TGQR 2010Q4 Report.pdf - Teragridforum.org

MCB070009
521. J. Lee, S. Ham, and W. Im (2009) Beta-Hairpin Restraint Potentials for Calculations ofPotentials of
Mean Force as a Function of Beta-Hairpin Tilt, Rotation, and Distance. J. Comput. Chem. 30:1334-1343.
522. W. Im, J. Lee, T. Kim, and H. Rui (2009) Novel Free Energy Calculations to Explore Mechanisms
and Energetics of Membrane Protein Structure and Function, J. Comput. Chem. 30:1622-1633.
523. S. Jo, J.B. Lim, J.B. Klauda, and W. Im (2009) CHARMM-GUI Membrane Builder for Mixed Bilayers
and Its Application to Yeast Membranes, Biophys. J. 97:50-58.
524. H. Rui, J. Lee, and W. Im (2009) Comparative Molecular Dynamics Simulation Studies of Protegrin-
1 Monomer and Dimer in Different Lipid Bilayers, Biophys. J. 97:787-795.
525. T. Rathinavelan, L. Zhang, W.L. Picking, D.D. Weis, R.N. De Guzman, and W. Im (2010) A
Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus, Biophys. J.
98:452-461 [cover].
526. T. Kim and W. Im (2010) Revisiting Hydrophobic Mismatch with Free Energy Calculations
ofTransmembrane Helix Tilt and Rotation. Biophys. J. (in press).
527. H. Rui and W. Im (2010) Protegrin-1 Orientation and Physicochemical Properties in Membrane
Bilayers Studied by Potential of Mean Force Calculations. J. Comput. Chem. (in press).
528. K.C. Song, P.W. Livanec, J.B. Klauda, K. Kuczera, R.C. Dunn, and W. Im (2010) Orientation of
Fluorescent Lipid Analog BODIPY-PC to Probe Lipid Membrane Properties: A Comparison of Simulation
with Experiment. submitted.
529. S. Jo, H. Rui, J.B. Lim, J.B. Klauda, and W. Im (2010) Cholesterol Flip-Flop: Insights from Free
Energy Simulation Studies, submitted.
MCB070118
530. Ruibo Wu, Shenglong Wang, Nengjie Zhou, Zexing Cao and Yingkai Zhang, A Proton-Shuttle
Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions. J. Am. Chem. Soc., in
press, 2010.
531. Yanzi Zhou, Shenglong Wang and Yingkai Zhang, Catalytic Reaction Mechanism of
Acetylcholinesterase Determined by Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations,
J. Phys. Chem. B, 114, 8817 - 8825, 2010.
532. Ruibo Wu, Po Hu, Shenglong Wang, Zexing Cao and Yingkai Zhang, Flexibility of Catalytic Zinc
Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics
Study, J. Chem. Theory Comput., 6, 337-343, 2010.
533. Kamau Fahie, Po Hu, Steven Swatkoski, Robert J. Cotter, Yingkai Zhang, and Cynthia Wolberger.
Side chain specificity of ADP-ribosylation by a sirtuin. FEBS J., 276, 7159-71767, 2009.
534. Zhenyu Lu, Jonathan Lai, Yingkai Zhang. Importance of Charge Independent Effects in Readout
the Trimethyllysine Mark by HP1 Chromodomain. J. Am. Chem. Soc., 131, 14928-14931, 2009.
MCB080015
535. “Structural Determinants of Cadherin-23 Function in Hearing and Deafness”. M. Sotomayor, W. A.
Weihofen, R. Gaudet, D. P. Corey. Neuron, 66: 85-100, 2010.
536. “Calmodulin-interaction sites are critical for the thermosensitivity of a heat-activated ion channel”.
E. Procko, S.-Y. Lau, M. Sotomayor, A. Beristain-Barajas, A. McFedries, R. Gaudet. In preparation.
537. “Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8
Hydrolase UCHL3”. K. Artavanis-Tsakonas, W. A. Weihofen, J. M. Antos, B. I. Coleman, C. Comeaux, M. T.
Duraisingh, R. Gaudet, H. L. Ploegh. Journal of Biological Chemistry, 285: 6857-6866, 2010.