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Geometrical Description of Protein Structural Motifs

Kozak, John J. and Gray, Harry B. and Wittung-Stafshede, Pernilla (2018) Geometrical Description of Protein Structural Motifs. Journal of Physical Chemistry B, 122 (49). pp. 11289-11294. ISSN 1520-6106. https://resolver.caltech.edu/CaltechAUTHORS:20180828-103040438

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Abstract

We present a geometrical method that can identify secondary structural motifs in proteins via angular correlations. The method uses crystal structure coordinates to calculate angular and radial signatures of each residue relative to an external reference point as the number of nearest-neighbor residues increases. We apply our approach to the blue copper protein amicyanin using the copper cofactor as the external reference point. We define a signature termed Δβ which describes the change in angular correlation as the span of nearest neighbor residues increases. We find that three turn regions of amicyanin harbor residues with Δβ near zero, while residues in other secondary structures have Δβ greater than zero: for β-strands, Δβ changes gradually residue by residue along the strand. Extension of our analysis to other blue copper proteins demonstrated that the noted structural trends are general. Importantly, our geometrical description of the folded protein accounts for all forces holding the structure together. Through this analysis, we identified some of the turns in amicyanin as symmetrical anchor points.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1021/acs.jpcb.8b07130DOIArticle
https://pubs.acs.org/doi/suppl/10.1021/acs.jpcb.8b07130PublisherSupporting Information
ORCID:
AuthorORCID
Gray, Harry B.0000-0002-7937-7876
Wittung-Stafshede, Pernilla0000-0003-1058-1964
Additional Information:© 2018 American Chemical Society. Received: July 25, 2018; Revised: August 22, 2018; Published: August 24, 2018. We thank Istvan Horvath (Chalmers University) for making structural images. Roberto Garza-Lopez (Pomona College) provided helpful insights in early stages. Work performed at Caltech was supported by NIH (R01 DK019038 to H.B.G.) and by the Barbro Osher Pro Svecia Foundation (funding a sabbatical for P.W.-S. at Caltech).
Funders:
Funding AgencyGrant Number
NIHR01 DK019038
Barbro Osher Pro Svecia FoundationUNSPECIFIED
Issue or Number:49
Record Number:CaltechAUTHORS:20180828-103040438
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20180828-103040438
Official Citation:Geometrical Description of Protein Structural Motifs. John J. Kozak, Harry B. Gray, and Pernilla Wittung-Stafshede. The Journal of Physical Chemistry B 2018 122 (49), 11289-11294. DOI: 10.1021/acs.jpcb.8b07130
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:89207
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:28 Aug 2018 18:25
Last Modified:03 Oct 2019 20:14

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