The Theoretical Studies Of The Modulation Of Micro-surroundings On The Transfer Of Proton/Excess Electron In Proteins

The mechanism of electron-induced dissociation of peptide chain cations and protein ions is one of the hot topics of research recently.Because the dissociation mechanism is conducive to the recognition of protein sequences,the localization of protein post-translational modifications and the development and enrichment of proteomics.Lysine（Lys,K）,histidine（His,H）,arginine（Arg,R）and other basic amino acid side chains are apt to be protonated,which capture excess electrons to form hypervalent radicals.The release of proton and electron for these hypervalent radicals takes place through different proton-coupled electron transfer（PCET）mechanism according to the surroundings of proteins.In addition,excess electrons can be produced in the cathode of the enzyme biofuel cell.It is beneficial to understand the mechanism of electron transfer in the cathode region by studying the proton and excess electron transfer mechanisms in proteins,thereby promoting the design and development of biofuel cells,a new energy source.The specific work of this topic is as follows:（1）The modulation of the micro-surroundings of proteins on the transfer of proton and excess electron in polypeptides containing lysine and histidine has been examined in this part.The transfer mechanism of proton and excess electron in the KH-N-HH system has been explored by B3LYP/6-31+G（d,p）.Combined the structure information of the reactants,transition states and products with their corresponding distributions of electron spin densities,the proton/electron transfer reaction of the KH-N-HH system can be described by a special orthogonal proton-coupled Rydberg electron transfer mechanism.The corresponding proton is transferred from the lysine side chain amino group to the adjacent backbone amide O-atom,while the electron is transferred from histidine side chain to the same backbone amide unit through the Rydberg orbital.Moreover,the results obtained by using B3PW91 and m PW1PW91 functional combined with 6-31+G（d,p）basis set are consistent with the B3LYP functional.This shows that it is reliable to use B3LYP to study the mechanism of this special proton-concerted excess electron transfer in the peptide systems.Therefore,we systematically study the KH-X-HH systems using B3LYP functional,and find that the difference of the X of structure,electronegativity,and other properties,but they do not change the transfer mechanism of proton/excess electron in the KH-X-HH systems.The side chain of X can produce a pull-push effect on the transfer of excess electron,resulting in the decrease or increase of the reaction energy barriers,which indicates that the protein micro-surroundings has a regulatory effect on proton transfer and excess electron transfer.（2）On the basis of the previous research,we examine the possible proton/electron transfer mechanisms in polypeptides containing two of the protonated lysine（KH）,the protonated histidine（HH）and the protonated arginine（RH）,which cause the competition in the binding sites for excess electron.At the same time,we also investigate the effects of different conformations of the same system on proton and excess electron transfer mechanism in order to better simulate the protein micro-surroundings.The double-protonated X-N-Y systems are optimized at the theoretical level of B3LYP/6-31+G（d,p）.According to the structures of the reactants,transition states and products and the maps of the corresponding electron spin density distribution,we can conclude that proton transfer and excess electron transfer are mutually motivated in these systems,which are described as a series of proton-coupled electron transfer mechanisms.Generally,proton transfer is less affected by the environment.Proton transfer takes place through the hydrogen bond channel formed between the side chain of lysine,histidine or arginine and a backbone peptide bond unit.However,the distributions of excess electron are greatly impacted by the surroundings,which causes different electron channels.The initial sites of excess electron transfer are different because of the difference in the electron affinities of the KH,HH and RH with the influence of the corresponding micro-surroundings（hydrogen bond）.These results are beneficial to enrich the theory of the proton-coupled electron transfer mechanisms.In general,the conformations closer to the real protein micro-surroundings are more favorable for proton and excess electron transfer.（3）Based onα-helix,the secondary structure of the proteins,we explore the regulation ofα-helix on the distribution of excess electron,which causes the difference in the coupling reactions of proton and excess electron transfer from the protonated lysine side chain（KH）to an adjacent amide unit.Structural optimizations and frequency analyses of a series ofα-helical models containing lysine side chains are performed using B3LYP/6-31+G（d,p）.In these systems,proton is transferred from the amino group of the lysine side chain to the amide oxygen.However,the distribution and transfer of excess electron is complicated due to the regulation of theα-helixes and the micro-surroundings in proteins.The N-terminal of theα-helix is a good“relay station”.As the length ofα-helix grows,the ability in capturing electron for the N-terminal increases,which can capture excess electron from the side chain of lysine.Therefore,a special proton-coupled multi-site Rydberg electron transfer mechanism occurs in the N-terminal of theα-helix（G_n-KH-G₂,n≥3）,and forward energy barriers firstly increase for 2≤n≤6 and then decrease for n≥6.However,the proton/electron transfer reaction in the T-G_n-KH-G₂（n≥5）systems occurs via the orthogonal proton-coupled Rydberg electron transfer mechanism,and the corresponding forward energy barriers gradually decrease with the increase of n.Moreover,for C-terminal ofα-helical（G₂-KH-G_n,n≥2）,the proton/electron transfer reaction takes place via the co-directional proton-coupled Rydberg electron transfer mechanism,and forward energy barriers gradually increase with the increase of n.In addition,to better simulate the protein micro-surroundings,the N-terminal of theα-helix structure has been capped with an acetate ion（CH₃COO^-）.For both A-G_n-KH-G₂（n≥2）and A-T-G_n-KH-G₂（n≥5）systems,protons and excess electrons are transferred through the co-directional proton-coupled Rydberg electron transfer mechanism,and both of their forward energy barriers tend to decrease with increase of theα-helix length.Therefore,the regulation of the protein micro-surroundings causes the difference in the microscopic mechanisms of the proton and excess electron transfer reactions and the different rate of reactions,which not only enriches the content of"relay stations"in proteins,but also promotes the understanding of electronic properties of micro-surroundings and electron transfer in proteins.