Zymogen and activated protein C have similar structural architecture

Stojanovski, Bosko M.; Pelc, Leslie A.; Zuo, Xiaobing; Di Cera, Enrico

doi:10.1074/jbc.RA120.014789

Title: Zymogen and activated protein C have similar structural architecture

Journal Article · Fri Nov 06 00:00:00 EST 2020 · Journal of Biological Chemistry

DOI:https://doi.org/10.1074/jbc.RA120.014789· OSTI ID:1774125

Stojanovski, Bosko M. ^[1]; Pelc, Leslie A. ^[1]; Zuo, Xiaobing ^[2];

^[1]

Saint Louis Univ., St. Louis, MO (United States). School of Medicine
Argonne National Lab. (ANL), Lemont, IL (United States)

Activated protein C is a trypsin-like protease with anticoagulant and cytoprotective properties that is generated by thrombin from the zymogen precursor protein C in a reaction greatly accelerated by the cofactor thrombomodulin. The molecular details of this activation remain elusive due to the lack of structural information. We now fill this gap by providing information on the overall structural organization of these proteins using single molecule Förster resonance energy transfer and small angle X-ray scattering. Under physiological conditions, both zymogen and protease adopt a conformation with all domains vertically aligned along an axis 76 Å long and maximal particle size of 120 Å. This conformation is stabilized by binding of Ca²⁺ to the Gla domain and is affected minimally by interaction with thrombin. Hence, the zymogen protein C likely interacts with the thrombin-thrombomodulin complex through a rigid body association that produces a protease with essentially the same structural architecture. This scenario stands in contrast to an analogous reaction in the coagulation cascade where conversion of the zymogen prothrombin to the protease meizothrombin by the prothrombinase complex is linked to a large conformational transition of the entire protein. The presence of rigid EGF domains in protein C as opposed to kringles in prothrombin likely accounts for the different conformational plasticity of the two zymogens. The new structural features reported here for protein C have general relevance to vitamin K-dependent clotting factors containing EGF domains, such as factors VII, IX, and X.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1774125

Journal Information:: Journal of Biological Chemistry, Vol. 295, Issue 45

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (48)

