Specializing in Biophysics Research


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 protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex. Sci Rep. 11(1):9354

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

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

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

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

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

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

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

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

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

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.” Biochemistry 47, 10933-39.

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

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

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

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 FunctionBiochemistry 44, 1225-1235.

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

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” Protein Science 13, 166-176.

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

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” Protein Science 11, 1300-1308.

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

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

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

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

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.” Journal of Molecular Biology, 1997 Nov 7, 273(4):913-26.

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. Proceedings of the National Academy of Sciences of the United States of America, 1996 Sep 17, 93(19):10177-82.

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” Protein Engineering 8, 1177 – 1187.