Halic acids, HOXO

Structure of Wool Proteins. The stmcture of wool proteins has been the subject of much research. Methods to solubilize, separate, and determine the amino acid sequence of these proteins have been reviewed (38—40). The proteins of wool basically belong to three groups low sulfur proteins, rich in amino acids that contribute to a-helix formation (glutamic acid, aspartic acid, leucine, lysine, arginine) high sulfur proteins rich in cystine, proline, serine, and threonine and high glycine—tyrosine proteins which are also rich in serine. The groups of proteins that constitute wool are not uniformly distributed throughout the fiber, but are aggregated within the various morphological regions.  [c.343]

Of specific interest are the unfolding simulation studies that highlight the role of the solvent in the folding and unfolding process, an insight that is very difficult to obtain experimentally. For example, simulations of the early stages of barnase unfolding at high temperamre [47] showed that solvent plays a key role in the denaturation process. It was found that an important element of the helix-unfolding transition is the replacement of an a-helical hydrogen bond (i to i + 4, where i is an amino acid residue) by water hydrogen bonds through an intermediate involving a 3io (i to i + 3), or reverse turn, hydrogen bond. Denaturation of a [3-sheet was also observed to start by the distortion of the [3-sheet hydrogen bonds, followed by the insertion of hydrogen-bonding water molecules between the strands. Finally, significant solvent participation was found even in the denaturation of the central stabilizing element of globular proteins—the hydrophobic core. This happens as some water molecules form cage structures around hydrophobic groups, often involving hydrogen bonds to water molecules outside the core. There are, however, concerns as to whether the observed water behavior corresponds to the actual denaturation process. The reason is that high temperature unfolding simulations are done either with a room temperature water density [47] or with low water density followed by rapid water penetration when the temperature is set equal to room temperature [48,49]. These procedures create an artificially high pressure, which may force water into protein cavities. Nonetheless, comparisons of unfolding simulations results at different temperatures seem to indicate that this effect is not very great [17].  [c.383]

The comparison of sequence-specific contacts shown in Figure 10.5 reveals that there is no specific correspondence between an amino acid residue in one of the four critical positions of the a helix and the hase that it contacts. Although contiguous zinc fingers contact contiguous sets of hase pairs, there is no simple rule that governs which bases the fingers contact. Furthermore, the number of bases in each set varies from three to five, and sometimes the sets of bases are strictly contiguous while in other cases they overlap or are spaced by one base pair that is not in contact with any finger. In addition, contacts are made in a seemingly random fashion to bases of both DNA strands. It is therefore not possible at present to predict from the amino acid sequence of a zinc finger the DNA sequence to which it will bind, or vice versa. However, one sequence-specific interaction occurs more  [c.180]

These hydrophobicity scales are frequently used to identify those segments of the amino acid sequence of a protein that have hydrophobic properties consistent with a transmemhrane helix. For each position in the sequence, a hydropathy index is calculated. The hydropathy index is the mean value of the hydrophobicity of the amino acids within a "window," usually 19 residues long, around each position. In transmemhrane helices the hydropathy index is high for a number of consecutive positions in the sequence. Charged amino acids are usually absent in the middle region of transmembrane helices because it would cost too much energy to have a charged residue in the hydrophobic lipid environment. It might be possible, however, to have two residues of opposite charge close together inside the lipid membrane because they neutralize each other. Such charge neutralization has been observed in the hydrophobic interior of soluble globular proteins.  [c.245]

Polymer molecules that have a high degree of regularity in their monomer sequence tend to assume helical rather than globular conformations, and fibers are formed when these helices become aligned with each other. This is well illustrated by the proteins keratin and collagen and by the nucleic acid, DNA. The regularity in the DNA double-helix is so high that fibers drawn from a concentrated DNA gel are highly ordered the long, thread-like DNA molecules extend parallel to the length of the fiber with a high degree of regularity in their side-by-side packing extending over many molecules. These regularly packed molecules form structures know as crystallites, and a typical fiber of 100 microns diameter contains a large number of such crystallites separated by less ordered regions where the molecules, while still largely parallel to the fiber length, are much less regularly packed. Because the crystallites are in random orientation about the direction of the fiber length, a diffraction pattern recorded from the fiber is similar to the pattern obtained when a single crystal is rotated 360° about the vertical axis while the data is being recorded. Therefore the diffraction pattern from a crystalline fiber can be analyzed using standard crystallographic techniques. The power of crystalline fiber diffraction analysis is illustrated by the detailed stereochemical information on the A and B conformations of DNA, reviewed in Chapter 7.  [c.384]

