Protein-protein interactions are ubiquitous in biological system. Recognition of binding is a key to high affinity interactions of protein complexes. The fasciculins (FAS), 61-amino-acid peptides, are potent inhibitors of synaptic acetylcholinesterase. Four fasciculins have been characterized to date: FAS1 and FAS2 from the venom of Dendroaspis angusticeps, toxin C from the venom of D.polylepis and FAS3 from the venom of D.viridis . The sequences of FAS1 and FAS2 are nearly identical and differ only by one residue at the position 47. The dynamic nature of the encounter between FAS molecules and acetylcholinesterase can shed light on conformational variations before and after bindings. This work presents the dynamical study, in terms of the accessible conformational space, at sub-microsecond time scale. Employing principle component analysis and clustering analysis methods in analyzing the sub-microsecond molecular dynamics (MD) trajectories of FAS1 and FAS2, and compared with a 15-nanosecond MD simulation of FAS bound to acetylcholinesterase, the important modes of conformational variations and transitions of FAS upon complexation have been identified and will be discussed.

Complex systems are often characterized by rough and complicated energy landscapes with high barriers, and the transitions over these barriers are infrequent. Even though they are rare, such transitions play a central role in conformational switching in biomolecules. However, many of these slow transitions cannot be simulated directly using traditional molecular dynamics (MD) because of nanosecond timescale limitations. We show that our MD approach can accelerate the conformational transitions and extend the time scale in all-atom simulations of biomolecules. We also show that this technique allows for the thermodynamic and kinetic rate information to be recaptured. In deducing the kinetic rates, the relationship between the local energetic roughness of the energy landscape and the effective diffusion coefficient is established. We do not only recapture the slow kinetic rate information of the isomerization of serine-proline motifs, but also obtain the underlying local roughness of the energy landscape at atomistic resolution.

Electrostatics plays a central role in many biological processes. Continuum electrostatics methods and particularly numerical solutions to the Poisson-Boltzmann equation (PBE) have been shown to provide valuable insights into molecular interactions and function. Adaptive Poisson-Boltzmann Solver (APBS), state of the art software package for studying molecular electrostatic potentials has been recently interfaced with a powerful molecular viewing environment the Python Molecule Viewer (PMV). This provides an integrated environment for studying electrostatic properties of molecular system at different scales - from small molecules to extended macromolecular systems. Demonstration will include application of PBS/PMV to acetylcholinesterase, an important enzyme which participates in a signal transduction process.

The nicotinic acetylcholine receptor (nAChR) is a well characterized ligand gated ion channel yet a proper description of the mechanisms involved in gating, opening, closing, ligand binding, and desensitization does not exist. Until recently, atomic resolution structural information on the protein was limited, but with the production of the X-ray crystal structure of the L.stagnalis acetylcholine binding protein (AChBP) and the electron microscopy (EM) image of the transmembrane domain of the torpedo electric ray nicotinic channel, we were provided with a window to examine the mechanism by which this channel operates. A 15 nanosecond (ns) all-atom simulation of a homology model of the homomeric human α7 form of the receptor was conducted, in a solvated POPC bilayer, and examined in detail. The receptor was unliganded. The structure undergoes a twist-to-close motion that correlates movements of the C-loop in the ligand binding domain, via the β10-strand that connects the two, with the 10° rotation and inward movement of two non-adjacent subunits. The Cys-loop appears to act as a stator around which the α-helical transmembrane domain can pivot and rotate relative to the rigid β-sheet binding domain. The M2-M3 loop may have a role in controlling the extent or kinetics of these relative movements. All of this motion, along with essential dynamics analysis, is suggestive of the direction of larger motions involved in gating of the channel.

Traditional molecular dynamics (MD) methods employ fixed protonation states and so cannot adequately model the coupling between conformation and protonation state. We have implemented a new method for constant pH MD, employing generalized Born (GB) electrostatics. Monte Carlo (MC) sampling is conducted across discrete protonation states, which are modeled as different sets of partial charges. Use of GB-derived energies for MC allows rapid sampling of protonation states under a potential consistent with that used for MD. Application of the method to hen egg-white lysozyme (HEWL) produces substantially accurate protonation state populations, from which pKa values can be predicted with RMS error of 0.82 from experiment. Results are independent of starting crystal structure. Constant pH trajectories show a strong correlation between conformation and protonation state, underscoring the importance of sampling these properties concurrently.

