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A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T - PLoS Comput. Biol. (2009)

Bottom Line: We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family.Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution.More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

View Article: PubMed Central - PubMed

Affiliation: Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America.

ABSTRACT
Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

Show MeSH
Description of the Backrub motional mechanism and ensemble selection.Backrub moves for (A) tripeptide segments and (B) segments of arbitrarily length from 2 through 12 residues. (C) Flowchart of the process used to select ensembles to match the RDC measurements.
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pcbi-1000393-g002: Description of the Backrub motional mechanism and ensemble selection.Backrub moves for (A) tripeptide segments and (B) segments of arbitrarily length from 2 through 12 residues. (C) Flowchart of the process used to select ensembles to match the RDC measurements.

Mentions: To test relation 1, our approach first uses unrestrained conformational sampling with the Backrub motional model to generate a large set of initial conformations, starting from the ubiquitin crystal structure (Protein Data Bank (PDB) code 1UBQ). We use a Monte Carlo protocol consisting of rotamer changes and Backrub moves. Backrub moves involve selection of a random peptide segment, followed by a rigid body rotation of all atoms in that segment about an axis defined by the endpoint C-alpha atoms [31]. The peptide segment length is chosen at random to be either 2 or 3 residues (denoted in the following as “maximum segment length of 3”; Figure 2A) or between 2–12 residues (“maximum segment length of 12”; Figure 2B). 10,000 Backrub-Monte-Carlo simulations are run to generate 10,000 possible conformations in an initial set (see Methods for details). The Backrub motional mechanism thus directly accounts for correlated motions of continuous peptide segments of up to length 3 or 12. Applying these moves repeatedly in randomly chosen regions of the protein using Monte Carlo sampling allows for correlated motions of residues distant in sequence yet close in tertiary structure. Correlations between side-chain and backbone dynamics have also been observed in numerous NMR studies, such as for Ribonuclease H on the relaxation time scale [59],[60] and on the RDC time scale for ubiquitin [61] and Protein G [38].


A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T - PLoS Comput. Biol. (2009)

Description of the Backrub motional mechanism and ensemble selection.Backrub moves for (A) tripeptide segments and (B) segments of arbitrarily length from 2 through 12 residues. (C) Flowchart of the process used to select ensembles to match the RDC measurements.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2682763&req=5

pcbi-1000393-g002: Description of the Backrub motional mechanism and ensemble selection.Backrub moves for (A) tripeptide segments and (B) segments of arbitrarily length from 2 through 12 residues. (C) Flowchart of the process used to select ensembles to match the RDC measurements.
Mentions: To test relation 1, our approach first uses unrestrained conformational sampling with the Backrub motional model to generate a large set of initial conformations, starting from the ubiquitin crystal structure (Protein Data Bank (PDB) code 1UBQ). We use a Monte Carlo protocol consisting of rotamer changes and Backrub moves. Backrub moves involve selection of a random peptide segment, followed by a rigid body rotation of all atoms in that segment about an axis defined by the endpoint C-alpha atoms [31]. The peptide segment length is chosen at random to be either 2 or 3 residues (denoted in the following as “maximum segment length of 3”; Figure 2A) or between 2–12 residues (“maximum segment length of 12”; Figure 2B). 10,000 Backrub-Monte-Carlo simulations are run to generate 10,000 possible conformations in an initial set (see Methods for details). The Backrub motional mechanism thus directly accounts for correlated motions of continuous peptide segments of up to length 3 or 12. Applying these moves repeatedly in randomly chosen regions of the protein using Monte Carlo sampling allows for correlated motions of residues distant in sequence yet close in tertiary structure. Correlations between side-chain and backbone dynamics have also been observed in numerous NMR studies, such as for Ribonuclease H on the relaxation time scale [59],[60] and on the RDC time scale for ubiquitin [61] and Protein G [38].

Bottom Line: We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family.Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution.More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

View Article: PubMed Central - PubMed

Affiliation: Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America.

ABSTRACT
Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR) Residual Dipolar Couplings (RDCs). Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i) a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii) a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

Show MeSH