title: Using the RosettaSurface algorithm to predict protein structure at mineral surfaces.
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.
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Pacella
authors.forename: Da Chen Emily
authors.initials: da CE
authors.lastname: Koo
authors.forename: Robin A
authors.initials: RA
authors.lastname: Thottungal
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Gray
mesh_terms: D000327:Adsorption; D000465:Algorithms; D003460:Crystallization; D017886:Durapatite / Q000737:chemistry; D006801:Humans; D062105:Molecular Docking Simulation; D009010:Monte Carlo Method; D015675:Osteocalcin / Q000737:chemistry; D012471:Salivary Proteins and Peptides / Q000737:chemistry; D012984:Software; D013499:Surface Properties
chemical_list: C018149:STATH protein, human; D012471:Salivary Proteins and Peptides; D015675:Osteocalcin; D017886:Durapatite
keywords: Biased sampling; Biomineralization; Experimental constraints; Hydroxyapatite; Monte Carlo docking; Osteocalcin; Protein–surface interactions; RosettaSurface; Statherin