Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects

2013 ◽  
Vol 135 (23) ◽  
pp. 8708-8719 ◽  
Author(s):  
Katarzyna Świderek ◽  
Iñaki Tuñón ◽  
Sergio Martí ◽  
Vicent Moliner ◽  
Juan Bertrán
Keyword(s):  
Isotope Effects ◽  
Bond Formation ◽  
Peptide Bond ◽  
Kinetic Isotope Effects ◽  
Formation Mechanisms ◽  
Peptide Bond Formation ◽  
Kinetic Isotope ◽  
Role Of Solvent

Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis

2021 ◽  
Author(s):  
Sofie Dekimpe ◽  
Joleen Masschelein
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Peptide Bond ◽  
Chemical Diversity ◽  
Peptide Bond Formation ◽  
Natural Product Biosynthesis

Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.

Secondary Kinetic Isotope Effects in Bimolecular Nucleophilic Substitutions. V. The Role of the Solvent in the Reaction Between Methyl Iodide and Pyridine

1972 ◽  
Vol 50 (7) ◽  
pp. 982-985 ◽  
Author(s):  
K. T. Leffek ◽  
A. F. Matheson
Keyword(s):  
Transition State ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
State Structure ◽  
Transition State Structure ◽  
Initial State ◽  
Nucleophilic Substitutions ◽  
Kinetic Isotope ◽  
Deuterium Isotope Effects

Secondary kinetic deuterium isotope effects are presented for the reaction of methyl-d3 iodide and pyridine in four different solvents. Calculations on mass and moment of inertia change with deuteration in the initial state and an assumed tetrahedral transition state, together with internal rotational effects, are used to rationalize the inverse isotope effects. It is concluded from the variation of the isotopic rate ratio, that the transition state structure varies with solvent.

scholarly journals The transition state for peptide bond formation reveals the ribosome as a water trap

2010 ◽  
Vol 107 (5) ◽  
pp. 1888-1893 ◽  
Author(s):  
Göran Wallin ◽  
Johan Åqvist
Keyword(s):  
Water Molecule ◽  
Transition State ◽  
Activation Enthalpy ◽  
Molecular Model ◽  
Isotope Effects ◽  
Bond Formation ◽  
Transition States ◽  
Peptide Bond ◽  
Hydroxyl Group ◽  
Peptide Bond Formation

Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered “double proton shuttle” mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation

1988 ◽  
Vol 18 (1-2) ◽  
pp. 107-119 ◽  
Author(s):  
Jack R. Collins ◽  
Gilda H. Loew ◽  
Brian T. Luke ◽  
David H. White
Keyword(s):  
Theoretical Investigation ◽  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation

scholarly journals Kinetic Isotope Effects for Alkaline Phosphatase Reactions:  Implications for the Role of Active-Site Metal Ions in Catalysis

2007 ◽  
Vol 129 (31) ◽  
pp. 9789-9798 ◽  
Author(s):  
Jesse G. Zalatan ◽  
Irina Catrina ◽  
Rebecca Mitchell ◽  
Piotr K. Grzyska ◽  
Patrick J. O'Brien ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Metal Ions ◽  
Active Site ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Kinetic Isotope
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