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Title

The role of Ca+ ions in the complex assembling of protein Z and Z-dependent protease inhibitor: A structure and dynamics investigation

 

Authors

Zahra Karimi1*, Sajad Falsafi-Zade1 & Hamid Galehdari2

 

Affiliation

1Bioinformatics unit, Department of Genetics, Shahid Chamran University, Ahvaz, Iran; 2Department of Genetics, Shahid Chamran University, Ahvaz, Iran

 

Email

z.karimi20@yahoo.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received April 16, 2012; Accepted April 18, 2012; Published May 15, 2012

Abstract

We investigated the solution structure and dynamics of the human anti-coagulation protein Z (PZ) in the complex with protein Z-dependent protease inhibitor (ZPI) to order to understand key structural changes in the presence and absence of Ca2+. Structural features of the complete complex of PZ-ZPI are poorly understood due to lack of complete atomic model of the PZ-ZPI complex. We have constructed a model of the complete PZ-ZPI complex and molecular dynamics (MD) simulation of the solvated PZ-ZPI complex with and without Ca2+ was achieved for 100ns. It is consider that the Ω-loop of GLA domains interacts with negatively charged biological membranes in the presence of Ca2+ ions. The PZ exerts its role as cofactor in a similar way. However, we used solvent-equilibrated dynamics to show structural features of the PZ-ZPI complex in the presence and the absence of Ca2+ions. We observed that the distance between the interacting sites of the ZPI with the PZ and the GLA domain decreases in the presence of Ca2+ ions. Further, we postulated that the calculated distance between the dominant plane of the Ca2+ ions and Ser196 of the pseudo-catalytic triad of the PZ is similar to the equivalent distance of FXa. This suggests that the central role of the PZ in the blood coagulation may be to align the inhibitory site of the ZPI with the active site of the FXa, which is depends on the interaction of the calcium bound GLA domain of the PZ with the active membrane.

 

Keywords

Protein Z, Protein Z-dependent protease inhibitor, Ca ion, blood coagulation, Molecular Dynamics simulation.

Citation

Karim et al. Bioinformation 8(9): 407-411 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.