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bioRxiv · 10.1101/2021.11.12.465807

Inhibition of Interactions Between NDPK-B and NDPK-C in Presence of Graphene Oxide

Zaznaev, A.·Macwan, I.
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Abstract

During a heart failure, higher amount of nucleoside diphosphate kinase (NDPK) enzyme in the sarcolemma membrane inhibits the synthesis of second messenger cyclic adenosine monophosphate (cAMP), which is required for the regulation of the calcium ion balance for normal functioning of the heart. In a dependent pathway, NDPK normally phosphorylates the stimulatory guanosine diphosphate, GDP(s), to a guanosine triphosphate, GTP(s), on the heterotrimeric (, {beta} and {gamma} subunits) guanine nucleotide binding protein (G protein), resulting in the stimulation of the cAMP formation. In case of a heart failure, an increased quantity of NDPK also reacts with the inhibitory GDP(i), which is converted to a GTP(i), resulting in the inhibition of the cAMP formation. Typically, the {beta}{gamma} dimer of the G protein binds with hexameric NDPK-B/C complex and receives the phosphate at the residue His266 from residue His118 of NDPK-B. It is known that NDPK-C is required for NDPK-B to phosphorylate the G protein. In this work, the interactions between NDPK-B and NDPK-C are quantified in the presence and absence of graphene oxide (GO) as well as those between NDPK-B and GO through stability analysis involving hydrogen bonds, center of mass (COM), root mean square deviation (RMSD), and salt bridges, and energetics analysis involving van der Waals (VDW) and electrostatic energies. Furthermore, the role of water molecules at the interface of NDPK-B and NDPK-C as well as between NDPK-B and GO is investigated to understand the nature of interactions. It is found that the adsorption of NDPK-B on GO triggers a potential conformational change in the structure of NDPK-B, resulting in a diminished interaction with NDPK-C. This is confirmed through a reduced center of mass (COM) distance between NDPK-B and GO (from 40 A{square} to 30 A{square}) and an increased COM distance between NDPK-B and NDPK-C (from 50 A{square} to 60 A{square}). Furthermore, this is also supported by fewer salt bridges between NDPK-B and NDPK-C, and an increased number of hydrogen bonds formed by the interfacial water molecules. As NDPK-C is crucial to be complexed with NDPK-B for successful interaction of NDPK-B with the G protein, this finding shows that GO can suppress the interactions between NDPK-B/C and G proteins, thereby providing an additional insight into the role of GO in the heart failure mechanism. AUTHOR SUMMARYWe report a novel computational understanding of the interactions between the enzymes NDPK-B and NDPK-C with GO as a potential inhibitor to such interactions and its implications. These types of interactions can play influential roles in many biochemical processes including those that take place during heart failure. A second messenger called cAMP is needed for proper cardiac contraction through the actions of NDPK-B/NDPK-C. It is needed to study the interactions between NDPK-B and NDPK-C to control the synthesis of cAMP. Towards this end, GO is tested through molecular simulations to understand the interactions between NDPK-B and NDPK-C. Influencing or modifying such enzyme active sites has been very less explored and, in this work, the molecular simulations suggest that GO is able to interact with the active site of NDPK-B to provide a sustained cAMP synthesis for longer duration. We found that conformational changes within NDPK-B and NDPK-C influence the interactions between them and such conformational changes are found to be governed by their adsorption on GO. Finally, we found the role of interfacial water molecules between NDPK-B and GO to be crucial in maintaining the interface between them.

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Zaznaev, A., Macwan, I.. 2021-11-13. Inhibition of Interactions Between NDPK-B and NDPK-C in Presence of Graphene Oxide. https://doi.org/10.1101/2021.11.12.465807

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