title: Cis-trans isomerization of omega dihedrals in proteins.
abstract: Peptide bonds in protein structures are mainly found in trans conformation with a torsion angle ω close to 180°. Only a very low proportion is observed in cis conformation with ω angle around 0°. Cis-trans isomerization leads to local conformation changes which play an important role in many biological processes. In this paper, we reviewed the recent discoveries and research achievements in this field. First, we presented some interesting cases of biological processes in which cis-trans isomerization is directly implicated. It is involved in protein folding and various aspect of protein function like dimerization interfaces, autoinhibition control, channel gating, membrane binding. Then we reviewed conservation studies of cis peptide bonds which emphasized evolution constraints in term of sequence and local conformation. Finally we made an overview of the numerous molecular dynamics studies and prediction methodologies already developed to take into account this structural feature in the research area of protein modeling. Many cis peptide bonds have not been recognized as such due to the limited resolution of the data and to the refinement protocol used. Cis-trans proline isomerization reactions represents a vast and promising research area that still needs to be further explored for a better understanding of isomerization mechanism and improvement of cis peptide bond predictions.
authors.affiliation: INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Université Denis Diderot-Paris 7, INTS, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France.
authors.forename: Pierrick
authors.initials: P
authors.lastname: Craveur
authors.forename: Agnel Praveen
authors.initials: AP
authors.lastname: Joseph
authors.forename: Pierre
authors.initials: P
authors.lastname: Poulain
authors.forename: Alexandre G
authors.initials: AG
authors.lastname: de Brevern
authors.forename: Joseph
authors.initials: J
authors.lastname: Rebehmed
mesh_terms: D018360:Crystallography, X-Ray; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry*; D019745:cis-trans-Isomerases / Q000378:metabolism
chemical_list: D011506:Proteins; D019745:cis-trans-Isomerases