21 research outputs found
Convex Constraint Decomposition of Circular Dichroism Curves of Proteins
A new algorithm, called convex analysis, has been developed
to deduce the chiral contribution of the common secondary structures
directly from experimental circular dichroism (CD) curves
of a large number of proteins. The analysis is based on CD data
reported by Yang et aU Test runs were performed on sets of artificial
protein spectra created by the Monte Carlo technique using
poly-u-Iysine based component spectra. Application of the decomposition algorithm for the created sets of spectra resulted in
component spectra [B (2, i)] and weights [C (i, k)] with excellent
Pearson correlation coefficients (r).2 The algori thm, independent
of X-ray data, revealed that the CD spectrum of a given protein
is composed of at least four independent sources of chirality. Three
of the computed component curves show remarkable resemblance
to the CD spectra of known protein secondary structures. This
approach yields a significant improvement compared to the eigenvector analysis of Hennessey and Johnson." The new method is a useful tool not only in analyzing CD spectra but also in treating
other decomposition problems where an additivity constraint is
valid
Analysis of hydrogen bonds in peptides, based on the hydration affinity of amides
The difference in the affinity for water of peptide groups embedded in different molecular environments was investigated. The chemical shift of an amide proton is sensitive to conformational variations, as well as to changes in the molecular environment [D.S. Wishat, B.D. Sykes and F.M. Richards, J. Mol. Biol., 222 (1991) 311\u2013333]. Therefore, if the conformational motions are minimized or excluded, the observed changes in the chemical shift can simply be related to the environmental effects. The conformation(s) of the cyclic \u3b2-turn models studied in this work has been previously reported using X-ray, NMR, circular dichroism, and (FT-IR) spectroscopic methods, as well as MD calculations. [M. Holl\uf3si, K.E. K\uf6ver, S. Holly, L. Radics and G.D. Fasman, Biopolymers, 26 (1987) 1527\u20131572; A. Perczel, M. Holl\uf3si, B.M. Foxman and G.D. Fasman, J. Am. Chem. Soc., 113 (1991) 9772\u20139784; and H.H. Mantsch, A. Perczel, M. Holl\uf3si and G.D. Fasman, Biopolymers, 33 (1993) 201\u2013207]. The backbone of the cyclo[(\u3b4)Ava\u2014Gly\u2014Pro\u2014Aaa\u2014Gly] (where Aaa = Ser(OtBu), Ser or Thr(OtBu), and \u3b4(Ava) is \u3b4-aminovaleric acid) compounds was found to be rigidly incorporated in the structure and to contain two intramolecular hydrogen bonds. These \u3b2-turn models also include one (or two) \u201cfree\u201d amide group(s) that are not involved in any type of interaction. The \u201cwater titration\u201d of these amide groups in acetonitrile, where they are involved in various degrees of hydrogen bonding, revealed their molecular environment. Owing to the rigidity of these structures, the observed changes in the amide proton chemical shifts, during titration were attributed to their involvement in hydrogen bonding. This was confirmed by monitoring the water titration simultaneously with FT-IR spectroscopy. The phenomenon described here, with the proposed characterization of the investigated peptide/water system, comprise an improvement in the NMR method for analyzing the hydrogen bonding of small rigid peptides.Peer reviewed: YesNRC publication: Ye