NMR and homology modeling studies of copper(II)-halocyanin from Natronobacterium pharaonis bacteria

• Published in: Inorganica Chimica Acta 2004-03, Vol.357 (4), p.1111-1118
• Main Authors: Monleón, Daniel, Ribes, Fernando, Jiménez, Hermas R, Moratal, José M, Celda, Bernardo
• Format: Article
• Language: English
• Subjects: Blue copper protein; Halocyanin; Metalloprotein; Natronobacterium pharaonis bacteria; Paramagnetic NMR; Restrained molecular dynamics homology modeling
• ISSN: 0020-1693; 1873-3255
• DOI: 10.1016/j.ica.2003.10.021

The copper coordination site of Cu(II)-halocyanin has been studied using paramagnetic NMR spectroscopy. We also reported first three-dimensional structure by modeling techniques for halocyanin and homology modeling was performed using two different structural templates and copper ion was added for further refinement of the coordination site. Halocyanin from the haloalkaliphilic archaean Natronobacterium pharaonis is a peripheral membrane type 1 blue copper protein with a single polypeptide chain of 163 amino acid residues. Halocyanin participates as putative electron carrier protein associated to an electron acceptor role for a terminal oxidase and has the lowest redox potential value reported to date for a BCP. NMR studies and homology modeling calculations were performed to evaluate the electronic properties of Cu(II)-halocyanin from Natronobacterium pharaonis. The copper coordination site properties of Cu(II)-halocyanin are discussed. The 1H NMR spectra, isotropic chemical shifts and relaxation times for halocyanin are compared with those of other BCPs such as azurin, amicyanin, plastocyanin and stellacyanin. The wild-type Cu(II)-halocyanin presents almost the same 1H NMR spectra in comparison with Cu(II)-plastocyanin as expected from a similar coordination symmetry. However, minor differences were found. In order to get some insight on these differences, a computational model for Cu(II)-halocyanin from N. pharaonis was built. Model is based on sequential homology of halocyanin with two different families of proteins: plastocyanins and pseudoazurins. Homology modeling was performed using two different structural templates and copper ion was added for further refinement of the coordination site. Proposed structure was in good agreement with NMR experimental information and is the first three-dimensional model reported to date of an halocyanin. Small differences were found in the copper coordination site with respect to other BCP with known structure. This work is also an interesting example of expertise-driven homology modeling across different protein families.