Anion induced conformational preference of CαNN motif residues in functional proteins |
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Authors: | Piya Patra Mahua Ghosh Raja Banerjee Jaydeb Chakrabarti |
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Affiliation: | 1. Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF‐142, Sector‐I, Saltlake, Kolkata, India;2. Department of Chemical, Biological and Macro‐Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, India;3. The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector‐III, Block JD, Salt Lake, Kolkata, India |
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Abstract: | Among different ligand binding motifs, anion binding CαNN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with CαNN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping CαNN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. |
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Keywords: | anion recognition conformational thermodynamics correlation plot molecular dynamics secondary structure |
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