Study on the cyclization tendency of backbone cyclic tetrapeptides.
The cyclization kinetics of five backbone-cyclic tetrapeptides was investigated both experimentally and computationally. The aim was to both accurately measure the cyclization rates in solution and develop a method that efficiently estimates the relative cyclization tendencies computationally. Progression of the cyclization reaction was monitored directly, yielding the kinetics of changes in the amounts of the linear precursor and the products. These measurements were used to calculate the reaction rates; the results were consistent with a first-order reaction kinetics. In order to predict the cyclization rates computationally, the conformation space of the linear precursors was mapped and used to construct an approximate partition function. We assumed that the cyclization tendency was correlated with the relative probability of being found in a cyclization-prone conformation of the backbone, this probability was estimated from the partition function. The results supported this assumption and demonstrated that, within reasonable accuracy, we are able to predict the relative cyclization tendencies of the peptides measured.
Besser
D
D
Institut für Biochemie und Biophysik, Friedrich-Schiller-Universität Jena, Germany. besser@merlin.biologie.uni-jena.de
Olender
R
R
Rosenfeld
R
R
Arad
O
O
Reissmann
S
S
D002845:Chromatography; D002851:Chromatography, High Pressure Liquid; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009010:Monte Carlo Method; D010452:Peptide Biosynthesis; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013696:Temperature; D013997:Time Factors
D010455:Peptides