Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.
Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding.
a State Key Laboratory of Non-food Biomass and Enzyme Technology , National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences , 98 Daling Road, Nanning , Guangxi 530007 , China.
Qi-Shi
QS
Du
Dong
D
Chen
Neng-Zhong
NZ
Xie
Ri-Bo
RB
Huang
Kuo-Chen
KC
Chou
D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary
D010455:Peptides
Hp–π interaction; hydrogen bond; protein loops; protein structures; secondary structure