Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding

The Utilization of Competing Unfolding Pathways of Monellin Is Dictated by Enthalpic Barriers

(2013) Nilesh Aghera et al.   BIOCHEMISTRY

Structural and energetic determinants of co-translational folding

(2013) Heinrich Krobath et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

How Well Does a Funneled Energy Landscape Capture the Folding Mechanism of Spectrin Domains?

(2013) Robert B. Best   JOURNAL OF PHYSICAL CHEMISTRY B

Single-molecule fluorescence probes dynamics of barrier crossing

(2013) Hoi Sung Chung et al.   NATURE

Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity

(2013) Hüseyin Kaya et al.   PHYSICAL REVIEW E

Native contacts determine protein folding mechanisms in atomistic simulations

(2013) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-level description of ubiquitin folding

(2013) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

(2013) Jianhui Song et al.   PLoS Computational Biology

Cooperativity in Cellular Biochemical Processes: Noise-Enhanced Sensitivity, Fluctuating Enzyme, Bistability with Nonlinear Feedback, and Other Mechanisms for Sigmoidal Responses

(2012) Hong Qian   Annual Review of Biophysics

The how’s and why’s of protein folding intermediates

(2012) Maksym Tsytlonok et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Coupled Folding-Binding in a Hydrophobic/Polar Protein Model: Impact of Synergistic Folding and Disordered Flanks

(2012) Arnab Bhattacherjee et al.   BIOPHYSICAL JOURNAL

Coarse-grained molecular simulations of large biomolecules

(2012) Shoji Takada   CURRENT OPINION IN STRUCTURAL BIOLOGY

Atomistic molecular simulations of protein folding

(2012) Robert B Best   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein folding: from theory to practice

(2012) D Thirumalai et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

(2012) Peter Csermely et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Why and how does native topology dictate the folding speed of a protein?

(2012) Mark Rustad et al.   JOURNAL OF CHEMICAL PHYSICS

The Folding Transition State of Protein L Is Extensive with Nonnative Interactions (and Not Small and Polarized)

(2012) Tae Yeon Yoo et al.   JOURNAL OF MOLECULAR BIOLOGY

Theory of the Molecular Transfer Model for Proteins with Applications to the Folding of the src-SH3 Domain

(2012) Zhenxing Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transition paths, diffusive processes, and preequilibria of protein folding

(2012) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Denaturant-dependent folding of GFP

(2012) G. Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

(2012) Tobias Sikosek et al.   PLoS Computational Biology

Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models

(2011) Hue Sun Chan et al.   Annual Review of Physical Chemistry

Current Computer Modeling Cannot Explain Why Two Highly Similar Sequences Fold into Different Structures

(2011) Jane R. Allison et al.   BIOCHEMISTRY

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

New Scenarios of Protein Folding Can Occur on the Ribosome

(2011) Edward P. O’Brien et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Population of Nonnative States of Lysozyme Variants Drives Amyloid Fibril Formation

(2011) Alexander K. Buell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins

(2011) Z. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncoupled binding and folding of immune signaling-related intrinsically disordered proteins

(2011) Alexander B. Sigalov   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain

(2011) Arash Zarrine-Afsar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme

(2011) Jin Wang et al.   PLoS Computational Biology

Theoretical Perspectives on Protein Folding

(2010) D. Thirumalai et al.   Annual Review of Biophysics

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Protein kinetic stability

(2010) Jose M. Sanchez-Ruiz   BIOPHYSICAL CHEMISTRY

Cooperativity and protein folding rates

(2010) John J Portman   CURRENT OPINION IN STRUCTURAL BIOLOGY

Enhanced sampling and applications in protein folding in explicit solvent

(2010) Cheng Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

The folding cooperativity of a protein is controlled by its chain topology

(2010) Elizabeth A. Shank et al.   NATURE

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins

(2010) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding

(2010) Jeffrey A. Rank et al.   PROTEIN SCIENCE

Atomic solvation parameters applied to molecular dynamics of proteins in solution

(2010) Laura Wesson et al.   PROTEIN SCIENCE

Dry molten globule intermediates and the mechanism of protein unfolding

(2010) Robert L. Baldwin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Topology-based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions

(2010) Debabani Ganguly et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Native Topology of the Designed Protein Top7 is Not Conducive to Cooperative Folding

(2009) Zhuqing Zhang et al.   BIOPHYSICAL JOURNAL

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments

(2009) Artem Badasyan et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Protein folding simulations: From coarse-grained model to all-atom model

(2009) Jian Zhang et al.   IUBMB LIFE

Desolvation Barrier Effects Are a Likely Contributor to the Remarkable Diversity in the Folding Rates of Small Proteins

(2009) Allison Ferguson et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding–Binding Process: A Critical Assessment of the “Fly-Casting” Mechanism

(2009) Yongqi Huang et al.   JOURNAL OF MOLECULAR BIOLOGY

Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt

(2009) Ariel Azia et al.   JOURNAL OF MOLECULAR BIOLOGY

Theory for Protein Folding Cooperativity: Helix Bundles

(2009) Kingshuk Ghosh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

All-or-none proteinlike folding transition of a flexible homopolymer chain

(2009) Mark P. Taylor et al.   PHYSICAL REVIEW E

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier

(2008) Hongxing Lei et al.   JOURNAL OF CHEMICAL PHYSICS

Probing Possible Downhill Folding: Native Contact Topology Likely Places a Significant Constraint on the Folding Cooperativity of Proteins with ∼40 Residues

(2008) Artem Badasyan et al.   JOURNAL OF MOLECULAR BIOLOGY

Biological switches and clocks

(2008) J. J Tyson et al.   Journal of the Royal Society Interface

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

(2008) A. Zarrine-Afsar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

(2008) E. P. O'Brien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions

(2007) Peter Tompa et al.   TRENDS IN BIOCHEMICAL SCIENCES

Spectrin R16: Broad energy barrier or sequential transition states?

(2005) Kathryn A. Scott et al.   PROTEIN SCIENCE