Structural changes in factor VIIa induced by Ca ²⁺ and tissue factor studied using circular dichroism spectroscopy Freskgård, Per-Ola; Olsen, Ole H.; Persson, Egon Protein Science, Vol. 5, Issue 8 https://doi.org/10.1002/pro.5560050809	journal	August 1996
PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data Schrimpf, Waldemar; Barth, Anders; Hendrix, Jelle Biophysical Journal, Vol. 114, Issue 7 https://doi.org/10.1016/j.bpj.2018.02.035	journal	April 2018
Uniqueness of ab initio shape determination in small-angle scattering Volkov, Vladimir V.; Svergun, Dmitri I. Journal of Applied Crystallography, Vol. 36, Issue 3, p. 860-864 https://doi.org/10.1107/S0021889803000268	journal	April 2003
Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis Torella, Joseph P.; Holden, Seamus J.; Santoso, Yusdi Biophysical Journal, Vol. 100, Issue 6 https://doi.org/10.1016/j.bpj.2011.01.066	journal	March 2011
Thrombomodulin Changes the Molecular Surface of Interaction and the Rate of Complex Formation between Thrombin and Protein C Xu, Hong; Bush, Leslie A.; Pineda, Agustin O. Journal of Biological Chemistry, Vol. 280, Issue 9 https://doi.org/10.1074/jbc.M412869200	journal	March 2005
Serine peptidases: Classification, structure and function Page, M. J.; Di Cera, E. Cellular and Molecular Life Sciences, Vol. 65, Issue 7-8 https://doi.org/10.1007/s00018-008-7565-9	journal	February 2008
Role of the activation peptide in the mechanism of protein C activation Stojanovski, Bosko M.; Pelc, Leslie A.; Di Cera, Enrico Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-68078-z	journal	July 2020
Time-resolved fluorescence study of a calcium-induced conformational change in prothrombin fragment 1 Hof, Martin; Fleming, Graham R.; Fidler, Vlastimil Proteins: Structure, Function, and Genetics, Vol. 24, Issue 4 https://doi.org/10.1002/(SICI)1097-0134(199604)24:4<485::AID-PROT7>3.0.CO;2-D	journal	April 1996
The function of calcium in protein C activation by thrombin and the thrombin-thrombomodulin complex can be distinguished by mutational analysis of protein C derivatives. Rezaie, A. R.; Esmon, C. T. Journal of Biological Chemistry, Vol. 267, Issue 36 https://doi.org/10.1016/S0021-9258(18)35723-5	journal	December 1992
Inflammation and thrombosis Esmon, C. T. Journal of Thrombosis and Haemostasis, Vol. 1, Issue 7 https://doi.org/10.1046/j.1538-7836.2003.00261.x	journal	July 2003
Calcium and Phospholipid Binding Properties of Synthetic .gamma.-Carboxyglutamic Acid-Containing Peptides with Sequence Counterparts in Human Protein C Colpitts, Tracy L.; Castellino, Francis J. Biochemistry, Vol. 33, Issue 12 https://doi.org/10.1021/bi00178a006	journal	March 1994
Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing Journal of Biological Chemistry, Vol. 291, Issue 35 https://doi.org/10.1074/jbc.M116.738310	journal	July 2016
X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B. Brandstetter, H.; Bauer, M.; Huber, R. Proceedings of the National Academy of Sciences, Vol. 92, Issue 21 https://doi.org/10.1073/pnas.92.21.9796	journal	October 1995
Thrombin Formation Mann, Kenneth G. Chest, Vol. 124, Issue 3 https://doi.org/10.1378/chest.124.3_suppl.4S	journal	September 2003
A new vitamin K-dependent protein. Purification from bovine plasma and preliminary characterization. Stenflo, J. Journal of Biological Chemistry, Vol. 251, Issue 2 https://doi.org/10.1016/S0021-9258(17)33886-3	journal	January 1976
Enhancing protein C interaction with thrombin results in a clot-activated anticoagulant Richardson, Mark A.; Gerlitz, Bruce; Grinnell, Brian W. Nature, Vol. 360, Issue 6401 https://doi.org/10.1038/360261a0	journal	November 1992
Determination of Domain Structure of Proteins from X-Ray Solution Scattering Svergun, Dmitri I.; Petoukhov, Maxim V.; Koch, Michel H. J. Biophysical Journal, Vol. 80, Issue 6 https://doi.org/10.1016/S0006-3495(01)76260-1	journal	June 2001
