A Novel United-Atom Force Field for Phosphatidylglycerols

150a Sunday, March 6, 2011 813-Pos Board B613 Ab-Initio Protein Folding and Small Molecule Dissociation by Potential Energy Based Biased Molecular Dynamics Gavin Bascom. Molecular dynamics simulations provide increasingly accurate methods for characterizing biomolecular dynamics. However such simulations typically explore dynamics on the ps to ns timescale, while most processes of interest tend to occur on the ms to s timescale. As such there is a need enhanced for sampling methods to overcome this timescale issue. We propose a novel enhanced sampling method in which the dihedral and/or non-bonded potential energy terms are gently biased, such that the system is driven towards lower or higher energy conformations. Preliminary results show particular promise in the area of protein folding and small molecule dissociation. Several small proteins including an alpha helix, hairpin beta sheet, and TRP-CAGE motifs have been folded from extended conformations to within 1 A of their crystal structures with no previous knowledge of said crystal structures. Furthermore, the technique was found to drive dissociation of the avidin-biotin drug complex in under 1 ns. It is anticipated that this method can be extended to all flexible polymers such as DNA, RNA, and proteins. It is also anticipated to increase viability of small molecule binding simulations, allowing for locally enhanced sampling of association/dissociation events. 814-Pos Board B614 Computational Studies of Interfacial Binding Dynamics of Phospholipase A2 Anna Manukyan, Themis Lazaridis. The primary function of secreted Phospholipase A2 (sPLA2) is to catalyze the hydrolysis of the sn-2 ester bond of phospholipids. The interaction of sPLA2 with phospholipid membranes has been considered to be a basic mechanism for the biological function of the protein. Despite a wealth of experimental data available, the conformational and energetic changes of these proteins during the adsorption process remain poorly understood. In this study, the interaction of sPLA2 with the lipid bilayer was investigated by MD simulations using an implicit membrane model (IMM1). The principal goal of this work is to identify the molecular determinants on PLA2 surface that are required for interfacial binding, and to characterize the conformational changes associated with the activation of enzyme. In 50ns MD simulations, starting from six different initial positions of the protein, sPLA2 consistently adopts an orientation with respect to the membrane, in very close agreement with the known EPR data. Our simulations have also predicted the experimentally obtained distribution of polar and hydrophobic residues on the interfacial binding surface. The association of sPLA2 with membrane is accompanied by conformational changes in the secondary structure of the protein. The most important change includes the movement of the N-terminal helix towards the calcium binding loop. The hydroxyl of the active site Tyr52, along with catalytic Asp49 residue, participates in a hydrogen-bonding network that connects the catalytic site to the N-terminal region on the enzyme surface. The determinants of substrate specificity are explored by investigating the energetic consequences of phospholipid binding and conformational changes in the active site during the binding process to anionic membrane. 815-Pos Board B615 Molecular Dynamics Simulation of Solid-Supported Lipid Bilayers In-Chul Yeh, Anders Wallqvist. Systems consisting of a solvated bilayer adsorbed on a solid surface and exposed to an air/vacuum interface occur in many experimental settings. Here, we investigated the effects of implementing different electrostatic boundary conditions in molecular dynamics simulations of a quartz-supported hydrated lipid bilayer exposed to vacuum. Since these interfacial systems have a net polarization, implementing the standard Ewald summation with the conducting boundary condition for the electrostatic long-range interactions introduced an artificial periodicity in the out-of-plane dimension. In particular, abnormal orientational polarizations of water were observed with the conducting boundary condition. Implementing the Ewald summation technique with the planar vacuum boundary condition and calculating electrostatic properties compatible with the implemented electrostatic boundary condition removed these inconsistencies. This formulation is generally applicable to similar interfacial systems in bulk solution. 816-Pos Board B616 Molecular Dynamics Study of Calmodulin-Target Complexes Dayle Smith, T.P. Straatsma, Thomas C. Squier. The change in calmodulin’s conformational entropy upon binding to target peptides favorably influences target binding thermodynamics. Experiments by Wand and co-workers (Nature 19, 2007, 325–329) demonstrated that calmodulin conformational entropy calculated from NMR order parameters correlates linearly with the overall binding entropy from isothermal titration calorimetry and is a significant contributor to binding affinity, a hypothesis that can be directly tested using computational molecular dynamics. We calculated 100 nanosecond trajectories for calcium-saturated calmodulin and five of the six calmodulin-target complexes from the Wand study for which structures are available (CaMKK, CaMK1, smMLCK, eNOS and nNOS) using fully atomistic, explicit solvent, constant temperature and pressure (300 K, 1 atm) molecular dynamics with the AMBER03 force field and the TIP3P solvent model. These simulations enabled us to compare the low- and high-frequency CaM motions associated with target binding and the conformational entropy changes associated with the process using the quasiharmonic approximation. The calculated entropies of CaM bound to the targets relative to unbound CaM correlate extremely well with the NMR-derived conformational entropies and ITC binding entropies (correlation coefficients R are 0.89), and trajectory analysis revealed that observed binding entropies are due to increased helix flexibility in calmodulin’s N-domain and the motion of CaM residues with long sidechains, particularly methionines and glutamates, consistent with the induced-disorder description of peptide binding to flexible proteins (Molecular Pharmaceutics, 2009, 430–437). 817-Pos Board B617 Characterization of Osteogenesis Imperfecta Mutations in Type I Collagen: A Molecular Dynamics Study Ashley E. Marlowe, Yaroslava G. Yingling. Osteogenesis Imperfecta is a disease characterized by too little collagen in the body, causing brittle bones, permanent disfigurement, and often death. Collagen, the most prevalent protein in the human body, could be used in tissue engineering if the mechanism of mutations is determined. To provide fundamental understanding of the molecular basis of this disease, extensive molecular dynamics simulations were conducted. A Glycine-Proline-Hydroxyproline tropocollagen molecule was used as a building block for a fibril that consists of seven tropocollagen strands. The central tropocollagen molecule was modified to include typical mutations present in the diseased collagen. Specifically, mutations of Glycine to Alanine, Aspartic Acid, Cysteine, and Serine and mutations of Hydroxyproline to Arginine, Asparagine, Glutamine, and Lysine were included in this study. We found that mutations disrupt hydration and the electrostatics pattern of the collagen fiber. Moreover, the fibril diameter increases as a result of mutations of both Glycine and Hydroxyproline amino acids. Steered molecular dynamics was used to determine the binding, shear, and tensile mechanical properties of the affected collagen fibrils. It was determined that the wild type tropocollagen molecule has better mechanical properties, which means that the point mutations weaken the tropocollagen. Our results indicate that the lysine mutation dramatically destabilized tropocollagen chemical and mechanical properties, which explains the high death rate related to this mutation. 818-Pos Board B618 The Equilibrium of Cholesterol DPPC Lipid Bilayers in Atomistic Molecular Dynamic Simulations Kun Huang, Angel E. Garcia. The lateral diffusion of lipids in lipid bilayers is a slow process accompanied with strong concerted motion of neighboring lipids. When a second component, e.g., cholesterol, is added to the bilayer the lateral organization of the bilayer relax slowly toward equilibrium. Here we explore the onset of equilibrium in simulations using molecular dynamics (MD) and constant pressure replica exchange molecular dynamics (REMD) simulations. We study the time evolution of structural ensembles that characterize the structure of the lipid-cholesterol mixture and show that in MD equilibrium is reached in the microsecond timescale. Replica Exchange Molecular Dynamics simulation (REMD) is able to take advantage of the larger diffusion rate at high temperature and consequently increase the mixing of different components. Comparing the result from REMD with MD simulations of 40% cholesterol-DPPC bilayers, we find that REMD not only achieves a faster equilibrium rate in the cholesterol lateral distribution, but also speeds up the dynamics of inner molecular structural properties such as cholesterol tilt angle and lipid acyl chain order parameters. Unreliable bilayers configurations induced by higher temperature replicas are not observed in the simulation. This work provides a novel method to quickly construct equilibrated binary lipids membranes that can be served as a startup to study the interaction between these bilayers and membrane proteins or peptides. 