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

PLoS One. 2020 Feb 27;15(2):e0229230. doi: 10.1371/journal.pone.0229230. eCollection 2020.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acids / chemistry*
  • Amino Acids / metabolism
  • Humans
  • Models, Molecular
  • Protein Conformation*
  • Protein Folding
  • Protein Interaction Domains and Motifs*
  • Proteins / chemistry*
  • Proteins / metabolism

Substances

  • Amino Acids
  • Proteins

Grants and funding

We acknowledge partial support by the Max Planck Society [NM, MT], the Deutsche Forschungsgemeinschaft (DFG) through SFB 755 (project A05) [SM], the Engineering and Physical Sciences Research Council (EPSRC) UK under grant no. EP/P022138/1 [AM], and the DFG through funding the Clusters of Excellence Center for Advancing Electronics Dresden (cfaed) and Physics of Life (PoL) [MT] The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.