Feb 14, 2017 - Michael F. Crowley1. 1National Renewable .... Joseph L. Baker1, Alexanndra Heyert2, Susan Knox3, Gerrick E. Lindberg2. 1Department of ...
Tuesday, February 14, 2017 2206-Pos Board B526 Systematic Parameterization of Lignin for the Charmm Force Field Josh V. Vermaas1, Loukas Petridis2, Gregg T. Beckham1, Michael F. Crowley1. 1 National Renewable Energy Laboratory, Golden, CO, USA, 2Oak Ridge National Laboratory, Oak Ridge, TN, USA. Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization for emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated, and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between disparate feedstocks, and guide further lignin engineering efforts. 2207-Pos Board B527 Simulated Forced Unbinding of Clustered Protocadherins Sanket P. Walujkar, Raul Araya-Sechhi, Marcos Sotomayor. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA. Clustered protocadherins belong to the cadherin superfamily of adhesion proteins and are involved in neuronal connectivity and self-recognition. Clustered protocadherins have six extracellular cadherin (EC) repeats with about 100 residues each. Recent crystallographic structures suggest an antiparallel homophilic binding interface that involves overlapped EC1 to EC4 repeats. Here, we present steered molecular dynamics simulations of a, b, and g clustered protocadherins homodimers exploring the forced unbinding of their adhesive interface. Constant velocity stretching simulations were performed on these homodimers at 10 nm/s, 1 nm/ns, 0.5 nm/ns, and 0.1 nm/ns. All protocadherins show some unfolding at the highest stretching speed, whereas simulations at slower speeds revealed unbinding pathways for the complex without unfolding. Force-extension profiles show broad force peaks that reflect the extended antiparallel interface of protocadherins, as well as the formation of transient interactions between protomers that break during unbinding. The unbinding pathways observed in simulations may help further elucidate the molecular basis of protocadherin binding specificity. 2208-Pos Board B528 Exploring Reaction Pathways for Peptidylprolyl-Isomerase Hiroshi Fujisaki1, Yasushige Yonezawa2, Motoyuki Shiga3, Luca Maragliano4, Shin-ichi Tate5. 1 Nippon Medical School, Musashino, Tokyo, Japan, 2Kindai Univ., Kainanshi, Wakayama, Japan, 3JAEA, Kashiwa, Chiba, Japan, 4Istituto Italiano di Tecnologia, Genova, Italy, 5Hiroshima Univ., Higashi-Hiroshima, Hiroshima, Japan. Pin1 enzyme is one of the peptidyl-prolyl cis/trans isomerases (PPIase), which isomerizes an omega bond of specific phospho-Serine/Threonine-Proline motifs, leading to many biological consequences. However, the isomerization mechanism has not been fully clarified yet though there are several experimental and numerical studies. For example, Tate and coworkers investigated a mutated (C113D) Pin1, and found that the isomerization rate is lower than that in the wild type [1], but it is difficult to understand the mechanism only from the experiment. Previously, Hamelberg and coworkers carried out molecular dynamics (MD) simulations of Pin1 with a model substrate, and because the isomerization process is a rare event, they used accelerated MD method
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[2] to enhance the sampling in configuration space. We here use temperature accelerated MD (TAMD) with several order parameters [3], and explore the free energy landscape for the isomerization process of Pin1. Combining with the string method [4], we will clarify the reaction pathways, and also examine the reaction rate using milestoning [5] or non-Markov type analysis of trajectories [6]. [1] Ning Xu et al. Biochemistry, 53, 5568-5578 (2014). [2] H.A. Velazquez and D. Hamelberg, J. Phys. Chem. B 117, 11509-11517 (2013). [3] H. Fujisaki, K. Moritsugu, Y. Matsunaga, T. Morishita, L. Maragliano, Front. Bioeng. and Biotechnol. 3: 125, Doi: 10.3389/fbioe.2015.00125. [4] L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 446, 182-190 (2007). [5] L. Maragliano, E. Vanden-Eijnden and B. Roux, J. Chem. Theory Comp. 5, 2589-2594 (2009). [6] E. Suarez, J.L. Adelman, and D.M. Zuckerman, J. Chem. Theor. Comput. DOI:10.1021/acs.jctc.6b00339. 2209-Pos Board B529 Mechanics of Cadherin Unbinding using Coarse-Grained Models Lahiru N. Wimalasena. Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA. Cell-cell adhesion is mediated by calcium-dependent proteins called cadherins, which are important in neuronal connectivity and tissue integrity. Cadherins are modular proteins with large extracellular domains that have typically been modeled using all-atom molecular dynamics (MD) simulations. However, these simulations are computationally expensive and most of them only include small fragments of these cadherin extracellular domains. To overcome these limitations, we used a coarse-grained (CG) model with the MARTINI force field to study large cadherin complexes over long time scales. All-atom MD simulations were used to find optimal parameters for an elastic network model that stabilized the protein secondary structure. The CG model allowed for a 5x increase in timestep and a 10-fold reduction of system sizes. Using this model we studied the dynamics and elastic response of classical cadherins and clustered protocadherins. In these simulations, the extracellular domains of classical cadherins straightened before unbinding, while protocadherins slipped past each other during unbinding. Overall, our results confirm that our model is an effective simulation tool for studying of the mechanics of cadherin complexes. 2210-Pos Board B530 Influence of an Ionic Liquid on TRP-Cage Structure and Xaa-Pro Dipeptide Conformational Sampling Joseph L. Baker1, Alexanndra Heyert2, Susan Knox3, Gerrick E. Lindberg2. 1 Department of Chemistry, The Collegeof New Jersey, Ewing, NJ, USA, 2 Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA, 3Department of Chemistry, Yale University, New Haven, CT, USA. Room temperature ionic liquids (RTILs) demonstrate great promise for the selective control of protein structure and function, however the fundamental aspects of RTIL effects on peptides and proteins remain unclear. Here we describe some recent results for the influence of the RTIL 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl) imide ([C4mpy][Tf2N]) on the structure of the miniprotein Trp-cage and on the behavior of Xaa-Pro dipeptides, where Xaa is any of the common amino acids. Starting from an unfolded configuration, we find that Trp-cage folds in water at 298 K in less than 500 ns of molecular dynamics (MD) simulation, but exhibits very little mobility in the RTIL at the same temperature, which is related to the RTIL viscosity. However, in simulations carried out at 365 K, the mobility of the RTIL is increased and initial stages of Trp-cage folding are observed. We employed scaled MD to expedite sampling, and demonstrate that Trp-cage in the RTIL can closely approach the aqueous folded state. While the RTIL is found to restrict Trpcage motion, cis/trans isomerization of peptide bonds involving proline occur that are not observed in aqueous simulations. Therefore, we studied Xaa-Pro dipeptides in several environments, including the same RTIL, water, octanol, and vacuum, in order to further explore this effect. The RTIL is found to restrict Ramachandran space sampling of the dipeptides, and for Trp-Pro, isomerization of the dipeptide bond to the cis state is observed. This suggests that RTILs can be used to stabilize otherwise infrequently observed dipeptide conformations. Our simulations imply that stacking of the Trp ring and Pro ring in the cis state versus the trans state might contribute to this effect for the Trp-Pro dipeptide.
