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

Decoding nonspecific interactions between human nuclear transport proteins: A computational study

View ORCID ProfileShravan B. Rathod
doi: https://doi.org/10.1101/2021.03.22.436462
Shravan B. Rathod
Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat, India
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Shravan B. Rathod
  • For correspondence: shravanathorizon93@gmail.com
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

The nuclear protein transport between the nucleus and cytosol can be considered a core process of cell regulation. Specially designed proteins in nature such as importins, exportins, and some other transporters facilitate this transport in the cell and control the cellular processes. Transient and weak protein–protein interactions are basis of these various biomolecular processes. Prior to cargo transports, the transport proteins recognize the Nuclear localization signals (NLSs) and Nuclear export signals (NESs) of cargo proteins and, bind to the RanGTP. Also, these proteins bind with other similar protein subunits along with RanGTP to transport cargos. Cell is enormously crowded place where DNA, RNA, proteins, lipids and small molecules cooperatively facilitate numerous cellular processes. In such environment, existence of nonspecific interactions between proteins is quite obvious. Considering this hypothesis, in this study, protein-protein docking approach was applied to determine the binding affinities of 12 human nuclear transport proteins. Results showed that KPNA1, TNPO1 and TNPO3 have greater affinity to bind with other transport proteins. Also, among 78 complexes (12 homodimers and 66 heterodimers), KPNA1-KPNB1, KPNA1-TNPO1 and KPNA1-TNPO3 complexes have the highest stability.

Figure
  • Download figure
  • Open in new tab

Graphical abstractInitially, 12 human nuclear transport proteins PDB structures were retrieved from the 1. Protein data bank (PDB). These proteins had some missing terminals and residues thus, we used 2. SWISS-MODEL and 3. MODELLER v.10.1 to model those regions in these proteins. Next, we used widely popular web server, 4. ClusPro v.2.0 for protein-protein docking analysis among 12 proteins. Then, we employed 5. PRODIGY web server to calculate the binding affinities of 78 complexes (12 homodimers & 66 heterodimers). Finally, we utilised three web tools, 6. Arpeggio, 7. PIMA and 8. PDBePISA to analyse top-three complexes (KPNA1-KPNB1, KPNA1-TNPO1 & TNPO3) for in-depth interactions and energetics.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Email: shravanathorizon93{at}gmail.com, Phone: +91-8200040941

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

Supplementary Material

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.
Decoding nonspecific interactions between human nuclear transport proteins: A computational study
(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
Decoding nonspecific interactions between human nuclear transport proteins: A computational study
Shravan B. Rathod
bioRxiv 2021.03.22.436462; doi: https://doi.org/10.1101/2021.03.22.436462
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Decoding nonspecific interactions between human nuclear transport proteins: A computational study
Shravan B. Rathod
bioRxiv 2021.03.22.436462; doi: https://doi.org/10.1101/2021.03.22.436462

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

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4237)
  • Biochemistry (9147)
  • Bioengineering (6786)
  • Bioinformatics (24020)
  • Biophysics (12137)
  • Cancer Biology (9544)
  • Cell Biology (13795)
  • Clinical Trials (138)
  • Developmental Biology (7642)
  • Ecology (11715)
  • Epidemiology (2066)
  • Evolutionary Biology (15517)
  • Genetics (10650)
  • Genomics (14332)
  • Immunology (9492)
  • Microbiology (22856)
  • Molecular Biology (9103)
  • Neuroscience (49028)
  • Paleontology (355)
  • Pathology (1484)
  • Pharmacology and Toxicology (2572)
  • Physiology (3848)
  • Plant Biology (8337)
  • Scientific Communication and Education (1472)
  • Synthetic Biology (2296)
  • Systems Biology (6196)
  • Zoology (1302)