Macwan, I. | Search bioRxiv

bioRxiv2024

Onset of Mismatch Repair by the Human Mismatch Repair Protein, MutSbeta for a Biosensing Device

Deficiency of MutSbeta protein has been proven to be a cause of Lynch Syndrome, which leads to hereditary colorectal cancer. In the absence of MutSbeta, or the energy source to initiate the conformational change of MutSbeta, the DNA repair pathway would not detect the DNA base pairing errors resulting in a failure to proceed. To examine the essential role of MutSbeta and the interface between MutSbeta and a mismatched DNA strand, 500ns of molecular dynamics simulations were performed and the results were compared with the controls. It is found that during the first 100ns, the outermost domain of MutSbeta (chain BP4) gets hold of the DNA, and the inner domains (AP1 and BP1) prepare to scan the DNA strand. An RMSD of 5-7[A] for the control MutSbeta compared to 3-6.5[A] in the presence of a mismatched DNA indicate that starting [~]75ns, MutSbeta stabilizes and initiates the scanning of the mismatched DNA. The reduction of the distance between the two biomolecules by [~]16[A], increase of Van der Waals energies by [~]75 kCal/mol and a crucial role played by the interfacial water molecules and their hydrogen bonds during the next 100ns also supports the manipulative nature and initiation of scanning by MutSbeta. Author SummaryAbout 1 and 23 men and 1 and 26 women have the chances of developing colorectal cancer and the chances only increase with old age. Cancer typically develops from mutated DNA, which emphasizes the importance of understanding how proteins a part of the DNA repair pathway process interact with a mutated strand of DNA. One such protein, MutSbeta, is the first protein that initiates the repair pathway process and scans DNA for any mutations. As the initiator, a deficiency of MutSbeta leads to higher chances of mutated DNA going undetected, and therefore forming cancerous cells. Using 3D simulations, we analyzed the interactions between MutSbeta and a mutated DNA strand. We found that the two outer domains, AP4 and BP4 grab hold of the DNA strand while the inner clamps, AP1 and BP1 scan the DNA strand. It was also discovered that Van der Waals play a more dominant role compared to electrostatics in terms of the driving force behind the interactions between DNA and MutSbeta. Overall, our data supported the attractive nature of MutSbeta towards DNA and its stability as it initiates the scanning process. Furthermore, this data was used to verify the presence of MutSbeta for a biosensor that was built previously; owing to the significance and applicatory effects of this work.

biophysics↗

bioRxiv2021

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

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.

bioengineering↗