Hydrogen Bonding Between Base Pairs UG, UU, AG, AT, GC And The Side Chains Of Arginine, Lysine, Histidine And Asparagine

It is important to study the hydrogen bonding sites between nucleic acid base pair and protein amino acid side chain to identify the recognition site and the interaction between protein and DNA,and to design new biomolecule material accurately.In this work,the density functional theory B3LYP/6-31+G（d,p）method was used to optimize the structures of the amino acid arginine,lysine,asparagine,and histidine side chains hydrogen bonding to the base pair AT,GC,UG,UU,and GA.61 stable hydrogen-bonded complexes was obtained,and the interaction energies of these complexes was calculated by using the density functional theory M06-2X-D3/aug-cc-pVDZ method with BSSE correction.The stable structure and the interaction energy of all the complexes in the aqueous phase was calculated by the same method and the PCM model.Using the M06-2X/aug-cc-pVDZ method,the electron densities at the hydrogen bond critical points of each complex was calculated.Research work can be summarized as the following aspects:1.Our calculation results show that the amino acid arginine,lysine,asparagine,and histidine side chains can form hydrogen-bonded complexes with the base pair AT,GC,UG,UU,and GA through multiple sites.U₁G,U₂G,U₃G and the asparagine and histidine side chains have strong hydrogen bonding interactions,namely site 1 and site 5,site 1 and site 4,site 1 and site 4.The strong hydrogen bonding interactions between UG and arginine side chains is site 5 of U₂G.The strong hydrogen bonding interactions between UG and lysine side chain hydrogen bonding is site 6 of U₂G.The strong hydrogen bonding interactions between UU and lysine side chain hydrogen bonding is the site 1 of U₂U₃.The asparagine or histidine side chain hydrogen bonding to the base pair GA is mainly through site 1 of GA.The asparagine or histidine side chains hydrogen bonding to the base pair TA is mainly through site 1 and site 3 of TA.The asparagine or histidine side chain hydrogen bonding to the base pair GC is mainly through site 1 and site 4 of GC.The order of stability of the complexes obtained from the electron density at the critical point is consistent with that obtained by the interaction energy.2.The stability of the hydrogen-bonded complexes is associated with the enthalpy change of the protonation reaction and the deprotonation reaction of the nucleic acid base pair.The more negative the enthalpy change of the protonation reaction or the smaller the enthalpy change of the deprotonation reaction,the more stable the hydrogen-bonded complexes.3.Water solvent has a certain influence on the interaction energy of these complexes,but the order of strength is consistent with that in the gas phase.