Abstract
α-crystallin is a major eye lens protein, comprising up to 40% of total lens protein. It is composed of two subunits, αA and αB and even shares a common central domain of about 90 residues with variable N- and C-terminal extensions. For the establishment of an evolutionary inter-relationship, an elucidation of the structure and alignment of protein sequences is crucial. In the present study, a bioinformatics approach was adopted to explore the possible structure, sequence and phylogenetic relationship of α-crystallin (both subunits αA and αB) from ten habitat-specific fish species, (freshwater and saltwater) and compared with a standard sequence of Bos taurus species. The sequence of Bos taurus was predicted to be a close homologue of the fish species. Wet lab experiments such as NMR are not only expensive and time consuming but are suitable for small proteins having less than 150 amino acids, so a preliminary computer-aided approach has been selected for structural analysis of α-crystallin of fish species. Our analysis shows that the secondary structures of bovine α-crystallin revealed no considerable differences as compared to that of the crystallins of the habitat-specific fish and that the presence of β- sheets was predominant in all structures. Though no significant differences in the αA subunits were revealed yet some structural variations were observed for αB subunits which had been confirmed by MSA analysis. The 3D structure of the protein hasn’t been elucidated yet so a computational analysis estimated no major differences in structures of crystallin for either bovine or the fish species except that saltwater fish proteins possess more favourable states and higher reliabilities. At the same time, the RMSF values of α-crystallin computed by CABS Flex 2.0 showed lesser values in the case of freshwater fish species which state the possible favourable structures of freshwater fish species. The stabilities of αB- subunits were revealed from the physiochemical parameters computed as compared to αA subunits of the respective proteins for all species. The Kyle-Doolittle Plots revealed the predominance of hydrophilic amino acids in both subunits of α-crystallin for all species and it is a cytosolic protein that has been determined using the TMHMM server. Considerate differences were revealed in the case of the αB subunit but not for the αA subunit, for all species as deciphered from Clustal omega which may indicate that the differences in α-crystallin occur primarily due to the αB subunit. Homology modeling revealed that bovine α-crystallin showed a greater sequence homology with most fish species, especially zebrafish. From our study, no major differences in α- crystallin structure could be deciphered between fish species in terms of habitat. The structure of human crystallin is a complex model so fish species were chosen as models which would be beneficial for humans in terms of drug designing as well.
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The study was designed by AC, SG, SS, PD. AC performed the dry lab analyses using various online bioinformatic tools, preparation of figures and preparing the manuscript. SG, SS, PD edited and revised the entire manuscript. All the authors have read and approved the final manuscript.
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Chakraborty, A., Ganguli, S., De, P. et al. An insight into the structural analysis of α-crystallin of habitat-specific fish: a computational approach. J Proteins Proteom 14, 111–127 (2023). https://doi.org/10.1007/s42485-023-00107-7
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DOI: https://doi.org/10.1007/s42485-023-00107-7