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

In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins

View ORCID ProfileThomas Tarenzi, View ORCID ProfileGiovanni Mattiotti, View ORCID ProfileMarta Rigoli, View ORCID ProfileRaffaello Potestio
doi: https://doi.org/10.1101/2022.06.21.497011
Thomas Tarenzi
1Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
2INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Thomas Tarenzi
Giovanni Mattiotti
1Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
2INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Giovanni Mattiotti
Marta Rigoli
3Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Marta Rigoli
Raffaello Potestio
1Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
2INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Raffaello Potestio
  • For correspondence: raffaello.potestio@unitn.it
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

The paradigmatic sequence-structure-dynamics-function relation in proteins is nowadays well established in the scientific community; in particular, large effort has been spent to probe the first connection, indeed providing convincing evidence of its strength and rationalising it in a quantitative and general framework. In contrast, however, the role of dynamics as a link between structure and function has eluded a similarly clear-cut verification and description. In this work, we propose a pipeline aimed at building a basis for the quantitative characterisation of the large-scale dynamics of a set of proteins, starting from the sole knowledge of their native structures. The method hinges on a dynamics-based clusterization, which allows a straightforward comparison with structural and functional protein classifications. The resulting basis set, obtained through the application to a group of related proteins, is shown to reproduce the salient large-scale dynamical features of the dataset. Most interestingly, the basis set is shown to encode the fluctuation patterns of homologous proteins not belonging to the initial dataset, thus highlighting the general applicability of the pipeline used to build it.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.5281/zenodo.6669245

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 June 22, 2022.
Download PDF

Supplementary Material

Data/Code
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.
In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins
(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
In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins
Thomas Tarenzi, Giovanni Mattiotti, Marta Rigoli, Raffaello Potestio
bioRxiv 2022.06.21.497011; doi: https://doi.org/10.1101/2022.06.21.497011
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins
Thomas Tarenzi, Giovanni Mattiotti, Marta Rigoli, Raffaello Potestio
bioRxiv 2022.06.21.497011; doi: https://doi.org/10.1101/2022.06.21.497011

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

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4663)
  • Biochemistry (10322)
  • Bioengineering (7648)
  • Bioinformatics (26266)
  • Biophysics (13487)
  • Cancer Biology (10655)
  • Cell Biology (15375)
  • Clinical Trials (138)
  • Developmental Biology (8473)
  • Ecology (12788)
  • Epidemiology (2067)
  • Evolutionary Biology (16807)
  • Genetics (11374)
  • Genomics (15440)
  • Immunology (10589)
  • Microbiology (25107)
  • Molecular Biology (10181)
  • Neuroscience (54272)
  • Paleontology (399)
  • Pathology (1663)
  • Pharmacology and Toxicology (2884)
  • Physiology (4329)
  • Plant Biology (9217)
  • Scientific Communication and Education (1583)
  • Synthetic Biology (2547)
  • Systems Biology (6765)
  • Zoology (1459)