Chemistry
Peptide Naming
Peptide naming follows a specific set of rules to describe the sequence of amino acids in a peptide or protein. The names are based on the one-letter abbreviations for each amino acid and are written in the order they appear in the sequence. The N-terminus is written first, followed by the C-terminus.
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3 Key excerpts on "Peptide Naming"
eBook - ePub- Stein(Author)
- 2017(Publication Date)
- CRC Press(Publisher)
An understanding of the relationship of a peptide or protein structure to its function is essential for the rational design of molecules with predicted properties that can be exploited for research and in the clinic. The chemical synthesis of peptides has a fundamental role in this area of modern biological research. Systematic variations in structure can be correlated with the properties of the resultant molecules; a direct approach to the identification of functional domains or of specific amino acids having specialized roles in the molecule of interest. These efforts are critically important since there is not yet a full appreciation of how the amino acid sequence of a peptide or protein directs its proper folding into a preferred bioactive conformation or a precise three-dimensional structure, giving rise to its unique properties. Macromolecular interactions, and the mechanisms governing biorecognition, particularly ligand/receptor interactions, must also be understood in order to design structures with predicted properties, and chemically synthesized peptides contribute to this goal as well. These and other applications of peptides have depended in large measure upon the accessibility of purified synthetic peptides ever since the first synthesis, in 1953, of a biologically active peptide hormone by du Vigneaud and his co-workers. The hormone was the cyclic octapeptide, oxytocin. Recent advances in the technology of chemical peptide synthesis, purification, and structural analysis have made such molecules more generally available, and the use of peptides in biomedical research and pharmaceutical development is expanding rapidly.BACKGROUNDThe term polypeptide was proposed in 1906 by Emil Fischer to describe structures consisting of variable numbers of amino acids linked together by amide bonds. The basic structural features of a linear peptide are illustrated in Figure 1 . A peptide bond is formed by a condensation reaction between two amino acids; the carboxyl group of one amino acid forms an amide bond with the amino group of a second amino acid, and a molecule of water is eliminated. The amino acids, which are called residues when they occur in peptide linkage, are conventionally numbered consecutively starting at the amino (N) terminus. The repetitive peptide backbone, which is all of the molecule except for the side-chain (R) groups, is defined by its length and by its direction. Each amino acid residue is distinguished by its side-chain moiety, which is attached to the alpha carbon atom (Fig. 1
eBook - PDF- R C Sheppard(Author)
- 2007(Publication Date)
- Royal Society of Chemistry(Publisher)
Rules and Tentative Rules on Nomenclature 48 1 SUMMARY WITH EXAMPLES The systematic application of these principles to the name of an imaginary pentapeptide ‘Iupaciubin’* may illustrate the symbolism. Rule Operation Short name Structure 1. 2a. 2b. 3. 4. 5a. 5b. 6. (Fundamental name) Replacement Extension (N terminal) Extension (C terminal) Insertion Removal Side chain substitution on amino group Side chain substitution on carboxyl group Partial sequence Iupaciubin [Phe*]iupaciubint Arginyl-iupaciubin, Arg-iupaciubin Iupaciubyl-met hionhe, iupaciubyl-Met Endo-Thr2&-iupaciubin Des-Glu3-iupaciubin NE2-Val-iupaciubin Iupaciubim(2-4)- tripeptide 1 2 3 4 5 Ala-Lys -Glu-Tyr -Leu Ala-Lys-Glu-Phe-Lue Arg-Ala-Lys-Glu-Tyr-Leu 4 1 5 1 5 Ala-Lys -Glu-Tyr-Leu-Met 2 2a 3 Ala-Lys -Thr-Glu-Tyr -Leu 2 4 Ala-Lys -Tyr -Leu Ala-Lys -Glu-Tyr-Leu Val Ala-Lys -Glu-Tyr-Leu 3 2 3 4 Lys-Glu-Tyr Val I& 2 IY To symbolize the harmonious cooperation of IUPAC and IUB. t Note that only for replacement are square brackets required. XI Abbreviated Nomenclature of Synthetic Polypeptides (Polymerized Amino Acids) (Reproduced by permission from Pure Appl. Chern., 1973, 33, 439444) The numerous studies on the physical, chemical, and biological properties of synthetic polypeptides have brought with them different ways of describing, in abbreviated form, these products whose structures are often incompletely known. The use of a variety of nomenclatures com- plicates the literature; hence, a consistent and clearly defined system for naming such polypeptides is desirable. The proposals set forth here, which represent the consensus of many discussions and suggestions, should aid in systematizing the nomenclature of a wide variety of synthetic polypeptides. They were published in tentative form in IUPA C Information Bulletin Nu. 30 (1967) and in revised form in several journals in 1972l.
eBook - PDF- Deniz Ekinci(Author)
- 2012(Publication Date)
- IntechOpen(Publisher)
14 Peptides and Peptidomimetics in Medicinal Chemistry Paolo Ruzza Institute of Biomolecular Chemistry of C.N.R. Italy 1. Introduction Peptides show great pharmaceutical potential as active drugs and diagnostics in several clinical areas such as endocrinology, urology, obstetrics, oncology, etc. and as functional excipients in drug delivery systems to overcome tissue and cellular membrane barriers (Nestor, 2009). From a pharmaceutical point of view, peptides are situated somewhere between classical organic drug substances and high molecular weight biopharmaceuticals. The importance of peptides to life is evident from the most primitive organism to man. In man, a myriad of roles is filled by peptides spanning hormonal, neuromodulatory, mucosal defense, et al. Despite the obvious importance of peptides to homeostasis in man, there are few peptides resulting from medicinal chemistry that are commercialized pharmaceutical products in the USA and Europe. The shortcomings of peptides as pharmaceutical products have been long known: typically short duration of action, lack of receptor subtype selectivity, lack of oral bioavailability. However medicinal chemistry offers solutions to the first two limitations and oral bioavailability issues have been addressed by novel routes of administration (e.g. intranasal, inhalation) and injectable depot formulations (Nestor, 2009). 2. Peptide design considerations The physical and chemical properties of peptides and proteins are determined by the nature of the constituent amino acid side chains and by the polyamide peptide backbone itself. The structures of the 20 primary amino acids are given in Figure 1. Amino acids are divided into hydrophobic and hydrophilic residues. The first group includes those with aliphatic side chains (Ala, Val, Ile, Leu, Met) and those with aromatic side chains (Phe, Tyr, Trp).
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