Post-translational Modifications of Cyclophilin D Fine-Tune Its Conformational Dynamics and Activity: Implications for Its Mitochondrial Function

Residue–Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways

(2022) Xin-Qiu Yao et al.   Journal of Chemical Theory and Computation

Protein folding and unfolding: proline cis ‐ trans isomerization at the c subunits of F 1 F O ‐ATPase might open a high conductance ion channel

(2022) Salvatore Nesci   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

p53 Is Potentially Regulated by Cyclophilin D in the Triple-Proline Loop of the DNA Binding Domain

(2021) Jacques Kumutima et al.   BIOCHEMISTRY

The Bio3D Packages for Structural Bioinformatics

(2020) Barry J. Grant et al.   PROTEIN SCIENCE

Cyclophilin D: An Integrator of Mitochondrial Function

(2020) Georgios Amanakis et al.   Frontiers in Physiology

Phosphorylation of cyclophilin D at serine 191 regulates mitochondrial permeability transition pore opening and cell death after ischemia-reperfusion

(2020) Stephen Hurst et al.   Cell Death & Disease

Indirubin and NAD+ prevent mitochondrial ischaemia/reperfusion damage in fatty livers

(2018) João Soeiro Teodoro et al.   EUROPEAN JOURNAL OF CLINICAL INVESTIGATION

Unraveling Allosteric Mechanisms of Enzymatic Catalysis with an Evolutionary Analysis of Residue–Residue Contact Dynamical Changes

(2018) Phuoc Jake Vu et al.   ACS Catalysis

Cyclophilin D phosphorylation is critical for mitochondrial calcium uniporter regulated permeability transition pore sensitivity

(2018) Rimpy Dhingra et al.   CARDIOVASCULAR RESEARCH

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

(2016) Urmi Doshi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of the mPTP by SIRT3-mediated deacetylation of CypD at lysine 166 suppresses age-related cardiac hypertrophy

(2016) Angela V. Hafner et al.   Aging-US

Structure and Dynamics of GeoCyp: A Thermophilic Cyclophilin with a Novel Substrate Binding Mechanism That Functions Efficiently at Low Temperatures

(2015) Michael J. Holliday et al.   BIOCHEMISTRY

Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis – trans isomerases

(2015) Safieh Tork Ladani et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Integrating protein structural dynamics and evolutionary analysis with Bio3D

(2014) Lars Skjærven et al.   BMC BIOINFORMATICS

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

(2014) Safieh Tork Ladani et al.   MOLECULAR SIMULATION

High-resolution crystal structures of two crystal forms of human cyclophilin D in complex with PEG 400 molecules

(2014) Koteswara Rao Valasani et al.   Acta Crystallographica Section F-Structural Biology Communications

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe 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

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

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

The Emerging Characterization of Lysine Residue Deacetylation on the Modulation of Mitochondrial Function and Cardiovascular Biology

(2009) Zhongping Lu et al.   CIRCULATION RESEARCH

Cyclophilin D Modulates Mitochondrial F0F1-ATP Synthase by Interacting with the Lateral Stalk of the Complex

(2009) Valentina Giorgio et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Activation of mitochondrial ERK protects cancer cells from death through inhibition of the permeability transition

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