819-Pos Board B619 A Novel United-Atom Force Field for Phosphatidylglycerols Jukka Määttä, Emppu Salonen, Luca Monticelli. Phosphatidylglycerols (PG)s are anionic lipids abundant both in prokaryotic membranes and in the chloroplast membrane of plants. In humans and animals PG lipids occur in minor amounts in pulmonary lung surfactants, blood cells and mitochondrial membranes. Similar to other negatively-charged phospholipids, PG has a very complex phase-behaviour: the phase transitions and structural organization of PG are affected both by temperature, pH, and concentration Sunday, March 6, 2011 of mono- and divalent cations. Furthermore, the glycerol moiety of the PG headgroup has a complex conformational space in aqueous media, because of the presence of vicinal hydroxyl groups that are capable of of stabilizing various conformers through hydrogen bonds (H-bonds). In this work a novel united-atom force field is constructed for PG lipids as a part of the ongoing development of a large, consistent lipid force field library. The torsional and partial atomic charge parameters were calculated based on highlevel ab initio quantum mechanical (QM) calculations with semiempirical molecular mechanics (MM) studies. The Lennard-Jones parameters were taken from the OPLS-UA force field developed by Jorgensen [1]. The QM and MM simulations were combined with experimental thermodynamic data of glycerol as target data for parameter optimization. The parameters were further optimized to reproduce the structural, dynamic and elastic properties of pure DMPG and POPG lipid bilayers. [1] W. L. Jorgensen, J. Phys. Chem. 1986, 90, 1276–1284. 820-Pos Board B620 Temperature Modulation of the Life Cycles of Phospholipid Bilayer Electropores Zachary A. Levine, P. Thomas Vernier. Molecular-scale details of the mechanism of electric field-driven pore formation in phospholipid bilayers are not well understood, in part because the nanoscopic domain at which individual pore formation occurs is not readily accessible to experimental observation. Analytical and numerical models can help to fill this void. Previous studies using molecular dynamics (MD) simulations defined the stages in the creation and annihilation of an electropore as a function of the externally applied electric field, from the formation of an initial water defect to the restoration of the intact bilayer [1]. Here we vary the temperature at which electropermeabilization occurs, and we extract heat capacity and energy profiles for each system. Results will be compared to and, to the extent possible at this time, reconciled with existing mathematical models of electroporation, presenting a more unified and complete framework for future studies. [1] Levine, Z. A. and P. T. Vernier. 2010. Life Cycle of an Electropore: FieldDependent and Field-Independent Steps in Pore Creation and Annihilation. Journal of Membrane Biology 236:27–36. 821-Pos Board B621 Nucleotide Modifications Change TRNA Dynamics and Base Pairing Christian Blau, Gerrit Groenhof, Helmut Grubmüller. Modified and unmodified yeast tRNA(Phe) in solution was simulated to understand the effect of nucleotide modifications on the dynamics of tRNA. High performance computing techniques were employed to obtain a ‘‘dynamic picture’’ at spacial and time resolutions hardly accessible experimentally for these systems. Local flexibility, secondary and tertiary structure, global rearrangements and movements of the whole tRNA were probed by a microsecond of all atom explicit solvent molecular dynamics simulations. The results of our simulations give new insight on experimentally observed biological impact of nucleotide modifications. Amongst other results we find that tRNA modification leads to a decrease in secondary structure and tertiary interactions in the anticodon stem loop. Nucleotides U16 and U17 show different orientations when modified to dihydrouridine. Modification of A58 to 1-methyladenosine causes local rearrangements in the elbow region. Implications of our results on external factor binding are discussed. 822-Pos Board B622 Molecular Dynamic Simulations of Blast Waves on Bilayers Rahul Bhowmik, Richard W. Pastor, Jeffrey T. Mason. Many studies using animal models have shown that blast waves cause injuries to the brain despite the lack of a direct physical impact to the brain or skull. Such injuries are manifested as biochemical, functional, or morphological alterations that result in motor and sensory deficits in addition to behavioral changes. Primary blast due to explosions causes an intense rise of atmospheric pressure, the positive phase, followed by a broader under-pressure, the negative phase. The peak overpressure reaches pressures up to 1724 kPa and the blast wave travels at speeds up to 670 m/s. Because of this high velocity, it is difficult to study the interaction of explosive blast waves with neural tissue in real time. Accordingly, we have performed molecular dynamic (MD) simulations of blast waves on myelin membranes to understand how blast waves interact with neural tissue to cause injury. In our simulations, we have created blast overpressure using a planar wall, which exerts a forces of -K(x0 - x)2; where K is the spring force constant, and x0 and x are the starting and final positions of the wall, respectively. The intensity of the overpressure wave is controlled by the spring stiffness (K) and the duration of the wave is controlled by how far the wall moves (x0 - x). Our findings demonstrate that the velocity of the blast wave is more deleterious to membranes than is the blast overpressure. At velocities above 600 m/s the negative phase can cause bilayers containing phospholipid 151a and cholesterol to bifurcate at the bilayer center. Such structural perturbations could result in diffuse axonal injury, which is believed to play a role in the pathology of blast injury. Emerging Single Molecule Techniques Fluorescence 823-Pos Board B623 Observation of Protein Adsorption Using a Synthetic Nanopore David J. Niedzwiecki, Liviu Movileanu. Using the coulter counter technique with a single nanopore, we probed the nonspecific adsorption of bovine serum albumin (BSA) to a silicon-based surface at the single molecule level. A potential bias was applied across a silicon nitride membrane containing a single nanopore that was immersed in KCl solution. Ionic current fluctuations across the nanopore revealed long-lived interactions of BSA with the silicon nitride. The nature of these interactions can be classified into two categories, suggesting that BSA adheres to the nitride surface in two distinct orientations. Knowing how proteins from the blood, like BSA, interact with silicon based materials is of growing importance as these materials are integrated into biosensors and medical devices. Acknowledgements: This research was supported by the NSF grant (DMR-0706517 and HRD0703452) and the National Institutes of Health (R01 GM088403). 824-Pos Board B624 Force-Free Three-Dimensional Measurements of DNA Conformations Reveals Its Behavior Close to a Wall Yuval Garini, Guy Nir, Shlomi Medalion, Yitzhak Rabin, Moshe Lindner. Using a combined setup of tethered particle motion (TPM) with gold nanobeads and total internal reflection (TIR) illumination, we measured the three dimensional end-to-end distribution of a DNA tethered to a wall. Although the lateral Gaussian distribution is well known and studied, the axial distribution was never measured before. The planar distribution (parallel to the wall) is found to be Gaussian, with good agreement to both the worm like chain (WLC) model and the commonly sued Gaussian random walk (GRW) model. The axial distribution (perpendicular to the surface) is found to be Rayleigh-like, in agreement with WLC simulations. The distribution that is found with these WLC simulations, however, deviates systematically from the GRW distributions for short DNA strands (less than 3 micrometer). The WLC simulations reveal that the presence of the wall increases the correlations between the orientations of neighboring segments with respect to free DNA. It can also be interpreted as an entropic repulsion due to rejection of polymer conformations from the wall. This repelling potential might play an important role in the DNA functioning when it is close to the nucleus membrane. 825-Pos Board B625 Tracking Degradations of Single DNA and Protein Molecules in Fluid Daisuke Onoshima, Noritada Kaji, Manabu Tokeshi, Yoshinobu Baba. Moving images obtained from optical microscopic studies with single biomolecules, including DNA and proteins, provide amazing insights into physico-chemical fundamentals such as dynamics and kinetics in a particular environment. Previously, the observation of large numbers of individual molecules has been used to detect identifiable individual chemical events or components of a chemical synthesis system. These may offer crucial clues towards intricate molecular mechanisms. Despite this importance, analytical applications still have lagged behind the establishment of theoretical principles. Based on the Michaelis-Menten equation, values for the reaction rate constants have traditionally been calculated from the solution phase reaction kinetics. This procedure is predictably effective for discussing a minimal model of the kinetics. However, most biomolecular interactions are thought to involve multiple steps, typically an initial binding followed by a structural rearrangement. Particular attention should be given to the fractionally-sampled molecular steps. Our analysis, described here, uses a technology to determine the detailed molecular information about interactions between DNA and DNA interactive protein. It uses motion capture technology that was originally developed for recording biomechanical movement onto a digital model. We applied it for motion tracking and position sensing of a single DNA molecule undergoing restriction enzyme digestion in a microfluidic device. Quantum dot and total internal reflection fluorescence microscope were used as a marker and a tracker respectively, which allowed motion capture of DNA during interfacial reactions. With our analysis, an enzymatic degradation time was detected at a single molecule level. It was also possible to calculate the observed catalytic rate constant. As an application case of our tracking measurement, protease activity of trypsin was monitored in real time. The geometrical features of the biological