Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble

Effect of ligand binding on a protein with a complex folding landscape

(2018) Hisham Mazal et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation

(2017) Lucas Sawle et al.   Journal of Chemical Theory and Computation

Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations

(2017) Álvaro Cortés Cabrera et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Time-resolved observation of protein allosteric communication

(2017) Sebastian Buchenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for the principle of minimal frustration in the evolution of protein folding landscapes

(2017) Franco O. Tzul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity

(2017) Katherine E. Larrimore et al.   Scientific Reports

Engineering ancestral protein hyperstability

(2016) M. L. Romero-Romero et al.   BIOCHEMICAL JOURNAL

Allosteric Mechanisms in Chaperonin Machines

(2016) Ranit Gruber et al.   CHEMICAL REVIEWS

Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

(2016) Ashini Bolia et al.   Journal of Chemical Information and Modeling

Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma

(2016) Lucas Sawle et al.   Journal of Chemical Theory and Computation

On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins

(2016) Devin L. Trudeau et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs

(2015) Zhen Li et al.   BIOCHEMISTRY

The E. coli thioredoxin folding mechanism: The key role of the C-terminal helix

(2015) Diego S. Vazquez et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?

(2015) Tom C.B. McLeish et al.   BIOPHYSICAL JOURNAL

The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin

(2015) Avishek Kumar et al.   BIOPHYSICAL JOURNAL

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine

(2015) Avishek Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using ancient protein kinases to unravel a modern cancer drug's mechanism

(2015) C. Wilson et al.   SCIENCE

A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins

(2015) Hanseong Kim et al.   STRUCTURE

Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

(2014) Valeria A. Risso et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme

(2014) T. Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins

(2014) Valeria A. Risso et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Thermodynamic System Drift in Protein Evolution

(2014) Kathryn M. Hart et al.   PLOS BIOLOGY

A Unified View of “How Allostery Works”

(2014) Chung-Jung Tsai et al.   PLoS Computational Biology

An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases

(2014) Jeffrey I Boucher et al.   eLife

Structural dynamics flexibility informs function and evolution at a proteome scale

(2013) Zeynep Nevin Gerek et al.   Evolutionary Applications

The Evolutionary Origins of Detoxifying Enzymes

(2013) Hagit Bar-Rogovsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian β-Lactamases

(2013) Valeria A. Risso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Experimental evidence for the thermophilicity of ancestral life

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

Conservation of Protein Structure over Four Billion Years

(2013) Alvaro Ingles-Prieto et al.   STRUCTURE

Functional Evolution of an Anthocyanin Pathway Enzyme during a Flower Color Transition

(2012) Stacey D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

The binding affinities of proteins interacting with the PDZ domain of PICK1

(2012) Ashini Bolia et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Collective Dynamics Differentiates Functional Divergence in Protein Evolution

(2012) Tyler J. Glembo et al.   PLoS Computational Biology

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

(2011) Raul Perez-Jimenez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

(2011) Z. Nevin Gerek et al.   PLoS Computational Biology

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

(2010) C. Atilgan et al.   BIOPHYSICAL JOURNAL

Allostery and population shift in drug discovery

(2010) Gozde Kar et al.   CURRENT OPINION IN PHARMACOLOGY

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

(2009) Jamie T. Bridgham et al.   NATURE

Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy

(2009) Raul Perez-Jimenez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Thermodynamics of replacing an α-helical Pro residue in the P40S mutant of Escherichia coli thioredoxin

(2009) Atis Chakrabarti et al.   PROTEIN SCIENCE

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

(2009) Z. Nevin Gerek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Evolution of Hormone Signaling in Elasmobranchs by Exploitation of Promiscuous Receptors

(2008) S. M. Carroll et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL

(2008) Chakra Chennubhotla et al.   Molecular BioSystems