Structure and Dynamics of Zymogen Human Blood Coagulation Factor X

Abstract

The solution structure and dynamics of the human coagulation factor X (FX) have been investigated to understand the key structural elements in the zymogenic form that participates in the activation process. The model was constructed based on the 2.3-A-resolution x-ray crystallographic structure of active-site inhibited human FXa (PDB:1XKA). The missing gamma-carboxyglutamic acid (GLA) and part of epidermal growth factor 1 (EGF1) domains of the light chain were modeled based on the template of GLA-EGF1 domains of the tissue factor (TF)-bound FVIIa structure (PDB:1DAN). The activation peptide and other missing segments of FX were introduced using homology modeling. The full calcium-bound model of FX was subjected to 6.2 ns of molecular dynamics simulation in aqueous medium using the AMBER6.0 package. We observed significant reorientation of the serine-protease (SP) domain upon activation leading to a compact multi-domain structure. The solution structure of zymogen appears to be in a well-extended conformation with the distance between the calcium ions in the GLA domain and the catalytic residues estimated to be approximately 95 A in contrast to approximately 83 A in the activated form. The latter is in close agreement with fluorescence studies on FXa. The S1-specificity residues near the catalytic triad show significant differences between the zymogen and activated structures.

Identification of coagulation factor (F)X binding sites on the adenovirus serotype 5 hexon: effect of mutagenesis on FX interactions and gene transfer

“…Cryo-em was used to determine low-resolution structures for Ad5 virions complexed with FX and also unlabeled particles. Fitting high-resolution coordinates for Ad5 hexon 34,38 and a molecular model of the FX structure 35 to these maps led to the synthesis of models of the complex based on density at 3 of the 4 possible unique capsomeres (hexon trimers) within the virion's asymmetric unit ( Figure 1C-E). The atomic resolution of 1 representative model viewed perpendicular to the capsid outer surface is shown ( Figure 1A).…”

“…A published high-resolution model was used as there are no crystallographic structures available for FX. 35 The docked hexon and FX coordinates were then integrated into single pdb files for each of the 3 models using UCSF Chimera. Interchain contact residues were identified in each model using the CCP4 program contact 36 and visualized using UCSF Chimera.…”

Identification of 31 novel mutations in the F8 gene in Spanish hemophilia A patients: structural analysis of 20 missense mutations suggests new intermolecular binding sites

“…34 Similar strategies have been followed by other authors to generate FIXa/FX models. 13,29,35 Model quality was assessed with MOLEMAN2 (http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl, Uppsala Software Factory, Uppsala, Sweden); for FVIIIa, that is, 89% of all residues were found in core regions of the Ramachandran plot. Docking was performed with ZDOCK (http://zdock.bu.edu/, Boston University) and structure figures were generated with PyMOL (http://www.pymol.…”

Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations

“…Thus, MD simulations have been used widely to solve problems in protein structural analysis [17][18][19][20][21][22][23][24][25][26][27] and rational drug design [28][29][30][31][32][33][34][35][36][37]. MD simulation was performed previously on FXa by Daura et al [38] and Venkateswarlu [39]. Due to the limitation of computing power at the time those studies were performed, their longest simulation times were 1.5 and 6.2 ns, respectively, which were not adequate to reveal the complete details of the conformational transitions of FXa.…”