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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The role and relative contributions of different forms of energy to the synthesis of amino acids and other organic compounds on the primitive earth, in the parent bodies or carbonaceous chondrites, and in the solar nebula are examined. A single source of energy or a single process would not account for all the organic compounds synthesized in the solar system. Electric discharges appear to produce amino acids more efficiently than other sources of energy and the composition of the synthesized amino acids is qualitatively similar to those found in the Murchison meteorite. Ultraviolet light is also likely to have played a major role in prebiotic synthesis. Although the energy in the sun's spectrum that can be absorbed by the major constituents of the primitive atmosphere is not large, reactive trace components such as H2S and formaldehyde absorb at longer wavelengths where greater amounts of energy are available and produce amino acids by reactions involving hot hydrogen atoms. The thermal reaction of CO + H2 + NH3 on Fischer-Tropsch catalysts generates intermediates that lead to amino acids and other organic compounds that have been found in meteorites. However, this synthesis appears to be less efficient than electric discharges and to require a special set of reaction conditions. It should be emphasized that after the reactive organic intermediates are generated by the above processes, the subsequent reactions which produce the more complete biochemical compounds are low temperature homogenous reactions occurring in an aqueous environment.
J Mol Evol 1976 Dec 31
PMID:Origin of organic compounds on the primitive earth and in meteorites. 101 32

Sterically permissible hydrogen bonds between side chains and the backbone, which fix a small number of angles of internal rotation have been identified. The hydrogen bonds on the ends and within the secondary structures, as well as the most important bonds in the alpha helix and in irregular structures, have been considered.
Mol Biol (Mosk)
PMID:Stereochemical analysis of the secondary structure of polypeptide chains with the aid of Courtauld three-dimensional models. II. Hydrogen and hydrophobic bonds. 102 51

1. The effects of oral hydrochloric acid, ammonium chloride, sodium bicarbonate and ammonium bicarbonate on urea and ammonium excretion in rats on a constant diet were studied. 2. Hydrochloric acid acidosis significantly reduced urea excretion in the rat, with an equimolar increase in NH+4 excretion and no change in their sum. In ammonium chloride acidosis, most of the additional nitrogen intake is excreted as NH+4 and a small percentage as urea. The converse holds true after administration of ammonium bicarbonate. The physiological significance of this is discussed. 3. The shift in nitrogen excretion from urea to NH+4 in acidosis is interpreted on the basis of bicarbonate production and utilization. Urea formation utilizes HCO-3. For amino acid sources, this utilization is offset by the metabolism of the carbon skeleton, which gives rise to HCO-3. When waste nitrogen is excreted as NH+4, no bicarbonate is utilized and the new HCO-3, generated by the carbon skeleton, hels to maintain hydrogen ion homeostasis.
Clin Sci Mol Med Suppl 1975 Jun
PMID:Adaptations in urea ammonium excretion in metabolic acidosis in the rat: a reinterpretation. 105 82

The stability of helical structures formed by polyuridylic acid with nucleosides and nucleotides derived from adenosine is not significantly affected by replacing hydroxyl groups by hydrogen, amino, or azido functions. Stability is affected by the position of the phosphate group.
J Mol Evol 1976 Jun 23
PMID:Triple helices formed by polyuridylic acid with some amino deoxyadenosine derivatives. 108 30

A description is provided for the effects of various concentrations of NaCl, MgC12, and urea on the precipitation of native and denatured DNA by histones. The solubility of complexes between total histones and fractions F1, F2a, F2b, and F3 with denatured and partially denatured DNA was greater than that of the complexes between histones and native DNA. The complexes formed between histones and denatured DNA were soluble in excess histones, unlike those formed between histones and native DNA. Electrophoresis of the individual histone fractions through a polyacrylamide gel layer containing DNA led to the determination of the amount of histones bound to native and denatured DNA under conditions of saturation (0.04 ionic strength). It was established that 1 mug of native DNA binds 2.4, 2.8, and 2.5 mug of histones F1, F2a, F2b and F3, respectively. The denatured DNA binds 1.4-1.5 times less of each histone fraction than does native DNA, but the binding seems stronger. It has been demonstrated that the histones inhibit to a lesser extent the template activity of denatured and partially denatured (about 5% disruption of hydrogen bonds) DNA in comparison with native DNA in an RNA polymerase system. It has been suggested that the properties of the complexes formed between histones and denatured or partially denatured DNA, may underlie the control mechanism for genome activity in the cells of higher organisms.
Mol Biol 1975 Jan
PMID:The interaction of histones with native and denatured DNA. 112 1

The structure of octylcarbamoyl-alpha-chymotrypsin to a resolution of 3.0 A is described. The n-octyl side chain of the active site directed irreversible inactivator octyl isocyanate is bound exclusively in the hydrophobic substrate binding pocket. The n-octyl isocyanate forms a planar urethane bond with the Ser-195 Ogamma and extends approximately 1 A deeper into the hydrophobic pocket than the indolyl group of indoleacryloyl-alpha-chymotrypsin (Henderson, R. (1970), J. Mol. Biol. 54, 341). All the structural changes are essentially identical with those observed in indoleacryloyl-alpha-chymotrypsin including the observation of a hydrogen bonded water molecule between the carbonyl oxygen of the octylcarbamoyl group and the imidazole group of His-57. The observed mode of n-octyl alkyl binding to chymotrypsin is consistent with the hypothesis proposed earlier (Brown, W. E. and Wold, F. (1973), Biochemistry 12, 828).
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PMID:Alkyl isocyanates as active site-specific reagents for serine proteases. Location of alkyl binding site in chymotrypsin by X-ray diffraction. 119 30

