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Inclusion of ph Effects in Molecular Dynamics Simulations of Membranes and Membrane Proteins
646a
Wednesday, March 2, 2016
glucose, mannose and galactose with water molecules to calculate spectra of water molecules. We demonstrate that the number of water molecules around typical hydroxyl is different between each monosaccharide. The result shows that the equatorial hydroxyl is more hydrated than the axial one because of steric inhabitation. However, hydroxyl next to oxygen doesn’t change between equatorial and axial. Spectra of water molecules in the bulk agree with that obtained by experiments. The spectra calculated by correlation function of relative velocity include three peeks which is related to typical motions of water molecule, angular, stretching and tumbling. The difference spectra between sugar solution and bulk shows that there are two larger changes around two peaks, angular and stretching motions, and the largest peak of angular is galactose, followed by mannose and glucose in this order. These results show the difference of hydration around carbohydrates can be identified by theoretical simulation and we can also identify the spectra change of water molecules. 3188-Pos Board B565 Inclusion of ph Effects in Molecular Dynamics Simulations of Membranes and Membrane Proteins Brian K. Radak1, Abhishek Singharoy2, Klaus Schulten2, Benoit Roux1. 1 Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA, 2Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA. Standard molecular simulation methods based on classical force fields typically assume only a fixed protonation state of systems. This assumption generally only permits a limited treatment of pH effects, for example, consideration of extreme acidic/basic conditions or situations where a small number of protonation states can be explicitly enumerated. Importantly, the standard approach cannot be scaled to chemical systems with a large number of titrateable sites such as lipid head groups or assemblies of protein subunits. Here we describe the development and application of a scalable and extensible method for including pH effects in molecular dynamics simulations. In contrast to other constant pH methods, the new method, based on a hybrid of non-equilibrium molecular dynamics and Monte Carlo, can be easily scaled to handle large heterogeneous systems, i.e., not only globular proteins. We present a validation of the method and its implementation in the program NAMD. Finally, we also present proof of concept studies on large biomolecular membrane systems. 3189-Pos Board B566 Improved Parameterization of Amine-Carboxyate, Amine-Phosphate, and Aliphatic Carbon-Carbon Interactions for Molecular Dynamics Simulations using the Charmm and Amber Force Fields Jejoong Yoo, Aleksei Aksimentiev. University of Illinois at Urbana-Champaign, Champaign, IL, USA. Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields—which were developed and validated using relatively short simulations of small molecules—become apparent. One common artifact is artificial aggregation of water-soluble biomolecules, which has been observed in a variety of systems, including electrolyte solutions, intrinsically disordered proteins, lipid bilayer membranes and DNA arrays. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine-carboxyate, aminephosphate, and aliphatic carbon-carbon interactions, which brings the results of MD simulations of proteins, nucleic acids, and lipids in remarkable agreement with experiments. To refine the amine-carboxylate and aliphatic carbon-carbon interactions, we matched the simulated osmotic pressure of amino acid solutions to the experimental data. Similarly, we refined the amine-phosphate interaction by matching the simulated and experimental osmotic pressure of a DNA array. We demonstrate the utility of our NBFIX corrections through simulations of lysine-mediated DNA—DNA forces, lipidbilayer membranes and folded proteins. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing any new artifacts. 3190-Pos Board B567 Improved Lennard-Jones Parameters for Accurate Molecular Dynamics Simulations Eliot Boulanger1, Lei Huang1, Alexander D. MacKerell, Jr.2, Benoit Roux1. 1 University of Chicago, Chicago, IL, USA, 2University of Maryland, Baltimore, MD, USA. The outcome of molecular dynamics simulation highly depends on the quality of the force field parameters used. While bonded and electrostatic parameters can be obtained automatically using gas phase quantum mechanical computations, the van der Waals parameters need systematic parameterization against experimental liquid phase data. In most cases, those parameters haven’t been
significantly refined since the early parameterization of additive force fields and their improvement appears as a mandatory step toward the development of a more accurate model. We collected the density, the heat of vaporization, and the solvation free energies of more than 500 compounds from experimental data. Those molecules were carefully picked to encompass all types of atomic van der Waals parameters for C, H, N, O, S, P, F, Cl and Br which are commonly used to simulate biomolecular systems and for drug design. As a starting point, we used the Lennard-Jones parameters of the General Amber Force Field (GAFF) as well as their bond and angle terms. The electrostatic and dihedral terms where reparameterized using the General Automated Atomic Model Parameterization (GAAMP). We ran liquid and gas phase simulations of the selected compounds to compute the different properties and optimize parameters by using analytical first derivatives of density and heat of vaporization. The solvation free energies will then be used for validation. Significant improvement on the prediction of the different experimental properties could be obtained. Further more, we could determine two additional atom types in order to reproduce experimental data more accurately. The parameters will be made globally accessible through the GAAMP web server and efforts are put into place to extend this approach to the Drude oscillator polarizable force field.
Optical Microscopy and Super-Resolution Imaging III 3191-Pos Board B568 Investigating the Dynamics of Vibrio Cholerae Virulence Initiation by Stics and Single Molecule Tracking Josh Karslake1, David J. Rowland1, Chanrith Siv1, Victor J. DiRita2, Julie S. Biteen3. 1 Biophysics, University of Michigan, Ann Arbor, MI, USA, 2Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA, 3 Chemistry, University of Michigan, Ann Arbor, MI, USA. Single molecule imaging techniques have provided insight into a vast realm of new biological processes. However, many of these techniques rely on capturing a sufficiently high number of emitted photons to localize a molecule and can thus fail when the photon count is low. In a system where a large fraction of the fluorescent labels are very dim and/or moving quickly, localization methods can fail or be biased toward the slowest and brightest molecules in the system. Fortunately, correlation-based methods can provide insight into dynamics in these systems. Spatio-Temporal Image Correlation Spectroscopy (STICS) uses the full spatiotemporal correlation of a fluorescent image time series to provide information such as the diffusion constants and the densities of fluorescent molecules. STICS does not rely on the emitters positions and thus operates with higher precision in systems where sub-diffraction limited localization fails. We have previously developed STICS for imaging single molecules in living bacteria cells, and here we apply STICS to the specific case of the V. cholerae virulence signaling pathway. In particular, the membrane-bound TcpP, which controls downstream expression of the cholera enderotoxin, is a dynamic protein whose behavior is believed to be affected by various environmental signals including temperature and specific small molecule hormones. Here, we examine the fluorescent signals from single molecules of TcpP fused at the native locus to the photoactivatable fluorescent protein PAmCherry. We analyze these data by STICS and single molecule tracking to compare these two techniques in realistic imaging conditions. Because each technique operates with higher precision in a different imaging regime, we conclude that these approaches used together can provide highly complementary information about the dynamics of TcpP. 3192-Pos Board B569 Super-Resolution Imaging of DNA Replisome Dynamics in Live Bacillus Subtilis Yilai Li1, Jeremy W. Schroeder1, Yi Liao2, Lyle A. Simmons1, Julie S. Biteen1. 1 University of Michigan, Ann Arbor, MI, USA, 2The University of Chicago, Chicago, IL, USA. DNA replication happens in all living organisms, and assures that the genome is accurately copied and maintained. The replisome is the molecular machine in cells that replicates DNA, and it is composed of several different proteins, including DNA polymerases, which directly synthesize DNA by adding nucleotides. Although the bacterial replisome has been studied extensively in vitro, little is known about the dynamics and architecture of replisome components in vivo. Here we use Bacillus subtilis, a Gram-positive bacterium commonly found in soil, as a model organism in which to study the architecture and
Wednesday, March 2, 2016
glucose, mannose and galactose with water molecules to calculate spectra of water molecules. We demonstrate that the number of water molecules around typical hydroxyl is different between each monosaccharide. The result shows that the equatorial hydroxyl is more hydrated than the axial one because of steric inhabitation. However, hydroxyl next to oxygen doesn’t change between equatorial and axial. Spectra of water molecules in the bulk agree with that obtained by experiments. The spectra calculated by correlation function of relative velocity include three peeks which is related to typical motions of water molecule, angular, stretching and tumbling. The difference spectra between sugar solution and bulk shows that there are two larger changes around two peaks, angular and stretching motions, and the largest peak of angular is galactose, followed by mannose and glucose in this order. These results show the difference of hydration around carbohydrates can be identified by theoretical simulation and we can also identify the spectra change of water molecules. 3188-Pos Board B565 Inclusion of ph Effects in Molecular Dynamics Simulations of Membranes and Membrane Proteins Brian K. Radak1, Abhishek Singharoy2, Klaus Schulten2, Benoit Roux1. 1 Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA, 2Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA. Standard molecular simulation methods based on classical force fields typically assume only a fixed protonation state of systems. This assumption generally only permits a limited treatment of pH effects, for example, consideration of extreme acidic/basic conditions or situations where a small number of protonation states can be explicitly enumerated. Importantly, the standard approach cannot be scaled to chemical systems with a large number of titrateable sites such as lipid head groups or assemblies of protein subunits. Here we describe the development and application of a scalable and extensible method for including pH effects in molecular dynamics simulations. In contrast to other constant pH methods, the new method, based on a hybrid of non-equilibrium molecular dynamics and Monte Carlo, can be easily scaled to handle large heterogeneous systems, i.e., not only globular proteins. We present a validation of the method and its implementation in the program NAMD. Finally, we also present proof of concept studies on large biomolecular membrane systems. 3189-Pos Board B566 Improved Parameterization of Amine-Carboxyate, Amine-Phosphate, and Aliphatic Carbon-Carbon Interactions for Molecular Dynamics Simulations using the Charmm and Amber Force Fields Jejoong Yoo, Aleksei Aksimentiev. University of Illinois at Urbana-Champaign, Champaign, IL, USA. Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields—which were developed and validated using relatively short simulations of small molecules—become apparent. One common artifact is artificial aggregation of water-soluble biomolecules, which has been observed in a variety of systems, including electrolyte solutions, intrinsically disordered proteins, lipid bilayer membranes and DNA arrays. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine-carboxyate, aminephosphate, and aliphatic carbon-carbon interactions, which brings the results of MD simulations of proteins, nucleic acids, and lipids in remarkable agreement with experiments. To refine the amine-carboxylate and aliphatic carbon-carbon interactions, we matched the simulated osmotic pressure of amino acid solutions to the experimental data. Similarly, we refined the amine-phosphate interaction by matching the simulated and experimental osmotic pressure of a DNA array. We demonstrate the utility of our NBFIX corrections through simulations of lysine-mediated DNA—DNA forces, lipidbilayer membranes and folded proteins. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing any new artifacts. 3190-Pos Board B567 Improved Lennard-Jones Parameters for Accurate Molecular Dynamics Simulations Eliot Boulanger1, Lei Huang1, Alexander D. MacKerell, Jr.2, Benoit Roux1. 1 University of Chicago, Chicago, IL, USA, 2University of Maryland, Baltimore, MD, USA. The outcome of molecular dynamics simulation highly depends on the quality of the force field parameters used. While bonded and electrostatic parameters can be obtained automatically using gas phase quantum mechanical computations, the van der Waals parameters need systematic parameterization against experimental liquid phase data. In most cases, those parameters haven’t been
significantly refined since the early parameterization of additive force fields and their improvement appears as a mandatory step toward the development of a more accurate model. We collected the density, the heat of vaporization, and the solvation free energies of more than 500 compounds from experimental data. Those molecules were carefully picked to encompass all types of atomic van der Waals parameters for C, H, N, O, S, P, F, Cl and Br which are commonly used to simulate biomolecular systems and for drug design. As a starting point, we used the Lennard-Jones parameters of the General Amber Force Field (GAFF) as well as their bond and angle terms. The electrostatic and dihedral terms where reparameterized using the General Automated Atomic Model Parameterization (GAAMP). We ran liquid and gas phase simulations of the selected compounds to compute the different properties and optimize parameters by using analytical first derivatives of density and heat of vaporization. The solvation free energies will then be used for validation. Significant improvement on the prediction of the different experimental properties could be obtained. Further more, we could determine two additional atom types in order to reproduce experimental data more accurately. The parameters will be made globally accessible through the GAAMP web server and efforts are put into place to extend this approach to the Drude oscillator polarizable force field.
Optical Microscopy and Super-Resolution Imaging III 3191-Pos Board B568 Investigating the Dynamics of Vibrio Cholerae Virulence Initiation by Stics and Single Molecule Tracking Josh Karslake1, David J. Rowland1, Chanrith Siv1, Victor J. DiRita2, Julie S. Biteen3. 1 Biophysics, University of Michigan, Ann Arbor, MI, USA, 2Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA, 3 Chemistry, University of Michigan, Ann Arbor, MI, USA. Single molecule imaging techniques have provided insight into a vast realm of new biological processes. However, many of these techniques rely on capturing a sufficiently high number of emitted photons to localize a molecule and can thus fail when the photon count is low. In a system where a large fraction of the fluorescent labels are very dim and/or moving quickly, localization methods can fail or be biased toward the slowest and brightest molecules in the system. Fortunately, correlation-based methods can provide insight into dynamics in these systems. Spatio-Temporal Image Correlation Spectroscopy (STICS) uses the full spatiotemporal correlation of a fluorescent image time series to provide information such as the diffusion constants and the densities of fluorescent molecules. STICS does not rely on the emitters positions and thus operates with higher precision in systems where sub-diffraction limited localization fails. We have previously developed STICS for imaging single molecules in living bacteria cells, and here we apply STICS to the specific case of the V. cholerae virulence signaling pathway. In particular, the membrane-bound TcpP, which controls downstream expression of the cholera enderotoxin, is a dynamic protein whose behavior is believed to be affected by various environmental signals including temperature and specific small molecule hormones. Here, we examine the fluorescent signals from single molecules of TcpP fused at the native locus to the photoactivatable fluorescent protein PAmCherry. We analyze these data by STICS and single molecule tracking to compare these two techniques in realistic imaging conditions. Because each technique operates with higher precision in a different imaging regime, we conclude that these approaches used together can provide highly complementary information about the dynamics of TcpP. 3192-Pos Board B569 Super-Resolution Imaging of DNA Replisome Dynamics in Live Bacillus Subtilis Yilai Li1, Jeremy W. Schroeder1, Yi Liao2, Lyle A. Simmons1, Julie S. Biteen1. 1 University of Michigan, Ann Arbor, MI, USA, 2The University of Chicago, Chicago, IL, USA. DNA replication happens in all living organisms, and assures that the genome is accurately copied and maintained. The replisome is the molecular machine in cells that replicates DNA, and it is composed of several different proteins, including DNA polymerases, which directly synthesize DNA by adding nucleotides. Although the bacterial replisome has been studied extensively in vitro, little is known about the dynamics and architecture of replisome components in vivo. Here we use Bacillus subtilis, a Gram-positive bacterium commonly found in soil, as a model organism in which to study the architecture and