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J Mol Graph Model. 2017 Nov;78:88-95. doi: 10.1016/j.jmgm.2017.09.023. Epub 2017 Oct 8.

Computational study to understand the energy transfer pathways within amicyanin.

Author information

1
Department of Chemistry, Pondicherry University, Puducherry, 605 014, India. Electronic address: gtrama@gmail.com.

Abstract

Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways. The major transport channels in the oxidised state are, Cu2+---> MET28---> LYS29---> TYR30---> GLU31 and Cu2+---> MET98---> TYR30---‚ÄČ> GLU31. And in the reduced state Cu+---> CYS9---> TYR30---> GLU31 and Cu+---> MET28---> LYS2---> TYR30---> GLU31. We studied further the interaction energies between the copper ion and neighbouring residues using B3LYP/QZVP method. Both the methods complement each other in predicting the energy flow pathways and the cooperative nature of residues.

KEYWORDS:

Amicyanin; Communication map; Energy flow pathways; Interaction energies; Vibrational energy diffusivity

PMID:
29054098
DOI:
10.1016/j.jmgm.2017.09.023
[Indexed for MEDLINE]

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