The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

Current structure predictors are not learning the physics of protein folding

(2022) Carlos Outeiral et al.   BIOINFORMATICS

Computational design of a thermolabile uracil-DNA glycosylase of Escherichia coli

(2022) Seongjun Park et al.   BIOPHYSICAL JOURNAL

Structural–Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble

(2022) Hemashree Golla et al.   ACS Central Science

Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein

(2022) Divya Rajendran et al.   Journal of Physical Chemistry Letters

Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains

(2021) Soundhararajan Gopi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS model

(2021) Achinta Sannigrahi et al.   eLife

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Folding Intermediates, Heterogeneous Native Ensembles and Protein Function

(2021) Athi N. Naganathan et al.   JOURNAL OF MOLECULAR BIOLOGY

Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression

(2021) Gloria Gamiz-Arco et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue

(2021) Juan Luis Pacheco-Garcia et al.   Redox Biology

pPerturb: A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations

(2020) Soundhararajan Gopi et al.   ACS Omega

Molecular origins of folding rate differences in the thioredoxin family

(2020) Athi N. Naganathan   BIOCHEMICAL JOURNAL

Electrostatic Frustration Shapes Folding Mechanistic Differences in Paralogous Bacterial Stress Response Proteins

(2020) Abhishek Narayan et al.   JOURNAL OF MOLECULAR BIOLOGY

A Disordered Loop Mediates Heterogeneous Unfolding of an Ordered Protein by Altering the Native Ensemble

(2020) Kabita Bhattacharjee et al.   Journal of Physical Chemistry Letters

Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape?

(2020) Sandhyaa Subramanian et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Weakening of interaction networks with aging in tip-link protein induces hearing loss

(2020) Surbhi Garg et al.   BIOCHEMICAL JOURNAL

Controlling Structure and Dimensions of a Disordered Protein via Mutations

(2019) Sneha Munshi et al.   BIOCHEMISTRY

Entropic Control of an Excited Folded-Like Conformation in a Disordered Protein Ensemble

(2018) Sneha Munshi et al.   JOURNAL OF MOLECULAR BIOLOGY

Effect of Mutations on the Global and Site-Specific Stability and Folding of an Elementary Protein Structural Motif

(2018) Jason K Lai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extracting the Hidden Distributions Underlying the Mean Transition State Structures in Protein Folding

(2018) Soundhararajan Gopi et al.   Journal of Physical Chemistry Letters

Switching Protein Conformational Substates by Protonation and Mutation

(2018) Abhishek Narayan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A new era for understanding amyloid structures and disease

(2018) Matthew G. Iadanza et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tunable order–disorder continuum in protein–DNA interactions

(2018) Sneha Munshi et al.   NUCLEIC ACIDS RESEARCH

Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein

(2017) Abhishek Narayan et al.   Journal of Physical Chemistry Letters

Graded Structural Polymorphism in a Bacterial Thermosensor Protein

(2017) Abhishek Narayan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Toward a quantitative description of microscopic pathway heterogeneity in protein folding

(2017) Soundhararajan Gopi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

A General Mechanism for the Propagation of Mutational Effects in Proteins

(2016) Nandakumar Rajasekaran et al.   BIOCHEMISTRY

Quantifying Protein Disorder through Measures of Excess Conformational Entropy

(2016) Nandakumar Rajasekaran et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880

(2016) Heeyoun Kim et al.   PLoS One

Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints?

(2015) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mapping the Topography of a Protein Energy Landscape

(2015) Richard D. Hutton et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Finite-size phase diagram of the Wako-Saitô-Mu˜noz-Eaton α-helix model

(2015) Julian Lee   JOURNAL OF THE KOREAN PHYSICAL SOCIETY

Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein

(2015) Sneha Munshi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Sequence, structure, and cooperativity in folding of elementary protein structural motifs

(2015) Jason K. Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding

(2015) Munehito Arai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics of Downhill Folding: Multi-Probe Analysis of PDD, a Protein that Folds Over a Marginal Free Energy Barrier

(2014) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evidence for the Sequential Folding Mechanism in RNase H from an Ensemble-Based Model

(2014) Abhishek Narayan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phase diagram of the Wako-Saitô-Muñoz-Eaton β hairpin model obtained from the partition-function zeros

(2014) Julian Lee   JOURNAL OF THE KOREAN PHYSICAL SOCIETY

Simplified lattice model for polypeptide fibrillar transitions

(2014) Xuhui Xiao et al.   PHYSICAL REVIEW E

A simple theoretical model goes a long way in explaining complex behavior in protein folding: Fig. 1.

