Author : Garry Paul Gippert
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (763 download)
Book Synopsis New Computational Methods for 3D NMR Data Analysis and Protein Structure Determination in High-dimensional Internal Coordinate Space by : Garry Paul Gippert
Download or read book New Computational Methods for 3D NMR Data Analysis and Protein Structure Determination in High-dimensional Internal Coordinate Space written by Garry Paul Gippert and published by . This book was released on 1995 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: New computational methods were developed for the determination of primary chemical shift assignments and measurement of three-bond scalar J-coupling constants using multi-dimensional NMR data; and high-dimensional, systematic search for poly-peptide conformations subject to distance geometry constraints. Two methods were developed for conformational search in a space consisting of variable torsion angles. Method I performs a recursive search for linear chains. Method II performs a binary tree search for linear or branched systems. Trial conformations are rejected based on distance and scalar coupling bounds violations, including novel bounds on distance ratios, coupling ratios, and a 'degenerate' treatment of equivalent and prochiral atoms. A hierarchical arrangement of sub-searches is used to prune the high-dimensional space. The binary search (Method II) employs Unix 'pipes' and may be distributed over a computer network in a multi-processor environment, and may additionally utilize bounds on relative orientations of chain segments. 1H, 13C and 15N chemical shift assignments were obtained for recombinant poplar plastocyanin (rPc) from homonuclear and heteronuclear 2D and 3D NMR spectra. A semi-automated reduction of 3D NH-based spectra into a series of interleaved 1D vectors facilitated the sequential assignment process. Sidechain assignments were completed by the prediction and interactive, visual correction of crosspeak locations based on expected scalar and through-space connectivities. A similar procedure was used to identify correct beta-strand alignment based on total integrated NOE volume. Secondary proton chemical shifts were compared for five homologous plastocyanins. Distinct chemical shift variations were correlated with changes in primary sequence and led to a critical analysis of structural differences observed within the protein family. Scalar J-coupling constants between backbone HN and H-alpha protons of rPc were measured in three different NMR spectra--by lineshape analysis for 1H COSY and 3D HNCA-J crosspeaks, and curve fitting to modulated 1H, 15N-HSQC crosspeak intensities. Solution measurements of J(HN,H-alpha) were compared to values predicted from the high-resolution X-ray crystal structure using the Karplus relationship. Notable deviations occur for residues that are involved in intermolecular backbone contacts in the crystal, or are likely to be due to conformational averaging in solution, and includes a subset of residues in the copper-binding loop.