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 influence of the natural polyamines [spermine (Sp) and spermidine (Spd)] on the conformation of thymus DNA molecule (M = 4 and 15 MDa) was studied by means of the viscometric method over the range of low supporting electrolyte concentrations (CNaCl = 0.6 divided by 8.4 mM). In was shown that at sufficiently low degrees of ligand binding (theta PA) which satisfy the condition ZPA theta PA less than 0.76 (where ZPA is the valence of PA), the PA addition results in a slight decrease of the volume effects in the DNA molecule due to the increase of the ionic strength (mu) of solution conditioned by the presence of polyvalent PA cations and also to the supplanting of "bound" Na+ cations. The further increase in CPA induces the corresponding increase in theta PA up to the value which provides ZPA theta PA greater than 0.76, and is accompanied by drastic decrease of macromolecule's dimensions and partial DNA condensation as well. At larger degrees of binding (ZPA theta PA approximately 0.90) a transition from the expanded to compact form of the DNA molecule is observed. The calculations of theta 1 = theta Na + theta PA and rcr = theta 1 + ZPA theta PA as a function of mu were carried out according to Manning's two-variables theory on the basis of the obtained dependences of the critical PA concentrations (Ccr PA), which correspond to the midpoint of the condensational transition, versus CNaCl. The increase of rcr and/or decrease of the effective site dimensions (ZPA) was shown to be necessary for the DNA molecule collapse over the range of low mu less than 0.01. The binding constants of the PA association to the compact DNA form were evaluated by the simplest model of McGhee and von Hippel. On the basis of the results obtained for Spd it was hypothesized that the non-electrostatic interactions are significant by the binding of the PA to the compact form of the DNA molecule.
Mol Biol (Mosk)
PMID:[Binding of polyamines by the double-helical DNA molecule in unfolded and compact forms]. 277 Jul 29

The application of McGhee and von Hippel's general equation [J. Mol. Biol., 86 (1974), 469-489, Eq. (15)] to the analysis of the interaction of intercalative drugs with DNA has been further simplified. The value of n can now be determined mathematically, using a simple function, and without any approximation. It is also established that the summation of squared deviation of (( (nu/c), nu)) points would be minimum for and only for the true set of (K,n,omega) of the interaction system. The method incorporating the simplification has been applied to determine the binding parameters of adriamycin-DNA interaction according to the above general equation.
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PMID:Further simplification of the general analysis of the intercalative drug-DNA interaction. 277 18

The six operators of phage lambda and their consensus sequence were synthesized as 21 base-pair DNAs and their interactions with Cro repressor were studied using a filter binding assay. The measured equilibrium dissociation constants suggest that Cro has the highest affinity to the consensus operator (KD = 1.2 X 10(-12) M) and then the OR3 operator (KD = 2.0 X 10(-12) M), after that the affinity becomes lower in the following order: OR1, OL1, OL2, OL3, OR2. The competition experiments show that Cro forms the most stable complex with the consensus operator (t1/2 = 150 min), which is followed by the complex with OR3 (t1/2 = 70 min), OR1, OL1, OL2, OL3 and OR2. The association rate constants (ka) were also measured. They are approximately the same (2 X 10(8) to 4 X 10(8) m-1 s-1) for the consensus, OR3, OR2 and OR1 operators. These experiments have thus shown that the sequence difference in the operator affects the dissociation (KD and kd) but not the association (ka) process. The operators' binding strengths relative to OR1 are 14 (for consensus operator), 7.6 (OR3), 0.73 (OL1), 0.42 (OL2), 0.16 (OL3) and 0.1 (OR2). Seven different lengths of OR-containing DNA fragments were prepared. Measurement of kinetic parameters shows that the affinity of Cro to operator DNA (measured by KD) is essentially constant and independent of the DNA length, while the association and dissociation rate constants increase as the DNA length increases. This is consistent with the idea that Cro locates and leaves its operator via a two-step mechanism. It appears that Cro binds first at an arbitrary site on DNA, then is transferred to its operator site by a facilitated mechanism. The process is reversed when Cro dissociates from the operator. Most of our data fit to the theoretical expression formulated by Berg, Winter & von Hippel for the sliding mechanism. We conclude that Cro slides along the DNA to locate and leave the operator.
J Mol Biol 1987 Jul 05
PMID:Kinetic studies on Cro repressor-operator DNA interaction. 295 36

