Proteins: Structure, Dynamics and Design

ISBN-13: 9789401090650 / Angielski / Miękka / 2011 / 423 str.

V. Renugopalakrishnan;Paul R. Carey;Ian C.P. Smith

Opis

The major goal of 'Expanding Frontiers in Polypeptide and Protein Structural Research' has been to bring the various avenues for the exploration of protein structures to a single forum. The idea of organizing the symposiwn was conceived by one of the editors, V. Renugopalakrislman, during the 9th International Biophysics Congress satellite symposium at Kibbutz Nof-Ginosar, Israel in 1987. It was originally supposed to dwell on 2D NMR and molecular dynamics of polypeptides and proteins. During the earlier part of the last decade, these two approaches began to emerge as powerful tools to probe protein structures at the atomic level in solution. The developments in molecular biology ushered in the capability to design polypeptides and proteins for specific application in science and technology. The emergence of 2D NMR and molecular dynamics was greatly facilitated by contemporary developments in molecular biology and protein engineering. Therefore an international symposiwn devoted exclusively to 2D NMR and molecular dynamics studies of proteins was felt necessary to bring two major approaches in a single forum. In addition to emphasis on 2D NMR and molecular dynamics simulation, the scope of the symposiwn included optical spectroscopy, protein design, and new horizons in protein structure. The symposiwn consisted of five plenary sessions devoted to NMR and optical spectroscopy as probes for protein structure, protein dynamics, computational methods in protein design, and new horizons in protein structure. In addition, five workshops in related areas, viz.

Spis treści

Section I: NMR as a probe for protein structure.- NMR structures of proteins: Improved precision through stereospecific resonance assignments.- Molecular dynamics of peptides and proteins investigated by NMR.- Stable-isotope-assisted multinuclear NMR investigations of proteins.- NMR studies of two related phosphotransfer proteins.- Motional properties of acyl carrier protein: Effects on NMR structural data.- Analysis of backbone dynamics of interleukin-1?.- Comparative study of solution conformation of bradykinin and its analogues.- Determination of locally accurate solution protein structures and unambiguous stereo-specific 1H NMR assignments.- Assessment of cheY binding regions using 2D NMR and paramagnetic ligands.- The determination of carbon-to-nitrogen distances in melanostatin using 13C, 15N-REDOR NMR spectroscopy.- Solution conformation of neuropeptide Y: 2D NMR and molecular dynamics studies.- Proline residues in bacteriorhodopsin: Conformation and temperature dependence.- A magnetic resonance study of solution conformation of Substance P and its N-terminal fragment.- Solution conformation of dermorphin in DMSO: 2D NMR studies.- An 1H NMR study of HTyr-D-Cys-Phe-D-PenOH (JOM-13), a highlyselective ligand for the ? opioid receptor.- The precision of protein structures determined from NMR data: Reality or illusion?.- Distance geometry in distance and torsion angle space: Flexibility, convergence and sampling properties.- Section II: Optical spectroscopy as a probe for protein structure.- Probing protein secondary structure by infrared spectroscopy.- Structural studies of cucumber mosaic virus: Fourier transform infrared spectroscopic studies.- Protein conformation and stability in relation to virus assembly: Investigation of bacteriophage P22 structural proteins by Raman spectroscopy.- Pursuit of higher order structural changes of proteins by time-resolved ultraviolet resonance Raman spectroscopy.- Femtosecond resonance Raman spectroscopy of photochemical and photophysical changes in the chromophores of some proteins.- Oriented fluorescent streptavidin conjugated phycoerythrin protein on biotinylated lipid LB monolayer films.- Conformational studies of proteins using vibrational circular dichroism.- Section III: Protein dynamics: Theory and experiment.- Protein dynamics: A brief overview.- Temperature and phase dependence of protein dynamics: A simulation study of myoglobin.- Protein dynamics from fluorescence resonance energy transfer.- Low-frequency dynamics of proteins: Comparison of experiment with theory.- Three-dimensional structure of amelogenin from 2D NMR: A molecular dynamics approach.- Analysis and interpretation of tryptophan fluorescence intensity decays in proteins.- Normal modes of crambin and molecular dynamics for structure prediction.- Analyses of statistical errors in dynamics simulations.- Derivation of solution conformers of peptide hormones via constrained molecular dynamics based on 2D NMR data.- Parallel processing and computational chemistry.- Section IV: Polypeptide and protein design: Protein engineering.- The N-terminal fragment of bovine phosphophoryn, an extracellular mineral matrix protein, shares sequence homology with viral, bacterial and eukaryotic transcriptional and post-translational regulatory proteins.- Computational and database retrieval approaches for determining polypeptide conformation 260.- Structure-activity relationships for 14-membered cyclic dermorphin analogs with two phenylalanines at the third and fourth positions.- Topographical considerations in the design of potent, receptor-selective peptide hormones and neurotransmitters.- Mimicry and antagonism in biotechnology drug discovery: Recognition peptides in protein scaffolds.- Comparative modeling of proteins in the design of novel cyclic renin inhibitors.- Helical transitions in peptides containing multiple ?,?-dialkyl amino acids.- Towards the design of structural mimics for proteins using helical peptide modules.- The polypeptide 310-helix.- Binding and translocation of Ca2+ by calcium channel drugs.- Morphology, conformation and stability of Alzheimer p-amyloid peptide fibrils.- ?-Helices in proteins: Strategies for detecting and analysing coiled-coil motifs.- Design of crystalline helices of short oligopeptides as a possible model for nucleation of the ?-helix.- A novel crepe ribbon representation for protein structures.- Molecular modeling of the interactions between Escherichia coli DNA polymerase I and substrates.- Molecular modeling of peptides on microcomputers.- Theory and simulation of protein folding: A personal view of problems and prospects.- Compact protein conformations.- Protein folding controlled by chemically shifting the temperatures of inverse temperature transitions.- Hydrophobic characteristics of folded proteins.- The localization of solvent in protein crystals.- The development of molecular mechanics parameters for carbohydrates.- On the use of conformationally dependent geometry trends from ab initio studies to determine empirical parameters for the CHARMm molecular mechanics force field.- Incomplete equilibration: A source of error in free energy calculations.- Free energy calculations on protein stability: The Thr157 ? Ala157 mutation of T4 Lysozyme.- Author index.