Cationic amino acids, arginine and lysine partition differentially from water into aqueous micellar sodium dodecanoate. Conversely, partitioning of serine, glycine, aspartic acid, glutamic acid, threonine, alanine, proline, valine, leucine, phenylalanine and isoleucine do not vary appreciably. Partitioning from neat hexane into dodecylammonium propionate trapped water in hexane is, however, dependent upon both electrostatic and hydrophobic interactions. These results imply that the interior of dedecylammonium propionate aggregates is negatively charged and is capable of hydrogen bonding in addition to providing a hydrophobic enviroment. The solubilities of amino acids in neat hexane substantiate the previously derived amino acid hydrophobicity scale. Relevance of partitioning in these systems to the postulated selective amino acid compartmentalization is discussed.
J Mol Evol 1975 Nov 04
PMID:Compartmentalization of amino acids in surfactant aggregates. Partitioning between water and aqueous micellar sodium deodecanoate and between hexane and dodecylammonium propionate trapped water in hexane. 120 27

The first UV-absorption band hypochromicity of poly(dA)-poly(dT), poly(dG)-poly(dC), poly(dA), poly(dT), poly(dG), poly(dC), is calculated with the help of the perturbation theory. The wave functions of the bases are computed by Pariser--Parr--Pople's method taking into account all the singly excited configurations. The results obtained show a good correlation between the theoretical and experimental values of hypochromicity. A considerable influence of the vaccum electron transitions on the hypochromicity of polynucleotides is revealed. The origin of the hypochromic effect in the double-stranded polynucleotides is investigated. It is shown that intrastrand interactions between the bases make the main contribution to hypochromicity (60-76%), while the contribution of the Watson-Crick pairs is small (2-12%). The essential part of hypochromicity (22-28%) is due to the interstrand interactions between the bases which are not coupled by hydrogen bonds. The discussion of the experimental data shows that the present theoretical investigation could serve as a basis for correct treatment of experimental results.
Mol Biol (Mosk)
PMID:[Theoretical study of the hypochromic effect in polynucleotides]. 121 3

A model is proposed for the structure of stereospecific sites in regulatory proteins. On its basis a possible code is suggested that governs the binding of regulatory proteins at specific control sites on DNA. Stereospecific sites of regulatory proteins are assumed to contain pairs of antiparallel polypeptide chain segments which form a right-hand twisted antiparallel beta-sheet, with single-stranded regions at the ends of the beta-structure. The model predicts that binding reaction between a regulatory protein and double-helical DNA is a cooperative phenomenon and is accompanied by significant structural alteration at the stereospecific site of the protein. Half of hydrogen bonds normally existing in beta-structure are broken upon complex formation with DNA and a new set of hydrogen bonds is formed between polypeptide amide groups and DNA base pairs. In a stereospecific site, one chain (t-chain) is attached through hydrogen bonds to the carbonyl oxygens of pyramides and N3 adenines lying in one DNA strand, while the second polypeptide chain (g chain) is hydrogen bonded to the 2-amino groups of guanine residues lying in the opposite DNA strand. The amide groups serve as specific reaction sites being hydrogen bond acceptors in g-chain and hydrogen bond donors in t-chain. The single-stranded portions of t- and g-chains lying in neighbouring subunits of regulatory protein interact with each other forming deformed beta-sheets. The recognition of regulatory sequences by proteins is based on the structural complementarity between stereospecific sites of regulatory proteins and base pairs sequences at the control sites. An essential feature of these sequences is the asymmetrical distribution of guanine residues between the two DNA strands. The code predicts that there are six fundamental amino acid residues (serine, threonine, asparagine, histidine, glutamine and cysteine) whose sequence in stereospecific site determines the base pair sequence to which a given regulatory protein would bind preferentially. The code states a correspondence between four amino acid residues at the stereospecific site of regulatory protein with the two residues being in t- and g-segments, respectively, and AT(GC) base pair at the control site. It is thus possible to determine which amino acid residues in the repressor and which base pairs in the operator DNA are involved in specific interactions with each other, as exemplified by lac repressor binding to lac operator.
Mol Biol (Mosk)
PMID:[A code governing specific binding of regulatory proteins to DNA and structure of stereospecific sites of regulatory proteins]. 121 4

An assumption is made on the substantial role of local hydrogen bonds in formation of irregular regions of globular protein polypeptide chains. The statistics of the amino acid composition of irregular regions is examined from this point of view. A statistical analysis of side group-backbone hydrogen bonds is carried out for three proteins: alpha-chy-motrypsin, lysozyme and myoglobin. It is shown that short side groups participate in formation of local hydrogen bonds more often than long ones. Conformations of amino acid residues in the first and the last positions are studied in beta-bends of 9 proteins. It is shown that over 70% of these residues are in conformations corresponding to the formation of local hydrogen bonds of three types: backbone-backbone, side groupbackbone, backbone-water molecule-backbone. Thus, the participation of the cooperative hydrogen-bonding network in stabilization of beta-bends is demonstrated.
Mol Biol (Mosk)
PMID:[The role of local hydrogen bonds in formation of irregular regions of globular protein polypeptide chains]. 121 11


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