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Intrinsically Disordered Proteins02:18

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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Updated: Aug 9, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web

Tongtong Li1, Emily Hendrix1, Yi He1,2

  • 1Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States.

The Journal of Physical Chemistry. B
|February 24, 2023
PubMed
Summary

Intrinsically disordered proteins (IDPs) exhibit structural heterogeneity crucial for their function. This study demonstrates that the UNited-RESidue (UNRES) web server effectively samples IDP conformational space, offering a computationally accessible alternative to all-atom simulations.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) lack stable structures, featuring high net charge and few hydrophobic residues.
  • Their structural heterogeneity is key to diverse biological functions and interactions.
  • Previous methods for sampling IDP structures, like all-atom force fields, demand significant computational resources.

Purpose of the Study:

  • To introduce a computationally inexpensive and accessible method for sampling the conformational space of IDPs.
  • To evaluate the efficacy of the UNited-RESidue (UNRES) web server for simulating IDP structures.
  • To compare UNRES simulation results with experimental data and established all-atom force field methods.

Main Methods:

  • Replica Exchange Molecular Dynamics (REMD) simulations using the UNRES force field.
  • Simulations were performed on eight disordered proteins across a temperature range of 270–430 K.
  • UNRES-generated ensembles were analyzed by comparing calculated NMR observables and radius of gyration with experimental data.

Main Results:

  • UNRES simulations successfully sampled heterogeneous structures of IDPs, yielding results comparable to all-atom force fields.
  • The UNRES model demonstrated accuracy across various temperatures when validated against experimental NMR observables and radius of gyration.
  • Optimal temperature selection was identified as crucial for accurate UNRES simulations.

Conclusions:

  • The UNRES web server provides a viable and resource-efficient alternative for exploring the conformational landscape of IDPs.
  • This approach democratizes the study of IDP structural dynamics, making it accessible without specialized hardware.
  • UNRES simulations, particularly at optimized temperatures, can accurately reproduce experimental characteristics of disordered proteins.