Computational evaluation of protein stability change upon mutations

Shuangye Yin, Feng Ding, Nikolay Dokholyan

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Citations (Scopus)

Abstract

When designing a mutagenesis experiment, it is often crucial to estimate the stability change of proteins induced by mutations (δδG). Despite the recent advances in computational methods, it is still challenging to estimate δ δG quickly and accurately. We recently developed the Eris protocols for in silico evaluation of the δ δG. Starting from the tertiary structure of the wide-type protein, the Eris protocols can model the structure of the mutant protein and estimate δ δG using the structure models. The Eris protocols not only efficiently optimize the side chains conformations, taking advantage of a fast rotamer-based searching algorithm, but also allow protein backbone flexibility during the modeling. As a result, the Eris protocols effectively resolve steric clashes induced by certain mutations and have more accurate δ δG predictions than a fixed-backbone approach. We discuss the general aspects of computational δ δG estimations and discuss in detail the principles and methodologies of the Eris protocols.

Original languageEnglish (US)
Title of host publicationIn Vitro Mutagenesis Protocols
Subtitle of host publicationThird Edition
EditorsBraman Jeff
Pages189-201
Number of pages13
DOIs
StatePublished - Dec 1 2010

Publication series

NameMethods in Molecular Biology
Volume634
ISSN (Print)1064-3745

Fingerprint

Protein Stability
Mutation
Mutant Proteins
Tertiary Protein Structure
Mutagenesis
Computer Simulation
Proteins
caN protocol

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Yin, S., Ding, F., & Dokholyan, N. (2010). Computational evaluation of protein stability change upon mutations. In B. Jeff (Ed.), In Vitro Mutagenesis Protocols: Third Edition (pp. 189-201). (Methods in Molecular Biology; Vol. 634). https://doi.org/10.1007/978-1-60761-652-8_14
Yin, Shuangye ; Ding, Feng ; Dokholyan, Nikolay. / Computational evaluation of protein stability change upon mutations. In Vitro Mutagenesis Protocols: Third Edition. editor / Braman Jeff. 2010. pp. 189-201 (Methods in Molecular Biology).
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Yin, S, Ding, F & Dokholyan, N 2010, Computational evaluation of protein stability change upon mutations. in B Jeff (ed.), In Vitro Mutagenesis Protocols: Third Edition. Methods in Molecular Biology, vol. 634, pp. 189-201. https://doi.org/10.1007/978-1-60761-652-8_14

Computational evaluation of protein stability change upon mutations. / Yin, Shuangye; Ding, Feng; Dokholyan, Nikolay.

In Vitro Mutagenesis Protocols: Third Edition. ed. / Braman Jeff. 2010. p. 189-201 (Methods in Molecular Biology; Vol. 634).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Yin S, Ding F, Dokholyan N. Computational evaluation of protein stability change upon mutations. In Jeff B, editor, In Vitro Mutagenesis Protocols: Third Edition. 2010. p. 189-201. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-60761-652-8_14