The frequency of base-pair occurrence in a set of recognition sequences for a particular DNA-binding protein is strongly related to the contributions to the binding free energy from the individual base pairs. Thus from the statistics of base-pair choice, it is possible to estimate the relative binding strengths of any base-pair sequences and to predict the effect of point mutations in specific sites. On the same basis, one can describe the binding properties of random DNA sequences and thereby the expected competitive effects from all the nonspecific DNA sites in the genome of a living cell. The statistical selection theory [Berg & von Hippel.J. Mol. Biol. 193 (1987) 723-750] describing these relations is extended and tested with computer simulations. The theory is shown to hold up well also in the case when base pairs contribute cooperatively to the binding interaction. The simulations also demonstrate the effects of the statistical small-sample uncertainty that appears due to the limited size of all sets of recognition sites identified.
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PMID:Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition. 327 24

The DNA sequences in the operator sites of the arginine regulon and of the SOS regulon have been subject to a statistical analysis. A quantitative correlation is found between the statistics of sequence choice and the activity at individual operator sites in both systems, as expected from theoretical considerations [Berg & von Hippel, J.Mol.Biol. (1987) 193, 723-750]. Based on these correlations it is possible to predict the effect of various sequence mutations. There is a significant difference in the slopes of the correlation lines between sequence and activity for the two systems. From this difference it can be expected that individual point mutations in the ARG boxes will have a much smaller effect on activity than similar changes in the SOS boxes. This difference may be related to a strong cooperative activity at tandem ARG boxes while the binding at SOS boxes appears to be mostly noncooperative.
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PMID:Selection of DNA binding sites by regulatory proteins: the LexA protein and the arginine repressor use different strategies for functional specificity. 329 Aug 47

Single-pulse (approximately 8 ns) ultraviolet laser excitation of protein-nucleic acid complexes can result in efficient and rapid covalent cross-linking of proteins to nucleic acids. The reaction produces no nucleic acid-nucleic acid or protein-protein cross-links, and no nucleic acid degradation. The efficiency of cross-linking is dependent on the wavelength of the exciting radiation, on the nucleotide composition of the nucleic acid, and on the total photon flux. The yield of cross-links/laser pulse is largest between 245 and 280 nm; cross-links are obtained with far UV photons (200-240 nm) as well, but in this range appreciable protein degradation is also observed. The method has been calibrated using the phage T4-coded gene 32 (single-stranded DNA-binding) protein interaction with oligonucleotides, for which binding constants have been measured previously by standard physical chemical methods (Kowalczykowski, S. C., Lonberg, N., Newport, J. W., and von Hippel, P. H. (1981) J. Mol. Biol. 145, 75-104). Photoactivation occurs primarily through the nucleotide residues of DNA and RNA at excitation wavelengths greater than 245 nm, with reaction through thymidine being greatly favored. The nucleotide residues may be ranked in order of decreasing photoreactivity as: dT much greater than dC greater than rU greater than rC, dA, dG. Cross-linking appears to be a single-photon process and occurs through single nucleotide (dT) residues; pyrimidine dimer formation is not involved. Preliminary studies of the individual proteins of the five-protein T4 DNA replication complex show that gene 43 protein (polymerase), gene 32 protein, and gene 44 and 45 (polymerase accessory) proteins all make contact with DNA, and can be cross-linked to it, whereas gene 62 (polymerase accessory) protein cannot. A survey of other nucleic acid-binding proteins has shown that E. coli RNA polymerase, DNA polymerase I, and rho protein can all be cross-linked to various nucleic acids by the laser technique. The potential uses of this procedure in probing protein-nucleic acid interactions are discussed.
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PMID:Laser cross-linking of nucleic acids to proteins. Methodology and first applications to the phage T4 DNA replication system. 394 76

