Structural and functional constraints in the evolution of protein families (Q37597886)

21 August 2017

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title

Structural and functional constraints in the evolution of protein families (English)

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21 August 2017

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2

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21 August 2017

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Tom L Blundell

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21 August 2017

Catherine Louise Worth

series ordinal

1

object named as

Catherine L Worth

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21 August 2017

publication date

16 September 2009

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Nature Reviews Molecular Cell Biology

21 August 2017

published in

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21 August 2017

volume

10

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21 August 2017

issue

10

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21 August 2017

page(s)

709-720

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A survey of left-handed polyproline II helices

21 August 2017

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Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

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Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins

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Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs

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An algorithm for secondary structure determination in proteins based on sequence similarity

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A revised set of potentials for beta-turn formation in proteins

31 March 2020

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Analysis and prediction of the different types of beta-turn in proteins

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31 March 2020

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Helix signals in proteins

31 March 2020

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31 March 2020

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A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations

31 March 2020

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A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations

31 March 2020

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Identification, classification, and analysis of beta-bulges in proteins

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The beta bulge: a common small unit of nonrepetitive protein structure

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Helix geometry in proteins

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Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures

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Properties of polyproline II, a secondary structure element implicated in protein-protein interactions

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Is the evolution of insulin Darwinian or due to selectively neutral mutation?

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On the conservation of protein sequences in evolution

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Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex

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Distinguishing structural and functional restraints in evolution in order to identify interaction sites

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Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction

31 March 2020

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

31 March 2020

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Protein stability promotes evolvability

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Thermodynamic prediction of protein neutrality

31 March 2020

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Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid

31 March 2020

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Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures

31 March 2020

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Hydrogen bonding increases packing density in the protein interior

31 March 2020

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Polar group burial contributes more to protein stability than nonpolar group burial

31 March 2020

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Do all backbone polar groups in proteins form hydrogen bonds?

31 March 2020

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Satisfying hydrogen bonding potential in proteins

31 March 2020

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Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains.

31 March 2020

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Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures

31 March 2020

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Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities

31 March 2020

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Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac

31 March 2020

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The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins

31 March 2020

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Analysis of the interaction between charged side chains and the alpha-helix dipole using designed thermostable mutants of phage T4 lysozyme

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Helix stop signals in proteins and peptides: the capping box

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Aromatic-aromatic interaction: a mechanism of protein structure stabilization

31 March 2020

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Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins

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Amino-aromatic interactions in proteins

31 March 2020

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Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?

31 March 2020

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Cation-pi interactions in structural biology

31 March 2020

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Crystal structure of an ancient protein: evolution by conformational epistasis

31 March 2020

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Conserved residues and the mechanism of protein folding

31 March 2020

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The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

31 March 2020

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How evolution makes proteins fold quickly

31 March 2020

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Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

31 March 2020

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Evolutionary conservation in protein folding kinetics.

31 March 2020

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Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation.

31 March 2020

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Are residues in a protein folding nucleus evolutionarily conserved?

31 March 2020

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Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

31 March 2020

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Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).

31 March 2020

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Protein co-evolution, co-adaptation and interactions

31 March 2020

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Evolutionary and physiological importance of hub proteins

31 March 2020

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Genomic function (communication arising): Rate of evolution and gene dispensability

31 March 2020

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Functional genomic analysis of the rates of protein evolution

31 March 2020

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Impact of transcriptional properties on essentiality and evolutionary rate

31 March 2020

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Why highly expressed proteins evolve slowly

31 March 2020

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A single determinant dominates the rate of yeast protein evolution

31 March 2020

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Understanding protein evolution: from protein physics to Darwinian selection

31 March 2020

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Gene expression and molecular evolution

31 March 2020

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Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

31 March 2020

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The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology

31 March 2020

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Protein misfolding, functional amyloid, and human disease

31 March 2020

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Competition between folding, native-state dimerisation and amyloid aggregation in beta-lactoglobulin.

31 March 2020

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Protein degradation and protection against misfolded or damaged proteins

31 March 2020

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Epigenetics: regulation through repression

31 March 2020

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CATH--a hierarchic classification of protein domain structures

31 March 2020

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PASS2: an automated database of protein alignments organised as structural superfamilies

31 March 2020

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A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease.

31 March 2020

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Searching protein structure databases with DaliLite v.3

31 March 2020

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Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

31 March 2020

1 reference

MMDB: Entrez's 3D structure database

31 March 2020

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The Pfam protein families database

31 March 2020

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InterPro: the integrative protein signature database

31 March 2020

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31 March 2020

The PROSITE database.

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PRINTS and its automatic supplement, prePRINTS.

31 March 2020

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SMART, a simple modular architecture research tool: identification of signaling domains

31 March 2020

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The TIGRFAMs database of protein families

31 March 2020

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Gene3D: structural assignments for the biologist and bioinformaticist alike

31 March 2020

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SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny

31 March 2020

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PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

31 March 2020

1 reference

CDD: a conserved domain database for interactive domain family analysis

31 March 2020

1 reference

PairsDB atlas of protein sequence space

31 March 2020

1 reference

Review: what can structural classifications reveal about protein evolution?

31 March 2020

1 reference

JOY: protein sequence-structure representation and analysis.

31 March 2020

1 reference

Amino acid substitution matrices from protein blocks

31 March 2020

1 reference

Ulla: a program for calculating environment-specific amino acid substitution tables

31 March 2020

1 reference

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

31 March 2020

1 reference

ProDom: automated clustering of homologous domains

31 March 2020

1 reference

12 December 2020

Conservation of protein interaction network in evolution.

1 reference

12 December 2020

SCOP: a structural classification of proteins database for the investigation of sequences and structures

1 reference

12 December 2020

Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering

1 reference

12 December 2020

Identifiers

DOI

10.1038/NRM2762

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21 August 2017

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