DOI: 10.1002/prot.22314. Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: An investigation by steered molecular dynamics simulation

Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: An investigation by steered molecular dynamics simulation

10.1002/prot.22314

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractLike the muscle protein Titin, proteins of the ubiquitin family exhibit a parallel strand arrangement, but otherwise having a distinctly different fold and not involved in an obvious load‐bearing function, exhibit high resistance to mechanical unfolding. We have applied all‐atom molecular dynamics simulation technique in implicit solvent to present a deep insight into the force‐induced unfolding pathway of three proteins—ubiquitin, NEDD8, and SUMO‐2—all having almost similar structural features. Two intermediates evolve in the unfolding pathway of each of the three proteins. The first intermediate, which has already been identified in case of ubiquitin by earlier simulation results, is similar for ubiquitin and NEDD8, but different in SUMO‐2. We have found a new intermediate with β3–β4 hairpin and some residual α‐helical character; and this intermediate is common for all the three proteins. Thus, proteins of the ubiquitin family pass through a well‐defined conformation in their force‐induced unfolding pathway. Reason behind the higher mechanical stability of the proteins with parallel strand structures like Titin has also been identified. Proteins 2009. © 2008 Wiley‐Liss, Inc.

Bibliography

Das, A., & Mukhopadhyay, C. (2008). Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: An investigation by steered molecular dynamics simulation. Proteins: Structure, Function, and Bioinformatics, 75(4), 1024â1034. Portico.

Authors 2

Atanu Das (first)
Chaitali Mukhopadhyay (additional)

References 43 Referenced 16

Dates

Type	When
Created	16 years, 10 months ago (Nov. 4, 2008, 4:51 p.m.)
Deposited	1 year, 11 months ago (Sept. 28, 2023, 2:49 p.m.)
Indexed	1 year, 1 month ago (Aug. 6, 2024, 11:02 a.m.)
Issued	16 years, 8 months ago (Dec. 16, 2008)
Published	16 years, 8 months ago (Dec. 16, 2008)
Published Online	16 years, 8 months ago (Dec. 16, 2008)
Published Print	16 years, 3 months ago (June 1, 2009)

Funders 0

None

BibTeX

@article{Das_2008, title={Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: An investigation by steered molecular dynamics simulation}, volume={75}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.22314}, DOI={10.1002/prot.22314}, number={4}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Das, Atanu and Mukhopadhyay, Chaitali}, year={2008}, month=dec, pages={1024–1034} }

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