title: Determination of the optimal position of adjacent proton-donor centers for the activation or inhibition of peptide bond formation--a computational model study.
abstract: The study reports a computational analysis of the influence of proton donor group adjacent to the reaction center during ester ammonolysis of an acylated diol as a model reaction for peptide bond formation. This analysis was performed using catalytic maps constructed after a detailed scanning of the available space around the reaction centers in different transition states, a water molecule acting as a typical proton donor. The calculations suggest that an adjacent proton donor center can reduce the activation barrier of the rate determining transition states by up to 7.2 kcal/mol, while no inhibition of the reaction can be achieved by such a group.
authors.affiliation: Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
authors.forename: Miroslav A
authors.initials: MA
authors.lastname: Rangelov
authors.forename: Galina P
authors.initials: GP
authors.lastname: Petrova
authors.forename: Vihra M
authors.initials: VM
authors.lastname: Yomtova
authors.forename: Georgi N
authors.initials: GN
authors.lastname: Vayssilov
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D010084:Oxidation-Reduction; D010455:Peptides / Q000737:chemistry*; D014176:Protein Biosynthesis; D011522:Protons; D012270:Ribosomes / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D010455:Peptides; D011522:Protons; D014867:Water