{"title":"Antibodies to DNA.","authors":"B D Stollar","doi":"10.3109/10409238609115899","DOIUrl":"https://doi.org/10.3109/10409238609115899","url":null,"abstract":"<p><p>Antibodies that recognize specific conformational variations of DNA structure provide sensitive reagents for testing the extent to which such conformational heterogeneity occurs in nature. A most dramatic recent example has been the development and application of antibodies to left-handed Z-DNA. They provided the first identification of Z-DNA in fixed nuclei and chromosomes, and of DNA sequences that form Z-DNA under the influence of supercoiling. Antibodies have also been induced by chemically modified DNA and by synthetic polydeoxyribonucleotides that differ from the average B-DNA structure. These antibodies recognize only the features that differ from native DNA. In most experiments, native DNA itself is not immunogenic. Antibodies that do react with native DNA occur in sera of patients with autoimmune disease, but even monoclonal anti-DNA autoantibodies usually react with other polynucleotides as well. Anti-DNA antibodies, especially those of monoclonal origin, provide a model for the study of protein-nucleic acid recognition.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"20 1","pages":"1-36"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609115899","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14636360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The mechanism of muscle contraction.","authors":"R Cooke","doi":"10.3109/10409238609113609","DOIUrl":"https://doi.org/10.3109/10409238609113609","url":null,"abstract":"<p><p>Knowledge of the mechanism of contraction has been obtained from studies of the interaction of actin and myosin in solution, from an elucidation of the structure of muscle fibers, and from measurements of the mechanics and energetics of fiber contraction. Many of the states and the transition rates between them have been established for the hydrolysis of ATP by actin and myosin subfragments in solution. A major goal is to now understand how the kinetics of this interaction are altered when it occurs in the organized array of the myofibril. Early work on the structure of muscle suggested that changes in the orientation of myosin cross-bridges were responsible for the generation of force. More recently, fluorescent and paramagnetic probes attached to the cross-bridges have suggested that at least some domains of the cross-bridges do not change orientation during force generation. A number of properties of active cross-bridges have been defined by measurements of steady state contractions of fibers and by the transients which follow step changes in fiber length or tension. Taken together these studies have provided firm evidence that force is generated by a cyclic interaction in which a myosin cross-bridge attaches to actin, exerts force through a \"powerstroke\" of 12 nm, and is then released by the binding of ATP. The mechanism of this interaction at the molecular level remains unknown.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"21 1","pages":"53-118"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609113609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14647340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Pseudogenes.","authors":"C D Wilde","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Pseudogenes are DNA sequences that bear significant homology to functional genes, yet they lack promoter sequences for their transcription or contain other mutations that preclude formation of a functional product. They appear to be a common feature of many eukaryotic genomes. Pseudogenes were first described among the 5S RNA genes of Xenopus; subsequently, they have been found for a wide range of genes, including globins, snRNAs, immunoglobulins, tubulins, and metallothionein. Some pseudogenes, like those of the beta-globins, lie within the gene cluster of their functional counterparts; they may simply have arisen by accumulation of mutations in a duplicated nonselected gene. Other pseudogenes appear to have arisen by a very different process. Characteristically, they are dispersed in the genome, lack introns, and have oligoA tracts at their 3' ends. Their structure suggests an origin from mRNAs through reverse transcription and integration into the genome. Pseudogenes have no known function. They may represent dead-end byproducts of normal cellular and evolutionary processes, yet they are also potential starting points from which new genes might evolve.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"19 4","pages":"323-52"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13569288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Solubilization of enzymes and nucleic acids in hydrocarbon micellar solutions.","authors":"P L Luisi, L J Magid","doi":"10.3109/10409238609081999","DOIUrl":"https://doi.org/10.3109/10409238609081999","url":null,"abstract":"<p><p>The present state of the field of biopolymers solubilized in apolar solvents via reverse micelles is reviewed. First, an extensive discussion of the physical and chemical properties of reverse micelles is presented. Particular attention is devoted to the nature of water in the water pools of reverse micelles; to the structure and shape of the micellar aggregates; and to the dynamic properties of the reverse micelles. In the second part of the paper, the mechanism of solubilization of proteins and nucleic acids in hydrocarbon reverse micelles is discussed. Spectroscopic data, mostly circular dichroism and fluorescence, are reviewed in order to clarify the conformational changes which the biopolymers undergo upon their uptake into the micellar environment and determine the location of the biopolymers inside the reverse micelles. Data from neutron scattering, light scattering, ultracentrifugation, and electron microscopy of the protein-containing micelles are reviewed and discussed with the aim of illustrating the structure of the micellar aggregates containing the biopolymer as guest molecules. The activity of enzymes and nucleic acids is discussed, with emphasis on the influence upon the chemical reactivity brought about by the micellar parameters. Finally, a brief review of the applications and potentialities of biopolymer-containing reverse micelles is presented.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"20 4","pages":"409-74"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609081999","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13574400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Kinetics of protein-nucleic acid interactions: use of salt effects to probe mechanisms of interaction.","authors":"T M Lohman","doi":"10.3109/10409238609084656","DOIUrl":"https://doi.org/10.3109/10409238609084656","url":null,"abstract":"<p><p>The kinetics of protein-nucleic acid interactions are discussed with particular emphasis on the effects of salt concentration and valence on the observed rate constants. A general review is given of the use of experimentally determined salt dependences of observed kinetic parameters as a tool to probe the mechanism of interaction. Quantitative analysis of these salt dependences, through the application of polyelectrolyte theory, can be used to distinguish reactions which occur in a single step from those reactions which involve distinct intermediates. For those rate constants which display a large salt dependence, in either the association or dissociation reaction, this is due to the high concentration of counterions (e.g., Na+) in the vicinity of the nucleic acid which are subsequently released (or bound in the case of dissociation) at some point before the rate limiting step of the reaction. A general discussion of other features which affect protein-nucleic acid kinetics, such as nucleic acid length and the ratio of nonspecific to specific DNA binding sites (in the case of sequence specific binding proteins), is also given. The available data on the nucleic acid binding kinetics of small ligands (ions, dyes, oligopeptides), nonspecific binding proteins (T4 gene 32 protein, fd gene 5 and Escherichia coli SSB), and sequence specific binding proteins (lac repressor, RNA polymerase, Eco RI restriction endonuclease) are discussed with emphasis on the interpretation of the experimentally determined salt dependences.