(2014) Victor Muñoz   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding pathway of a multidomain protein depends on its topology of domain connectivity

(2014) Takashi Inanami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonequilibrium dynamics of an exactly solvable Ising-like model and protein translocation

(2013) A. Pelizzola et al.   EPL

Frustration-induced protein intrinsic disorder

(2013) Katsuyoshi Matsushita et al.   JOURNAL OF CHEMICAL PHYSICS

The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator

(2013) Athi N. Naganathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exact partition function zeros of the Wako-Saitô-Muñoz-Eatonβhairpin model

(2013) Julian Lee   PHYSICAL REVIEW E

Exact Partition Function Zeros of The Wako-Saitô-Muñoz-Eaton Protein Model

(2013) Julian Lee   PHYSICAL REVIEW LETTERS

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations

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

A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα

(2013) Srinivasan Sivanandan et al.   PLoS Computational Biology

Worm-Like Ising Model for Protein Mechanical Unfolding under the Effect of Osmolytes

(2012) Daniel Aioanei et al.   BIOPHYSICAL JOURNAL

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model

(2012) Min-Yeh Tsai et al.   JOURNAL OF BIOLOGICAL PHYSICS

Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics

(2012) Athi N. Naganathan   Journal of Chemical Theory and Computation

Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model

(2012) M Caraglio et al.   PHYSICAL BIOLOGY

Calculations of Free Energy Surfaces for Small Proteins and a Protein-RNA Complex Using a Lattice Model Approach

(2011) Eun-Sang Lee et al.   BULLETIN OF THE KOREAN CHEMICAL SOCIETY

Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations

(2011) Kazuhito Itoh et al.   JOURNAL OF CHEMICAL PHYSICS

Analysis of the equilibrium and kinetics of the ankyrin repeat protein myotrophin

(2011) Mauro Faccin et al.   JOURNAL OF CHEMICAL PHYSICS

Microsecond Subdomain Folding in Dihydrofolate Reductase

(2011) Munehito Arai et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model

(2011) Pierpaolo Bruscolini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis

(2011) Athi N. Naganathan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Direction-dependent mechanical unfolding and green fluorescent protein as a force sensor

(2011) M. Caraglio et al.   PHYSICAL REVIEW E

Observing the osmophobic effect in action at the single molecule level

(2011) Daniel Aioanei et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How Fast-Folding Proteins Fold

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

Pathways of mechanical unfolding of FnIII10: Low force intermediates

(2010) M. Caraglio et al.   JOURNAL OF CHEMICAL PHYSICS

Different Folding Pathways Taken by Highly Homologous Proteins, Goat α-Lactalbumin and Canine Milk Lysozyme

(2010) Takashi Nakamura et al.   JOURNAL OF MOLECULAR BIOLOGY

Transfer matrix solution of the Wako–Saitô–Muñoz–Eaton model augmented by arbitrary short range interactions

(2010) V I Tokar et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Simplified Exactly Solvable Model forβ-Amyloid Aggregation

(2010) M. Zamparo et al.   PHYSICAL REVIEW LETTERS

Entropic mechanism of large fluctuation in allosteric transition

(2010) Kazuhito Itoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early intermediates in the folding of dihydrofolate reductase from escherichia coli detected by hydrogen exchange and NMR

(2010) Bryan E. Jones et al.   PROTEIN SCIENCE

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Multidimensional theory of protein folding

(2009) Kazuhito Itoh et al.   JOURNAL OF CHEMICAL PHYSICS

Nearly symmetrical proteins: Folding pathways and transition states

(2009) Marco Zamparo et al.   JOURNAL OF CHEMICAL PHYSICS

Equilibrium Properties and Force-Driven Unfolding Pathways of RNA Molecules

(2009) A. Imparato et al.   PHYSICAL REVIEW LETTERS

The Protein Folding Problem

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

Conserved Folding Pathways of α-Lactalbumin and Lysozyme Revealed by Kinetic CD, Fluorescence, NMR, and Interrupted Refolding Experiments

(2008) Kai Schlepckow et al.   JOURNAL OF MOLECULAR BIOLOGY

Estimating Free-Energy Barrier Heights for an Ultrafast Folding Protein from Calorimetric and Kinetic Data†

(2008) Raquel Godoy-Ruiz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The folding transition state theory in simple model systems

(2008) Szymon Niewieczerzał et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Mechanical Unfolding and Refolding Pathways of Ubiquitin

(2008) A. Imparato et al.   PHYSICAL REVIEW LETTERS

Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics

(2008) O. Halskau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

(2008) W. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperativity, connectivity, and folding pathways of multidomain proteins

(2008) K. Itoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring internal friction of an ultrafast-folding protein

(2008) T. Cellmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

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

Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface

(2008) Hoi Sung Chung et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE