Bulletin of the American Physical Society
2017 Annual Meeting of the APS Mid-Atlantic Section
Volume 62, Number 19
Friday–Sunday, November 3–5, 2017; Newark, New Jersey
Session M1: Protein and DNA II |
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Chair: Brigita Urbanc, Drexel University Room: 235, Campus Center, NJIT |
Sunday, November 5, 2017 10:00AM - 10:36AM |
M1.00001: Enabling proton transfer in classical simulations Invited Speaker: Themis Lazaridis An important limitation of mainstream classical molecular dynamics simulations is the inability to make or break chemical bonds. This limitation is especially restrictive in regard to protons and hinders our ability to model processes involving proton transfer. Existing approaches for allowing proton transfer in the context of classical mechanics are still cumbersome and have not achieved widespread use and routine status. Here we consider a simple combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, hydroxide, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton and hydroxide diffusion in bulk water and carbon nanotubes and proton conductance in the gramicidin A channel. [Preview Abstract] |
Sunday, November 5, 2017 10:36AM - 10:48AM |
M1.00002: Role of interfacial water in the binding of two proteins Jose Caro, Kathleen Valentine, Josh Wand Molecular recognition by proteins is fundamental to biology. Specific contacts at the interface ($\Delta $H) and the release of solvating water (T$\Delta $S$_{\mathrm{solv}})$ are often assumed to govern binding energetics. Typically, T$\Delta $S$_{\mathrm{solv}}$ is obtained by calculating the surface area that becomes buried on binding, and by assuming a generic contribution from the hydrophobic effect. For some protein complexes, however, crystal structures display a large number of water molecules at the binding interface. This is the case for barnase-barstar, a protein-protein complex with over a dozen waters buried at the interface. Based on the entropy of fusion of water, this represents a very large energetic penalty. Yet, the complex forms with femtomolar affinity ($\Delta $G$_{\mathrm{bind}}$ \textasciitilde 80 kJ/mol). Interestingly, 9 of the buried waters are also observed in the crystal structure of unbound barnase. To evaluate the role of specific hydration in barnase-barstar, we used nuclear Overhauser (NOE) NMR methods to detect magnetization transfer between amide protons and water. The NOEs detected for both the free and bound states of barnase are consistent with the crystallographic waters observed. Order parameters of side chains directly hydrogen bonded to the rigid waters are also consistent with a pre-organized interface. NOE experiments performed in the confined, water-depleted space of a reverse micelle enabled detection of binding-induced changes in protein-water interactions far from the interface. [Preview Abstract] |
Sunday, November 5, 2017 10:48AM - 11:00AM |
M1.00003: Effects of Trimethylamine-N-oxide on the Conformation of Peptides and Proteins Zhaoqian Su, Farbod Mahmoudinobar, Cristiano Dias To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. Effects of TMAO on the charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins which would accounts for swelling of hydrophobic cores and stabilization of charge-charge interactions. These mechanisms are studied from replica exchange molecular dynamics simulations of the Trp cage miniprotein.~ [Preview Abstract] |
Sunday, November 5, 2017 11:00AM - 11:12AM |
M1.00004: Computational study of DNA-mediated self-assembly using coase-grained model Runfang Mao, Jeetain Mittal The ability to rationally design and synthesize complex nano-, micro-, and hierarchically structured materials with tunable functionality represents a holy grail that holds exciting promise for revolutionizing materials applications spanning catalysis, molecular sensing, drug delivery, molecular and charge manipulation, and beyond. Such applications hinge upon precise control over morphology, topology, material connectivity, and function, and demand accommodation of a wide range of materials compositions spanning organic, inorganic, and hybrid structures. One of the most promising approach to achieve such unprecedented control over colloidal self-assembly is to use DNA-mediated interactions between particles functionalized with partially complementary DNA sequences. In general, DNA functionalized particles have several adjustable parameters: the hybridization interaction strength, temperature, DNA chain length and so on. Using molecular dynamics simulations of a coarse-grained model developed specifically to study such systems, we show that variations in these key factors leads structure from amorphous to crystallization. In addition, the optimized design parameters that favored crystallization is carefully investigated. [Preview Abstract] |
Sunday, November 5, 2017 11:12AM - 11:48AM |
M1.00005: Asymmetric Breathing Motions of Nucleosomal DNA and the Role of Histone Tails Invited Speaker: Sharon Loverde The most important packing unit of DNA in the eukaryotic cell is the nucleosome [1]. It undergoes large-scale structural re-arrangements during different cell cycles [1,2]. For example, the disassembly of the nucleosome is one of the key steps for DNA replication, whereas reassembly occurs after replication. Thus, conformational dynamics of the nucleosome is crucial for different DNA metabolic processes. We perform three different sets of atomistic molecular dynamics (MD) simulations of the nucleosome core particle at varying degrees of salt conditions for a total of 0.7 microseconds simulation time. We find that the conformational dynamics of the nucleosomal DNA tails are oppositely correlated from each other during the initial breathing motions [3]. Furthermore, the strength of the interaction of the nucleosomal DNA tail with the neighboring H2A histone tail modulates the conformational state of the nucleosomal DNA tail. With increasing salt concentration, the degree of asymmetry in the conformation of the nucleosomal DNA tails decreases as both tails tend to unwrap. This direct correlation between the asymmetric breathing motions of the DNA tails and the H2A histone tails, and its decrease at higher salt concentrations, may play a significant role in the molecular pathway of unwrapping. [1] McGinty, R. K, Tan, S. Chemical Reviews 115, 2255 (2015). [2] Muller, M. M, Muir, T. W. Chemical Reviews 115, 2296 (2015). [3] Chakraborty, K., Loverde, S.M. Journal of Chemical Physics 147, 165101 (2017). [Preview Abstract] |
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