title: Capturing conformational States in proteins using sparse paramagnetic NMR data.
abstract: Capturing conformational changes in proteins or protein-protein complexes is a challenge for both experimentalists and computational biologists. Solution nuclear magnetic resonance (NMR) is unique in that it permits structural studies of proteins under greatly varying conditions, and thus allows us to monitor induced structural changes. Paramagnetic effects are increasingly used to study protein structures as they give ready access to rich structural information of orientation and long-range distance restraints from the NMR signals of backbone amides, and reliable methods have become available to tag proteins with paramagnetic metal ions site-specifically and at multiple sites. In this study, we show how sparse pseudocontact shift (PCS) data can be used to computationally model conformational states in a protein system, by first identifying core structural elements that are not affected by the environmental change, and then computationally completing the remaining structure based on experimental restraints from PCS. The approach is demonstrated on a 27 kDa two-domain NS2B-NS3 protease system of the dengue virus serotype 2, for which distinct closed and open conformational states have been observed in crystal structures. By changing the input PCS data, the observed conformational states in the dengue virus protease are reproduced without modifying the computational procedure. This data driven Rosetta protocol enables identification of conformational states of a protein system, which are otherwise difficult to obtain either experimentally or computationally.
authors.affiliation: Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
authors.forename: Kala Bharath
authors.initials: KB
authors.lastname: Pilla
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States of America.
authors.forename: Julia Koehler
authors.initials: JK
authors.lastname: Leman
authors.affiliation: Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
authors.forename: Gottfried
authors.initials: G
authors.lastname: Otting
authors.affiliation: Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
authors.forename: Thomas
authors.initials: T
authors.lastname: Huber
mesh_terms: D000595:Amino Acid Sequence; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012697:Serine Endopeptidases / Q000737:chemistry / Q000378:metabolism; D012996:Solutions; D013329:Structure-Activity Relationship; D017361:Viral Nonstructural Proteins / Q000737:chemistry; D000085242:Viral Proteases
chemical_list: D011506:Proteins; D012697:Serine Endopeptidases; D012996:Solutions; D017361:Viral Nonstructural Proteins; C504449:NS3 protease, dengue virus; D000085242:Viral Proteases