Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

(2013) Joseph A. Marsh et al.   CELL

Molecular origins of binding affinity: seeking the Archimedean point

(2013) Panagiotis L Kastritis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dynamics and adaptive benefits of modular protein evolution

(2013) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Describing intrinsically disordered proteins at atomic resolution by NMR

(2013) Malene Ringkjøbing Jensen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

(2013) Marija Buljan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Buried and Accessible Surface Area Control Intrinsic Protein Flexibility

(2013) Joseph A. Marsh   JOURNAL OF MOLECULAR BIOLOGY

What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

(2013) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Conformational Diversity Correlates with Evolutionary Rate

(2013) Diego Javier Zea et al.   MOLECULAR BIOLOGY AND EVOLUTION

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

(2013) Gira Bhabha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins

(2013) Wade Borcherds et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

From Sequence and Forces to Structure, Function, and Evolution of Intrinsically Disordered Proteins

(2013) Julie D. Forman-Kay et al.   STRUCTURE

The Role of Salt Bridges, Charge Density, and Subunit Flexibility in Determining Disassembly Routes of Protein Complexes

(2013) Zoe Hall et al.   STRUCTURE

The emergence of protein complexes: quaternary structure, dynamics and allostery

(2012) Tina Perica et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Characterization of disordered proteins with ENSEMBLE

(2012) Mickaël Krzeminski et al.   BIOINFORMATICS

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

(2012) M�rton M�nz et al.   BMC BIOINFORMATICS

Probing the diverse landscape of protein flexibility and binding

(2012) Joseph A Marsh et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

(2012) Donald Gagné et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Conservation of Functionally Important Global Motions in an Enzyme Superfamily across Varying Quaternary Structures

(2012) Emily K. Luebbering et al.   JOURNAL OF MOLECULAR BIOLOGY

A Phylogenetic Analysis of Normal Modes Evolution in Enzymes and Its Relationship to Enzyme Function

(2012) Jason Lai et al.   JOURNAL OF MOLECULAR BIOLOGY

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution

(2012) Roberto Mosca et al.   MOLECULAR & CELLULAR PROTEOMICS

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification

(2012) Harry Amri Moesa et al.   Molecular BioSystems

Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

(2012) Cristian Micheletti   Physics of Life Reviews

Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

(2012) Ulf Hensen et al.   PLoS One

Evolution of oligomeric state through geometric coupling of protein interfaces

(2012) T. Perica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

(2012) E. D. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Why are the low-energy protein normal modes evolutionarily conserved?

(2012) Julian Echave   PURE AND APPLIED CHEMISTRY

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution

(2011) Duncan C. Ramsey et al.   GENETICS

Molecular Evolution of Protein Conformational Changes Revealed by a Network of Evolutionarily Coupled Residues

(2011) Jouhyun Jeon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slow protein evolutionary rates are dictated by surface-core association

(2011) A. Toth-Petroczy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein topology from predicted residue contacts

(2011) William R. Taylor et al.   PROTEIN SCIENCE

Ensemble modeling of protein disordered states: Experimental restraint contributions and validation

(2011) Joseph A. Marsh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Dynamics alignment: Comparison of protein dynamics in the scop database

(2011) Dror Tobi   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding

(2011) Joseph A. Marsh et al.   STRUCTURE

Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis

(2011) Arvind Ramanathan et al.   PLOS BIOLOGY

Bringing order to protein disorder through comparative genomics and genetic interactions

(2011) Jeremy Bellay et al.   GENOME BIOLOGY

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

(2010) K. Hashimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quaternary dynamics and plasticity underlie small heat shock protein chaperone function

(2010) F. Stengel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds

(2010) John Overington et al.   PROTEIN SCIENCE

Exploring the factors determining the dynamics of different protein folds

(2010) S. M. Hollup et al.   PROTEIN SCIENCE

Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily

(2010) Francesco Raimondi et al.   STRUCTURE

Structural Diversity in Free and Bound States of Intrinsically Disordered Protein Phosphatase 1 Regulators

(2010) Joseph A. Marsh et al.   STRUCTURE

Structure/Function Implications in a Dynamic Complex of the Intrinsically Disordered Sic1 with the Cdc4 Subunit of an SCF Ubiquitin Ligase

(2010) Tanja Mittag et al.   STRUCTURE

On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm

(2010) Enrique Marcos et al.   PLoS Computational Biology

Evolution of Protein Binding Modes in Homooligomers

(2009) Judith E. Dayhoff et al.   JOURNAL OF MOLECULAR BIOLOGY

Solvent Exposure Imparts Similar Selective Pressures across a Range of Yeast Proteins

(2009) G. C. Conant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparing Models of Evolution for Ordered and Disordered Proteins

(2009) C. J. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level

(2009) E. A. Franzosa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Self-Assembly and Evolution of Homomeric Protein Complexes

(2009) Gabriel Villar et al.   PHYSICAL REVIEW LETTERS

A perturbative view of protein structural variation

(2009) Julián Echave et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

(2009) Javier A Velazquez-Muriel et al.   BMC STRUCTURAL BIOLOGY

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

(2009) Gregory D. Friedland et al.   PLoS Computational Biology

Evolutionary conservation of protein vibrational dynamics

(2008) Sandra Maguid et al.   GENE

Assembly reflects evolution of protein complexes

(2008) Emmanuel D. Levy et al.   NATURE

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

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

Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families

(2008) Andrea Zen et al.   PROTEIN SCIENCE

Do viral proteins possess unique biophysical features?

(2008) Nobuhiko Tokuriki et al.   TRENDS IN BIOCHEMICAL SCIENCES