Peptides small

Conformational Properties of the Commonly Occurring Amino Acids 

Properties of Some Conformationally Constrained Amino Acids 

A large number of amino acid and dipeptide derivatives with built-in conformational constraints have been synthesized and incorporated into biologically active peptides (reviewed in Hruby, 1982). In this review we shall consider only those modifications that appear to be generally applicable and for which the amino acids are either commercially available or can be prepared relatively easily. 

Another change that is commonly made in peptides is the reversal of the chirality of one or more amino acid residues (reviewed in Rose et al., 1985). This is a particularly popular modification, because protected d-amino acids are commercially available, and the resulting analogs, if active, would have enhanced stabilities to enzymatic degradation. The chirality of the amino acids in the central two positions (/ + 1 and i + 2) of a turn have a profound effect on the type of turn that is formed. If the central two residues are both of the l configuration, a type I turn is often formed. If the residue at position + 1 is l and that at position i + 2 is d (an l, d pair) then a type II turn is stabilized, while a d, l pair at the central position will stabilize a type II turn (Rose et al., 1985). For this reason, type II turns are often referred to as l, d turns and type II turns as d, l turns. 

Yet another substitution that restricts the conformational freedom of amino acids is the introduction of a double bond at the Ca and atoms. In addition to the obvious effect that a, /3-unsaturation has on the side-chain mobility, this modification also affects the conformation of the backbone. The effects of Ca-Cp unsaturation have been explored experi- 

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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... 

The major disadvantage of solid-phase peptide synthesis is the fact that ail the by-products attached to the resin can only be removed at the final stages of synthesis. Another problem is the relatively low local concentration of peptide which can be obtained on the polymer, and this limits the turnover of all other educts. Preparation of large quantities (> 1 g) is therefore difficult. Thirdly, the racemization-safe methods for acid activation, e.g. with azides, are too mild (= slow) for solid-phase synthesis. For these reasons the convenient Menifield procedures are quite generally used for syntheses of small peptides, whereas for larger polypeptides many research groups adhere to classic solution methods and purification after each condensation step (F.M. Finn, 1976). 

Dowex 1-X2 0.6 0.65 Strongly basic anion exchanger with S-DVB matrix for separation of small peptides, nucleotides, and large metal complexes. Molecular weight exclusion is <2700. 

General trends in radiopharmaceutical research emphasize the use of small peptides. These molecules, of which the agents mentioned for thrombosis localization are an example, exhibit rapid and specific binding, and rapid blood clearance, two important parameters for a successflil radiopharmaceutical. Peptides are readily labeled with Tc and lend themselves to formulation as lyophilized kits that can be rapidly and rehably reconstituted. Possible targets for these molecules are quite varied, ranging from atherosclerotic plaque to P-amyloid (for Alzheimer s disease), to a variety of somatic receptors the populations of which are increased or decreased in disease. 

One important class of integral equation theories is based on the reference interaction site model (RISM) proposed by Chandler [77]. These RISM theories have been used to smdy the confonnation of small peptides in liquid water [78-80]. However, the approach is not appropriate for large molecular solutes such as proteins and nucleic acids. Because RISM is based on a reduction to site-site, solute-solvent radially symmetrical distribution functions, there is a loss of infonnation about the tliree-dimensional spatial organization of the solvent density around a macromolecular solute of irregular shape. To circumvent this limitation, extensions of RISM-like theories for tliree-dimensional space (3d-RISM) have been proposed [81,82],... 

The basic chemical description of rare events can be written in terms of a set of phenomenological equations of motion for the time dependence of the populations of the reactant and product species [6-9]. Suppose that we are interested in the dynamics of a conformational rearrangement in a small peptide. The concentration of reactant states at time t is N-n(t), and the concentration of product states is N-pU). We assume that we can define the reactants and products as distinct macrostates that are separated by a transition state dividing surface. The transition state surface is typically the location of a significant energy barrier (see Fig. 1). 

Inhibitors as well as substrates bind in this crevice between the domains. From the numerous studies of different inhibitors bound to serine pro-teinases we have chosen as an illustration the binding of a small peptide inhibitor, Ac-Pro-Ala-Pro-Tyr-COOH to a bacterial chymotrypsin (Figure 11.9). The enzyme-peptide complex was formed by adding a large excess of the substrate Ac-Pro-Ala-Pro-Tyr-CO-NHz to crystals of the enzyme. The enzyme molecules within the crystals catalyze cleavage of the terminal amide group to produce the products Ac-Pro-Ala-Pro-Tyr-COOH and NHs. The ammonium ions diffuse away, but the peptide product remains bound as an inhibitor to the active site of the enzyme. 

Wrighton, N.C., et al. Small peptides as potent mimetics of the protein hormone erythropoietin. Science 273 458-463, 1996. 

