Charge Transfer Network Of Biomolecule Based On Transfer Integral

The growing amounts of high-quality experimental structures(X-ray,NMR,and cryo-electron microscopy)of protein and DNA have opened space to improve our theoretical understanding of interactions within biomolecule in the foreseen big data scenario.Although previous studies have analyzed the relative abundance of different forms of amino acids-amino acids and amino acids-DNA base contacts(van der Waals,hydrogen bonds)based on the statistical distance distribution and interaction energy,etc.there are relatively few studies on their internal physical and chemical properties.In this work,we directly calculate the charge-transfer integrals among millions of amino acid side-chain combinations in the Protein and Protein-DNA database under the tight-binding approximation.A representative complex network model is constructed to reveal the charge-transfer within biomolecules,which is large enough to sufficiently represent possible occurrences of amino acid and DNA base pairs contacts and comprehensively understand the charge transfer network as a whole in realistic biomolecules.Thus,the charge transfer network as a powerful directly look-up map,enable us to directly obtain the overall charge-transfer preferences for any biomolecules structures and find a unanimous recognition code.In addition,we calculate the charge-transfer integrals of the model system,catechol O-methyl-transferase(COMT)under the tight binding approximation and construct the charge transfer network,which transforms the abstract problem of QM regions selection into an intuitive and complex network problem in QM/MM calculation.Then we can efficiently select several optimized QM regions by the visual inspection of the network connections or community detection algorithms and compares the results of the previous contact map research by investigate the convergence of key catalytic properties with increasing QM region size.Finally,we suggest the charge transfer network provides us an alternative tool for confirming the QM/MM boundary,which is computational efficient in a convenient and intuitive manner.