The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor Banner, David W.; D'Arcy, Allan; Chène, Christiana Nature, Vol. 380, Issue 6569 https://doi.org/10.1038/380041a0	journal	March 1996
Calcium-dependence of the interactions between protein C, thrombin and the elastase fragment of thrombomodulin. Analysis by ultracentrifugation Olsen, Philip H.; Esmon, Naomi L.; Esmon, Charles T. Biochemistry, Vol. 31, Issue 3 https://doi.org/10.1021/bi00118a016	journal	January 1992
The linker connecting the two kringles plays a key role in prothrombin activation Pozzi, N.; Chen, Z.; Pelc, L. A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 21 https://doi.org/10.1073/pnas.1403779111	journal	May 2014
Identification of structural domains in protein C involved in its interaction with thrombin-thrombomodulin on the surface of endothelial cells. Hogg, P. J.; Ohlin, A. K.; Stenflo, J. Journal of Biological Chemistry, Vol. 267, Issue 2 https://doi.org/10.1016/S0021-9258(18)48340-8	journal	January 1992
Interplay between conformational selection and zymogen activation Chakraborty, Pradipta; Acquasaliente, Laura; Pelc, Leslie A. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-21728-9	journal	March 2018
How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin Pozzi, Nicola; Chen, Zhiwei; Di Cera, Enrico Journal of Biological Chemistry, Vol. 291, Issue 12 https://doi.org/10.1074/jbc.M115.700401	journal	January 2016
Nucleotide sequence of the gene for human prothrombin Degen, Sandra J. Friezner; Davie, Earl W. Biochemistry, Vol. 26, Issue 19 https://doi.org/10.1021/bi00393a033	journal	September 1987
Tryptophans 231 and 234 in Protein C Report the Ca2+-Dependent Conformational Change Required for Activation by the Thrombin-Thrombomodulin Complex Rezaie, Alireza R.; Esmon, Charles T. Biochemistry, Vol. 34, Issue 38 https://doi.org/10.1021/bi00038a016	journal	September 1995
The Protein C Pathway Esmon, Charles T. Chest, Vol. 124, Issue 3 https://doi.org/10.1378/chest.124.3_suppl.26S	journal	September 2003
Structural basis for the anticoagulant activity of the thrombin–thrombomodulin complex Fuentes-Prior, Pablo; Iwanaga, Yoriko; Huber, Robert Nature, Vol. 404, Issue 6777 https://doi.org/10.1038/35006683	journal	March 2000
The X-ray Crystal Structure of Full-Length Human Plasminogen Law, Ruby H. P.; Caradoc-Davies, Tom; Cowieson, Nathan Cell Reports, Vol. 1, Issue 3 https://doi.org/10.1016/j.celrep.2012.02.012	journal	March 2012
Thrombomodulin as a model of molecular mechanisms that modulate protease specificity and function at the vessel surface Esmon, Charles T. The FASEB Journal, Vol. 9, Issue 10 https://doi.org/10.1096/fasebj.9.10.7615164	journal	July 1995
The Conformation of the Activation Peptide of Protein C Is Influenced by Ca2+ and Na+ Binding Yang, Likui; Prasad, Swati; Di Cera, Enrico Journal of Biological Chemistry, Vol. 279, Issue 37 https://doi.org/10.1074/jbc.M407304200	journal	September 2004
Activated protein C: biased for translation Griffin, John H.; Zlokovic, Berislav V.; Mosnier, Laurent O. Blood, Vol. 125, Issue 19 https://doi.org/10.1182/blood-2015-02-355974	journal	May 2015
Charge reversal at the P3′ position in protein C optimally enhances thrombin affinity and activation rate: Charge reversal at the P3′ position in protein C optimally enhances thrombin affinity and activation rate Richardson, Mark A.; Gerlitz, Bruce; Grinnell, Brian W. Protein Science, Vol. 3, Issue 4 https://doi.org/10.1002/pro.5560030420	journal	April 1994
Enhancing the anticoagulant profile of meizothrombin Stojanovski, Bosko M.; Pelc, Leslie A.; Zuo, Xiaobing Biomolecular Concepts, Vol. 9, Issue 1 https://doi.org/10.1515/bmc-2018-0016	journal	December 2018
Isolation of a membrane-bound cofactor for thrombin-catalyzed activation of protein C. Esmon, N. L.; Owen, W. G.; Esmon, C. T. Journal of Biological Chemistry, Vol. 257, Issue 2 https://doi.org/10.1016/S0021-9258(19)68276-1	journal	January 1982
The 2.8 A crystal structure of Gla-domainless activated protein C. Mather, T.; Oganessyan, V.; Hof, P. The EMBO Journal, Vol. 15, Issue 24 https://doi.org/10.1002/j.1460-2075.1996.tb01073.x	journal	December 1996
