Studying Solvation of Small Biomolecules via Molecular Dynamics using a Polarizable Force Field

Wednesday, February 15, 2017 bind to the C-terminal a7-helix of aL I domain at the lovastatin (L) site. Lovastatin, a drug primarily used for the prevention of cardiovascular disease and the treatment of hypercholesterolemia, was found to inhibit the interaction of aLb2 with ICAM-1. In this study, we analyze the effect of lovastatin and several related small molecules on the aI domain of aLb2 via several m-second long allatom explicit solvent molecular dynamics simulations. We focus on the MIDAS and the a7 helix of the aI domain, which have been reported to play key roles in binding aLb2 to ICAM-1, and illustrate the allosteric effects induced by these small molecules acting at aLb2. The largest movement was observed at the a7 helix upon the removal of lovastatin. Besides, we also observe the change of Mg2þ position and the remodeling of MIDAS, as well as changes of dynamical modes of the aI domain, elucidated by referencefree time-dependent principal component analysis. 2444-Pos Board B51 The Structural and Dynamic Effects of Inhibitor Binding to Protein Kinase C bII Shashank Jariwala1, Sivaraj Sivaramakrishnan2, Barry J. Grant1. 1 Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Ann Arbor, MI, USA, 2Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA. Protein kinase C bII (PKCbII) regulates diverse cellular signaling pathways involved in B-cell activation, insulin signaling, and oxidative stress-induced apoptosis. Aberrant PKCbII activity has been implicated in a variety of human diseases including diabetic retinopathy and B-cell immunodeficiency. Accordingly, PKCbII has become a popular target for small molecule based inhibition. However, the effects of available inhibitors on the conformational dynamics and allosteric couplings essential for PKCbII function remains largely unknown. This lack of knowledge hampers the development of improved inhibitors and limits our understanding of how disease-associated mutations in distal sites can interfere with inhibitor efficacy. Here we characterize distinct flexibilities and internal dynamical couplings upon inhibitor binding using molecular dynamics (MD) simulations and bioinformatics analysis. MD simulations revealed increased flexibility of the nucleotide-binding P-loop and the regulatory C-terminal tail when bound to the ATP-competitive inhibitor Bisindolylmaleimide I (BIM1). Community partitioning of the dynamical cross-correlations, based on network approaches, reveal further variations between ATP and inhibitor states. Specifically, the inhibitor state exhibits overall dynamical tightening, with stronger couplings between communities encompassing the C-terminal tail in the N-lobe and helices aE, aG, aH and activation loop in the C-lobe. In contrast, the ATP state displays distinct couplings between active-site residues that are lost upon inhibitor binding. Furthermore, mutational simulations of residues exhibiting state specific couplings demonstrate a shift towards inhibitorstate dynamics, indicating their role in allosteric modulation. Collectively, this study elucidates the effect of inhibitor binding on conformational dynamics and furthers our understanding of allosteric mechanisms in PKCbII. 2445-Pos Board B52 Studying Solvation of Small Biomolecules via Molecular Dynamics using a Polarizable Force Field Saurabh Belsare1, Alexander Esser2, Dominik Marx2, Teresa Head-Gordon3. 1 UCB-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA, 2Lehrstuhl f€ur Theoretische Chemie, RuhrUniversit€at Bochum, Bochum, Germany, 3Departments of Chemistry, Bioengineering, Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. Interactions with solvent have been shown to affect the dynamics of small biomolecules. While bulk properties of solvation can be studied via experiments like spectral measurements, understanding the precise impact of solvent interactions on specific motions of biomolecules, and the spatial extent of impact of the biomolecules on the solvent are accessible through simulations. We have used the polarizable AMOEBA molecular mechanics force field to simulate terahertz (THz) spectra of two zwitterionic peptides, glycine and valine in aqueous solution. Ab initio molecular dynamics (AIMD) simulations have been previously used to study these spectra. An analysis method has been previously developed by Marx and co-workers (Sun et. al. JACS 2014) to decompose the THz spectrum into the component motion modes for specific molecules, as well as modes arising from intermolecular interactions, for AIMD simulations. We present here an approach whereby classical MD simulations performed via the AMOEBA forcefield can be analyzed with that mode decomposition method to obtain dynamic modes for the zwitterions. Based on this decomposition, overall we find very good agreement of the AMOEBA classical MD simulations with AIMD. THz spectral assignments and the spectral decomposition of the total spectrum into intramolecular peptide motions and peptide-water cross-correlation modes shows substantial agreement between AMOEBA and AIMD. The

