Peptides molecular structure

The comparison of the amino acid sequence of the above-mentioned bitter peptides shows a large proportion of hydrophobic amino acids in each peptide. And the amino acid sequence of peptides also plays an important role in the intensity of the bitter taste. For example, the bitterness of Phe-Pro is more intense than that of Pro-Phe, and the bitterness of Gly-Phe-Pro is more intense than that of Phe-Pro-Gly (23). C-terminal groups of all bitter peptides in pepsin hydrolysates of the above-mentioned soy protein were characterized by the location of the Leu residue (14-17). The research on the relationship between the structure and bitter taste intensity of Arg-Gly-Pro-Pro-Phe-Ile-Val (BP-Ia) showed that Pro and Arg located on center and the N-terminal site, respectively, played an important role in the increment of bitter taste intensity besides the hydro-phobic amino acids located on C-terminal site (24-26). This may indicate that the peptide molecular structure formed by the arrangement of Arg, Pro and hydrophobic amino acid residues contributes to the bitter taste intensity of the peptide. 

The importance of linked scanning of metastable ions or of ions formed by induced decomposition is discussed in this chapter and in Chapter 34. Briefly, linked scanning provides information on which ions give which others in a normal mass spectrum. With this sort of information, it becomes possible to examine a complex mixture of substances without prior separation of its components. It is possible to look highly specifically for trace components in mixtures under circumstances in which other techniques could not succeed. Finally, it is possible to gain information on the molecular structures of unknown compounds, as in peptide and protein sequencing (see Chapter 40). 

Most of the 2D QSAR methods are based on graph theoretic indices, which have been extensively studied by Randic [29] and Kier and Hall [30,31]. Although these structural indices represent different aspects of molecular structures, their physicochemical meaning is unclear. Successful applications of these topological indices combined with multiple linear regression (MLR) analysis are summarized in Ref. 31. On the other hand, parameters derived from various experiments through chemometric methods have also been used in the study of peptide QSAR, where partial least square (PLS) [32] analysis has been employed [33]. 

Bella, J., et al. Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution. Science 266 ... 

Now, it is seen that polar groups dominate the molecular structure, resulting from hydroxyl groups from the two serine and threonine fragments in addition to the peptide bonds themselves. Only weak dispersive interactions will be contributed by glycine fragments (CH2 groups). 

Hybrid Molecular Structure with Peptide and Nonpeptide Sequences. 124... 

In terms of their molecular structures, the nucleotide and protein realms are usually considered to be rather independent of each other. However, these two families of molecules are covalently linked in the translational aminoacyl- RNAs and ribonucleoproteins as well as in the nucleoproteins involved in cellular and viral replication. In these hybrid biomolecules, a (deoxy)ribose phosphate moiety serves as the structural connection between the nucleoside and peptide moieties. 

Sweetness is a quality that defies definition, but whose complexity can be appreciated merely by examining the molecular structures of those compounds that elicit the sensation. They come in all molecular shapes and sizes, and they belong to such seemingly unrelated classes of compounds as aliphatic and aromatic organic compounds, amino acids, peptides and proteins, carbohydrates, complex glycosides, and even certain inorganic salts. 

The N-terminal peptide fragment of des-angiotensinogen Val-Ile-His-Asn contains two strongly hydrophobic amino acid residues on the N-terminal site of His-3. The potentiometric data have shown that the NiH.2L complex with this albumin-like sequence is more than two orders of magnitude more stable than the respective complex with Gly-Gly-His.1744 The NMR-based molecular structure has shown that the side chains of Val-1 and lie-2 form a well-ordered hydrophobic fence (Figure 21) shielding one side of the coordination plane from the bulk of... 

The concept of molecular structure implies a reduction in the freedom of motion for the involved atoms. Thus an indirect strategy for identifying structured segments is to search for restricted motion for contiguous sets of amino acid residues. Relaxation of the 15N nucleus in the peptide bond provides a quantitative measure of the rates and angular range of motion experienced by individual amino acids under equilibrium conditions (Palmer, 2001). 

Schaefer, M., Bartels, C., and Karplus, M. (1998). Solution conformations and thermodynamics of structured peptides Molecular dynamics simulation with an implicit solvation model./. Mol. Biol. 284, 835-848. 

Scarsdale, J. N., C. Van Alsenoy, V. J. Klimkowski, L. Schafer, and F. A. Momany. 1983. Ab Initio Studies of Molecular Geometries. 27. Optimized Molecular Structures and Conformational Analysis of N-Acetyl-N-methylalaninamide and Comparison with Peptide Crystal Data and Empirical Calculations. J. Am. Chem. Soc. 105,3438-3445. 

Schafer, L., C. Van Alsenoy, and J. N. Scarsdale. 1982. Ab Initio Studies of Structural Features Not Easily Amenable to Experiment. 23. Molecular Structures and Conformational Analysis of the Dipeptide N-acetyl-N -methyl Glycyl Amide and the Significance of Local Geometries for Peptide Structures. J. Chem. Phys. 76, 1439-1444. 

Conformation of a System of Three Linked Peptide Units. Biopol. 6, 1425-1436. von Carlowitz, S., H. Oberhammer, H. Willner, and J. E. Boggs. 1986. Structural Determination of a Recalcitrant Molecule (S2F4). J. Mol. Struct. 100,161-177. von Carlowitz, S., W. Zeil, P. Pulay, and J. E. Boggs. 1982. The Molecular Structure, Vibrational Force Field, Spectral Frequencies, and Infrared Intensities of CH3POF2. J. Mol. Struct. (Theochem) 87, 113-124. 

Daniel, H. Function and molecular structure of brush border membrane peptide/H+ symporters. J. Membr. 

Peptide and protein folding. Journal of Molecular Structure Theochem 537, 319-361. 

I Abdelmoty, F Albericio, LA Carpino, BM Foxman, SA Kates. Structural studies of reagents for peptide bond formation crystal and molecular structures of HBTU and HATU. Lett Pept Sci 1, 57, 1994. 

An opposite case is found, for example, in the reduction of Cu(III) complexes with some deprotonated peptides. For example, Figure 9 illustrates the molecular structure of the trideprotonated Cu(II) tetraglycine [Cun(H 3G4)].2 15... 

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