Structure of the Ca2+-free GLA domain sheds light on membrane binding of blood coagulation proteins Sunnerhagen, Maria; Forsén, Sture; Hoffrén, Anna-Marja Nature Structural & Molecular Biology, Vol. 2, Issue 6 https://doi.org/10.1038/nsb0695-504	journal	June 1995
Protein S Alters the Active Site Location of Activated Protein C above the Membrane Surface Yegneswaran, Subramanian; Wood, Gary M.; Esmon, Charles T. Journal of Biological Chemistry, Vol. 272, Issue 40 https://doi.org/10.1074/jbc.272.40.25013	journal	October 1997
Structure of prothrombin in the closed form reveals new details on the mechanism of activation Chinnaraj, Mathivanan; Chen, Zhiwei; Pelc, Leslie A. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-21304-1	journal	February 2018
Evolution of enzyme cascades from embryonic development to blood coagulation Krem, Maxwell M.; Cera, Enrico Di Trends in Biochemical Sciences, Vol. 27, Issue 2 https://doi.org/10.1016/S0968-0004(01)02007-2	journal	February 2002
Calcium-induced conformational change in fragment 1-86 of factor X Häfner, A.; Merola, F.; Duportail, G. Biopolymers, Vol. 57, Issue 4 https://doi.org/10.1002/1097-0282(2000)57:4<226::AID-BIP4>3.0.CO;2-I	journal	January 2000
Thrombomodulin Structure and Function Sadler, J. Thrombosis and Haemostasis, Vol. 78, Issue 01 https://doi.org/10.1055/s-0038-1657558	journal	June 1997
Exposure of R169 controls protein C activation and autoactivation Pozzi, Nicola; Barranco-Medina, Sergio; Chen, Zhiwei Blood, Vol. 120, Issue 3 https://doi.org/10.1182/blood-2012-03-415323	journal	July 2012
Modeling Zymogen Protein C Perera, Lalith; Foley, Charles; Darden, Thomas A. Biophysical Journal, Vol. 79, Issue 6 https://doi.org/10.1016/S0006-3495(00)76530-1	journal	December 2000
Three-dimensional Model of Coagulation Factor Va Bound to Activated Protein C Pellequer, Jean-Luc; Gale, Andrew; Getzoff, Elizabeth Thrombosis and Haemostasis, Vol. 84, Issue 11 https://doi.org/10.1055/s-0037-1614127	journal	January 2000
Probing prothrombin structure by limited proteolysis Acquasaliente, Laura; Pelc, Leslie A.; Di Cera, Enrico Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42524-z	journal	April 2019
Structure of the Metal-free γ-Carboxyglutamic Acid-rich Membrane Binding Region of Factor IX by Two-dimensional NMR Spectroscopy Freedman, Steven J.; Furie, Barbara C.; Furie, Bruce Journal of Biological Chemistry, Vol. 270, Issue 14 https://doi.org/10.1074/jbc.270.14.7980	journal	April 1995
Study of the ?molten globule? intermediate state in protein folding by a hydrophobic fluorescent probe Semisotnov, G. V.; Rodionova, N. A.; Razgulyaev, O. I. Biopolymers, Vol. 31, Issue 1 https://doi.org/10.1002/bip.360310111	journal	January 1991
Role of the I16-D194 ionic interaction in the trypsin fold Stojanovski, Bosko M.; Chen, Zhiwei; Koester, Sarah K. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-54564-6	journal	December 2019

Similar Records

Structural architecture of prothrombin in solution revealed by single molecule spectroscopy

Journal Article · Tue Jul 19 00:00:00 EDT 2016 · Journal of Biological Chemistry · OSTI ID:1774125

Pozzi, Nicola; Bystranowska, Dominika; Zuo, Xiaobing; +1 more

Crystal structure of prethrombin-1

Journal Article · Mon Nov 15 00:00:00 EST 2010 · Proc. Natl. Acad. Sci. USA · OSTI ID:1774125

Chen, Zhiwei; Pelc, Leslie A; Di Cera, Enrico

Enhancing the anticoagulant profile of meizothrombin

Journal Article · Wed Dec 26 00:00:00 EST 2018 · Biomolecular Concepts · OSTI ID:1774125

Stojanovski, Bosko M.; Pelc, Leslie A.; Zuo, Xiaobing; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
BioSAXS
ligand-binding protein
protein C
protein conformation
serine protease
single molecule biophysics
thrombin

Title: Zymogen and activated protein C have similar structural architecture

Citation Formats

References (48)

Similar Records

Related Subjects