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Updated: Apr 7, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model.

Govardhan Reddy¹, D Thirumalai²

¹Solid State and Structural Chemistry Unit, Indian Institute of Science , Bangalore, Karnataka, India 560012.

The Journal of Physical Chemistry. B

|July 2, 2015

Summary

Ubiquitin folding mechanisms change with pH. Simulations reveal pH-dependent pathways and metastable states, offering insights into protein folding dynamics.

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Area of Science:

Biophysics
Computational Biology
Protein Science

Background:

Ubiquitin (Ub) is a crucial protein in eukaryotic organisms.
Understanding protein folding is vital for comprehending biological functions.

Purpose of the Study:

Investigate Ubiquitin folding at varying pH and temperatures.
Elucidate the pH-dependent folding pathways and mechanisms.

Main Methods:

Coarse-grained self-organized-polymer model with side chains (SOP-SC) simulations.
Analysis of heat capacity, radius of gyration, and conformational clustering.
Pfold analysis for transition state structures.

Main Results:

Melting temperatures decrease with decreasing pH.
Simulated radius of gyration agrees well with experimental data.
Ubiquitin folding exhibits a pH-dependent dominant pathway and metastable states.
Folding mechanisms shift between nucleation-collapse and diffusion-collision models based on pH and temperature.

Conclusions:

Protein folding mechanisms are significantly influenced by pH.
Simulations provide detailed insights into Ubiquitin folding thermodynamics and kinetics.
The study predicts pH-dependent folding variations, suggesting avenues for experimental validation.