Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

(2018) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations

(2018) Fabian Paul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

New protein structures provide an updated understanding of phenylketonuria

(2017) Eileen K. Jaffe   MOLECULAR GENETICS AND METABOLISM

PKU mutation p.G46S prevents the stereospecific binding ofl-phenylalanine to the dimer of human phenylalanine hydroxylase regulatory domain

(2017) João Leandro et al.   FEBS Open Bio

Identification of the Allosteric Site for Phenylalanine in Rat Phenylalanine Hydroxylase

(2016) Shengnan Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Domain Movements upon Activation of Phenylalanine Hydroxylase Characterized by Crystallography and Chromatography-Coupled Small-Angle X-ray Scattering

(2016) Steve P. Meisburger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

(2016) Vladimiras Oleinikovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer

(2016) Emilia C. Arturo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for ligand-dependent dimerization of phenylalanine hydroxylase regulatory domain

(2016) Dipali Patel et al.   Scientific Reports

The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor

(2016) Nathaniel Stanley et al.   Scientific Reports

Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase

(2015) Carla Carluccio et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Variational cross-validation of slow dynamical modes in molecular kinetics

(2015) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

(2015) Gregory R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Allostery through the computational microscope: cAMP activation of a canonical signalling domain

(2015) Robert D. Malmstrom et al.   Nature Communications

Phenylalanine Binding Is Linked to Dimerization of the Regulatory Domain of Phenylalanine Hydroxylase

(2014) Shengnan Zhang et al.   BIOCHEMISTRY

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

(2014) Shuo Gu et al.   PLoS Computational Biology

A new model for allosteric regulation of phenylalanine hydroxylase: Implications for disease and therapeutics

(2013) Eileen K. Jaffe et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

(2013) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

Structural Features of the Regulatory ACT Domain of Phenylalanine Hydroxylase

(2013) Carla Carluccio et al.   PLoS One

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Direct evidence for a phenylalanine site in the regulatory domain of phenylalanine hydroxylase

(2010) Jun Li et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Regulation of Phenylalanine Hydroxylase: Conformational Changes Upon Phenylalanine Binding Detected by Hydrogen/Deuterium Exchange and Mass Spectrometry

(2010) Jun Li et al.   BIOCHEMISTRY

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation