Polypeptide chain fragmentation

Rather more sound seem to be numerous attempts to analyze the hydrophobic character of proteins and polypeptide chain fragments on the basis of the aforementioned quantitative estimates of the relative hydrophobicity of the amino acids side chains obtained by the experimental methods considered above 41 54,71,80,81). It should be noted that many of these estimates seem to be questionable due to the above drawbacks of the methods based on the study of transfer of a solute from water into... 

Polypeptide chain fragment from protein tetrabrachion (Staphylothermus marinus) a-Helix/coiled coil Cisplatin Eriksson et al. (2009), Stetefeld et al. (2000)... 

A polymer is a macromolecule that is constructed by chemically linking together a sequent of molecular fragments. In simple synthetic polymers such as polyethylene or polystyrer all of the molecular fragments comprise the same basic unit (or monomer). Other poly me contain mixtures of monomers. Proteins, for example, are polypeptide chains in which eac unit is one of the twenty amino acids. Cross-linking between different chains gives rise to j-further variations in the constitution and structure of a polymer. All of these features me affect the overall properties of the molecule, sometimes in a dramatic way. Moreover, or... 

Superficially, the lambda repressor protein is very different from lambda Cro. The polypeptide chain is much larger, 236 amino acids, and is composed of two domains that can be released as separate fragments by mild proteolysis. In repressor the domain responsible for dimerization is separate from the... 

C-terminal tail (Tyr 527 in c-Src). Phosphorylation of Tyr 419 activates the kinase phosphorylation of Tyr 527 inhibits it. Crystal structures of a fragment containing the last four domains of two members of this family were reported simultaneously in 1997—cellular Src by the group of Stephen Harrison and Hck by the group of John Kuriyan. The two structures are very similar, as expected since the 440 residue polypeptide chains have 60% sequence identity. The crucial C-proximal tyrosine that inhibits the activity of the kinases was phosphorylated in both cases the activation loop was not. 

Each polypeptide chain is cleaved into smaller fragments, and the amino acid composition and sequence of each fragment are determined. 

The fragmentation of Ca -ATPase by proteolytic enzymes [42,85,235,236] and by vanadate-catalyzed photocleavage [104,105] occurs at well defined and conforma-tionally sensitive cleavage sites that delineate functional domains within the Ca -ATPase. The functional changes that follow the cleavage of the polypeptide chain provide useful hints about the role of various domains in the mechanism of Ca transport. 

Soltes, L., Sebille, B. (1997). Reversible binding interactions between the tryptophan enantiomers and albumins of different animal species as determined by novel high performance liquid chromatographic methods an attempt to localize the d- and L-tryptophan binding sites on the human serum albumin polypeptide chain by using protein fragments. Chirality 9, 373-379. 

Edelman, G.M., Gall, W.E., Waxdal, M.J., and Konigsberg, W.H. (1968) The covalent structure of a human gG-immunoglobulin. I. Isolation and characterization of the whole molecules, the polypeptide chains, and the tryptic fragments. Biochemistry 7, 1950-1958. 

Figure 2.3 Fragment of polypeptide chain backbone illustrating rigid peptide bonds and the intervening N—Ca and Ca—C backbone linkages, which are free to rotate...

Figure 12.5 Proteolytic cleavage of prothrombin by factor Xa, yielding active thrombin. Although prothrombin is a single-chain glycoprotein, thrombin consists of two polypeptides linked by what was originally the prothrombin intrachain disulfide bond. The smaller thrombin polypeptide fragment consists of 49 amino acid residues, and the large polypeptide chain contains 259 amino acids. The N-terminal fragment released from prothrombin contains 274 amino acid residues. Activation of prothrombin by Xa does not occur in free solution, but at the site of vascular damage...

Most HPLC instruments monitor sample elution via ultraviolet (UV) light absorption, so the technique is most useful for molecules that absorb UV. Pure amino acids generally do not absorb UV therefore, they normally must be chemically derivatized (structurally altered) before HPLC analysis is possible. The need to derivatize increases the complexity of the methods. Examples of derivatizing agents include o-phthaldehyde, dansyl chloride, and phenylisothiocyanate. Peptides, proteins, amino acids cleaved from polypeptide chains, nucleotides, and nucleic acid fragments all absorb UV, so derivatization is not required for these molecules. 

E. Haas, G. T. Montelione, C. A. McWherter, and H. A. Scheraga, Local structure in a tryptic fragment of performic acid oxidized ribonuclease A corresponding to a proposed polypeptide chain-folding initiation site detected by tyrosine fluorescence lifetime and proton magnetic resonance measurements, Biochemistry 26, 1672-1683 (1987). 

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