The RBVI DASH (DAta SHaring) infrastructure meets the data-sharing and pipline management needs of collaborative team-based research projects by managing updates within a distributed set of data sources. DASH has a robust yet lightweight event-processing engine, which matches arbitrary "events" (a series of attribute / value pairs) to registered "handlers" based on configurable criteria. A graphical user interface will enable users to describe multi-step computational pipelines in terms of the data and processing protocols involved. DASH monitors registered data for changes, and then automatically invokes the appropriate processing pipeline(s). We describe the overall design of the DASH system and the application of a preliminary DASH implementation to a collaborative pharmacogenomics research project involving several dozen researchers located at different sites.

End-point free energy calculations have received increasing attention over the last decade. These methods combine gas phase energies from explicit solvent simulations with continuum solvation energies to evaluate the free energy of the bound and free states of a binding reaction. This work explores the importance of using compatible implicit and explicit solvent models. We report the effects of using different continuum parameter sets including a set of radii that have been recently optimized for Poisson-Boltzmann calculations with the AMBER (parm99) partial charges. These radii were benchmarked against explicit solvent electrostatic solvation energies to provide the optimal explicit and implicit energetic agreement. Different radii were reported for abrupt and cubic spline smoothed surface definitions. We report the effect of these surface definitions on the measured free energies as well as their relative computational demand.

We will describe our research that has lead to a successful integration of sequence-based bioinformatics and atomic scale simulation on the Aldehyde Dehydrogenase (ALDH) family. This integration has resulted in compelling hypotheses concerning the molecular basis for two metabolic diseases as well as a novel enzyme mechanism. We developed and applied analyses that identify residues in biological macromolecules that confer specificity of interaction on the members of a paralogous family of molecules. The analysis uses the Kullback-Leibler (KL) distance; an information theory measure of entropy. Residues that have a high KL distance represent positions in the alignment where there are large systematic differences in the kinds of residues present in the two subfamilies (i.e., the defined subfamily under investigation and the rest of the alignment). This KL distance corresponds to the biological question of "What columns in an alignment most completely discriminate the subfamily or group from the rest of the alignment?" We also sought to better understand how these residues impact on the ALDH chemical mechanism. Therefore, we employed molecular dynamics (MD) simulation methods using both Molecular Mechanical (MM) potentials for studies of substrate binding and hybrid Quantum Mechanical (QM)/MM potentials for the subsequent reactions. The results suggest that the intermediate formed upon nucleophilic attack of the enzyme on the substrate is stabilized by a proton transfer from a mainchain amide. This proton transfer is supported by interactions with a residue with high group entropy. Mutating residues that disrupt this "second sphere" interaction could be the molecular basis behind two metabolic diseases.

The tetramer is the most important form for acetylcholinesterase in physiological conditions, i.e., in the neuromuscular junction and the nervous system. It is important to study the diffusion of acetylcholine to the active sites of the tetrameric enzyme in order to understand the overall signal transduction process in these cellular components.

Crystallographic studies revealed two different forms of tetramers, suggesting a flexible tetramer model for acetylcholinesterase. Using a recently developed finite element solver for the steady-state Smoluchowski equation, we have calculated the reaction rate for three mouse acetylcholinesterase tetramers using these two crystal structures and an intermediate structure as templates. Our results show that the reaction rates differ for different individual active sites in the compact tetramer crystal structure, and the rates are similar for different individual active sites in the other crystal structure and the intermediate structure. At 0 M ionic strength the reaction rates per active site for the tetramers are the same as that for the monomer, while at higher ionic strength, the rates per active site for the tetramers are about 67% to 75% of the rate for the monomer. As a comparison, the reaction rates per active site of a neutral ligand for the tetramers are only 1/4 to 1/3 of the rate for the monomer, indicating a strong rate enhancement by the electrostatic steering forces. This study also shows that the finite element solver is well suited for solving the diffusion problem within complicated geometries.