Curdlan is insoluble in water, but does absorb some water to become swollen. It can be dissolved in alkaline solutions, formic acid (see Formic acid AND derivatives), and certain organic solvents such as dimethyl sulfoxide (322). Suspensions of curdlan heated above 54°C form a firm gel. A closely related polysaccharide, pachyman, which has a P(1 — 3)-D-glucan main chain and a small number of P(1 — 6)-1inked D-glucose branches, does not form gels when heated, even at higher concentrations. The lack of side groups in curdlan apparently allows the polymer to form aggregates that are insoluble and to form gels at moderately warm temperatures. Curdlan forms a low set gel when heated to 55°C and allowed to cool (324) high set gels obtained by heating curdlan suspensions at higher temperatures have melting temperatures of 140—160°C (325). According to conformational studies, the soHd and low set gelled polymer is a single-stranded helix (326) whereas the high set gelled polymer is a triple-stranded helix (322,327,328) with strands from several heflces intertwining to form three-dimensional networks.  [c.301]

The structure of this fragment, which like the high pH fragment is a trimer, confirms that the HA2 subunit undergoes major structural changes at low pH. Most of the secondary structure elements are essentially preserved but there are two important exceptions (Figure 5.26). First, the loop region B between the two long a helices A and C + D in the high pH structure changes into an a helix. Second, an a-helical region in the middle of helix C + D changes into a loop region (Figure 5.26). The resulting helix A -t- B + C comprises 65 residues and is about 100 A long. Previous examination of the amino acid sequence of this whole region, residues 40-106, had shown a very dear heptad repeat typical of coiled-coil structures (see Chapter 3). It was therefore surprising that in the high pH structure only a part of this region, helix C, actually has a coiled-coil structure. Reassuringly, in the low pH structure the whole region is a coiled coil which is involved in trimerization (Figure 5.25).  [c.82]

The crystal structure of the b/HLH domain of one myogenic protein, MyoD, complexed with a DNA fragment containing the consensus recognition sequence has been determined by the group of Carl Pabo at Massachusetts Institute of Technology, Boston. The DNA fragment, having two symmetric binding sites, binds to one dimer of the b/HLH domain. Each monomer of the protein has a very simple structure comprising two a helices joined by a loop region (Figure 10.24). The first a helix contains the basic region followed by the HI region the second helix, joined to the first by a loop, contains the H2 region of the HLH motif. The helical HI and H2 regions of each monomer are involved in the dimer interface and participate in forming the four-helix bundle of the dimer (Figure 10.25). Conserved hydrophobic residues in both HI and H2 form the hydrophobic core of the four-helix bundle. This core stabilizes the dimer and keeps the monomers together with the precise geometry that allows the two basic regions to interact properly with the two recognition sites of the DNA fragment, which are separated by two base pairs. These rather stringent stereochemical requirements impose constraints on the amino acid sequence of the HLH motif this is reflected in the high degree of sequence homology that allows new proteins to be identified from their sequences as members of this family.  [c.197]

Today s predictive methods rely on prediction of secondary structure in other words, which amino acid residues are a-helical and which are in p strands. We have emphasized in Chapter 12 that secondary structure cannot in general be predicted with a high degree of confidence with the possible exceptions of transmembrane helices and a-helical coiled coils. This imposes a basic limitation on the prediction of tertiary stmcture. Once the correct secondary stmcture is known, we know enough about the rules for packing elements of secondary structure against each other (see Chapter 2 for helix packing) to derive a very limited number of possible stable globular folds. Consequently, secondary structure prediction lies at the heart of the prediction of tertiary stmcture from the amino acid sequence.  [c.350]

Until recent years the only syntheses of 3-hydroxy quinoline involved multistep processes, the last step of which consisted of the conversion of 3-aminoquinoline to 3-hydroxyquinoline via the diazonium salt. " Small quantities of quinoline have been oxidized to 3-hydroxyquinoline in low yields by using oxygen in the presence of ascorbic acid, ethylenediaminetetraacetic acid, ferrous sulfate, and i)hosi)halc buffer. The decarboxylation of 3-hydroxycinchoninic, acid in boiling nitrobenzene has been re-  [c.59]

See pages that mention the term Halic acids, HOXO : [c.107]    [c.293]    [c.543]    [c.198]    [c.387]   
Chemistry of the elements (1998) -- [ c.2 , c.862 ]