Biochemistry, peptides

Williams S, Causgrove T P, Gilmanshin R, Fang KS, Callender R H, Woodruff WH and Dyer R B 1996 Fast events in protein folding helix melting and formation in a small peptide Biochemistry ZS 691-7... 

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

As m most aspects of chemistry and biochemistry structure is the key to function We 11 explore the structure of proteins by first concentrating on their fundamental building block units the a ammo acids Then after developing the principles of peptide structure we 11 see how the insights gamed from these smaller molecules aid our under standing of proteins... 

S. B 2ick cn2cn, Mmino Mcid Determination Methods and Techniques, Marcel Dekker, New York, 1968 A. Niederweiser and G. Pataki, eds., Neiv Techniques in Mmino Mcids, Peptide and Protein Mnalysis, Ann Arbor Science Pubhshers, Ann Arbor, Mich., 1971 The Chemical Society of Japan, eds., Neiv Experimental Chemistry Series, Vol. 1 (Biochemistry 1) (in Japanese), Mamzen, Tokyo, Japan, 1978, pp. 141—160. 

MK Eidsness, AK Burden, KA Richie, DMJ Kurtz, RA Scott, ET Smith, T Ichiye, C Kang. Modulation of the redox potential of the Ee(SCys)4 site m rubredoxm by the orientation of a peptide dipole. Biochemistry 38 14803-14809, 1999. 

Qnadroni, M., et al., 1996. Analy.sis of global re.spon.ses by protein and peptide fingerprinting of protein.s i.solated by two-dimensional electrophore-.sis. Application to snlfate-starvation re.sponse of Escherichia coli. European Journal of Biochemistry 239 773-781. This paper de.scribes the n.se of tandem MS in the analysis of protein.s in cell extracts. 

Harper, E., and Rose, G. D., 1993. Helix stop signals in proteins and peptides The capping box. Biochemistry 32 7605-7609. 

I. Ugi, D. Marquarding, R. Urban in Chemistry and Biochemistry of Amino Acids, Peptides and Proteins, B. Weinstein, Ed., p 245, Marcel Dckkcr, New York 1982. 

Figure 5.27 Selective detection of lactolated peptides from a tryptic digest of / -lacto-globulins by LC-electrospray-MS-MS, showing (a) the total-ion-cnrrent trace in full-scan mode, and (b) the total-ion-current trace in neutral-loss-scanning mode. Figure from Selective detection of lactolated peptides in hydrolysates by liquid chromatography/ electrospray tandem mass spectrometry , by Molle, D., Morgan, F., BouhaUab, S. and Leonil, J., in Analytical Biochemistry, Volume 259, 152-161, Copyright 1998, Elsevier Science (USA), reproduced with permission from the publisher.

Reese, R.N. Wagner, G.J. (1987). Properties of tobacco Nicotiana tabacum) cadmium-binding peptide(s). Biochemistry Journal, 241, 641-7. 

Bentin T., Nielsen P. E. Enhanced peptide nucleic acid binding to supercoiled DNA possible implications for DNA breathing dynamics. Biochemistry 1996 35 8863-8869. 

Kaihatsu K., Braasch D.A., Cansizo-GLU A., Corey D.R. Enhanced strand invasion by peptide nucleic acid-peptide conjugates. Biochemistry 2002 41 11118-11125. 

Karras J.G., Maier M.A., Lu T, Watt A., Manoharan M. Peptide nucleic acids are potent modulators of endogenous pre-mRNA splicing of the murine inter-leukin-5 receptor-alpha chain. Biochemistry 2001 40 7853-7859. 

Belotserkovskii B.P., Zarling D.A. Peptide nucleic acid (PNA) facilitates multistranded hybrid formation between linear double-stranded DNA targets and RecA protein-coated complementary single-stranded DNA probes. Biochemistry 2002 41 3686-3692. 

C. G., Janowski B.A., Corey D. R. Inhibition of gene expression inside cells by peptide nucleic acids effect of mRNA target sequence, mismatched bases, and PNA length. Biochemistry 2001 40 53-64. 

Yang JJ, Pitkeathly M, Radford SE (1994) Far-uv circular-dichroism reveals a conformational switch in a peptide fragment Irom the beta-sheet of hen lysozyme. Biochemistry 33 7345-7353... 

In between the above two extremes are the monoamines (1-lOnmol/g) which are preformed and stored in terminals but at much lower concentrations than the amino acids and when released are removed primarily by reuptake for re-use, or intraneuronal metabolism to inactive metabolites. Thus the appropriate synaptic organisation, biochemistry and receptor pharmacology of the NTs also varies in keeping with their function. It is often assumed, incorrectly, that the NTs found in the highest concentration are the most potent. In fact the opposite is true. Those like the amino acids while having high affinity for their receptors have low potency while the peptides found at much lower concentration have high potency but low affinity. 

Balaram, P., Bothner-By, A. A., Breslow, E. Nuclear magnetic resonance smdies of interaction of peptides and hormones with bovine neurophysin. Biochemistry 1973, 12, 4695 704. 

Guichard, G., Briand, J. P., Muller, S., Cung, M. T. Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach. Biochemistry 2001, 40, 5720-5727. 

Mayer KL, Stone Ml. NMR solution structure and receptor peptide binding of the CC chemokine eotaxin-2. Biochemistry 2000 39 8382-95. 

Y2. Yandle, T. G The natriuretic peptide hormones. Biochemistry of natriuretic peptides. J. Intern. Med. 235,561-576(1994). 

Maraganore J. M., Bourdon P Jablonskj J., Ramachandran K. L. Design and characterization of hirulogs A novel class of bivalent peptide inhibitors of thrombin. Biochemistry 1990 229, 7095-101. 

Esler WP, Stimson ER, Ghilardi JR, Lu YA, Felix AM, Vinters HV, Mantyh PW, Lee JP, Maggio JE. Point substitution in the central hydrophobic cluster of a human beta-amyloid congener disrupts peptide folding and abolishes plaque competence. Biochemistry 1996 35 13914-13921. 

Lee JP, Stimson ER, Ghilardi JR, Mantyh PW, Lu Y-A, Felix AM, Llanos W, Behbin A, Cummings M, Criekinge MV, Timms W, Maggio JE. 1H NMR of A(i amyloid peptide congeners in water solution. Conformational changes correlate with plaque competence. Biochemistry 1995 34 5191-5200. 

Salomon AR, Marcinowski KJ, Friedland RP, Zagorski MG. Nicotine inhibits amyloid formation by the beta-peptide. Biochemistry 1996 35 13568-13578. 

Osterhout JJ Jr, Baldwin RL, York EJ, Stewart JM, Dyson HJ, Wright PE (1989) 11 NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A. Biochemistry 28 7059-7064. 

Selective cleavage of peptides and proteins is an important procedure in biochemistry and molecular biology. The half-life for the uncatalyzed hydrolysis of amide bonds is 350 500 years at room temperature and pH 4 8. Clearly, efficient methods of cleavage are needed. Despite their great catalytic power and selectivity to sequence, proteinases have some disadvantages. Peptides 420,423,424,426 an(j proteins428 429 can be hydrolytically cleaved near histidine and methionine residues with several palladium(II) aqua complexes, often with catalytic turnover. 

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