1.Kinetics of peptide synthesis studied by fluorescence of fluorophenyl esters.
Permyakov EA1, Medvedkin VN, Klimenko LV, Mitin YV, Permyakov SE Jr. Int J Pept Protein Res. 1994 Nov;44(5):472-6.
The kinetics of the reaction of Boc-alanine-trifluorophenyl, Boc-alanine-tetrafluorophenyl, Boc-alanine-pentafluorophenyl, and Boc-alanine-p-chlorotetrafluorophenyl esters (BocAlaOTrf, BocAlaOTfp, BocAlaOPfp, and BocAlaTfc, respectively) with leucine amide and with valine methyl ester have been measured using changes in fluorophenyl chromophore emission at 375 nm. The kinetic data cannot be well fit with a simple second-order reaction scheme. Measurements of the reaction kinetics at different concentrations of the reagents showed that the expression for the reaction rate is V = kC(N)0.5C(AE)1.5, in which k is the reaction rate constant, CN is the concentration of either LeuNH2 or ValOCH3, and CAE is the concentration of the fluorophenyl ester. This reaction equation indicates a complex, probably chain-like, reaction mechanism. The order of reactivity for these active esters with ValOCH3 is BocAlaOTfc > BocAlaOPfp > BocAlaOTfp > BocAlaTrf.
2.Conformational preferences of heterochiral peptides. Crystal structures of heterochiral peptides Boc-(D) Val-(D) Ala-Leu-Ala-OMe and Boc-Val-Ala-Leu-(D) Ala-OMe--enhanced stability of beta-sheet through C-H...O hydrogen bonds.
Fabiola GF1, Bobde V, Damodharan L, Pattabhi V, Durani S. J Biomol Struct Dyn. 2001 Feb;18(4):579-94.
The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P2(1),2(1),2(1), with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)A. V = 5,884 (3) A3, Z = 8, R = 0.086. VALa crystallises in space group P2(1) with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) A, beta = 95.84 (8) degrees , V = 3,040(4) A3, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel beta-sheet arrangement in both the structures. Several of the Calpha hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand. An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and alphaL conformation though the frequence of occurence may not be equal.
3.Design of peptides: synthesis, crystal structure and molecular conformation of N-Boc-L-Val-delta Phe-L-Val-OC H3.
Mitra SN1, Dey S, Bhatia S, Singh TP. Int J Biol Macromol. 1996 Aug;19(2):103-12.
The dehydropeptide Boc-L-Val-delta Phe-L-Val-OC H3 was synthesized by azlactone method in solution phase. The peptide crystallized from its solution in a methanol/water mixture (70:30) in space group P2(1)2(1)2(1) with a = 13.638(1)A, b = 22.864(3)A, c = 27.600(2)A, V = 8606(1)A3. The structure was determined by direct methods and refined to an R value of 0.089 for 3326 observed [1 > or = 2 sigma(I)] reflections. The structure contains three crystallographically independent molecules. Two molecules (A and B) adopt identical conformations with phi 1(A) = -130(1), phi 1(B) = -139(1), psi 1(A) = 153(1), psi 1(B) = 145(1), phi 2(A) = 62(1), phi 2(B) = 56(1), psi 2(A) = 33(1), psi 2(B) = 33(1), phi 3(A) = -75(1), phi 3(B) = -77(1) psi 3T(A) = 152(1) and psi 3T(B) = 163(1) degrees. The conformation of the third molecule (C) is different as in that torsion angle psi 1 is rotated by 180 degrees. The backbone torsion angles are phi 1 = -128(2), psi 1 = -37(2), phi 2 = 65(1), psi 2 = 35(1), phi 3 = -84(1) and psi 3T = 169(1).
4.Reengineering a type II beta-turn as a potential helix nucleator. Part I. Crystal structure of Boc-Val-Pro-(D)Asp-Asp-Val-OMe monohydrate.
Fabiola F1, Pattabhi V, Raju EB, Durani S. J Pept Res. 1997 Nov;50(5):352-6.
The crystal structure of Boc-Val1-Pro2-(D)Asp3-Asp4-Val5-OMe is described as a type II beta-turn reengineered into a potential helix nucleator. (D)Asp3 in the peptide is responsible for the configurationally guided LD chiral type II beta-turn centered at Pro2-(D)Asp3, as well as the partially developed LL chiral type I beta-turn centered at Asp4-Val5 by acceptance of a conformation nucleating H-bond from Val5NH to its carboxylic oxygen.