The situation is different for other examples—for example, the peptide hormone glucagon and a small peptide, metallothionein, which binds seven cadmium or zinc atoms. Here large discrepancies were found between the structures determined by x-ray diffraction and NMR methods. The differences in the case of glucagon can be attributed to genuine conformational variability under different experimental conditions, whereas the disagreement in the metallothionein case was later shown to be due to an incorrectly determined x-ray structure. A re-examination of the x-ray data of metallothionein gave a structure very similar to that determined by NMR. 

Small peptides may be difficult to chromatograph by aqueous GFC due to complex nonsize effects such as ionic and hydrophobic interactions. Elution... 

Small peptides are among the most difficult compounds to analyze by aqueous SEC, although conditions for good separations have been developed for both TSK-GEL SW and TSK-GEL PW column types (15,16). Pigure 4.27 (page 124) compares the results of separating two mixtures of peptides on... 

The neutral hydrophilic surface and the wide range of pore diameters available for SynChropak GPC allow many compounds from small peptides to nucleic acids and other polymers to be analyzed. Table 10.2 lists the approximate exclusion limits for both linear and globular solutes. Although this information... 

For proteins, the most useful columns are those with pores of 100-500 A, as seen in Fig. 10.2, because most proteins elute on the linear portions of the calibration curves. Figure 10.5 illustrates an analysis of a protein mixture on SynChropak GPC100. Small peptides can be analyzed on the 50-A SynChro-pak GPC Peptide column with appropriate mobile-phase modifications. Many peptides have poor solubility in mobile phases standardly used for protein analysis, as discussed later in this chapter. 

Mabbott, G., 1990. Qualitative amino acid analysis of small peptides by GC/ S. Journal of Chemical Education 67 441—445. 

FIGURE 5.2 The peptide bond is shown in its usnal trans conformation of carbonyl O and amide H. The atoms are the oi-carbons of two adjacent amino acids joined in peptide linkage. The dimensions and angles are the average valnes observed by crystallographic analysis of amino acids and small peptides. The peptide bond is the light gray bond between C and N. (Adapted from Ramachandran, G. A., ct ai, 1974. Biochimica Biophysica Acta 359 298-302.)... 

Profens Small peptides N-bloeked amino aeids... 

For most free amino acids and small peptides, a mixture of alcohol with water is a typical mobile phase composition in the reversed-phase mode for glycopeptide CSPs. For some bifunctional amino acids and most other compounds, however, aqueous buffer is usually necessary to enhance resolution. The types of buffers dictate the retention, efficiency and - to a lesser effect - selectivity of analytes. Tri-ethylammonium acetate and ammonium nitrate are the most effective buffer systems, while sodium citrate is also effective for the separation of profens on vancomycin CSP, and ammonium acetate is the most appropriate for LC/MS applications. 

Human brain natriuretic peptide (BNP) is a small peptide of 32 amino acids used in the treatment of congestive heat failure. How many nitrogen bases are present in the DNA that codes for BNP ... 

Heveker, N., Montes, M., Germeroth, L., Amara, A., Trautmann, A., Alizon, M., and Schneider-Mergener, J. (1998). Dissociation of the signalling and antiviral properties of SDF-1-derived small peptides. Current Biology 8 369-376. 

It is notable that small peptides were retained on a cross-linked PEI column [37] but polypeptides over 20 residues were weakly retained or not at all. Possibly, small peptides were able to penetrate into the depth of the bonded phase while larger peptides could not. These packings were more useful for the separation of oligonucleotides, i.e. more acidic compounds. Lawson et al. [39] have shown the applicability of PEI-silicas for assessing the purity of precursor blocks, monitoring the chemical synthesis and isolating reaction products after synthesis. 

Penicillin has an interesting mode of action it prevents the cross-linking of small peptide chains in peptidoglycan, the main cell wall polymer of bacteria. Pre-existing cells are unaffected, but all newly produced cells are abnormally grown. The newborn cells are unable to maintain their wall rigidity, and they are susceptible to osmotic lysis. 

PTB domains recognize small peptides containing a phosphotyrosine, usually with the consensus sequence, NPXpY. Some PTB-containing proteins, such as Numb, are able to bind to the consensus peptide in the absence of phosphorylated tyrosine, suggesting phosphotyrosine is dispensable for the function of certain PTB domains. Hydrophobic residues N-termi-nal to the phosphotyrosine provide some specificity of target and distinction from SH2 domains. PTB domains appear to be particularly important in docking... 

Fibrin is an elastic filamentous protein elaborated from its precursor, fibrinogen, which is present in plasma at high concentration. Fibrin is formed in response to the actions of thrombin. Thrombin cleaves small peptides from the fibrinogen molecule, forming fibrin monomers that will begin to polymerize and become crosslinked. 

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