Conformation in proteins

Fig. 7.14 Nomenclature for characteristic regions of peptide c >,t /-space taken from Karplus (1996). The frequencies of observed peptide conformations in protein crystal structures decrease from areas enclosed by a heavy solid line to regions enclosed by a plain solid line, to dashed outlines. Areas outside the dashed lines are disallowed in peptide conformational space. The lines are an approximate rendering of the exact contours given by Karplus (1996).

Quantification of ORD and CD Data. In principle ORD and CD can be used to calculate the amounts of a, / , and random conformations in protein, but in practice such estimates are subject to large errors. The Moffitt-Yang plot is probably the best estimate of percentage of a-helicity, but it is unable to distinguish between the ft and random structures. A detailed analysis of CD bands and their resultant Cotton effects, combined with infrared data, is the most promising approach even here the limits of error are large (82). Traditional estimates have been based on combinations of a-helix and random coil, and attention has been centered upon estimation of helical content. Consideration of j3 structure has been introduced more recently. The technique must be calibrated empirically with synthetic polypeptides of known conformation, and the proper choice of reference is not obvious. The /3 structure seems to be particularly variable in its rotational properties (27, 82). 

Both amide I and amide III bands are seen in Raman spectra of proteins.30 Lippert et al. devised the following method for estimating the fractions of a-helix, (3 sheet, and random coil conformations in proteins.31 The amide I Raman bands are recorded at 1632 and 1660 cm 1 in DzO (amide I ). The amide III band, which is weak in DzO, is measured at 1240 cm-1 in H20. The intensities of the three bands relative to the intensity of an internal standard (the 1448 cm 1 CH2... 

CONTENTS Introduction to the Series An Editor s Foreword. Albert Padwa Preface, C. Allen Bush. Raman Spectroscopy ol Nucleic Acids and Their Complexes. George J. Thomas. Jr. and Masamichi Tsuboi. Oligosaccharide Conformation in Protein/Carbohydrate Complexes, Anne Imberty. Yves Bourne. Christian Cambillau and Serge Perez. Geometric Requirements of Proton Transfers, Steve Schemer. Structural Dynamics of Calcium-Binding Proteins. Robert F. Steiner. Determination of the Chemical Structure ol Complex Polysaccharides, C. Abeygunawandana and C. Allen Bush. Index. 

Matthews BW (1972) The y-turn, evidence for a new folded conformation in proteins. Macromolecules 5 818-819... 

J. Habazettl, C. Cieslar, H. Oschkinat, IH NMR assignments of sidechain conformations in proteins using a high-dimensional potential in the simulated annealing calculations, Febs Letters, 268 (1990) 141. 

Fig. 3. a Left-handed (A) and right-handed (B) a-helix conformation in proteins, b Screw arrangement of proteins in the tobacco mosaic virus (TMV) ... 

Fig. 10a implies that shared (bifurcated) hydrogen bonds dominate the statistical picture of helical conformation in proteins and must be considered in helical mimetic design. 

J. L. Pellequer, S. W. Chen. Does conformational free energy distinguish loop conformations in proteins Biophys J. 1997, 73, 2359-2375. 

The frequencies of the infrared peptide backbone vibrations (the so-called Amide vibrations) of proteins can be used to differentiate secondary structures (conformations) in proteins in aqueous solutions. 

Hartmann, C., Antes, 1., and Lengauer, T. (2007) IRECS a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Science, 16 (7), 1294-1307. 

Geddes AJ, Parker KD, Atkins ED, Beighton E (1968) Cross-beta conformation in proteins. J Mol Biol 32 343-358... 

A simple and popular method for the prediction of conformation is the application of empirical conformational parameters. From the study of numerous protein structures determined by x-ray crystallography it became obvious that certain amino acids are frequent constituents of helical portions while others are more likely to occur in j -sheets and still others are often found in reverse turns. Statistical treatment of such frequencies (Chou and Fasman 1978) produced sets of conformational parameters (Table 5) which were applied for the prediction of conformation in proteins with considerable success. A cluster of four helical residues (P > 1.00) in a six residue stretch of a chain is predictive for a helical region that can be extended in both directions until a... 

Chakrabarti, R and D. Pal. 2001. The interrelationships of side-chain and main-chain conformations in proteins. Prog Biophys Mol Biol 76 1. 

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