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PreprintCited by 7Protein Structure and DynamicsEnzyme Structure and FunctionChemical Synthesis and Analysis

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Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA

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Chandra, Soumyanetra, Manjunath, Kavyashree, Asok, Aparna, Varadarajan, Raghavan·2022·Protein Science
DOI 10.1101/2022.04.08.487678PMC PMC9951195

Preprint — published as 10.1002/pro.4580 · Paper page

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Abstract

Unlike globular proteins, mutational effects on the function of Intrinsically Disordered Proteins (IDPs) are not well-studied. Deep Mutational Scanning of a yeast surface displayed mutant library yields insights into sequence-function relationships in the CcdA IDP. The approach enables facile prediction of interface residues and local structural signatures of the bound conformation. In contrast to previous titration-based approaches which use a number of ligand concentrations, we show that use of a single rationally chosen ligand concentration can provide quantitative estimates of relative binding constants for large numbers of protein variants. This is because the extended interface of IDP ensures that energetic effects of point mutations are spread over a much smaller range than for globular proteins. Our data also provides insights into the much-debated role of helicity and disorder in partner binding of IDPs. Based on this exhaustive mutational sensitivity dataset, a model was developed to predict mutational effects on binding affinity of IDPs that form alpha-helical structures upon binding.

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Metadata

Authors
Chandra, S., Manjunath, K., Asok, A., & Varadarajan, R.
Affiliations
  • Indian Institute of Science Bangalore (IN)
  • Institute for Stem Cell Biology and Regenerative Medicine (IN)
Corresponding author
Varadarajan, Raghavan
ORCID
Venue
Protein Science
Publisher
openRxiv
Published
2022-04-08
Volume
32
Issue
3
Pages
e4580-e4580
ISSN
0961-8368 (ISSN-L)
DOI
10.1101/2022.04.08.487678
PMC
PMC9951195
OpenAlex
W4318474348
Cited by
7
References
2
Citations by year
2025: 3 · 2023: 1 · 2022: 3
FWCI
0.36
Type
journal article
Language
en
Open access
Locations
  • Protein Science (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • NOT FOUND REPOSITORY (Indian Institute of Science Bangalore) (submittedVersion)
Funders
  • Indian Institute of Science
  • Department of Biotechnology, Ministry of Science and Technology, India (BT/COE/34/SP15219/2015, DT.20/11/2015, BT/COE/34/SP15219/2015, DT.20/11/2015)
  • Department of Science and Technology, Ministry of Science and Technology, India
  • Ministry of Education, India
  • Science and Engineering Research Board (SR/S2/JCB‐10/2007, EMR/2017/0040S4)
  • Division of Human Resource Development
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
Keywords
intrinsically disordered proteins, CcdA, deep mutational scanning, protein-ligand binding affinity, binding energetics, alpha-helix formation, sequence-function relationships, yeast surface display, point mutations
MeSH terms
Protein Conformation, alpha-Helical, Ligands, Mutation, Protein Binding, Protein Conformation, Intrinsically Disordered Proteins

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