Dataset Information

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl ¹H-¹³C residual dipolar couplings.

ABSTRACT: Modelling of protein structures based on backbone chemical shifts, using programs such as CS-ROSETTA, is becoming increasingly popular, especially for systems where few restraints are available or where homologous structures are already known. While the reliability of CS-ROSETTA calculations can be improved by incorporation of some additional backbone NMR data such as those afforded by residual dipolar couplings or minimal NOE data sets involving backbone amide protons, the sidechain conformations are largely modelled by statistical energy terms. Here, we present a simple method based on methyl residual dipolar couplings that can be used to determine the rotameric state of the threefold symmetry axis of methyl groups that occupy a single rotamer, determine rotameric distributions, and identify regions of high flexibility. The method is demonstrated for methyl side chains of a deletion variant of the human chaperone DNAJB6b.

SUBMITTER: Karamanos TK

PROVIDER: S-EPMC7083688 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Determining methyl sidechain conformations in a CS-ROSETTA model using methyl <sup>1</sup>H-<sup>13</sup>C residual dipolar couplings.

Karamanos Theodoros K TK Tugarinov Vitali V Clore G Marius GM

Journal of biomolecular NMR 20200116 2-3

Modelling of protein structures based on backbone chemical shifts, using programs such as CS-ROSETTA, is becoming increasingly popular, especially for systems where few restraints are available or where homologous structures are already known. While the reliability of CS-ROSETTA calculations can be improved by incorporation of some additional backbone NMR data such as those afforded by residual dipolar couplings or minimal NOE data sets involving backbone amide protons, the sidechain conformatio ...[more]

PMID: 31950428

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Project description:Disulfide bridges in proteins are formed by the oxidation of pairs of cysteine residues. These cross-links play a critical role in stabilizing the 3D-structure of small disulfide rich polypeptides such as hormones and venom toxins. The arrangement of the multiple disulfide bonds directs the peptide fold into distinct structural motifs that have evolved for resistance against biochemical and physical insults. These structural scaffolds have, therefore, proven to be very attractive in bioengineering efforts to develop novel biologics with applications in health and agriculture. Structural characterization of small disulfide rich peptides (DRPs) presents unique challenges when using commonly applied biophysical methods. NMR is the most commonly used method for studying such molecules, where the relatively small size of these molecules results in highly precise structural ensembles defined by a large number of distance and dihedral angle restraints per amino acid. However, in NMR the sulfur atoms that are involved in three of the five dihedral angles in a disulfide bond cannot be readily measured. Given the central role of disulfide bonds in the structure of these molecules, it is unclear what the inherent resolution of such NMR structures is when using traditional NMR methods. Here, we use an extensive set of long-range residual dipolar couplings (RDCs) to assess the resolution of the NMR structure of a disulfide-rich peptide. We find that structures based primarily on NOEs, yield ensembles that are equivalent to a crystallographic resolution of 2-3 Å in resolution, and that incorporation of RDCs reduces this to ~1-1.5 Å resolution. At this resolution the sidechain of ordered amino acids can be defined accurately, allowing the geometry of the cysteine bridges to be better defined, and allowing for disulfide-bond connectivities to be determined with high confidence. The observed improvements in resolution when using RDCs is remarkable considering the small size of these peptides.

Dataset Information

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl ¹H-¹³C residual dipolar couplings.

Publications

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl <sup>1</sup>H-<sup>13</sup>C residual dipolar couplings.

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Dataset Information

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl 1H-13C residual dipolar couplings.

Publications

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl <sup>1</sup>H-<sup>13</sup>C residual dipolar couplings.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl ¹H-¹³C residual dipolar couplings.