Folding Intermediates, Heterogeneous Native Ensembles and Protein Function

NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function

(2021) T. Reid Alderson et al.   CELL

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

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

Tackling Covid‐19 using disordered‐to‐order transition of residues in the spike protein upon angiotensin‐converting enzyme 2 binding

(2021) Dhanusha Yesudhas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

(2021) Maxwell I. Zimmerman et al.   Nature Chemistry

Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS)

(2020) Tobias W. Gräwert et al.   JOURNAL OF MOLECULAR BIOLOGY

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

(2020) Amir Bitran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

(2020) Zhenming Jin et al.   NATURE

Colloidal stability of the living cell

(2020) Håkan Wennerström et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complementarity of Hydrogen/Deuterium Exchange Mass Spectrometry and Cryo-Electron Microscopy

(2020) John R. Engen et al.   TRENDS IN BIOCHEMICAL SCIENCES

Single-Molecule Studies of Protein Folding with Optical Tweezers

(2020) Carlos Bustamante et al.   Annual Review of Biochemistry

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

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

Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor

(2020) C. Köhler et al.   Science Advances

Lessons about Protein Folding and Binding from Archetypal Folds

(2020) Luis Alberto Campos et al.   ACCOUNTS OF CHEMICAL RESEARCH

Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography

(2020) Mateusz Sikora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase

(2020) Alexander E. Conicella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein-complex stability in cells and in vitro under crowded conditions

(2020) Samantha S Stadmiller et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Local frustration around enzyme active sites

(2019) Maria I. Freiberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frustration and folding of a TIM barrel protein

(2019) Kevin T. Halloran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural dynamics of membrane-protein folding from single-molecule FRET

(2019) Georg Krainer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Successes and challenges in simulating the folding of large proteins

(2019) Anne Gershenson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Dynamic Core in Human NQO1 Controls the Functional and Stability Effects of Ligand Binding and Their Communication across the Enzyme Dimer

(2019) Vankova et al.   Biomolecules

Protein engineers turned evolutionists—the quest for the optimal starting point

(2019) Devin L Trudeau et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineering protein assemblies with allosteric control via monomer fold-switching

(2019) Luis A. Campos et al.   Nature Communications

How does solvation in the cell affect protein folding and binding?

(2018) Caitlin M Davis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conformational dynamics and enzyme evolution

(2018) Dušan Petrović et al.   Journal of the Royal Society Interface

Dynamic activation and regulation of the mitogen-activated protein kinase p38

(2018) Ganesan Senthil Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution cryo-EM structures of actin-bound myosin states reveal the mechanism of myosin force sensing

(2018) Ahmet Mentes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local energetic frustration affects the dependence of green fluorescent protein folding on the chaperonin GroEL

(2017) Boudhayan Bandyopadhyay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

The Power of Force: Insights into the Protein Folding Process Using Single-Molecule Force Spectroscopy

(2016) Jörg Schönfelder et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantifying Protein Disorder through Measures of Excess Conformational Entropy

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

How cooperative are protein folding and unfolding transitions?

(2016) Pooja Malhotra et al.   PROTEIN SCIENCE

Structural Determinants of Misfolding in Multidomain Proteins

(2016) Pengfei Tian et al.   PLoS Computational Biology

Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints?

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

Reversal of the DNA-Binding-Induced Loop L1 Conformational Switch in an Engineered Human p53 Protein

(2014) Soheila Emamzadah et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR

(2014) Celia Sanchez-Medina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

(2014) Stefano Gianni 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

Fast protein folding kinetics

(2014) Hannah Gelman et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Folding of a large protein at high structural resolution

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

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

Force as a single molecule probe of multidimensional protein energy landscapes

(2012) Gabriel Žoldák et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

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

How, when and why proteins collapse: the relation to folding

(2011) Gilad Haran   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integrated prediction of protein folding and unfolding rates from only size and structural class

(2011) David De Sancho et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Fast-Folding Proteins Fold

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

Theoretical Perspectives on Protein Folding

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

Choreographing an enzyme's dance

(2010) Janice Villali et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

Dry molten globule intermediates and the mechanism of protein unfolding

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

A one-dimensional free energy surface does not account for two-probe folding kinetics of protein α3D

(2009) Feng Liu et al.   JOURNAL OF CHEMICAL PHYSICS

Functional features cause misfolding of the ALS-provoking enzyme SOD1

(2009) A. Nordlund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Multiple Routes and Structural Heterogeneity in Protein Folding

(2008) Jayant B. Udgaonkar   Annual Review of Biophysics

d-Ribose-5-Phosphate Isomerase B from Escherichia coli is Also a Functional d-Allose-6-Phosphate Isomerase, While the Mycobacterium tuberculosis Enzyme is Not

(2008) Annette K. Roos et al.   JOURNAL OF MOLECULAR BIOLOGY

Expanding the Realm of Ultrafast Protein Folding: gpW, a Midsize Natural Single-Domain with α+β Topology that Folds Downhill

(2008) Adam Fung et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Backtracking on the folding landscape of the  -trefoil protein interleukin-1 ?

(2008) D. T. Capraro 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