Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A

The Underappreciated Role of Allostery in the Cellular Network

(2013) Ruth Nussinov et al.   Annual Review of Biophysics

Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover

(2013) Lauren C. McGowan et al.   BIOPHYSICAL JOURNAL

Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design

(2013) Mulpuri Nagaraju et al.   Journal of Chemical Information and Modeling

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions

(2012) Urmi Doshi et al.   Journal of Chemical Theory and Computation

Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A

(2012) Safieh Tork Ladani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Does Pin1 Catalyze the Cis–Trans Prolyl Peptide Bond Isomerization? A QM/MM and Mean Reaction Force Study

(2012) Esteban Vöhringer-Martinez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Resolving the complex role of enzyme conformational dynamics in catalytic function

(2012) U. Doshi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Dependence of Isotropic Polarizabilities

(2011) Pär Söderhjelm et al.   Journal of Chemical Theory and Computation

Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

(2011) Moran Grossman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cyclophilin A

(2010) Kimio Satoh et al.   CIRCULATION JOURNAL

Water’s Contribution to the Energetic Roughness from Peptide Dynamics

(2010) Quentin Johnson et al.   Journal of Chemical Theory and Computation

Crystal structure of the FTO protein reveals basis for its substrate specificity

(2010) Zhifu Han et al.   NATURE

Role of conformation transitions in adenylate kinase

(2010) Martin Karplus   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Karplus: Conformational dynamics have no role in the chemical step

(2010) Shina C. L. Kamerlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl-Prolyl Isomerases

(2010) Tara L. Davis et al.   PLOS BIOLOGY

A Library of Fluorescent Peptides for Exploring the Substrate Specificities of Prolyl Isomerases

(2009) Gabriel Zoldák et al.   BIOCHEMISTRY

Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics

(2009) Urmi Doshi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intra- and Intermolecular Interaction Inducing Pyramidalization on Both Sides of a Proline Dipeptide during Isomerization: An Ab Initio QM/MM Molecular Dynamics Simulation Study in Explicit Water

(2009) Yasushige Yonezawa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A

(2009) Donald Hamelberg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enzyme millisecond conformational dynamics do not catalyze the chemical step

(2009) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cortical Factor Feedback Model for Cellular Locomotion and Cytofission

(2009) Shin I. Nishimura et al.   PLoS Computational Biology

(Thermo)dynamic Role of Receptor Flexibility, Entropy, and Motional Correlation in Protein–Ligand Binding

(2008) Riccardo Baron et al.   CHEMPHYSCHEM

Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2′ Domains in Ligand Binding to PPAR-γ

(2008) C. G. Ji et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY