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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.

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Chi angle distributions of residues in or near the core of ubiquitin.Distributions are shown for the best RDC-optimized Backrub ensemble with maximum segment length of 12 and kT = 1.2, as well as modeled and experimental relaxation order parameters corresponding to these chi angles (chi1 and chi2 correspond to the Cγ and Cδ methyl groups, respectively). The Leucine Cδ methyl group relaxation order parameters were averaged.
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pcbi-1000393-g005: Chi angle distributions of residues in or near the core of ubiquitin.Distributions are shown for the best RDC-optimized Backrub ensemble with maximum segment length of 12 and kT = 1.2, as well as modeled and experimental relaxation order parameters corresponding to these chi angles (chi1 and chi2 correspond to the Cγ and Cδ methyl groups, respectively). The Leucine Cδ methyl group relaxation order parameters were averaged.

Mentions: We showed above that our RDC-optimized Backrub ensemble (i) gives similar Q-factors to reference ensembles including an RDC-restrained MD ensemble (EROS) [4], a ubiquitin X-ray ensemble and an ensemble of snapshots from a 100-nanosecond MD trajectory [63] and (ii) has similar regions of structural variability (Figure 4B). As an additional point of comparison and validation of our approach, we asked whether the RDC-optimized Backrub ensemble also supports other structural and functional insights derived from previous ensemble descriptions of ubiquitin. Lindorff-Larsen et al. [58] as well as Richter et al. [57] used MD simulations with side chain and backbone relaxation order parameters as restraints. These ensembles displayed liquid-like flexibility of side chains buried in the protein core. The RDC-optimized Backrub ensemble also has this property, with buried or near buried residues 13, 23, 44, 61, and 67 correctly modeled as flexible with calculated order parameters close to their respective values from NMR relaxation experiments. As shown in Figure 5, Ile 13 chi2, Ile 44 chi2, and Leu 67 chi2 have modeled order parameters within 0.04 of the experimental values. Ile 13 chi 1 and Ile 61 chi2 have modeled order parameters that are substantially lower than the experimental values but these differences can be due to the short timescale of the relaxation measurements compared to the longer timescale of the RDCs fit by the RDC-optimized Backrub ensemble. (See Figure S5 for comparison to more side chains analyzed in [58].) Side chain order parameters derived from the 100 ns MD simulation discussed earlier are also shown in Figure S5 for comparison. In several cases, the side chain order parameters from the MD simulation are higher than those obtained from the relaxation experiments, possibly due to sampling limitations at the side chain level. Exceptions are the modeled order parameters for L15 chi2 and I61 chi2, which are significantly lower than the measured relaxation order parameters (this may be because the timescale of the MD simulation is longer than the rotational correlation time of the molecule).


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)

Chi angle distributions of residues in or near the core of ubiquitin.Distributions are shown for the best RDC-optimized Backrub ensemble with maximum segment length of 12 and kT = 1.2, as well as modeled and experimental relaxation order parameters corresponding to these chi angles (chi1 and chi2 correspond to the Cγ and Cδ methyl groups, respectively). The Leucine Cδ methyl group relaxation order parameters were averaged.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2682763&req=5

pcbi-1000393-g005: Chi angle distributions of residues in or near the core of ubiquitin.Distributions are shown for the best RDC-optimized Backrub ensemble with maximum segment length of 12 and kT = 1.2, as well as modeled and experimental relaxation order parameters corresponding to these chi angles (chi1 and chi2 correspond to the Cγ and Cδ methyl groups, respectively). The Leucine Cδ methyl group relaxation order parameters were averaged.
Mentions: We showed above that our RDC-optimized Backrub ensemble (i) gives similar Q-factors to reference ensembles including an RDC-restrained MD ensemble (EROS) [4], a ubiquitin X-ray ensemble and an ensemble of snapshots from a 100-nanosecond MD trajectory [63] and (ii) has similar regions of structural variability (Figure 4B). As an additional point of comparison and validation of our approach, we asked whether the RDC-optimized Backrub ensemble also supports other structural and functional insights derived from previous ensemble descriptions of ubiquitin. Lindorff-Larsen et al. [58] as well as Richter et al. [57] used MD simulations with side chain and backbone relaxation order parameters as restraints. These ensembles displayed liquid-like flexibility of side chains buried in the protein core. The RDC-optimized Backrub ensemble also has this property, with buried or near buried residues 13, 23, 44, 61, and 67 correctly modeled as flexible with calculated order parameters close to their respective values from NMR relaxation experiments. As shown in Figure 5, Ile 13 chi2, Ile 44 chi2, and Leu 67 chi2 have modeled order parameters within 0.04 of the experimental values. Ile 13 chi 1 and Ile 61 chi2 have modeled order parameters that are substantially lower than the experimental values but these differences can be due to the short timescale of the relaxation measurements compared to the longer timescale of the RDCs fit by the RDC-optimized Backrub ensemble. (See Figure S5 for comparison to more side chains analyzed in [58].) Side chain order parameters derived from the 100 ns MD simulation discussed earlier are also shown in Figure S5 for comparison. In several cases, the side chain order parameters from the MD simulation are higher than those obtained from the relaxation experiments, possibly due to sampling limitations at the side chain level. Exceptions are the modeled order parameters for L15 chi2 and I61 chi2, which are significantly lower than the measured relaxation order parameters (this may be because the timescale of the MD simulation is longer than the rotational correlation time of the molecule).

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