Theoretical study on the polar hydrogen-π (Hp-π) interactions between protein side chains

Chemistry Central Journal

Qi-Shi Du²  Qing-Yan Wang¹  Li-Qin Du¹  Dong Chen¹  Ri-Bo Huang¹ 

[1] Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China

[2] Gordon Life Science Institute, San Diego, CA 92130, USA

关键词: Ghost atom;    CCSD;    Protein backbones;    Hydrogen-π interactions;    Molecular interactions;    Protein structures;   

Others  :  787901
DOI  :  10.1186/1752-153X-7-92

 received in 2013-03-13, accepted in 2013-05-20,  发布年份 2013

【 摘 要 】

Background

In the study of biomolecular structures and interactions the polar hydrogen-π bonds (Hp-π) are an extensive molecular interaction type. In proteins 11 of 20 natural amino acids and in DNA (or RNA) all four nucleic acids are involved in this type interaction.

Results

The Hp-π in proteins are studied using high level QM method CCSD/6-311 + G(d,p) + H-Bq (ghost hydrogen basis functions) in vacuum and in solutions (water, acetonitrile, and cyclohexane). Three quantum chemical methods (B3LYP, CCSD, and CCSD(T)) and three basis sets (6-311 + G(d,p), TZVP, and cc-pVTZ) are compared. The Hp-π donors include R₂NH, RNH₂, ROH, and C₆H₅OH; and the acceptors are aromatic amino acids, peptide bond unit, and small conjugate π-groups. The Hp-π interaction energies of four amino acid pairs (Ser-Phe, Lys-Phe, His-Phe, and Tyr-Phe) are quantitatively calculated.

Conclusions

Five conclusion points are abstracted from the calculation results. (1) The common DFT method B3LYP fails in describing the Hp-π interactions. On the other hand, CCSD/6-311 + G(d,p) plus ghost atom H-Bq can yield better results, very close to the state-of-the-art method CCSD(T)/cc-pVTZ. (2) The Hp-π interactions are point to π-plane interactions, possessing much more interaction conformations and broader energy range than other interaction types, such as common hydrogen bond and electrostatic interactions. (3) In proteins the Hp-π interaction energies are in the range 10 to 30 kJ/mol, comparable or even larger than common hydrogen bond interactions. (4) The bond length of Hp-π interactions are in the region from 2.30 to 3.00 Å at the perpendicular direction to the π-plane, much longer than the common hydrogen bonds (~1.9 Å). (5) Like common hydrogen bond interactions, the Hp-π interactions are less affected by solvation effects.

【 授权许可】

   
2013 Du et al.; licensee Chemistry Central Ltd.

【 图 表 】

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