Substrate tunnels in enzymes: Structure-function relationships and computational methodology

Including ligand-induced protein flexibility into protein tunnel prediction

(2014) Laura J. Kingsley et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Atomic Picture of Ligand Migration in Toluene 4-Monooxygenase

(2014) Ali Hosseini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes

(2014) Laura J. Kingsley et al.   PLoS One

Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor

(2014) A. Stsiapanava et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gates of Enzymes

(2013) Artur Gora et al.   CHEMICAL REVIEWS

Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst–Planck equation

(2013) Dezső Boda et al.   JOURNAL OF MOLECULAR LIQUIDS

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

(2013) David Sehnal et al.   Journal of Cheminformatics

A molecular pathway for the egress of ammonia produced by nitrogenase

(2013) Ian Dance   Scientific Reports

Allostery and the Monod-Wyman-Changeux Model After 50 Years

(2012) Jean-Pierre Changeux   Annual Review of Biophysics

Structural determinants of substrate specificity in aldehyde dehydrogenases

(2012) Héctor Riveros-Rosas et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels

(2012) Ying-Lu Cui et al.   CHEMISTRY-A EUROPEAN JOURNAL

Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450?

(2012) Michal Otyepka et al.   CURRENT DRUG METABOLISM

Insights into the Substrate Specificity of a Thioesterase Rv0098 ofMycobacterium Tuberculosisthrough X-ray Crystallographic and Molecular Dynamics Studies

(2012) Koustav Maity et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study

(2012) Jacopo Sgrignani et al.   Journal of Chemical Information and Modeling

BDflex: A method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations

(2012) Nicholas Greives et al.   JOURNAL OF CHEMICAL PHYSICS

Motion and Flexibility in Human Cytochrome P450 Aromatase

(2012) Wenhua Jiang et al.   PLoS One

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

Catalytic versus Inhibitory Promiscuity in Cytochrome P450s: Implications for Evolution of New Function

(2011) Robert S. Foti et al.   BIOCHEMISTRY

Investigation by site-directed mutagenesis of the role of cytochrome P450 2B4 non-active-site residues in protein-ligand interactions based on crystal structures of the ligand-bound enzyme

(2011) P. Ross Wilderman et al.   FEBS Journal

Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2

(2011) Tao Zhang et al.   Journal of Chemical Information and Modeling

Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites

(2011) Jorge L. Barreda et al.   JOURNAL OF CHEMICAL PHYSICS

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9

(2011) Vlad Cojocaru et al.   PLoS Computational Biology

Protein dynamics and ligand migration interplay as studied by computer simulation

(2010) Pau Arroyo-Mañez et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Pharmacophore modeling and applications in drug discovery: challenges and recent advances

(2010) Sheng-Yong Yang   DRUG DISCOVERY TODAY

The structure of maize polyamine oxidase K300M mutant in complex with the natural substrates provides a snapshot of the catalytic mechanism of polyamine oxidation

(2010) Annarita Fiorillo et al.   FEBS Journal

Induced-fit upon Ligand Binding Revealed by Crystal Structures of the Hot-dog Fold Thioesterase in Dynemicin Biosynthesis

(2010) Chong Wai Liew et al.   JOURNAL OF MOLECULAR BIOLOGY

The influence of key residues in the tunnel entrance and the active site on activity and selectivity of toluene-4-monooxygenase

(2010) Moran Brouk et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

POVME: An algorithm for measuring binding-pocket volumes

(2010) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

(2009) Martin Klvana et al.   JOURNAL OF MOLECULAR BIOLOGY

Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism

(2009) Dan Fishelovitch et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

(2009) Martina Pavlova et al.   Nature Chemical Biology

Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein

(2009) Dong Long et al.   PLoS One

Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex

(2008) Harish Vashisth et al.   BIOPHYSICAL JOURNAL

Identification and Analysis of Conserved Sequence Motifs in Cytochrome P450 Family 2

(2008) Numan Oezguen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences

(2008) Josef Skopalík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural consequences of effector protein complex formation in a diiron hydroxylase

(2008) L. J. Bailey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MolAxis: Efficient and accurate identification of channels in macromolecules

(2008) Eitan Yaffe et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Quantitative Index of Substrate Promiscuity†

(2007) Abhinav Nath et al.   BIOCHEMISTRY

Sequence of the lid affects activity and specificity of Candida rugosa lipase isoenzymes

(2003) Stefania Brocca et al.   PROTEIN SCIENCE