Tetrapeptide

A similar algorithm has been used to sample the equilibrium distribution [p,(r )] in the conformational optimization of a tetrapeptide[5] and atomic clusters at low temperature.[6] It was found that when g > 1 the search of conformational space was greatly enhanced over standard Metropolis Monte Carlo methods. In this form, the velocity distribution can be thought to be Maxwellian. 

A dipeptide is a molecule consisting of two ammo acids joined by a peptide bond A tnpeptide has three ammo acids joined by two peptide bonds a tetrapeptide has four ammo acids and so on Peptides with more than 30-50 ammo acids are polypeptides Proteins are polypeptides that have some biological function... 

There are several levels of pepfide sfrucfure The primary structure is the ammo acid sequence plus any disulfide links With the 20 ammo acids of Table 27 1 as building blocks 20 dipeptides 20 tripeptides 20" tetrapeptides and so on are possible Given a peptide of unknown structure how do we determine its ammo acid sequence" ... 

Ammo acid analysis of a certain tetrapeptide gave alanine... 

Digestion of the tetrapeptide of Problem 27 13 with chy motrypsin gave a dipeptide that on ammo acid analysis gave phenylalanine and valine in equimolar amounts What ammo acid sequences are possible for the tetrapeptide ... 

The sequences of the four tetrapeptides shown m red m Figure 27 10 bridge the gaps between three of the four blue peptides to give an unbroken sequence from 1 through 24... 

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

The sequence of each different peptide or protein is important for understanding the activity of peptides and proteins and for enabling their independent synthesis, since the natural ones may be difficult to obtain in small quantities. To obtain the sequence, the numbers of each type of amino acid are determined by breaking down the protein into its individual amino acids using concentrated acid (hydrolysis). For example, hydrolysis of the tetrapeptide shown in Figure 45.3 would give one unit of glycine, two units of alanine, and one unit of phenylalanine. Of course, information as to which amino acid was linked to which others is lost. 

H-Tyr-D-Ala-Pile-Asp-Val-Val-Gly-NH2 (D-Ala -deltorpliiu I) and H-Tyr-D-Ala-Plie-Glu-Val-Val-Gly-NH2 (D-Ala -deltorpliiu II) display greater 5-selectivity than DPDPE owiag to their higher 5-receptor affinity (96). These compounds both contain the same N-terminal tripeptide sequence as the. -selective dermorphins, which underscores the importance of the C-terminal tetrapeptide sequence in conferring 5-selectivity. 

Several methods are being studied to enhance the stabiUty of peptide mimics and improve their stereochemical similarity to the endogenous peptides. For example, the tetrapeptide Cys—Val—Phe—Met, a potent inhibitor of Ras famesyltransferase, is proposed to exist in a turned conformation, which mimics the endogenous peptide during enzyme binding. This conformation is successhiUy mimicked by 3-amino-l-carboxymethyl-5-phenyl-benzodiazepin-2-onederivatives (198) (142). 

Czerminski and Elber [64], who generated an almost complete map of the minima and barriers of an alanine tetrapeptide in vacuum. Using the master equation approach they were able to smdy aspects of this system s kinetics, which involve the crossing of barriers of different heights. 

Caution The order of elution of solutes smaller than a tetrapeptide may be in order of decreasing polarity rather than decreasing molecular weight. This reflects the relative size of their spheres of hydration. 

Peptide is the name assigned to short polymers of amino acids. Peptides are classified by the number of amino acid units in the chain. Each unit is called an amino acid residue, the word residue denoting what is left after the release of HgO when an amino acid forms a peptide link upon joining the peptide chain. Dipeptides have two amino acid residues, tripeptides have three, tetrapeptides four, and so on. After about 12 residues, this terminology becomes cumbersome, so peptide chains of more than 12 and less than about 20 amino acid residues are usually referred to as oligopeptides, and, when the chain exceeds several dozen amino acids in length, the term polypeptide is used. The distinctions in this terminology are not precise. 

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