Bond distances protein backbone

L. Schafer, M. Cao, and M. J. Meadows, Predictions of Protein Backbone Bond Distances and Angles from First Principles, Biopol., 35 (1995) 603-606. 

Predictions of Protein Backbone Bond Distances and Angles from First Principles... 

When a biomolecular system is separated into QM and MM regions one must usually cut amino acid side chains or the protein backbone at covalent bonds (Fig. 5.2 a). The construction of the covalent boundary between the QM and MM parts is key to accurate results from QM/MM calculations. Because there is no unique way to treat the covalent boundary, several different approaches have been described. In the first applications of coupled QM/MM simulations link atoms were used to create the covalent QM/MM boundary (Fig. 5.2b). Link atoms are atoms added to the QM part to fill the broken valences of the boundary QM atoms. These atoms are placed along the broken QM/MM bond at a distance appropriate for the QM bond added. The link atoms have usually been hydrogen atoms but methyl groups and pseudohalogen atoms have also been used [35]. 

Rusticyanin has a high reduction potential (680 mV), which is similar to that for the Type 1 Cu center in fungal as opposed to tree laccase (785 mV) (73). This trend is so far unexplained. From the sequence and EXAFS studies, His-Cys-His-Met coordination is a reasonable possibility for rusticyanin (55). It may well be that the reduction potential is determined by effects of a polypeptide backbone on Cu—S(Cys) and Cu—S(Met) bond distances and the Cu ligand field (74). If this is the case, however, rusticyanin would be expected to have one or both Cu—S distances shorter than in other blue copper proteins, which is not borne out by information from EXAFS (Table IV). A further possibility that the Cu(I) form is three-coordinate, as in the case of plasto-cyanin at low pH (Fig. 2), has no strong support at present (75). 

EJectron-tunneling pathway for myoglobin modified at His-48, The pathway moves along the protein backbone from His-48 to Arg-45, and then to the heme via an H-bond (=) to the heme propionate. The His-48 to heme edge-edge distance is 12.7 A. ... 

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