Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease

Neha Samant, Gily Nachum, Tenzin Tsepal, Daniel N.A. Bolon
doi: https://doi.org/10.1101/2022.04.18.488666
Neha Samant
Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gily Nachum
Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tenzin Tsepal
Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel N.A. Bolon
Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation St, Worcester, MA 01605 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: Daniel.Bolon@umassmed.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

The infectivity of HIV-1 requires its protease cleave multiple cut-sites with low sequence similarity. The diversity of cleavage sites has made it challenging to investigate the underlying sequence properties that determine binding and turnover of substrates by PR. We engineered a mutational scanning approach utilizing yeast display, flow cytometry, and deep sequencing to systematically measure the impacts of all individual amino acid changes at 12 positions in three different cut-sites (MA/CA, NC/p1, and p1/p6). The resulting fitness landscapes revealed common physical features that underlie cutting of all three cut-sites at the amino acid positions closest to the scissile bond. In contrast, positions more than two amino acids away from the scissile bond exhibited a strong dependence on the sequence background of the rest of the cut-site. We observed multiple amino acid changes in cut-sites that led to faster cleavage rates, including a preference for negative charge five and six amino acids away from the scissile bond at locations where the surface of protease is positively charged. Analysis of individual cut sites using full-length matrix-capsid proteins indicate that long-distance sequence context can contribute to cutting efficiency such that analyses of peptides or shorter engineered constructs including those in this work should be considered carefully. This work provides a framework for understanding how diverse substrates interact with HIV-1 protease and can be extended to investigate other viral proteases with similar properties.

Competing Interest Statement

The authors have declared no competing interest.

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-NC 4.0 International license.
Back to top
PreviousNext
Posted April 18, 2022.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease
Neha Samant, Gily Nachum, Tenzin Tsepal, Daniel N.A. Bolon
bioRxiv 2022.04.18.488666; doi: https://doi.org/10.1101/2022.04.18.488666
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease
Neha Samant, Gily Nachum, Tenzin Tsepal, Daniel N.A. Bolon
bioRxiv 2022.04.18.488666; doi: https://doi.org/10.1101/2022.04.18.488666

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biochemistry
Subject Areas
All Articles
  • Animal Behavior and Cognition (4369)
  • Biochemistry (9546)
  • Bioengineering (7068)
  • Bioinformatics (24768)
  • Biophysics (12560)
  • Cancer Biology (9924)
  • Cell Biology (14297)
  • Clinical Trials (138)
  • Developmental Biology (7930)
  • Ecology (12074)
  • Epidemiology (2067)
  • Evolutionary Biology (15954)
  • Genetics (10904)
  • Genomics (14706)
  • Immunology (9844)
  • Microbiology (23582)
  • Molecular Biology (9454)
  • Neuroscience (50691)
  • Paleontology (369)
  • Pathology (1535)
  • Pharmacology and Toxicology (2674)
  • Physiology (3997)
  • Plant Biology (8639)
  • Scientific Communication and Education (1505)
  • Synthetic Biology (2388)
  • Systems Biology (6415)
  • Zoology (1344)