Local and Nonlocal Environments around Cis Peptides - Journal of

Dec 13, 2007 - Sreetama Das , Pratiti Bhadra , Suryanarayanarao Ramakumar , and Debnath ... Kantharaju , Srinivasarao Raghothama , Upadhyayula Surya ...
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Local and Nonlocal Environments around Cis Peptides Brent Wathen and Zongchao Jia* Department of Biochemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6 Received June 28, 2007

Although the vast majority of peptide bonds in folded proteins are found in the trans conformation, a small percentage are found in the less energetically favorable cis conformation. Though the mechanism of cis peptide bond formation remains unknown, the role of local aromatics has been emphasized in the literature. This paper presents results from a comprehensive statistical analysis of both the local and nonlocal (i.e., tertiary) environment around cis peptides. In addition to an increased frequency of aromatic residues in the local environment around cis peptides, a number of nonlocal differences in protein secondary and tertiary structure between cis and trans peptides are found: (i) coil regions containing cis peptides are almost twice as long as those without cis peptides and include more Tyr and Pro residues; (ii) cis peptides occur with high frequencies in coil regions near large β-structures; (iii) there is a nonlocal enrichment of Cys, His, Tyr, and Ser in the tertiary environment surrounding cis peptides when compared to trans peptides; and (iv) on average, cis peptides make fewer mediumrange and more long-range contacts than trans peptides do. On the basis of these observations, it is concluded that nonlocal factors play a significant role in cis peptide formation, which has not been fully appreciated previously. An autocatalytic model for cis peptide formation is discussed as are consequences for protein folding. Keywords: cis peptides • isomerization • protein folding • nonlocal environments

Introduction The peptide bond joining two adjacent amino acids acquires a partial double-bond character through a redistribution of electron density from the amide nitrogen of one amino acid to the carbonyl oxygen of the other. This electron delocalization results in a rotational barrier about this bond of between 13 and 20 kcal/mol,1–9 sufficient to ensure that the linkage between successive amino acids in a polypeptide chain remains planar. The overwhelming majority of the peptide bonds found in protein structures solved thus far by NMR or X-ray crystallography are in the trans conformation. A small percentage of these bonds, however, adopt the energetically less favorable cis conformation. The energy difference between the trans and cis conformations has been estimated to be ∼2.5 kcal/mol, primarily due to an increase in steric hindrance between adjacent R carbons that are brought into close proximity in the cis conformation.10 Typically, >80% of cis peptides are reported to occur within imide (X-Pro, where X is any amino acid) bonds and