Covalent structures proteins

In Section 18-6.3 the composition of proteins was given. They are large, amide-linked polymers of amino acids. However, the long chain formula (Figure 18-14, p. 348) does not represent all that is known about the structure of proteins. It shows the covalent structure properly but does not indicate the relative positions of the atoms in space. 

Important products derived from amino acids include heme, purines, pyrimidines, hormones, neurotransmitters, and biologically active peptides. In addition, many proteins contain amino acids that have been modified for a specific function such as binding calcium or as intermediates that serve to stabilize proteins—generally structural proteins—by subsequent covalent cross-hnk-ing. The amino acid residues in those proteins serve as precursors for these modified residues. Small peptides or peptide-like molecules not synthesized on ribosomes fulfill specific functions in cells. Histamine plays a central role in many allergic reactions. Neurotransmitters derived from amino acids include y-aminobutyrate, 5-hydroxytryptamine (serotonin), dopamine, norepinephrine, and epinephrine. Many drugs used to treat neurologic and psychiatric conditions affect the metabolism of these neurotransmitters. 

Model analogs of the green type chromophore HBI have been chemically synthe-tized in different forms carrying blocking groups in place of the protein polypeptide chain [21, 24, 68, 69]. However, the covalent structure of HBI does not uniquely define its optical properties, because the molecule undergoes several protonation and conformational equilibria that directly affect its electronic structure. 

The presence of chemically reactive structural features in potential drug candidates, especially when caused by metabolism, has been linked to idiosyncratic toxicity [56,57] although in most cases this is hard to prove unambiguously, and there is no evidence that idiosyncratic toxicity is correlated with specific physical properties per se. The best strategy for the medicinal chemist is avoidance of the liabilities associated with inherently chemically reactive or metabolically activated functional groups [58]. For reactive metabolites, protein covalent-binding screens [59] and genetic toxicity tests (Ames) of putative metabolites, for example, embedded anilines, can be employed in risky chemical series. 

Hydrogen-bonding interactions are considerably weaker than ionic interactions and covalent bonds but have a profound effect on many chemical and physical properties [221] and determine the shapes of large molecules such as proteins and nucleic acids. Protein secondary structure is determined by H bonding between the carbonyl oxygen of one amide unit and the N—H bond of another. The two strands of the double helix of... 

As in the case of protein structure (Chapter 4), it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity (primary, secondary, tertiary). The primary structure of a nucleic acid is its covalent structure and nucleotide sequence. Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid can be referred to as secondary structure. All structures considered in the remainder of this chapter fall under the heading of secondary structure. The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure this is discussed in Chapter 24. 

The covalent structure of insulin was established by Frederick Sanger in 1953 after a 10-year effort. This was the first protein sequence determination.237 238 Sanger used partial hydrolysis of peptide chains whose amino groups had been labeled by reaction with 2,4-dinitrofluorobenzene239 to form shorter end-labeled fragments. These were analyzed for their amino acid composition and labeled and hydrolyzed again as necessary. Many peptides had to be analyzed to deduce the sequence of the 21-residue and 30-residue chains that are joined by disulfide linkages in insulin.237 238... 

Figure 31-4 Schematic structure of one-fifth of an IgM molecule. From Putnam et al A (A) Covalent structure. (B) Schematic three-dimensional representation. (C) Ribbon diagram of an IgG molecule. From Cochran et al,64a (D) Folding patterns of one chain in a constant and a variable domain of a Bence-Jones protein. From Schiffer et al.66 Green arrows indicate hypervariable regions. (E) MolScript drawing of the common core structure of Ig-like domains. The lighter shaded strands (b, c, e, f) form the core common to all Ig-like domains, which is surrounded by structurally more varied additional strands (darker). The front sheet has up to five strands (a, f, c, e, c") and the back sheet up to four (a, b, e, d). Strand c" is very flexible and is not always a part of the (3 sheet. From Bork, Holm, and Sander.65 See also Fig. 2-16.

The assays referred to in the right-hand columns employed RN A as a substrate unless otherwise indicated. These data cannot be used to provide accurate S-protein S-peptide derivative binding constants (see reference 234), but they do give a qualitative picture of the effect on binding and activity of the indicated changes in covalent structure. The peptides are indicated by the horizontal lines with reference to the sequence at the top. Only altered residues are specifically indicated. 

These correspond to the S Is — M d7t(e) and Sis > M d<7(t2) transitions split in energy by 10Dq (in the d6 final state). The resolved intensities provide the n and cr covalencies (i.e., thiolate S character) in the d-orbitals of this site. In a comparison of the S K-edge data for the iron-sulfur model complexes of Holm and collaborators58 to the proteins with structurally congruent sites, the intensity is generally decreased... 

For conformational energy calculations on structures involving loops (e.g. the loop of gramicidin-S involving only N—C , C —C and peptide bonds, or the loops in proteins involving closure by the S—S bonds of cystine), it is necessary to assure that the loop will close properly to satisfy all the requirements (proper bond distances, bond angles, etc.) of the covalent structure. For this purpose, an empirical loop-closing potential is required. 

Although most of the focus on solute effects on macromolecular systems has involved proteins, there is evidence that some of the patterns of solute accumulation reflect the dangers that high salt concentrations pose for the covalent structure of DNA. Using cultured mammalian kidney cells Kiiltz and Chakravarty (2001) showed that hyperosmotic stress could cause double strand breaks (dsb) in DNA. Hyperosmolality due to elevated [NaCl] in the culture medium caused the most dsb. Potassium chloride and mannitol led to less damage and, interestingly, no damage to DNA was found in cells exposed to elevated levels of urea. 

MALDI has also been successfully used to study a number of intact non-covalent complexes such as protein quaternary structures [132-135]. However, MALDI has not yet contributed widely to the study of these complexes because it requires the crystallization of the sample with the matrix. Furthermore, the energy deposited to desorb the ions is not clearly known. In consequence, MALDI generally induces dissociation of the non-covalent interactions and leads to the formation of non-specific aggregates. Nevertheless, weak non-covalent interactions can survive during the MALDI process to allow the direct detection of intact complexes if specific methods, which have been developed to preserve these interactions, are followed [136],... 

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