{"id":407,"date":"2018-09-13T16:22:14","date_gmt":"2018-09-13T16:22:14","guid":{"rendered":"http:\/\/komiveslab.ucsd.edu\/?page_id=407"},"modified":"2023-02-08T05:00:21","modified_gmt":"2023-02-08T05:00:21","slug":"thrombin-publications","status":"publish","type":"page","link":"https:\/\/komiveslab.ucsd.edu\/?page_id=407","title":{"rendered":"Thrombin Publications"},"content":{"rendered":"

<\/a>
\nThrombin-Thrombomodulin<\/a><\/strong><\/p>\n

Peacock RB, McGrann T, Zaragoza S, Komives EA. (2022) How Thrombomodulin Enables W215A\/E217A Thrombin to Cleave Protein C but Not Fibrinogen.<\/a> Biochemistry. 61(2):77-84<\/p>\n

Peacock RB, Komives EA. (2021) Hydrogen\/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin.<\/a> Biochemistry 60(46):3441-3448<\/p>\n

Peacock RB, McGrann T, Tonelli M, Komives EA. (2021) Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex.\u00a0<\/a>Sci Rep. 11(1):9354<\/p>\n

Markwick PRL, Peacock RB, Komives EA. (2019) Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thromobin Allostery.<\/a> Biophys J. 116(1):49-56<\/p>\n

Peacock RB, Davis JR, Markwick PRL, Komives EA. (2018) Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin.<\/a> Biochemistry. 2018;57(18):2694-2703.<\/p>\n

Handley, LD, Fuglestad, B, Stearns, K, Tonelli, M, Fenwick, RB, Markwick, PRL, and Komives, EA (2017) NMR reveals a dynamic allosteric pathway in thrombin. <\/a> Scientific Reports 7:39575. PMC5216386<\/p>\n

Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. (2015)Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin <\/a>Biochemistry 54(43):6650-8. PMC4697735<\/p>\n

Boechi L, Pierce L, Komives EA, McCammon JA. (2014)Trypsinogen activation as observed in accelerated molecular dynamics simulations.<\/a>Protein Sci. 2014 Nov;23(11):1550-8. PMC4241106<\/p>\n

Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives EA. (2013) Correlated Motions and Residual Frustration in Thrombin. <\/a>J Phys Chem B. 117(42):12857-63 PMC3808083<\/p>\n

Gasper, PM, Fuglestad, B., Komives, EA, Markwick, PRL, McCammon, JA. (2012) Allosteric networks in thrombin distinguish procoagulant and anticoagulant activities. <\/a>Proc Natl Acad Sci USA 109(52):21216-22. PMC3535651<\/p>\n

Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives EA. (2012) The dynamic structure of thrombin in solution. <\/a>Biophys J. 103(1):79-88. PMC3388214<\/p>\n

Treuheit, NA, Beach, MA. and Komives, EA. (2011) Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin. <\/a>Biochemistry 50, 4590-6. PMC3107735<\/p>\n

Koeppe, J. R., Beach, M.S. and Komives, E. A. (2008) “Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin.<\/a>” Biochemistry 47, 10933-39.<\/p>\n

Koeppe, J. R. and Komives, E. A. (2006) “Amide H\/2H Exchange Reveals a Mechanism of Thrombin Activation.<\/a>” Biochemistry 45, 7724-32.<\/p>\n

Wood, M. J., Prieto, J. H. & Komives, E. A. (2005) Structural and functional consequences of methionine oxidation in thrombomodulin<\/a> Biochim. Biophys. Acta 1703, 141-147.<\/p>\n

Koeppe, J. R., Seitova, A., Mather, T., Komives, E. A. (2005) “Thrombomodulin tightens the thrombin active site loops to promote protein C activation.<\/a>” Biochemistry 44, 14784-91.<\/p>\n

Prieto, J. H., Sampoli Benitez, B., Melacini, G., Johnson, D. A., Wood, M. J., & Komives, E. A. (2005) Dynamics of the Fragment of Thrombomodulin Containing the Fourth and Fifth EGF-Like Domains Correlate with Function<\/a>Biochemistry 44, 1225-1235.<\/p>\n

Croy, C.H., Koeppe, J.R., Bergqvist, S., Komives, E.A.(2004) “Allosteric changes in solvent accessibility observed in thrombin upon active site occupation.<\/a>” Biochemistry 43, 5246-55.<\/p>\n

Baerga-Ortiz, A., Bergqvist, S. P., Mandell, J. G. & Komives, E. A. (2004) “Two different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles<\/a>” Protein Science 13, 166-176.<\/p>\n

Wood, M. J., Becvar, L. A., Prieto, J. H., Melacini, G., & Komives, E. A. (2003) NMR Structures Reveal How Oxidation Inactivates Thrombomodulin<\/a> Biochemistry 42, 11932-42.<\/p>\n

Baerga-Ortiz, A., Hughes, C. A., Mandell, J. G. & Komives, E. A. (2002) “Epitope Mapping of a monoclonal antibody against human thrombin by H\/D exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein<\/a>” Protein Science 11, 1300-1308.<\/p>\n

Mandell, J. G. Baerga-Ortiz, A., Akashi, S., Takio, K. & Komives, E. A. (2001) “Solvent Accessibility of the Thrombin-Thrombomodulin Interface<\/a>” J. Mol. Biol. 306, 575-589.<\/p>\n

Baerga-Ortiz, A. J., Rezaie, A. R. & Komives, E. A. (2000) “Electrostatic Dependence of the Thrombin-Thrombomodulin interaction<\/a>” J. Mol. Biol. 296: 651 – 658.<\/p>\n

Sampoli Benitez, B.& Komives, E. A. (2000) “Disulfide bond plasticity in EGF<\/a>” Proteins, Structure, Function and Genetics 40, 168 – 174.<\/p>\n

Wood, M. J., Sampoli Benitez, B., Komives, E. A. Solution structure of the smallest cofactor-active fragment of thrombomodulin.<\/a> Nature Structural Biology, 2000 Mar, 7(3):200-4.<\/p>\n

Sampoli Benitez, BA; Hunter, MJ; Meininger, DP; Komives, EA. Structure of the fifth EGF-like domain of thrombomodulin: An EGF-like domain with a novel disulfide-bonding pattern.<\/a>” Journal of Molecular Biology, 1997 Nov 7, 273(4):913-26.<\/p>\n

White, CE; Hunter, MJ; Meininger, DP; Garrod, S; Komives, EA. The fifth epidermal growth factor-like domain of thrombomodulin does not have an epidermal growth factor-like disulfide bonding pattern.<\/a> Proceedings of the National Academy of Sciences of the United States of America, 1996 Sep 17, 93(19):10177-82.<\/p>\n

White, C. E., Hunter, M. J., Meininger, D. P., White, L. R. & Komives, E. A. (1995) ““Large Scale Expression, Purification and Characterization of the Smallest Active Fragment of Thrombomodulin: The Roles of the Sixth Domain and of Methionine-388<\/a>” Protein Engineering 8, 1177 – 1187.<\/p>\n","protected":false},"excerpt":{"rendered":"

Thrombin-Thrombomodulin Peacock RB, McGrann T, Zaragoza S, Komives EA. (2022) How Thrombomodulin Enables W215A\/E217A Thrombin to Cleave Protein C but Not Fibrinogen. Biochemistry. 61(2):77-84 Peacock RB, Komives EA. (2021) Hydrogen\/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin. Biochemistry 60(46):3441-3448 Peacock RB, McGrann T, Tonelli M, Komives EA. (2021) Serine<\/p>\n

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