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Quantum chemical studies on anion specificity of CαNN motif in functional proteins

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Abstract

Anion binding CαNN motif is found in functionally important regions of protein structures. This motif based only on backbone atoms from three adjacent residues, recognizes free sulphate or phosphate ion as well as phosphate groups in nucleotides and in a variety of cofactors. The mode of anion recognition and microscopic picture of binding interaction remains unclear. Here we perform self-consistent quantum chemical calculations considering sulphate and phosphate bound CαNN motif fragments from crystal structures of functional proteins in order to figure out microscopic basis of anion recognition. Our calculations indicate that stability and preference of the anion in the motif depends on the sequence of the motif. The stabilization energy is larger in case of polar residue containing motif fragment. Nitrogen atom of the polar residue of motif mainly participates in the coordination at the lowest energy levels. Anion replacement decreases stabilization energy along with coordination between motif atoms and oxygen atoms of anion shifted to higher energies, suggesting preference of the motif residues to specific anion. Our analysis may be helpful to understand microscopic basis of interaction between proteins and ionic species.

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Acknowledgements

PP thanks to Dr. Manas Mondal for helping in VASP calculation. RB and PP thank the TEQIP-III, MAKAUT, WB and DBT-BIF for funding. PP is also thankful to SNBNCBS, Kolkata for giving the computational facility. JC thanks DST for financial support.

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Authors and Affiliations

  1. Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as WBUT), BF-142, Sector-I, Salt Lake, Kolkata, 700064, India

    Piya Patra & Raja Banerjee

  2. Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India

    Mahua Ghosh & Jaydeb Chakrabarti

  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, 700106, India

    Jaydeb Chakrabarti

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  1. Piya Patra
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  2. Mahua Ghosh
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  4. Jaydeb Chakrabarti
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Correspondence to Piya Patra or Jaydeb Chakrabarti.

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Patra, P., Ghosh, M., Banerjee, R. et al. Quantum chemical studies on anion specificity of CαNN motif in functional proteins. J Comput Aided Mol Des 32, 929–936 (2018). https://doi.org/10.1007/s10822-018-0157-3

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