Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The formation of compact particles from double-stranded DNA molecules in water-salt solutions containing spermidine was studied. It has been shown that in solutions of low ionic strength (0.01 M NaCl) DNA-spermidine complexes have the form of large particles which scatter UV-light. Electron micrographs show that such complexes formed at certain molar ratios spermidine/DNA may exist both as intermolecular aggregates and as toroidal particles 1500 A in diameter. The CD spectra of solutions containing DNA-spermidine complexes are characterized by the positive band (delta epsilon max = 10) at 265--270 nm. The appearance of the positive CD band may be caused by two factors: interaction between DNA and spermidine may lead to the alteration of the DNA secondary structure "in direction to A-form" or intermolecular aggregation, which may change the initial shape of the CD spectrum. The exclusion of spermidine molecules from DNA-spermidine complexes by Na+ ions in presence of poly(ethylene glycol) which occurs as the ionic strength increases from 0.01 to 0.3 does not lead to decompactization of DNA molecules but is accompained by the appearance of the intense negative CD band at 270 nm.
Mol Biol (Mosk)
PMID:[Formation of the compact form of DNA in solution after reaction with spermidine]. 34 64

We have investigated the nonspecific interactions of Escherichia coli RNA polymerase core and holoenzyme with double-stranded (ds) and single-stranded (ss) DNA. Binding constants for these interactions as functions of such solution variables as monovalent and/or divalent cation concentration, temperature, or pH were determined by the method of deHaseth et a. [deHaseth, P.L., Gross, C.A., Burgess, R.R. and Record, M.T. (1977), Biochemistry 16, 4777--4783] from analysis of the elution of the proteins from small columns containing immobilized DNA. This technique, although as yet empirical, has been demonstrated to yield accurate binding constants fot the nonspecific interation of lac repressor with ds DNA. We find that observed binding constants (Kobsd) are extraordinarily sensitive functions of the monovalent cation concentration for the interactions of both core and holoenzyme with ds DNA. In the absence of divalent cations, the derivatives --(d log Kobsd/d log [Na+]) are 11 +/- 2 for the holo--ds DNA interaction and 21 +/- 3 for the core--ds DNA interaction. Consequently, approximately 11 and 21 low-molecular-weight ions are released, iin the thermodynamic sense, in the formation of the holo--ds and core--ds complexes, respectively (Record, M.T., Jr., Lohman, T.M., and deHaseth, P.L. (1976), J. Mol. Biol. 107, 145--158; Record, M.T., Jr., Anderson, C.F., and Lohman, T.M. (1978), Q. Rev. Biophys., in press). Ion release is a thermodynamic driving force for these nonspecific interactions and causes the stability of the complexes to increase very substantially with a reduction in monovalent ion concnetration. Possible molecular models which account for the different salt sensitivities of the holo--ds and core--ds complexes are discussed. Effects of the competitive ligand Mg2+ on these interactions are also examined. Substantial ion release (approximately 18 monovalent ions) also accompanies the interaction of either holo or core polymerase with ss DNA. Over the range of ion concentrations investigated the holo--ss interaction is substantially stronger than the core--ss interaction; furthermore, we conclude that the interactions of polymerase with ss DNA are, in general, stronger than the nonspecific interations of the enzyme with ds DNA. It is likely that the nonspecific interactions of RNA polymerase with DNA have physiological relevance. Not only is it plausible to assume that the same regions of the protein are involved in both specific and nonspecific interactions, but in addition nonspecific interactions of RNA polymerase and DNA may play role in determining the availability of this protein, in both the thermodynamic and the kinetic sense, for promoter binding and RNA chain initiation [von Hippel. P.H., Revzin, A., Gross, C.A., and Wang, A.C. (1974), Proc. Natl. Acad. Sci U.S.A. 71, 4808--4812]. Consequently, the strong dependences of the nonspecific interactions of RNA polymerase on ionic conditions suggest the possibility of a modulating role of ion concentrations in the control of transcription.
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PMID:Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: differences in the binding behavior of core and holoenzyme. 35 Feb 71

A conditional lethal mutator, dnaQ49, was found in Escherichia coli K12. The dnaQ49 mutation caused stimulation of rifampicin-, nalidixic acid- and streptomycin-resistant mutation frequencies 100 to 2000 fold at 30 degrees C and the frequencies were further increased 50 to 100 fold at 35 degrees C or higher temperatures. Cells carrying dnaQ49 were unable to grow in salt-free L-broth at 44.5 degrees C, and DNA synthesis but not protein synthesis of the cells was suppressed under the restrictive conditions. The dnaQ gene was located at about 5 min on the E. coli linkage map and the order of the genes residing in this region was determined to be ton A-dnaE-metD-dnaQ-pro A.
Mol Gen Genet 1978 Jul 25
PMID:A new conditional lethal mutator (dnaQ49) in Escherichia coli K12. 35 54

The influence of peptidyl-tRNA on the dissociation of yeast 80 S ribosomes into subunits was studied. For this purpose temperature-sensitive (ts) suppressor strain of yeast Saccharomyces cervisiae carrying a defect in peptide chain termination was used. It was found that peptidyl-tRNA did not influence the dissociation of ribosomes either at high salt concentration or in the presence of dissociation factor (DF) from yeast. After dissociation of yeast ribosomes in 0.5 M KCl, peptidyl-tRNA remains bound to the 60 S subunit. Some characteristics of the termination process and release of nascent polypeptides from yeast ribosomes are discussed.
Mol Biol Rep 1978 Jun 16
PMID:Dissociability of free and peptidyl-tRNA bound ribosomes. 35 60

A structural gene for sigma factor (rpoD) of DNA-dependent RNA polymerase (RNA nucleotidyltransferase; nucleoside-triphosphate: RNA nucleotidyltransferase, E.C. 2.7.7.6) was mapped precisely by a set of F' factors including those already published (Proc. Natl. Acad. Sci. USA. 74, 1831-1835 (1977)). Based on the result that rpoD is located at the dnaG-uxaAC region, a number of mutants containing a temperature-sensitive mutation at or near the uxaA gene were isolated by localized mutagenesis. One of these mutants was found to produce RNA polymerase altered in both thermostability and optimum salt concentration as a result of structural alteration of sigma factor. This mutation, U303, maps at 66 min on the genetic map of E. coli, near the dnaG locus, and affects normal growth of cells.
Mol Gen Genet 1978 Sep 20
PMID:RNA polymerase mutant with altered sigma factor in Escherichia coli. 36 59

The native T2 DNA in solutions with different LiCl concentrations was oriented by pumping through a capillary device similar to that described in rf. 1. The change of the parallel, deltaepsilon parallel, and perpendicular, 2 delta epsilon perpendicular, components of circular dichroism tensor was studied as a function of salt concentration. Positive (delta epsilon parallel 280) and negative (2 delta epsilon perpendicular 280) components were shown to increase in absolute magnitude, so that there was a monotonous drop in the longwave band magnitude of the isotropic delta epsilon 280 as a result of compensation; the shortwave band magnitude of the isotopic delta 245 and its anisotropic components were constant. It is proposed that while the helix is winding as a result of LiCl rise progressive tilting of base pairs takes place. It was also shown that the glucosylated T2 DNA in solution is wound to a greater extent than the non-glucosylated DNA of the same GC-content.
Mol Biol (Mosk)
PMID:[Conformational transition of DNA within the B-family as revealed by anisotropy circular dichroism]. 37

