Biochemistry peptide bond

Zurawski, V. R., Jr., Kohr, W. J. and Foster, J. F. 1976. Conformational properties of bovine plasma albumin with a cleaved internal peptide bond. Biochemistry 14, 5579-5586. 

Odom, O.W., Picking, W.D., and Hardesty, B. (1990) Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes. Biochemistry 29, 10734-10744. 

M. N. James, and A. R. Sielecki, Stereochemical analysis of peptide bond hydrolysis catalyzed by the aspartic proteinase penicillopepsin, Biochemistry 24 3701 (1985). 

The amino acids link together by the reaction of an amino group of one amino acid with the carboxylic acid group of another amino acid. This forms a peptide bond. (For the sake of clarity the + signs in the reaction have been omitted.) A peptide bond is an amide group in molecules that are not biochemical. Many functional groups have different names in organic chemistry and in biochemistry. 

Wolfenden, R. V. Interaction of the peptide bond with solvent water a vapor phase analysis. Biochemistry, 17(1) 201-204,1978. 

In biochemistry, the amide linkage is traditionally referred to as a peptide bond. Whether the resultant polymer is classified as a peptide or a protein is not clearly defined generally, a chain length of more than 40 residues confers protein status, whereas the term polypeptide can be used to cover all chain lengths. 

Abrahmsen, L., Tom, J., Bumier, J., Butcher, K.A., Kossiakoff, A. and Wells, J.A. (1991) Engineering subtihsin and its substrates for efficient ligation of peptide bonds in aqueous solution. Biochemistry, 30,4151 159. 

Figure 16.7 Mechanism of aspartyl proteases involving general acid-base catalysis and the formation of a protonated terahedral intermediate. Bottom Proposal by T. J. Rodriguez. T. A. Angeles, and T. D. Meek, Biochemistry 32, 12380 (1993), that the first step is peptide bond isomerization. This accounts for the observed inverse 15N/14N kinetic isotope effect, which implies that bonding with the N atom becomes stiffer in the transition state.

Chaffotte, A.F., Guillou, Y., and Goldberg, M.E. 1992. Kinetic resolution of peptide bond and side chain far-UV circular dichroism during the folding of hen egg white lysozyme. Biochemistry 31 9694-9702. 

The International Union of Biochemistry and Molecular Biology recommends that the term peptidase be used synonymously with the term peptide hydrolase (IUBMB, 1992). Thus, in this unit the term peptidase is used in reference to any enzyme that catalyzes the hydrolysis of peptide bonds, without distinguishing between exo- and endopeptidase activities. Peptidases may be assayed using native or modified proteins, peptides, or synthetic substrates. In this unit, the focus is on assays based on the hydrolysis of common, commercially available, protein substrates. Thus, the assays are not intended to be selective for a given peptidase they are designed to provide estimates of overall peptidase activity. Other units in this publication focus on synthetic or model substrates, which can be designed for the measurement of specific endo- and/or exopeptidase activities. 

M. Laskowski Jr., Synthesis of peptide bonds by proteinases. Addition of organic cosolvents shifts peptide bond equilibriums toward synthesis, Biochemistry 1978, 37, 5220-5227. 

CY Shiau, MF Byford, RT Aplin, JE Baldwin, CJ Schofield. L-Delta-(alpha-amino-adipoyl)-L-cysteinyl-D-valine synthetase thioesterification of valine is not obligatory for peptide bond formation. Biochemistry 36 8798-8806, 1997. 

Horsthemke B, Bauer K (1982) Substrate specificity of an adenohypophyseal endopeptidase capable of hydrolyzing LHRH preferential cleavage of peptide bonds involving the carboxyl terminus of lower of it of hydrophobic and basic amino acids. Biochemistry 21 1033-1036 Horsthemke B, Knisataschek H, Rivier J, Sandow J, Bauer K (1981) Degradation of LHRH and analogs by adenohypophyseal peptidases. Biochem biophys Res Commun 100 753-759... 

Mahoney, W. C., and Hermodson, M. A. (1979). High-yield cleavage of tryptophanyl peptide bonds by o-iodosobenzoic acid. Biochemistry 18, 3810-3814. 

R. Wolfenden, Biochemistry, 17, 201 (1978). Interaction of a Peptide Bond with Solvent Water—Vapor Phase Analysis. 

As peptide chemists undertook the synthesis of peptides of increasing complexity and size the need for improved methods of amide bond formation became a central issue. In the 1950s, a significant expansion of the number of avaUable methods for peptide bond formation was apparent in the literature. Many of these methods were rooted in discoveries in biochemistry that showed that phosphoanhydrides and thioesters could be used to efficiently drive reactions of carboxy groups. 

Fig. 4.3 Collagen helix. This secondary structure is created by peptide bond conformation around the proline and hydroxyproline residues (From Fig. 2-39 in Biochemistry. L. Stryer, 4th Ed. 1995. W.H. Freeman Co., New York)...

Amides are notable for their role in biochemistry, i.e., the special amide bond between two amino acids is called a peptide bond. 

In 19S3, Frederick Sanger determined the amino acid sequence of insulin, a protein hormone (Figure 2.22). This work is a landmark in biochemistry because it showed for the first time that a protein has a precisely defined amino acid sequence consisting only of L amino acids linked by peptide bonds. This accomplishment stimulated other scientists to carry out sequence studies of a wide variety of proteins. Currently, the complete amino acid sequences of more than 2,000,000 proteins are known. The striking fact is that each protein has a unique, precisely defined amino acid sequence. The amino acid sequence of a protein is referred to as its primary structure. 

Lin L, Sulea T, Szittner R, Kor C, Purisima E, Meighen E. Implications of the Reactive Thiol and the proximal non-proline cis-peptide bond in the structure and function of Vibrio harveyi luciferase. Biochemistry 2002 41 9938-45. 

Jayaraman, J., and Goldberg, I. H. (1968). Localization of sparsomycin action to the peptide-bond-forming step. Biochemistry 7,418 21. 

G.A. Homandberg, M. Laskowski Jr, Enzymatic resynthesis of the hydrolyzed peptide bond(s) in ribonuclease S, Biochemistry 1979, 18, 586-592. 

The ability of proteinases to catalyze peptide bond hydrolysis and synthesis has long been known [29,30,31,32,33,34], and there is a renewed interest in it in present food protein biochemistry [10,25,27,28,35,36,37,59],... 

Carles, C., and Ribadeau-Dumas, B. (1984). Kinetics of action of chymosin (rennin) on some peptide bonds of bovine /3-casein. Biochemistry 23, 6839-6843. 

Chymotrypsin catalyzes the hydrolysis of peptide bonds adjacent to aromatic amino acid residues in the protein being hydrolyzed other residues are attacked at a lower frequency. In addition, chymotrypsin catalyzes the hydrolysis of esters in model studies in the laboratory. The use of model systems is common in biochemistry because a model provides the essential features of a reaction in a simple form that is easier to work with than the one found in nature. The amide (peptide) bond and the ester bond are similar enough that the enzyme can accept both types of compounds as substrates. Model systems based on the hydrolysis of esters are frequendy used to study the peptide hydrolysis reaction. 

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