Biophysical Society 60th Annual Meeting

3170-Pos Board B547 HOW TO EASILY EXTRACT PHYSICAL PROPERTIES FROMMD SIMULA- TIONS OF LIPID MEMBRANES WITH FATSLIM. Sebastien Buchoux 3171-Pos Board B548 A RIEMANNIAN FRAMEWORK FOR TACKLING LARGE-SCALE CONFORMA- TIONAL CHANGES OF PROTEINS USING ALL-ATOMMOLECULAR DYNAM- ICS SIMULATIONS. Mahmoud Moradi 3172-Pos Board B549 ESTIMATING THE RUGGEDNESS OF PROTEIN FREE ENERGY LANDSCAPES FROMMOLECULAR DYNAMICS SIMULATIONS. Andreas Volkhardt , Helmut Grubmüller 3173-Pos Board B550 ON THE EFFECT OF MAPPING IN THE COARSE GRAINING OF ELASTIC NET- WORKS. Patrick M. Diggins , Changjiang Liu, Potestio Raffaello, Markus Deserno 3174-Pos Board B551 A QUANTITATIVE COARSE-GRAINED MODEL OF SUGARS.  James A. Graham , Syma Khalid, Jonathan Essex 3175-Pos Board B552 EXPLORING N-GLYCAN CONFORMERS: ASSESSMENT OF ENHANCED SAM- PLING ALGORITHMS. Raimondas Galvelis , Suyong Re, Yuji Sugita 3176-Pos Board B553 EXTENDING THE ADRESS MULTISCALE SCHEME FOR PROTEIN AND BI- LAYER APPLICATIONS. Manuel N. Melo , Julija Zavadlav, Matej Praprotnik, Siewert J. Marrink 3177-Pos Board B554 UNIVERSAL METRICS OF INTERSTRUCTURE DISTANCE FOR FLEXIBLE AND INTRINSICALLY DISORDERED PROTEINS. Timothy G. Connolly , David Ando, Shawn D. Newsam, Ajay Gopinathan, Michael E. Colvin 3178-Pos Board B555 CID TRAVEL AWARDEE STRUCTURAL-FUNCTION STUDY OF MEMBRANE PROTEINS WITH RE- STRAINED-ENSEMBLE AND DUMMY SPIN-LABEL MOLECULAR DYNAMICS SIMULATIONS. Shahidul M. Islam , Giacomo Florin, Yifei Qi, Rong Shen, Wei Han, Richard A. Stein, Klaus Schulten, Hassane S. Mchaourab, Wonpil Im, Benoit Roux 3179-Pos Board B556 PEPTIDE BOND ISOMERIZATION IN HIGH-TEMPERATURE SIMULA- TIONS. Chris Neale , Régis Pomès, Angel E. García 3180-Pos Board B557 MECHANICAL ASPECTS OF PROTEIN THERMOSTABILITY. Guillaume Stirnemann , Fabio Sterpone 3181-Pos Board B558 MD MODELING OF OXIDATIVE FOLDING IN PEPTIDES AND PROTEINS.  Sergei A. Izmailov , Ivan S. Podkorytov, Nikolai R. Skrynnikov 3182-Pos Board B559 SEQUENCE-SPECIFIC BINDING AND DIFFUSION OF TRF1 ON TELOMERIC DNA STUDIED BY MOLECULAR DYNAMICS. Milosz Wieczor , Jacek Czub 3183-Pos Board B560 SIMULATION STUDIES OF TWIST-STRETCH COUPLING IN NUCLEIC AC- IDS. Anupam Chatterjee 3184-Pos Board B561 SOLVATION STRUCTURE AND QUASIDYNAMICS OF BIOMOLECULES STEERED WITH EFFECTIVE SOLVATION FORCES OBTAINED FROMMO- LECULAR THEORY OF SOLVATION. Andriy Kovalenko 3185-Pos Board B562 EFFECT OF DMSO ON WATER MOLECULES NEAR PHOSPHOLIPID BILAYER SURFACES. Yuno Lee , Changbong Hyeon

3155-Pos Board B532 DESIGN AND DEVELOPMENT OF A TELOMERE SENSOR BASED ON FLUO- RESCENCE ENERGY TRANSFER. Haitao Li 3156-Pos Board B533 BEYOND AN ‘ON˗OFF’ ACTIVATION MODEL OF G˗PROTEIN˗COUPLED RE- CEPTORS.  Julia Wagner , Mike Friedrich, Martin J. Lohse, Katrin G. Heinze 3157-Pos Board B534 DETERMINING THE STOICHIOMETRY OF EGFR AND ADRβ2 USING CELL FUSION AND SINGLE MOLECULE IMAGING. Maria Sirenko , Avtar Singh, Alexander Song, Paul Kammermeier, Warren Zipfel 3158-Pos Board B535 BIFUNCTIONAL RHODAMINE LINKER SIMPLIFIES COLOCALIZATION STUD- IES IN SINGLE-MOLECULE IMAGING. Richard A. Haack , Patrick J. Macdonald, Qiaoqiao Ruan, Richard J. Himmelsbach, Sergey Y. Tetin 3159-Pos Board B536 SINGLE-MOLECULE APPROACHES TO MEMBRANE NANOTUBES.  Minhyeok Chang , Jungsic Oh, Ryangguen Lee, Jong-Bong Lee 3160-Pos Board B537 INVESTIGATING THE KINETICS AND SPECIFICITY OF TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR BINDING USING HIGH THROUGHPUT SINGLE MOLECULE IMAGING. Alexander L. Van Slyke , Avtar Singh, Fabio Cupri Rinaldi, Adam J. Bogdanove, John T. Lis, Warren R. Zipfel Molecular Dynamics II (Boards B538 - B567) 3161-Pos Board B538 GNEIMOSIM: MULTISCALE INTERNAL COORDINATES MOLECULAR DYNAMICS FOR PROTEINS. Saugat Kandel , Adrien B. Larsen, Abhinandan Jain, Nagarajan Vaidehi 3162-Pos Board B539 LOOS: A TOOLKIT FOR ANALYZING MOLECULAR SIMULATIONS AND MAKING NEW TOOLS. Tod D. Romo, Alan Grossfield 3163-Pos Board B540 CHARMM-GUI INPUT GENERATOR FOR NAMD, GROMACS, AMBER, OPENMM, AND CHARMM/OPENMM SIMULATIONS USING THE CHARMM36 ADDITIVE FORCE FIELD.  Jumin Lee , Xi Cheng, Sunhwan Jo, Alexander D. MacKerell Jr., Jeffery B. Klauda, Wonpil Im 3164-Pos Board B541 EASY AND FAST SETUP OF MOLECULAR DYNAMICS SIMULATIONS: COM- BINING VMD AND NAMD FOR EXPERIMENTALISTS.  Joao V. Ribeiro , Rafael C. Bernardi, Till Rudack, Klaus Schulten 3165-Pos Board B542 ACCELERATING ORTHOGONAL SPACE SAMPLING WITH REPLICA EXCHANGE WITH SOLUTE TEMPERING (REST2) THROUGH A GENERIC IMPLEMENTATION IN NAMD. Wei Jiang , Sunhwan Jo 3166-Pos Board B543 IMPROVED ESTIMATION OF LONG-TIME KINETICS USING NON-MARKOV- IAN ANALYSIS OF TRAJECTORY SEGMENTS: APPLICATION TO PROTEIN FOLDING AND UNFOLDING. Ernesto Suarez , Daniel M. Zuckerman 3167-Pos Board B544 HDGB IMPLICIT MEMBRANE MODEL WITH A VAN DER WAALS DISPER- SION TERM. Bercem Dutagaci , Maryam Sayadi, Michael Feig 3168-Pos Board B545 OBTAINING BINDING FREE ENERGY FROM A PATH SAMPLING WITHOUT FORCE BIAS. Duy Phuoc Tran , Akio Kitao 3169-Pos Board B546 A MULTISCALE APPROACH TO UNDERSTANDING PROTEIN LIGAND BIND- ING PROCESS. Tohru Terada , Tatsuki Negami, Kentaro Shimizu

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