Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding

(2015) Tao Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling

(2015) Franco O. Tzul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modeling Non-Native Interactions in Designed Proteins

(2014) Shilpa Yadahalli et al.   ISRAEL JOURNAL OF CHEMISTRY

Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding

(2014) Cristiano L. Dias et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins

(2014) Ignacia Echeverria et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

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

(2014) Tao Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Energetic Frustrations in Protein Folding at Residue Resolution: A Homologous Simulation Study of Im9 Proteins

(2014) Yunxiang Sun et al.   PLoS One

Benchmarking all-atom simulations using hydrogen exchange

(2014) John J. Skinner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frustration in biomolecules

(2014) Diego U. Ferreiro et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Molecular origins of internal friction effects on protein-folding rates

(2014) David de Sancho et al.   Nature Communications

Funneling and frustration in the energy landscapes of some designed and simplified proteins

(2013) Ha H. Truong et al.   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

Quantitative Analysis of the Effects of Photoswitchable Distance Constraints on the Structure of a Globular Protein

(2012) Andrew A. Beharry et al.   BIOCHEMISTRY

Configuration-Dependent Diffusion Dynamics of Downhill and Two-State Protein Folding

(2012) Weixin Xu 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

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

(2012) A. N. Adhikari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonnative interactions regulate folding and switching of myristoylated protein

(2012) D. Shental-Bechor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

(2012) A. Soranno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Improvement of Structure-Based Potentials for Protein Folding by Native and Nonnative Hydrogen Bonds

(2011) Marta Enciso et al.   BIOPHYSICAL JOURNAL

Conformational Properties of the Unfolded State of Im7 in Nondenaturing Conditions

(2011) Clare L. Pashley et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

The folding of single domain proteins—have we reached a consensus?

(2010) Tobin R Sosnick et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective

(2010) Nicolas Guex et al.   ELECTROPHORESIS

Desolvation and Development of Specific Hydrophobic Core Packing during Im7 Folding

(2010) Alice I. Bartlett et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Extremely slow intramolecular diffusion in unfolded protein L

(2010) S. A. Waldauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-native interactions play an effective role in protein folding dynamics

(2010) Patrícia F. N. Faísca et al.   PROTEIN SCIENCE

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

Amino Acid Insertion Reveals a Necessary Three-Helical Intermediate in the Folding Pathway of the Colicin E7 Immunity Protein Im7

(2009) Stuart E. Knowling 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

The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints

(2009) Claire T Friel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Following evolutionary paths to protein-protein interactions with high affinity and selectivity

(2009) Kalia Bernath Levin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms

(2009) Alice I Bartlett et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

(2008) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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