Using the Rosetta surface algorithm to predict protein structure at mineral surfaces

Michael S. Pacella, Da Chen Emily Koo, Robin A. Thottungal, Jeffrey J. Gray

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Determination of protein structure on mineral surfaces is necessary to understand biomineralization processes toward better treatment of biomineralization diseases and design of novel protein-synthesized materials. To date, limited atomic-resolution data have hindered experimental structure determination for proteins on mineral surfaces. Molecular simulation represents a complementary approach. In this chapter, we review RosettaSurface, a computational structure prediction-based algorithm designed to broadly sample conformational space to identify low-energy structures. We summarize the computational approaches, the published applications, and the new releases of the code in the Rosetta 3 framework. In addition, we provide a protocol capture to demonstrate the practical steps to employ RosettaSurface. As an example, we provide input files and output data analysis for a previously unstudied mineralization protein, osteocalcin. Finally, we summarize ongoing challenges in energy function optimization and conformational searching and suggest that the fusion between experiment and calculation is the best route forward.

Original languageEnglish (US)
Title of host publicationResearch Methods in Biomineralization Science
PublisherAcademic Press Inc.
Pages343-366
Number of pages24
ISBN (Print)9780124166172
DOIs
StatePublished - 2013

Publication series

NameMethods in Enzymology
Volume532
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Keywords

  • Biased sampling
  • Biomineralization
  • Experimental constraints
  • Hydroxyapatite
  • Monte Carlo docking
  • Osteocalcin
  • Protein-surface interactions
  • RosettaSurface
  • Statherin

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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  • Cite this

    Pacella, M. S., Koo, D. C. E., Thottungal, R. A., & Gray, J. J. (2013). Using the Rosetta surface algorithm to predict protein structure at mineral surfaces. In Research Methods in Biomineralization Science (pp. 343-366). (Methods in Enzymology; Vol. 532). Academic Press Inc.. https://doi.org/10.1016/B978-0-12-416617-2.00016-3