Nucleotide triphosphate (NTP) binding domains, also known as P-loops, are protein structural motifs that play crucial biochemical and catalytic functions. Upon interaction with NTPs the geometric structures of the P-loops rearrange themselves to accommodate, often preferentially, substrates such as ATP or GTP. Members of the Flavivirus genus, including dengue (DENV) and zika (ZIKV), rely on NS3 helicase proteins for their pathogenic function. The latter, in turn, depend on their NTP binding domains for substrate and cation (Mg2+, Mn2+) recognition and binding. We present a comprehensive computational study of the physico-chemical mechanisms which lead to P-loop…ATP binding in various proteins. We study, <i>via</i> semiempirical and quantum chemical methods, P-loop…ATP binding for NS3 helicase and RecA DNA-repairing proteins and discern, qualitatively and quantitatively, the nature and role of their non-covalent (van der Waal, electrostatic and hydrogen bonding) interactions.<br/>

Semiempirical and quantum chemical prediction of ATP affinities and non-covalent binding to P-loops of proteins

253rd National Meeting (2017)

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