The adenovirus type 7 (Ad7) single-stranded DNA-binding protein (DBP) structural gene has been sequenced and located between 66.7 and 62.3 map units. This region codes for a protein that contains 517 amino acid residues with a calculated molecular mass of 58,240 daltons. We compared the Ad7 amino acid sequence with those reported for the Ad5 (Kruijer, W., van Schaik, F.M.A., and Sussenbach, J.S. (1981) Nucleic Acids Res. 9, 4439-4457) and Ad12 (Kruijer, W., van Schaik, F.M.A., Speijer, J.G., and Sussenbach, J.S. (1983) Virology 128, 140-153) DNA-binding proteins. A greater amount of amino acid sequence homology was found in the carboxyl-terminal DNA-binding domain of the molecule. This homology is 61% between Ad7 and Ad5 and 49% when Ad12 was included in the comparison. The NH2-terminal domain of DBP retained a 49% homology between Ad7 and Ad5 and a 23% homology for all three serotypes. The greatest difference between the Ad7 and Ad5 DBPs is the absence, in the Ad7 protein, of 12 amino acids located between the two functional domains in the Ad5 protein (amino acids 151-162). In addition, three regions of high amino acid conservation between Ad5, Ad7, and Ad12 consisting of 9 (178-186), 9 (322-330), and 12 (464-475) consecutive amino acids (numbers refer to Ad5) in the DNA-binding portion of the molecule were revealed. These three regions contain a centrally located basic amino acid (183, 326, and 470) as well as an aromatic amino acid residue (181, 324, and 469). Since basic and aromatic amino acids have been implicated in other single-stranded DNA-binding protein/DNA interactions (Anderson, R.A., Nakashima, V., and Coleman, J.E. (1975) Biochemistry 14,907-917; Kowalczykowski, S.C., Lonberg, N., Newport, J.W., and von Hippel, P.H. (1981). J. Mol. Biol. 145, 75-104), these three conserved regions may represent DBP/DNA contact points.
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PMID:Sequence of the DNA-binding protein gene of a human subgroup B adenovirus (type 7). Comparisons with subgroup C (type 5) and subgroup A (type 12). 632 15

The dissociation kinetics of bacteriophage T4 coded gene 32 protein-single-stranded nucleic acid complexes have been examined as a function of monovalent salt concentration, temperature, and pH in order to investigate the details of the dissociation of cooperatively bound protein. Fluorescence stopped-flow techniques were used, and irreversible dissociation was induced by a combination of [NaCl] jumps and mixing with excess nucleic acid competitor. This made it possible to directly investigate the irreversible dissociation process over a wide range of NaCl concentrations [e.g., from 50 mM to 0.60 M for the gene 32 protein-poly(A) complex], in the absence of reassociation. Over the entire salt range, the only dissociable species observed is the singly contiguously bound gene 32 protein which dissociates from the ends of protein clusters. However, the [NaCl] dependence of the dissociation rate constant suggests that two competing pathways exist for dissociation of cooperatively bound gene 32 protein from the ends of protein clusters. At high monovalent salt concentrations, dissociation is dominated by a single-step process, with log ke/log [NaCl] = 6.5 +/- 0.5; i.e., the dissociation rate constant increases with increasing NaCl concentration due to the uptake of approximately six monovalent ions upon dissociation. This indicates that singly contiguous protein dissociates directly into solution. However, at much lower [NaCl] the data suggest that gene 32 protein, when bound at the end of a protein cluster, dissociates by first sliding off the end to form a noncooperatively bound intermediate which subsequently dissociates. A quantitative model which incorporates the sliding pathway [Berg, O. G., Winter, R. B., & von Hippel, P. H. (1981) Biochemistry 20, 6929-6948] in the dissociation mechanism fits the data reasonably well and suggests that noncooperatively bound monomers of gene 32 protein may be capable of one-dimensional translocation along single-stranded nucleic acids as suggested by independent kinetic data on the association reaction [Lohman, T. M., & Kowalczykowski, S. C. (1981) J. Mol. Biol. 152, 67-109]. It is also observed that both the absolute dissociation rate constant for T4 gene 32 protein and its salt dependence are sensitive to the average molecular weight and polydispersity of the nucleic acid sample used. This is a general phenomenon exhibited by proteins that bind to nucleic acids in a highly cooperative manner.
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PMID:Kinetics and mechanism of dissociation of cooperatively bound T4 gene 32 protein-single-stranded nucleic acid complexes. 2. Changes in mechanism as a function of sodium chloride concentration and other solution variables. 638 32

