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Difference contact maps: from what to why in the analysis of the conformational flexibility of proteins

Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, View ORCID ProfileMayy Sedova, View ORCID ProfileAdam Godzik
doi: https://doi.org/10.1101/575696
Mallika Iyer
1Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
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Zhanwen Li
2Biosciences Division, University of California Riverside School of Medicine, 900 University Ave., Riverside, CA, 92521, USA
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Lukasz Jaroszewski
2Biosciences Division, University of California Riverside School of Medicine, 900 University Ave., Riverside, CA, 92521, USA
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Mayy Sedova
2Biosciences Division, University of California Riverside School of Medicine, 900 University Ave., Riverside, CA, 92521, USA
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  • ORCID record for Mayy Sedova
Adam Godzik
2Biosciences Division, University of California Riverside School of Medicine, 900 University Ave., Riverside, CA, 92521, USA
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  • ORCID record for Adam Godzik
  • For correspondence: adam@godziklab.org
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Abstract

Protein structures, usually visualized in various highly idealized forms focusing on the three-dimensional arrangements of secondary structure elements, can also be described as lists of interacting residues or atoms and visualized as two-dimensional distance or contact maps. We show that contact maps provide an ideal tool to describe and analyze differences between structures of proteins in different conformations. Expanding functionality of the PDBFlex server and database developed previously in our group, we describe how analysis of difference contact maps (DCMs) can be used to identify critical interactions stabilizing alternative protein conformations, recognize residues and positions controlling protein functions and build hypotheses as to molecular mechanisms of disease mutations.

Author Summary Protein folding is driven, and the three-dimensional structures of proteins are defined, by the non-local interactions between amino acid chains. However, the usual visualizations of protein structures focus on the overall chain topology and do not provide much information about the interactions defining them. Here we explore contact map visualization of protein structures, which directly focuses on interactions stabilizing the structure and thus can be easily used to understand effects of mutations on protein structure. We show that contact map visualization is particularly useful for comparing alternative conformations of proteins and identifying critical positions controlling functional flexibility.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 12, 2019.
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Difference contact maps: from what to why in the analysis of the conformational flexibility of proteins
Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Mayy Sedova, Adam Godzik
bioRxiv 575696; doi: https://doi.org/10.1101/575696
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Difference contact maps: from what to why in the analysis of the conformational flexibility of proteins
Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Mayy Sedova, Adam Godzik
bioRxiv 575696; doi: https://doi.org/10.1101/575696

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