of its infected host cell after replication. This alarming discovery, that the virus has gained an upper hand on medicine, has raised grave concerns regarding an effective defense against subsequent influenza outbreaks. The H1N1pdm "swine" influenza virus is closely related to the 2003 H5N1 "avian" influenza virus for which oseltamivir-resistance due to two individual point mutations, H274Y and N294S, is well known. However, the mechanism behind why these mutations actually inhibit successful binding of oseltamivir to neuraminidase is not well understood. Furthermore the mutations are actually located some distance from the drug-protein binding site, suggesting that the mutations may disrupt the actual drug binding process rather than just forming an inhospitable environment for drug-protein endpoint interactions.

flu_res

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Influenza viral infections affect all populations of the world and represent a leading cause of mortality in elderly and immunecompromised populations. The 2009 A/H1N1 pandemic, now believed to have caused as many as ten times more deaths than originally estimated, clearly illustrated how drug resistant mutants can impact a population before a vaccine is available. The development of potent and effective antiviral drugs, therefore, is of paramount importance for stemming future epidemics. The influenza virus capsid contains two glycoproteins, namely hemagglutinin and neuraminidase. Neuraminidase in particular binds with sialic acid on respiratory tract epithelial cells, allowing attachment of the virus and the subsequent release of viral replicants. This sialic acid binding site is a viable target for neuraminidase inhibitors such as Tamiflu (oseltamivir) and Relenza (zanamivir); however, the emergence of drug resistant mutations (H274Y, N294S, and Y252H) to the A/H1N1 strain as well as the more common H5N1 strain has significantly limited the effectiveness of Tamiflu in particular, inducing a drug resistance anywhere from 81- to 256-fold over the wild type strains.

Lung surfactant protein

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Influenza is a highly contagious respiratory disease, estimated to cause 250,000 to 500,000 deaths worldwide each year. Before Influenza A virus (IAV) infection of the host is established, the virus encounters various lines of innate defenses, including an important class of mammalian innate immune proteins, namely proteins called collectins. Lung collectins are involved in the early pulmonary response to limit infection and spread of IAVs and other pathogens in the airways. By now, it is well established that among these collectins, surfactant protein D (SP-D) appears particularly important in the context of IAV. SP-D-mediated protection is primarily established by reducing the number of infectious particles via aggregation of viral particles, which prevents attachment of virus to the host respiratory epithelium and induces phagocytic responses resulting in enhanced viral clearance.

Methylated DNA

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Methylation of cytosine is a covalent modification of DNA, in which hydrogen H5 of cytosine is replaced by a methyl group. In mammals, 60% - 90% of all CpGs are methylated. Methylation adds information not encoded in the DNA sequence, but it does not interfere with the Watson-Crick pairing of DNA - the methyl group is positioned in the major groove of the DNA. The pattern of methylation controls protein binding to target sites on DNA, affecting changes in gene expression and in chromatin organization, often silencing genes, which physiologically orchestrates processes like differentiation, and pathologically leads to cancer.

RHDV

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made with VMD

DNA, a long linear molecule, is the carrier of genetic information. In the cell, each DNA molecule is packaged in a structure called chromosome. The ends of linear chromosomes are capped by structures known as telomeres to prevent fusion with neighboring chromosomes. Telomeres are maintained by an enzyme called telomerase during DNA replication. In order to do so, telomerase has to find the telomere region on DNA quickly and precisely. One telomerase is the protelomerase TelK, which binds to the ends of DNA, cleaves DNA strands and refolds cleaved DNA ends into hairpin telomeres in linear chromosomes of prokaryotes and viruses. Previous studies have shown that TelK is only active as a dimer. Researchers investigated the target-search mechanism of protelomerase TelK through single-molecule experiments and molecular dynamics simulation. It was revealed that as a monomer, TelK undergoes one-dimensional diffusion along non-specific DNA (without telomere sequence), and is able to bind to the target site preferentially. There, the target-immobilized monomer waits for a second binding partner to form an active protein complex. More on our TelK website.

Two pigment molecules (BChls) vibrating

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Excitation transfer between pigment molecules, such as bacteriochorophylls (BChls), and between pigment-protein light harvesting complexes, such as light harvesting complex 2 (LH2), has been investigated for many years using many different theoretical descriptions. Typically these descriptions include a priori assumptions about the dynamics of the system. Such assumptions are often made due to incomplete knowledge to make the system numerically tractable so that further insight can be gained. In the theoretical models of excitation transfer, it is often assumed that one parameter is much larger than another, allowing the system to be treated perturbatively. These assumptions, however, should be physically reasonable and should be tested if possible.

The Force Field Toolkit

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Structural biologists are increasingly turning to simulation methods to investigate the connections between molecular structure and biological function. Classical molecular dynamics (MD) simulations, such as those performed by the simulation software NAMD, rely on potential energy functions requiring parameters to describe atomic interactions within the molecular system. While these parameters are available for the most commonly simulated biopolymers (e.g., proteins, nucleic acids, carbohydrates), many small molecules and other chemical species lack adequate descriptions. The complexity of developing these parameters severly restricts the application of MD technologies across many fields, including most notably drug discovery. Researchers have developed software, the Force Field Toolkit (ffTK), that greatly reduces these limitations by facilitating the development of parameters directly from first principles. ffTK, distributed as a plugin for the molecular modeling softare VMD, addresses both theoretical and practical aspects of parameterization by automating tedious and error-prone steps, performing multidimensional optimizations, and providing quantitative assessment of parameter performance--all from within an easy-to-use graphical user interface. Additional information on ffTK, including documentation and screencast tutorials, can be found here.

Multilevel Summation Method in NAMD

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Long-range electrostatic interactions control macromolecular processes within living cells as prominent charges appear everywhere, such as in DNA or RNA, in membrane lipid head groups, and in ion channels. Reliable and efficient description of electrostatic interactions is crucial in molecular dynamics simulations of such processes. Recently a new mathematical approach for calculating electrostatic interactions, known as multilevel summation method (MSM), has been developed and programmed into NAMD 2.10 as reported here. Compared to the earlier decades-long approach, the particle-mesh Ewald (PME) method, MSM provides more flexibility as it permits non-periodic simulations like ones with asymmetric charge distributions across a membrane or of a water droplet with a protein folding inside. Furthermore, MSM is ideally suited for modern parallel computers, running, for example, simulations of large virus particles. More information here.