English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Self-organized emergence of folded protein-like network structures from geometric constraints

Molkenthin, N., Mühle, S., Mey, A. S. J. S., & Timme, M. (2020). Self-organized emergence of folded protein-like network structures from geometric constraints. PLoS One, 15(2): e0229230. doi:10.1371/journal.pone.0229230.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/21.11116/0000-0005-BF0F-5 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-F1AD-8
Genre: Journal Article

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Molkenthin, Nora1, Author              
Mühle, S., Author
Mey, A. S. J. S., Author
Timme, Marc1, Author              
Affiliations:
1Max Planck Research Group Network Dynamics, Max Planck Institute for Dynamics and Self-Organization, Max Planck Society, ou_2063295              

Content

show
hide
Free keywords: -
 Abstract: The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical environment and the temporal sequence of distinct interactions yield a complex folding process that cannot yet be easily tracked for all proteins. To gain qualitative insights into the fundamental mechanisms behind the folding dynamics and generic features of the folded structure, we propose a simple model of structure formation that takes into account only fundamental geometric constraints and otherwise assumes randomly paired connections. We find that despite its simplicity, the model results in a network ensemble consistent with key overall features of the ensemble of Protein Residue Networks we obtained from more than 1000 biological protein geometries as available through the Protein Data Base. Specifically, the distribution of the number of interaction neighbors a unit (amino acid) has, the scaling of the structure's spatial extent with chain length, the eigenvalue spectrum and the scaling of the smallest relaxation time with chain length are all consistent between model and real proteins. These results indicate that geometric constraints alone may already account for a number of generic features of protein tertiary structures.

Details

show
hide
Language(s): eng - English
 Dates: 2020-02-272020
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1371/journal.pone.0229230
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: PLoS One
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: 13 Volume / Issue: 15 (2) Sequence Number: e0229230 Start / End Page: - Identifier: -