The avaliable data on equilibrium fluctuations in DNA are critically analyzed. Fluctuations of these types are considered: bending and torsional fluctuations and fluctuational opening of base pairs. The latest experimental and theoretical work has made it possible to estimate the bending and torsional stiffnesses of the double helix. Either of these stiffnesses has been determined by at least two different methods that have led to the same results. The stiffness of the double helix is definitely shown to be independent of the concentration of counterions when it exceeds 10(-2) M Na+. As to the fluctuational opening, the current literature is controversial and different methods lead to contradictory results. The method based on DNA unwinding by formaldehyde is considered in some detail. Strong evidence is presented in favour of the modification of base pairs without their complete opening, through an "outside" reaction. Incorporation of this modification route into the theoretical model of DNA unwinding eliminates the last descrepancies between theory and experiment. The successful accounting for all details of the process of DNA unwinding by formaldehyde is argued to prove the adequacy of the helix-coil transition theory as a basis for describing the process of base-pairs opening. The conclusion of McGhee and von Hippel, who obtained a highly overestimated value of the base-pair opening probability proceeding from the formaldehyde kinetics, is shown to be based on an erroneous assumption. The NMR data of Early et al. are briefly discussed. They strongly support the author's concept. A critical comment is made concerning the interpretation of the hydrogen exchange data by Mandel, Kallenbach and Englander. The highly overestimated value of the probability of base-pair opening claimed by these authors is most probably based on unjustified assumptions.
Mol Biol (Mosk)
PMID:[Fluctuational mobility of DNA]. 687 35

Loss of heterozygosity (LOH) studies have suggested that somatic mutations of a tumour suppressor gene or genes on chromosome 3p are a critical event in the pathogenesis of non-familial renal cell carcinoma (RCC). Germline mutations of the von Hippel-Lindau (VHL) disease gene predispose to early onset and multifocal clear cell renal cell carcinoma, and the mechanism of tumorigenesis in VHL disease is consistent with a one-hit mutation model. To investigate the role of somatic VHL gene mutations in non-familial RCC, we analysed 99 primary RCC for VHL gene mutations by SSCP and heteroduplex analysis. Somatic VHL gene mutations were identified in 30 of 65 (46%) sporadic RCC with chromosome 3p allele loss and one of 34 (3%) tumours with no LOH for chromosome 3p. The VHL gene mutations were heterogeneous (17 frameshift deletions, eight missense mutations, four frameshift insertions, one nonsense and one splice site mutation), but no mutations were detected in the first 120 codons of cloned coding sequence. Most RCCs with somatic VHL mutations (23 of 27 (85%) informative cases) had chromosome 3p25 allele loss in the region of the VHL gene so that both alleles of the VHL gene had been inactivated as expected from a two-hit model of tumorigenesis. Detailed histopathology was available for 59 of the tumours investigated: 18 of 43 (42%) RCC with a clear cell appearance had a somatic VHL gene mutation but none of 16 non-clear cell RCC (eight chromophilic, three chromophobe and five oncocytoma) (chi2 = 7.77, P < 0.025).(ABSTRACT TRUNCATED AT 250 WORDS)
Hum Mol Genet 1994 Dec
PMID:Somatic mutations of the von Hippel-Lindau disease tumour suppressor gene in non-familial clear cell renal carcinoma. 788 15


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