Sequence and Conformation

The amino-acid sequence has been determined for the SOD of four species (Table 2). There are minor differences for the yeast enzyme Asn-55 and Asn-92 against Asp-55 and Asp-92 and for the human enzyme concerning the amidation of six residues and Ser-17 and Val-98 against He-17 and Ser-98 . Characteristic is the very low amount or the absence of methionine and tryptophan. There is no methionine in human SOD, the yeast SOD contains only Met-84, the bovine SOD Met-115, and the equine SOD Met-99 and Met-117. Tryptophan is absent with the exception of Trp-32 in human SOD. 

A sequence homology of 54 % was observed between the yeast and bovine SOD of 80% between equine and bovine SOD , and of 82% between the bovine and human SOD 

The conformation of BESOD has been determined by X-ray diffraction to a resolution of 0.3 nm and of 0.2 nm, as quoted in Almost 50% of the amino-acid residues form a p barrel made up of 8 antiparallel strands. There is a 

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Table 5.7 Theoretically predicted polypeptides from the trypsin digestion of S-lacto-globulin (/3LG) . Reprinted from J. Chromatogr., A, 763, Turula, V. E., Bishop, R. T., Ricker, R. D. and de Haseth, J. A., Complete structure elucidation of a globular protein by particle beam liquid chromatography-Fourier transform infrared spectrometry and electrospray liquid chromatography-mass spectrometry - Sequence and conformation of /3-lactoglobulin , 91-103, Copyright (1997), with permission from Elsevier Science...

Early conformational studies by HOESY experiments are illustrated by the work of Batta and Kover54 who were able to access oligosaccharide sequencing and conformational distribution around the glycosidic bond in model compounds. These determinations make use of relayed proton-proton-carbon cross-relaxation. 

Asakura, T., Yoshimizy, H., and Yoshizawa, F. (1988). NMR of silk fibroin. 9. Sequence and conformation analysis of the silk fibroins from Bombyx mod and Philosamia cynthia ricini by 15N NMR spectroscopy. Macromolecules 21, 2038-2041. 

Magnetic resonance techniques have again been popular for studying enzymes which are involved in phosphate hydrolysis and transfer. 31P or 19F N.m.r.1-2 and spinlabelling3 have all been used to study the interaction of substrates with these enzymes, while affinity labelling4 5 6 7 is another technique which has been used to obtain information about the sequence and conformation of amino-acid chains at the active sites of enzymes. Recently, these experimental methods have been applied to the study of cell membranes,6-7 and these are mentioned in a new series of books concerned with enzymes in biological membranes.8 A new journal, Trends in Biochemical Sciences, which contains concise, up-to-date reviews on these and other topics is published by Elsevier on behalf of the International Union of Biochemistry. 

There are always numerous H-bond contacts formed between the recognition sequence and the binding protein. The pattern of H-bond donors and H-bond acceptors is determined by the sequence and conformation of the DNA as well as by the specific structure of the protein. Both together lay the foundation for a specific recognition of the DNA by the protein. 

Macromolecules are very much like the crystalline powder just described. A few polymers, usually biologically-active natural products like enzymes or proteins, have very specific structure, mass, repeat-unit sequence, and conformational architecture. These biopolymers are the exceptions in polymer chemistry, however. Most synthetic polymers or storage biopolymers are collections of molecules with different numbers of repeat units in the molecule. The individual molecules of a polymer sample thus differ in chain length, mass, and size. The molecular weight of a polymer sample is thus a distributed quantity. This variation in molecular weight amongst molecules in a sample has important implications, since, just as in the crystal dimension example, physical and chemical properties of the polymer sample depend on different measures of the molecular weight distribution. 

NMR analysis allows characterization of proteins to an atomic level. The most frequently used nuclei on protein NMR are 41, 2H, 13C, 15N, and 170 with proton NMR (Jefson, 1988). The use of NMR methods for protein sequence and conformational studies was limited to the small proteins or peptides because high magnetic fields were required but not widely available to study larger molecules and it was very time consuming with the capability of instruments in the past. 

Simultaneous evolution of sequences and conformations. In the work [71], the simultaneous evolution of sequences and conformations was studied. This design procedure leads to the final state that depends on the set of interaction parameters and on the rearrangements both in conformational space... 

To compute the free energy of an oligopeptide, it is first necessary to express the Cartesian coordinates of every atom of the molecule (in any conformation) in the same coordinate system. The coordinates of each amino acid residue and those of the end groups of the chain are first expressed in local coordinate systems. The chain is then built in a prespecified amino acid sequence and conformation by connecting the individual residues and end groups, with proper adjustment of the dihedral angles. 

STEVEN E. ROKITA, PhD, is Professor in the Department of Chemistry and Biochemistry at the University of Maryland. His research interests lie in sequence and conformation specihc reachons of nucleic acids, enzyme-mediated activation of substrates and coenzymes, halogenation and dehalogenation reactions in biology, and aromatic substitution and quinone methide generation in bioorganic chemistry. 

Feig M, Pettitt BM. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. J. Mol. Biol. 1999 286 1075-1095. 

PrP-res can induce its own formation (Kocisko et al, 1994), an essential prerequisite for a protein-only infectious agent. This replication is clearly influenced by PrP primary sequence and conformation. Supporting data are now available for how, in the absence of any nucleic acid component, these variations in PrP sequence and conformation could account for TSE species and strain characteristics. It is important to remember, however, that the link between these properties of PrP-res at the molecular level and the in vivo events in TSE disease remains... 

Aldehyde chemistry has been used to preferentially PEGylate the N-terminus of proteins [64]. These selective methods as well as nonselective PEGylation have been used successfully when native sequences and conformations are amenable to conjugation away from active sites. 

Colson, P., Jennings, H. J., and Smith, I. . P. (1974)./. Amer. Chem. Soc. 96, 8081. Composition, Sequence, and Conformation of Polymers and Oligomers of Glucose as Revealed by Carbon-13 Nuclear Magnetic Resonance. 

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