A series of five alternating poly(leucyl-lysyl) samples with varying amounts of L-and D-residues randomly distributed along the chain, but evenly shared out amongst leucyl and lysyl residues were synthesized by condensation of a mixture of the four diastereoisomeric dipeptide p-nitro-phenylesters. Their behavior in aqueous solution at various ionic strengths was studied by infrared spectroscopy which allowed measurement of the total amount of beta-structures, and by circular dichroism which gives the excess of L-residues over D-residues in the same structures. Comparison with the properties of the all L-poly(Lys-Leu-Lys-Leu) shows that incorporation of a few D-residues in a L-chain seems to reduce the width of the beta-sheets obtained in presence of salt. Higher proportions of D-isomers prevent the coil leads to beta transition from occurring when the ionic strength is increased except for segments containing at least 6 to 7 adjacent residues of the same configuration.
J Mol Evol 1979 Jun 08
PMID:Beta-structures of polypeptides with L-and D-residues. Part I. Synthesis and conformational studies. 45 71

Conditions of formation of the DNA optically-active compact particles (e. g. particles which are characterized by intense negative band in CD spectrum) in PEG-containing solutions of NaCl, NaClO4, KCl, KBr, KI and CsCL have been studied. It has been shown that the region of existence of the DNA optically-active compact particles is restricted not only by the definite concentration of PEG, but also by the definite ionic strength of solution. Above this region the intense band in CD spectra of the DNA compact particles is practically absent. The nature of cation influences the process of compactization (condensation) of the DNA double-stranded molecules; the nature of anion does not influence this process (up to 0,3 M salt concentration).
Mol Biol (Mosk)
PMID:[Conditions of formation of DNA optically-active particles in polyethyleneglycol-containing solutions of different salts]. 47 Sep 38

Different physico-chemical methods (CD, ORD, small-angle X-ray diffraction, etc) were used for investigating the properties of the DNA compact particles formed in PEG-containing water-salt solutions. It has been shown that small-angle reflection, characteristic of the DNA compact particles, changes from 36.8 A (CPEG = 140 mg/ml) to 25 A (CPEG = 300 mg/ml). The maximal optical activity (the intense negative CD-band and optical rotation [alpha] = 60 000 degrees) are inherent properties of the DNA compact particles formed at CPEG 120--180 mg/ml. The high optical activity points to the twist of DNA chromophores through the DNA molecule resulting in a long-rang pitch (P approximately 2000A). Such macroscopic superhelical structure (diameter 40--30 A) is due to conformational distortion of the DNA double-helix with alternating "left" and "right" orientation of chromophoes. Disappearance of conformation distortion is accompanied by disappearance of the high optical activity of the DNA compact particles and results in a small-angle reflection of 25 A. Taking into account the reasons of formation of the optically-active DNA compact particles conditions are suggested to conserve high optical activity at CPEG equal to 400 mg/ml.
Mol Biol (Mosk)
PMID:[Correlation between conformation distortion of the DNA sugar-phosphate backbone and high optical activity of its compact form]. 50 60

The fluorescence method was used to reveal some differences in the interaction of gene 5 protein of phage f1 with single- and double-stranded polynucleotides (DNA). The binding with the duplexes is non-cooperative and the Kapp is twice lower than that for the cooperative formation of the complex with single-stranded structures. In the complex with a double-stranded polynucleotide (DNA) the protein cover 3 nucleotide pairs. The complex dissociates with a lower concentration of salt and the contribution of the energy of nonelectrostatic interactions to the total energy of complex formation for it is lower than for the complex with single-stranded DNA. In the complex of protein with single-stranded structure the fluorescence of the tyrosine (Tyr) residues is quenched to a greater degree and their accessibility to the external quencher is lower than that of the complex with double-stranded polynucleotides (DNA). The suggestion is made that in destabilization of nucleic double helices by gene 5 protein of phage f1, a great role belongs to Tyr residues because of their high affinity to single-stranded structures and because of their different localization in the complexes with single- and double-stranded polynucleotides.
Mol Biol (Mosk)
PMID:[Interaction of gene 5 protein of phage f1 with single and double-stranded DNA and polynucleotides]. 50 62


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