Proteins and polypeptides

Two amino adds can react to form an amide bond (see Section 23-19). Compounds formed by the linking of small numbers of amino acids are called peptides, and the amide bond linking the amino acid monomers is called the peptide bond. 

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The prefixes di-, tri-, and so on are used tx) indicate the number of amino acid monomers that are joined to form the peptide. The peptide indicated in the preceding equation is a dipeptide. 

General. The possibility that infra-red methods would throw some light on the problem of the structures of proteins and similar 

Fraction A The removal of dinitrophenol is recommended if much is present this may be done in one of two ways  

Svblimatum. Binitrophenol largely sublimes when heated in high vacuum at 70—80 0 in a special apparatus designed by Mills [169]. Some DNP-methionine and, as observed in our laboratory, also di-D15P-cystine may be lost. If necessary, the sublimation procedure may have to be interrupted, the substance dissolved in a little acetone and redeposited as a thin film on the walls of the vessel by evaporation. 

The residue from removal of dinitrophenol is dissolved in acetone (ca. 1 ml per 10 xmole protein) and amounts of about 1 d can be chromatographed directly. 

Fraction B The acid-soluble DNP-amino acids can often be directly identified by chromatography even when free amino acids are present. The solution is repeatedly evaporated to dryness, some water being added each time. The residue is taken up on 0.5 N hydrochloric acid or in acetic acid (about 1 ml per 10 pmole protein) and 1 d amounts applied . 

In order to remove the free amino acids, the residue from evaporation (see above) is dissolved in 2 ml IN hydrochloric acid and this solution passed through a column (diameter 2.5 cm) of a mixture of 20 g Hyflo-Super-Cel and 50 g talcum (pretreated with 0.01 N and IN hydrochloric acid [171]). All the DNP-amino acids (apart from DNP-cysteic acid) are adsorbed, in contrast to the free amino acids. The column is rinsed with 100 ml IN hydrochloric acid and finally the DNP-amino acids are eluted with alcoholic hydrochloric acid (alcohol-1 N hydrochloric acid, 40 + 10) or, better, with ammoniacal alcohol (alcohol-0.3% ammonium hydroxide, 40 + 10). The eluate is evaporated to dryness and the residue chromatographed as indicated above. 

Polylysine in neutral solution is evidently much more reactive than lysine (k = 2 x 107 at pH = 7-8) or lysyl-lysine (k 5x 108 M-1 sec-1 at pH = 8). This enhancement in reactivity is probably related to the multi- 

It may be concluded, therefore, that an electron that encounters a polyelectrolyte molecule is removed from solution by an irreversible process and, although it may not be incorporated into any particular orbital for a considerable length of time ( 10-9 sec), it has little chance to escape the high concentration of trapping sites provided by the polyelectrolyte. Another explanation would be that the polyelectrolyte has a kind of conductivity band. In the latter case, it is expected that the reactivity of the polymer should be the sum of the reactivities of the individual trapping sites. 

The latter theory of intramolecular electron transfer in nonconjugated polyelectrolytes, which may find support in the behaviour of the ribonuclease-copper(n) system (Levitzky and Anbar, 1967), is in accord with the observed agreement between the specific rates of gelatine, lysozyme and ribonuclease and the sum of specific rates of the constituent amino-acid residues (Braams, 1965, 1967). The latter agreement may, however, be fortuitous, and these proteins, which react at rates approaching the diffusion-controlled limit, may act as overall electron traps according to the first mechanism. 

In any case, it is evident that the behaviour of polymeric molecules differs qualitatively from that of low-molecular-weight substrates. This conclusion puts serious doubts on any direct extrapolation of the behaviour of monomeric constituents of living matter to that of biopolymers. Moreover, it should be remembered that the latter conclusion has been drawn from the behaviour of biopolymers in dilute solution in contrast to the even more complex situation inside a living cell. 

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Ramachandran G N and Sasisekharan V 1968 Conformation of polypeptides and proteins Adv. Prof. Chem. 23 283-438... 

M.J. Sippl, M. Hendlich and P. Lackner, Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments. Protein Sci. 1 (1992), 625-640. 

MM2 was, according the web site of the authors, released as MM2 87). The various MM2 flavors are superseded by MM3, with significant improvements in the functional form [10]. It was also extended to handle amides, polypeptides, and proteins [11]. The last release of this series was MM3(%). Further improvements followed by starting the MM4 series, which focuses on hydrocarbons [12], on the description of hyperconjugative effects on carbon-carbon bond lengths [13], and on conjugated hydrocarbons [14] with special emphasis on vibrational frequencies [15]. For applications of MM2 and MM3 in inorganic systems, readers are referred to the literature [16-19]. 

A key biochemical reaction of ammo acids is their conversion to peptides polypeptides and proteins In all these substances ammo acids are linked together by amide bonds The amide bond between the ammo group of one ammo acid and the carboxyl of another IS called a peptide bond Alanylglycme is a representative dipeptide... 

Although the natural abundance of nitrogen-15 [14390-96-6] leads to lower sensitivity than for carbon-13, this nucleus has attracted considerable interest in the area of polypeptide and protein stmcture deterrnination. Uniform enrichment of is achieved by growing protein synthesi2ing cells in media where is the only nitrogen source. reverse shift correlation via double quantum coherence permits the... 

Proteins. The most abundant and physiologically diverse natural biopolymers are proteins, which make up enzymes, hormones, and stmctural material such as hair, skin, and connective tissue. The monomer units of natural proteins, a-amino acids, condense to form dipeptides, tripeptides, polypeptides, and proteins. 

The amide linkage between monomer units in a protein is called a peptide bond. Peptides and polypeptides, which often exhibit biological activity (see Antibiotics, peptides Neuroregulators), are smaller than proteins. Although the differentiation between polypeptide and protein is somewhat arbitrary, the usual distinction is drawn around 100 monomer units. Proteins are also characterized by higher levels of stmcture resulting from internal interactions. 

M Vasquez, G Nemethy, ElA Scheraga. Conformational energy calculations on polypeptides and proteins. Chem Rev 94 2183-2239, 1994. 

It follows, that the peak width of a solute could give an indication of its molecular weight and, although the data may not be precise, approximate values could be extremely valuable when dealing with very large molecular weight substances such as polypeptides and proteins. In particular, the technique would be very useful for those substances that are extremely difficult, or impossible, to vaporize in the ion source of a mass spectrometer to provide mass data. 

Iteration of the reaction shown in Figure 4.2 produces polypeptides and proteins. The remarkable properties of proteins, which we shall discover and come to appreciate in later chapters, all depend in one way or another on the unique properties and chemical diversity of the 20 common amino acids found in proteins. 

The terms polypeptide and protein are used interchangeably in discussing single polypeptide chains. The term protein broadly defines molecules composed of one or more polypeptide chains. Proteins having only one polypeptide chain are monomeric proteins. Proteins composed of more than one polypeptide chain are multimeric proteins. Multimeric proteins may contain only one kind of polypeptide, in which case they are homomultimeric, or they may be composed of several different kinds of polypeptide chains, in which instance they are heteromultimeric. Greek letters and subscripts are used to denote the polypeptide composition of multimeric proteins. Thus, an ag type protein is a dimer of identical polypeptide subunits, or a homodimer. Hemoglobin (Table 5.1) consists of four polypeptides of two different kinds it is an hetero-multimer. 

The structures of amino acids incorporated into polypeptides and proteins may be characterized by a pair of dihedral angles involving the so-called a carbon for each amino acid. 

S. Fox, K. Harada, and D. Rohlfmg, Polyamino Acids, Polypeptides and Proteins, (M. Stahman, ed.), U. Wisconsin Press, Maddison, Wisconsin (1952). 

Fig. 7. Scheme of the intermolecular forces stabilizing ordered structures in polypeptides and proteins m... 

Weidner, H., Engel, J., Fietzek, P, Peptides, Polypeptides and Proteins, Part V., John Wiley and Sons, New York 1974... 

Sela, M., Synthetic antigens and recent progi ss in immunology, in Peptides. Polypeptides and Proteins. Proceedings of the Rehovot Symposium on Poly (Amino Acids), Polypeptides and Proteins, John Wiley and sons, New York, 1974, pp. 495-509... 

The way that Pn peptides self-assemble is important for polypeptides and proteins amyloid-type structures are believed to have the same core stmcture, and in fact the propensity to self-assemble in this manner is hypothesized to be a general property of polypeptides [52]. It is therefore unsurprising that systems featuring this motif are common. In recent years, a push towards the use of peptide-based self-assembled materials has led to increasing interest in extending their functionality by derivatising them. 

Thorton JM, Barlow DJ (1991) In Hider RC, Barlow DJ (eds) Polypeptide and protein drags. Ellis Horwood, Chichester, p 9... 

Production of medically important polypeptides and proteins 7 Further reading... 

The promise of the isolation and production of therapeutic polypeptides and proteins demands that for treatment of a chronic disease state an oral delivery system be developed which will protect these valuable agents from the hostile gastric environment. Subsequently, the drugs will have to be completely released in the intestine, preferably in a state that will enhance their rapid dissolution and transport across the gut wall minimizing interaction with intestinal proteases. 

Schaumann T, Braun W, Wilthrich K. The program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. Biopolymers 1990 29 679-694. 

III. Survey of Polypeptide and Protein Raman Optical Activity. 59... 

The application of ROA to studies of unfolded and partially folded proteins has been especially fruitful. As well as providing new information on the structure of disordered polypeptide and protein sequences, ROA has provided new insight into the complexity of order in denatured proteins and the structure and behavior of proteins involved in misfold-ing diseases. All the ROA data shown in this chapter have been measured in our Glasgow laboratory because, at the time of writing, ROA data on typical large biomolecules had not been published by any other group. We hope that this review will encourage more widespread use of ROA in protein science. 

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