Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure. (Q30356000)

20 June 2017

title

Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure. (English)

1 reference

20 June 2017

0 references

1 reference

2

1 reference

20 June 2017

Joseph A Marsh

1

0 references

language of work or name

English

0 references

publication date

25 November 2013

1 reference

20 June 2017

1 reference

20 June 2017

volume

36

1 reference

20 June 2017

issue

2

1 reference

20 June 2017

page(s)

209-218

1 reference

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins

20 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The nature of the accessible and buried surfaces in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Probing the diverse landscape of protein flexibility and binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Buried and accessible surface area control intrinsic protein flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Conformational change of proteins arising from normal mode calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Relative solvent accessible surface area predicts protein conformational changes upon binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Probes of Subunit Assembly and Reconstitution Pathways in Multisubunit Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Assembly reflects evolution of protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Protein complexes are under evolutionary selection to assemble via ordered pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structural characterisation and functional significance of transient protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Morpheeins--a new structural paradigm for allosteric regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Quaternary dynamics and plasticity underlie small heat shock protein chaperone function

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Dynamics and adaptive benefits of modular protein evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

3D domain swapping: a mechanism for oligomer assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Evolution of oligomeric state through geometric coupling of protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

On Some Principles Governing Molecular Evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Solvent exposure imparts similar selective pressures across a range of yeast proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The relationship between relative solvent accessibility and evolutionary rate in protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The stability effects of protein mutations appear to be universally distributed

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Flexibility and packing in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Describing intrinsically disordered proteins at atomic resolution by NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Evolutionary rate heterogeneity in proteins with long disordered regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Comparing models of evolution for ordered and disordered proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Slow protein evolutionary rates are dictated by surface-core association

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structural determinants of the rate of protein evolution in yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Why highly expressed proteins evolve slowly

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Protein conformational diversity correlates with evolutionary rate.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

An analysis of core deformations in protein superfamilies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Comparison of molecular dynamics and superfamily spaces of protein domain deformation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Relation between native ensembles and experimental structures of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Recapitulation of protein family divergence using flexible backbone protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Proteins with similar architecture exhibit similar large-scale dynamic behavior

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Exploring the common dynamics of homologous proteins. Application to the globin family.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Evolutionary conservation of protein backbone flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Exploring the factors determining the dynamics of different protein folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Conservation of functionally important global motions in an enzyme superfamily across varying quaternary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Conservation and specialization in PAS domain dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Comparative molecular dynamics--similar folds and similar motions?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Conservation of flexible residue clusters among structural and functional enzyme homologues

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Exploring protein dynamics space: the dynasome as the missing link between protein structure and function

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Dynamics alignment: comparison of protein dynamics in the SCOP database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Protein dynamism and evolvability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

3D complex: a structural classification of protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Novel methods for studying multiprotein complexes in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Self-assembly and evolution of homomeric protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Molecular origins of binding affinity: seeking the Archimedean point

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Evolution of protein binding modes in homooligomers

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Detecting protein function and protein-protein interactions from genome sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

An evolutionary trace method defines binding surfaces common to protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Sequence evolution correlates with structural dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structural basis for regulation of protein phosphatase 1 by inhibitor-2

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Characterization of the unfolded state of bovine alpha-lactalbumin and comparison with unfolded states of homologous proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The role of structural disorder in the rewiring of protein interactions through evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Bringing order to protein disorder through comparative genomics and genetic interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The relationship between evolutionary and physiological variation in hemoglobin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The Energy Landscapes and Motions of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Evolutionarily conserved pathways of energetic connectivity in protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Ligand-dependent dynamics and intramolecular signaling in a PDZ domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Molecular evolution of protein conformational changes revealed by a network of evolutionarily coupled residues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Protein 3D structure computed from evolutionary sequence variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Protein topology from predicted residue contacts

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Characterization of disordered proteins with ENSEMBLE.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

Structural Determinants of Protein Dynamics: Analysis of 15N NMR Relaxation Measurements for Main-Chain and Side-Chain Nuclei of Hen Egg White Lysozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

The accessible surface area and stability of oligomeric proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201300134

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

21 January 2018

1 reference

20 August 2023

https://opencitations.net/index/coci/api/v1/citations/10.1351/PAC-CON-12-02-15

Identifiers

DOI

10.1002/BIES.201300134

1 reference

20 June 2017

1 reference