Chemical bond peptide

In a recent study of the transferability of moments, it has shown that stable trends are actually observed for the chemical bond features along investigated test peptide chains (Figure 6-4 and Table 6-4). 

Enzyme specificity is often explained in terms of the geometric configuration of the active site of the enzyme. The active site includes the side chains and peptide bonds that either come into direct contact with the substrate or perform some direct function during catalysis. Each site is polyfunctional in that certain parts of it may hold the substrate in a position where the other parts cause changes in the chemical bonding of... 

Yarovsky, L, Aguilar, M.I., and Hearn, M.T.W., High-performance liquid-chromatography of amino-acids, peptides and proteins. 125. Molecular-dynamics simulation of n-butyl chains chemically bonded to sihca-based reversed-phase high-performance liquid-chromatography sorbents, 7. Chromatogr. A, 660, 75, 1994. 

TTie TOCSY 2D NMR experiment correlates all protons of a spin system, not just those directly connected via three chemical bonds. For the protein example, the alpha proton, Ft , and all the other protons are able to transfer magnetization to the beta, gamma, delta, and epsilon protons if they are connected by a continuous chain—that is, the continuous chain of protons in the side chains of the individual amino acids making up the protein. The COSY and TOCSY experiments are used to build so-called spin systems—that is, a list of resonances of the chemical shift of the peptide main chain proton, the alpha proton(s), and all other protons from each aa side chain. Which chemical shifts correspond to which nuclei in the spin system is determined by the conventional correlation spectroscopy connectivities and the fact that different types of protons have characteristic chemical shifts. To connect the different spin systems in a sequential order, the nuclear Overhauser effect spectroscopy... 

The simplest approach to disulfide bond formation of chemically synthesized peptides and proteins involves (i) complete deprotection including that of the cysteine thiol functions, and (ii) mild oxidation of the thiol groups to form the folded product with the native cystine connectivity. With careful attention to experimental conditions, the native-type folding of the peptide can be accomplished however, misfolded disulfide isomers are often produced as the main products in spite of efforts to optimize the reaction conditions. 

Table 2 Selection of Commonly Used Ion-Pairing/Dynamic Liquid-Liquid Ion Exchange/ Mobile-Phase Additive Species, Which at pH <7.0 Modify the Retention Characteristics of Unprotected Peptides on Chemically Bonded Hydrocarbonaceous Stationary Phases3-11...

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

The use of nonpolar chemically bonded stationary phases with a polar mobile phase is referred to as reverse-phase HPLC. This technique separates sample components according to hydrophobicity. It is widely used for the separation of all types of biomolecules, including peptides, nucleotides, carbohydrates, and derivatives of amino acids. Typical solvent systems are water-methanol, water-acetonitrile, and water-tetrahydrofiiran mixtures. Figure 3.15 shows the results of protein separation on a silica-based reverse-phase column. 

N and 13C labeling of peptides facilitates the study of their molecular dynamics in solution by measurements of relaxation parameters (42,43). Heteronuclear relaxation times and heteronuclear NOEs are predominantly affected by the dipole-dipole interaction of the heteronucleus with the directly attached proton. Since the intemuclear (i.e., chemical bonding) distances are known from the molecular geometry, correlation times for overall and internal motions can be determined. 

The operating principle of such devices relies on materials whose volume changes abruptly, i.e., that display a volume phase transition (VPT), when an appropriate stimulus is applied. Thermosensitive poly(N-isopropylacrylamide) (PNIPA) hydrogel, where the cross-links are chemical, namely peptide bonds, is widely used for this purpose since its VPT in pure water is close to 34°C.1 3... 

Amino acids The basic units that join together to make proteins. They contain functional groups amines (-NH2) and carboxylic acids (-COOH), hence their name. The chemical bonds formed between amino acids when joining together to form proteins are called peptide links. 

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