Abstract
C–H/O interactions of aromatic C–H donors within proteins have been studied by analyzing the data in the Protein Data Bank (PDB). The C–H/O interactions were studied between aromatic donors; phenylalanine, tyrosine, and tryptophan and the acceptors; alcohol, backbone amide, and side-chain amide groups. The analysis of the C–H–O angle indicates that protein C–H donors do not show a preference for linear contacts. Although there is no tendency for linear C–H/O interactions, there are only around 3% of bifurcated C–H/O interactions. Furthermore, the analyses of the C–H/O interactions indicate an influence of simultaneous classical hydrogen bonds, especially for the tyrosine systems. The calculated electrostatic potential maps for model systems can explain the results of the crystallographic analysis. These results can be important for recognizing the C–H/O interaction of aromatic rings in the crystal structures of proteic systems.
Highlights
IntroductionC–H/O interactions represent a wide group of weak hydrogen bonds that have important roles in many biological macromolecule structures like in the stability of proteins, in different types of interactions e.g. protein-protein, protein-ligand and protein nucleic acid interactions as well as in crystal structures and in enzymatic activity.[1,2,3] A few studies have presented that weak C–H/O interactions exist between parallel and anti-parallel beta sheets in proteins.[4,5,6] It was established that the role of C–H/O interactions is primarily to stabilize protein structures where they contribute up to 25% among the total number of hydrogen bonds detected in proteins.[5,6,7,8,9,10,11,12,13]The C–H/O interactions are widely studied using spectroscopic methods,[14,15,16,17] theoretical calculations,[9,11,14,18,19,20,21,22,23] and structure analysis of data in the Cambridge Structural Database (CSD)[24,25] and the Protein Data Bank (PDB).[10,12,13,26] C–H/O interactions are considered to belong to the group of weak, linear interactions, their energies can vary from very weak, -0.3 kcal/mol, to quite strong, E < -4 kcal/mol.[8]
It was shown that the hydrogen bond can influence C–H/O interactions of pyridine.[29]
There is no tendency for linear C–H/O interactions, there is no significant number of bifurcated C–H/O interactions, while in previous work it was shown that benzene in crystal structures forms significant number of bifurcated interactions.[30]
Summary
C–H/O interactions represent a wide group of weak hydrogen bonds that have important roles in many biological macromolecule structures like in the stability of proteins, in different types of interactions e.g. protein-protein, protein-ligand and protein nucleic acid interactions as well as in crystal structures and in enzymatic activity.[1,2,3] A few studies have presented that weak C–H/O interactions exist between parallel and anti-parallel beta sheets in proteins.[4,5,6] It was established that the role of C–H/O interactions is primarily to stabilize protein structures where they contribute up to 25% among the total number of hydrogen bonds detected in proteins.[5,6,7,8,9,10,11,12,13]The C–H/O interactions are widely studied using spectroscopic methods,[14,15,16,17] theoretical calculations,[9,11,14,18,19,20,21,22,23] and structure analysis of data in the Cambridge Structural Database (CSD)[24,25] and the Protein Data Bank (PDB).[10,12,13,26] C–H/O interactions are considered to belong to the group of weak, linear interactions, their energies can vary from very weak, -0.3 kcal/mol, to quite strong, E < -4 kcal/mol.[8]. C–H/O interactions represent a wide group of weak hydrogen bonds that have important roles in many biological macromolecule structures like in the stability of proteins, in different types of interactions e.g. protein-protein, protein-ligand and protein nucleic acid interactions as well as in crystal structures and in enzymatic activity.[1,2,3] A few studies have presented that weak C–H/O interactions exist between parallel and anti-parallel beta sheets in proteins.[4,5,6] It was established that the role of C–H/O interactions is primarily to stabilize protein structures where they contribute up to 25% among the total number of hydrogen bonds detected in proteins.[5,6,7,8,9,10,11,12,13]. In the case of aromatic C–H donors, the interaction energy depends on the aromatic ring substituents and on the acceptor.[20,27,28]
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