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Title

Molecular dynamics analysis of conserved water mediated inter-domain recognition of His667-Trp669 in human ceruloplasmin

 

Authors

Bishnu Prasad Mukhopadhyay*

 

Affiliation

Department of Chemistry, National Institute of Technology-Durgapur, West Bengal, Durgapur 713209, India; *Corresponding author.

 

Email

Bishnu P Mukhopadhyay Tel.: 0091- 0343 2547074; FAX: 0091-0343-2547375 / 2546753; Email address: bpmk2@ch.nitdgp.ac.in. bpmukhopadhyay17@gmail.com

 

Article Type

Research Article

 

Date

Received February 19, 2020; Accepted March 5, 2020; Published March 31, 2020

 

Abstract

The human ceruloplasmin (hCP) is the copper containing ferroxidase enzyme with multifunctional activities (NO-oxidase, NO2-synthase, oxidation of neurotransmitters including antioxidants). Therefore, it is of interest to probe the multi-domain hCP using molecular dynamics simulation. Results explain the role played by several conserved water centers in the intra and inter-domain recognition through H-bond interaction with the interacting residues. We observed seventeen conserved water centers in the inter-domain recognition. We show that five invariant water centers W13, W14, W18, W23 and W26 connect the Domain 5 to Domain 4 (D5WW4). We also show that five other water centers W19, W20, W27, W30 and W31 connects the Domain 5 to Domain 6 (D5WW6) that is unique in the simulated form. The W7 and W32 water centers are involved in the D1WW6 recognition. This is important for the water-mediated interaction of Glu1032 to the trinuclear copper cluster present at the interface between these domains. The involvement of W10 water center in the D3W10D4 recognition through Gln552W10His667 H-bond interaction is critical in the complexation of CP with myeloperoxidase (Mpo). These observations provide insights to the molecular recognition of hCP with other biomolecules in the system.

 

Keywords

Conserved water molecules; MD-simulation; Ceruloplasmin.

 

Citation

Mukhopadhyay, Bioinformation 16(3): 209-218 (2020)

 

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.