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unique feature of this approach comes from the good agreement of the peptide-water cross-correlation modes, which involve distortions of the electron density as a result of polarization and hence cannot be captured by fixed charge force fields. This is a promising first step towards future studies for simulating and decomposing the THz observable for larger solutes such as polymers or proteins where AIMD studies are currently intractable. 2446-Pos Board B53 Molecular Allostery in Dengue NS3 Helicase along the ATP Hydrolysis Cycle Russell B. Davidson1, Brian J. Geiss2, Martin McCullagh1. 1 Chemistry, Colorado State University, Fort Collins, CO, USA, 2 Microbiology, Immunology, Pathology, Colorado State University, Fort Collins, CO, USA. The flavivirus non-structural 3 (NS3) protein is a viral helicase that plays a pivotal role during the replication of the viral genome. Specifically, this enzyme uses energy released from ATP hydrolysis to translocate and cause the unwinding of a double-stranded RNA substrate, thereby preparing the RNA for the replication machinery. Microsecond molecular dynamic simulations of the dengue NS3 helicase are performed on seven structures, five of which represent important RNA-bound structures that model the ATP hydrolysis cycle (apo, pre-hydrolysis, post-hydrolysis, and product release states). These simulations demonstrate that the RNA binding cleft is affected by the different ATP substrates and suggest a hold-release mechanism for the translocation of the enzyme along the RNA substrate. Also, comparisons made between the five RNA-bound and remaining two RNA-unbound simulations indicate that the RNA substrate influences the water dynamics of the ATP binding pocket. These results provide molecular insights into the experimentally observed RNA-enhanced ATPase activity of dengue NS3 helicase. The allosteries observed between both the ATP and RNA binding sites will be discussed in relation to the ATP hydrolysis cycle. 2447-Pos Board B54 How the Barrierless Folding Helps DNA Recognition: Theoretical Investigation on Ultrafast Folding Protein Engrailed Homeodomain Xiakun Chu1, Victor Mun˜oz2,3. 1 IMDEA-Nanociencia, Madrid, Spain, 2Centro Nacional de Biotecnologı´a (CNB), Consejo Superior de Investigaciones Cientı´ficas (CSIC), Madrid, Spain, 3School of Engineering, University of California Merced, Merced, CA, USA. Engrailed homeodomain (EngHD), a 3-helix bundle fast-folding protein, has been found to play a critical role in transcription regulation during its binding to DNA. Evidence shows that protein efficiently recognizes the short target DNA sequence from the enormous pool of binding sites via the process of ‘‘facilitated diffusion’’, including sliding and hopping. During the facilitated diffusion, protein is supposed to go through ‘‘speed’’ mode, where protein nonspecifically interacts with DNA in fast diffusion, and ‘‘stability’’ mode, where protein strongly and specifically scans the base pairs in DNA with slow displacement. How the conformational dynamics in protein participating into the balance of the two modes to optimize the non-specific searching and specific binding to DNA remains unclear. Here, we developed a variable-barrier structure-based model to investigate EngHD’ folding and DNA-binding process. The folding barriers of EngHD can be achieved from 2-state (>3 kT) to global downhill (~0.5 kT) folding regimes by modulating the interplay between the local dihedral and non-local native contact energy. During the DNA binding process, the folding energy landscape of EngHD undergoes dynamical changes at different diffusion processes. EngHD is found to preferentially fold in sliding, where EngHD binds to DNA in the specific manner, reminiscent of the ‘‘stability’’ mode, while hopping favors unfolded states, in which the fluctuating protein-DNA interfaces are formed, corresponding to the ‘‘speed’’ mode. We also addressed the important roles of conformational disorder and salt concentrations in modulating the two modes during EngHD-DNA recognition process. Finally, we found folding with marginal barrier possessing significantly conformational flexibility, is able to fulfill the two modes at the same time. In summary, the conformational rheostat in downhill folding protein optimizes the DNA recognition process by solving the speed-stability paradox. 2448-Pos Board B55 The Folding Mechanism and Kinetics of the Domains of a-Spectrin: Results from a Variational Model Daniel Gavazzi, John J. Portman. Department of Physics, Kent State University, Kent, OH, USA. Although the three domains of a-spectrin (R15, R16, and R17) are highly homologous, experiments reveal striking differences in their folding mechanism and kinetics. In particular, the R15 domain’s folding rate is measured to be three orders of magnitude greater than the other two domains, with R17 being