Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein (Q30164542)

9 June 2017

Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein (English)

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9 June 2017

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2

Vijay S Pande

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9 June 2017

Stefan M Larson

1

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PubMed ID

12946364

9 June 2017

language of work or name

English

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publication date

1 September 2003

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Journal of Molecular Biology

9 June 2017

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9 June 2017

332

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9 June 2017

1

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9 June 2017

275-286

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Why are proteins so robust to site mutations?

9 June 2017

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Roles of mutation and recombination in the evolution of protein thermodynamics

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Native protein sequences are close to optimal for their structures

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Thoroughly sampling sequence space: large-scale protein design of structural ensembles

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Prediction of amino acid sequence from structure

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Implications of SH3 domain structure and dynamics for protein regulation and drug design.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

The identification of conserved interactions within the SH3 domain by alignment of sequences and structures

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

In silico design for protein stabilization

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

De novo protein design: fully automated sequence selection

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

De novo protein design: towards fully automated sequence selection

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Computer search algorithms in protein modification and design.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

De novo design of the hydrophobic cores of proteins

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

New strategies in protein design

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Energy functions for protein design

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

High-resolution protein design with backbone freedom

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

De novo protein design. I. In search of stability and specificity.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Review: protein design--where we were, where we are, where we're going.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Computational protein design

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Automatic protein design with all atom force-fields by exact and heuristic optimization

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Bayesian statistical analysis of protein side-chain rotamer preferences

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Side-chain and backbone flexibility in protein core design

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

De novo design of the hydrophobic core of ubiquitin

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Experiment and theory highlight role of native state topology in SH3 folding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Functional rapidly folding proteins from simplified amino acid sequences.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

The native state conformational ensemble of the SH3 domain from alpha-spectrin

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Conformational strain in the hydrophobic core and its implications for protein folding and design

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Computer-assisted re-design of spectrin SH3 residue clusters

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Hydrophobic core packing in the SH3 domain folding transition state

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

De novo protein design. II. Plasticity in sequence space

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Folding free energy function selects native-like protein sequences in the core but not on the surface

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

An analysis of simultaneous variation in protein structures

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Scoring residue conservation

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Protein folding theory: from lattice to all-atom models

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Evolutionary conservation in protein folding kinetics.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Obligatory steps in protein folding and the conformational diversity of the transition state

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

The sequences of small proteins are not extensively optimized for rapid folding by natural selection

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

Solvation energy in protein folding and binding

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900832-5

10.1016/S0022-2836(03)00832-5

7 January 2021

Identifiers

DOI

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9 June 2017

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PubMed ID

12946364