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"19 3","pages":"191-245"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609084656","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14635630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structure-activity relationships of the yeast alpha-factor.","authors":"F Naider, J M Becker","doi":"10.3109/10409238609113612","DOIUrl":"https://doi.org/10.3109/10409238609113612","url":null,"abstract":"<p><p>The yeast Saccharomyces cerevisiae produces a peptide pheromone, termed the alpha-factor, as a prelude to sexual conjugation. Haploid MAT alpha-cells, but not haploid MAT a-cells or MAT a/alpha-diploids, produce this tridecapeptide of the structure: Trp-His-Trp-Leu-Gln-Leu-Lys-Pro-Gly-Gln-Pro-Met-Tyr. Structural analogues of the alpha-factor have been prepared with alterations in many of the residues, derivatized peptides have been synthesized, and truncated and elongated peptides have been studied. These peptides have been analyzed for their biological activities by various assays. Mutants of S. cerevisiae have been isolated that do not respond to alpha-factor or are supersensitive to the pheromone and its analogues. The mating system of S. cerevisiae provides a powerful model in which genetics, biochemistry, and molecular biology can be used to unravel the mysteries of peptide hormone structure and function.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"21 3","pages":"225-48"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609113612","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14659155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structure of transcriptionally active chromatin.","authors":"M Yaniv, S Cereghini","doi":"10.3109/10409238609113607","DOIUrl":"https://doi.org/10.3109/10409238609113607","url":null,"abstract":"<p><p>Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"21 1","pages":"1-26"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609113607","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14148823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Protein translocation across and integration into membranes.","authors":"T A Rapoport","doi":"10.3109/10409238609115901","DOIUrl":"https://doi.org/10.3109/10409238609115901","url":null,"abstract":"<p><p>This review concentrates mainly on the translocation of proteins across the endoplasmic reticulum membrane and cytoplasmic membrane in bacteria. It will start with a short historical review and will pinpoint the crucial questions in the field. Special emphasis will be given to the present knowledge on the molecular details of the first steps, i.e., on the function of the signal recognition particle and its receptor. The knowledge on the signal peptidase and the ribosome receptor(s) will also be summarized. The various models for the translocation of proteins across and the integration of proteins into membranes will be critically discussed. In particular, the function of signal, stop-transfer, and insertion sequences will be dealt with and molecular differences discussed. The cotranslational mode of membrane transfer will be compared with the post-translational transport found for mitochondria and chloroplasts. This review will conclude with open questions and an outlook.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"20 1","pages":"73-137"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609115901","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14140155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular biology of terminal transferase.","authors":"L M Chang, F J Bollum","doi":"10.3109/10409238609113608","DOIUrl":"https://doi.org/10.3109/10409238609113608","url":null,"abstract":"<p><p>Terminal transferase is an unusual deoxynucleotide polymerizing enzyme found only in prelymphocytes. The protein was purified to homogeneity from calf thymus glands in 1971 as a 32 kDa protein with a two peptide structure. Subsequent biochemical and immunological analyses of terminal transferase protein in crude extracts from a number of animal species showed a single peptide with a molecular weight of about 58,000. The two peptide structure found earlier was caused by proteolysis. Homogeneous 58 kDa terminal transferase has now been produced from human lymphoblastoid cells and calf thymus glands by immunoaffinity chromatography. In vitro phosphorylation studies showed that the terminal transferase protein contains one phosphorylation site near one end of the polypeptide chain, and the phosphorylation of the enzyme has been confirmed by in vivo labeling experiments. Unambiguous demonstration of the molecular weight of the human terminal transferase was obtained by translation of the cloned human terminal transferase DNA sequence to a 58,308 Da protein. The translated amino acid sequence also provided a possible phosphorylation site near the amino-terminus of the protein. Preliminary analysis of the genomic structure shows a simple intron/exon pattern with the total human terminal transferase gene spanning at least 65 Kb.</p>","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"21 1","pages":"27-52"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3109/10409238609113608","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14647341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The interferon receptors.","authors":"M. Rubinstein, P. Orchansky","doi":"10.1002/0471684228.egp06422","DOIUrl":"https://doi.org/10.1002/0471684228.egp06422","url":null,"abstract":"Early studies on the mode of action of interferons have indicated that a receptor system on the cell surface is involved in its action. The first direct evidence to a high-affinity binding site was found only after pure interferon was available. Two different receptors, one specific for interferons-alpha and beta, and the other for interferon-gamma were recognized. A correlation between affinity to the receptor and specific activity was established. Cross-linked complexes of labeled interferons with their receptors were visualized on gel electrophoresis and even partially purified. Internalization of interferons after binding to the receptor was reported. The role of gangliosides as helpers of interferon binding was recently investigated. Fragments of interferons which still retained binding capacity were described and helped in elucidating the binding site on the interferon molecule.","PeriodicalId":75744,"journal":{"name":"CRC critical reviews in biochemistry","volume":"26 5","pages":"249-75"},"PeriodicalIF":0.0,"publicationDate":"1986-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50951457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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