Evidence of reduced flexibility in disulfide bridge-depleted azurin: a molecular dynamics simulation study.
Two molecular dynamics simulations have been performed for 2 ns, at room temperature, on fully hydrated wild type and Cys3Ala/Cys26Ala double-mutant azurin, to investigate the role of the unique disulfide bridge on the structure and dynamics of the protein. The results show that the removal of the [bond]SS[bond] bond does not affect the structural features of the protein, whereas alterations of the dynamical properties are observed. The root mean square fluctuations of the atomic positions are, on average, considerably reduced in the azurin mutant with respect to the wild type form. The number of intramolecular hydrogen bonds between protein backbone atoms that are lost during the simulation, with respect to the starting configuration, are reduced in the absence of the disulfide bond. The analysis of the dynamical cross-correlation map, characterising the protein co-ordinated internal motions, demonstrates in the mutated azurin a significant decrease in anti-correlated displacements between protein residues, with the only exception occurring in the region of the mutation sites. The overall findings show a relevant reduction in flexibility as a consequence of the disulfide bridge depletion in azurin, suggesting that the [bond]SS[bond] bond is a structural element which significantly contributes to the dynamic properties of the native protein.
Rizzuti
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Dipartimento di Fisica e Unità INFM, Laboratorio di Biofisica Molecolare, Università della Calabria, Ponte P. Bucci, Cubo 30C, 87030 Rende (CS), Italy.
Sportelli
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Guzzi
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D001400:Azurin / Q000737:chemistry*; D019295:Computational Biology; D004220:Disulfides / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation
D004220:Disulfides; D001400:Azurin