Glycine in Water Favors the Polyproline II State

Biomolecules

卷:10

Reinhard Schweitzer-Stenner¹  Brian Andrews²  Brigita Urbanc²  Shuting Zhang² 

[1] Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA;

[2] Department of Physics, Drexel University, Philadelphia, PA 19104, USA;

关键词: molecular dynamics;    protein folding;    glycine;   

DOI  :  10.3390/biom10081121

来源: DOAJ

【 摘 要 】

Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.

【 授权许可】

Unknown