Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain

(2020) Khatuna Kachlishvili et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition

(2020) Jennifer E. Dawson et al.   Nature Communications

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

(2019) Adam Liwo et al.   JOURNAL OF CHEMICAL PHYSICS

Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes

(2019) Adam K. Sieradzan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein tertiary structure and the myoglobin phase diagram

(2019) Alexander Begun et al.   Scientific Reports

Multifunnel Energy Landscapes for Phosphorylated Translation Repressor 4E-BP2 and Its Mutants

(2019) Wei Kang et al.   Journal of Chemical Theory and Computation

Mechanism of Phosphorylation-Induced Folding of 4E-BP2 Revealed by Molecular Dynamics Simulations

(2016) Juan Zeng et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation

(2016) Rainer Bomblies et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phosphorylation as Conformational Switch from the Native to Amyloid State: Trp-Cage as a Protein Aggregation Model

(2015) József Kardos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water

(2015) Marta Wiśniewska et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch

(2015) Soundhararajan Gopi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

(2014) Francois-Xavier Theillet et al.   CHEMICAL REVIEWS

Kinks, loops, and protein folding, with protein A as an example

(2014) Andrey Krokhotin et al.   JOURNAL OF CHEMICAL PHYSICS

Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch

(2014) Alaji Bah et al.   NATURE

Local vs Global Motions in Protein Folding

(2013) Gia G. Maisuradze et al.   Journal of Chemical Theory and Computation

Soliton driven relaxation dynamics and protein collapse in the villin headpiece

(2013) Andrey Krokhotin et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Elucidating Human Phosphatase-Substrate Networks

(2013) X. Li et al.   Science Signaling

Coexistence of Phases in a Protein Heterodimer

(2012) Andrey Krokhotin et al.   JOURNAL OF CHEMICAL PHYSICS

Deciphering a global network of functionally associated post-translational modifications

(2012) Pablo Minguez et al.   Molecular Systems Biology

Soliton concepts and protein structure

(2012) Andrei Krokhotin et al.   PHYSICAL REVIEW E

Solitons and collapse in theλ−repressor protein

(2012) Andrey Krokhotin et al.   PHYSICAL REVIEW E

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

(2012) Y. Cote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural scaffold for eIF4E binding selectivity of 4E-BP isoforms: crystal structure of eIF4E binding region of 4E-BP2 and its comparison with that of 4E-BP1

(2011) Ai Fukuyo et al.   JOURNAL OF PEPTIDE SCIENCE

Towards quantitative classification of folded proteins in terms of elementary functions

(2011) Shuangwei Hu et al.   PHYSICAL REVIEW E

Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins

(2011) Shuangwei Hu et al.   PHYSICAL REVIEW E

Discrete Nonlinear Schrödinger Equation and Polygonal Solitons with Applications to Collapsed Proteins

(2011) Nora Molkenthin et al.   PHYSICAL REVIEW LETTERS

Relation between Free Energy Landscapes of Proteins and Dynamics

(2010) Gia G. Maisuradze et al.   Journal of Chemical Theory and Computation

Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

(2010) Gia G. Maisuradze et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Topological solitons and folded proteins

(2010) Maxim Chernodub et al.   PHYSICAL REVIEW E

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

(2009) Cezary Czaplewski et al.   Journal of Chemical Theory and Computation

Conformational Switch upon Phosphorylation: Human CDK Inhibitor p19INK4dbetween the Native and Partially Folded State

(2008) Christian Löw et al.   ACS Chemical Biology

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

Is there a code embedded in proteins that is based on post-translational modifications?

(2008) Robert J. Sims et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

How main-chains of proteins explore the free-energy landscape in native states

(2008) P. Senet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA