scholarly journals Nucleic acid specificity of a vertebrate telomere-binding protein: evidence for G-G base pair recognition at the core-binding site.

1992 ◽  
Vol 6 (5) ◽  
pp. 815-824 ◽  
Author(s):  
A Gualberto ◽  
R M Patrick ◽  
K Walsh
Keyword(s):  
Nucleic Acid ◽  
Binding Site ◽  
Base Pair ◽  
Binding Protein ◽  
The Core ◽  
Telomere Binding Protein

Helicase mechanisms and the coupling of helicases within macromolecular machines Part I: Structures and properties of isolated helicases

2002 ◽  
Vol 35 (4) ◽  
pp. 431-478 ◽  
Author(s):  
Emmanuelle Delagoutte ◽  
Peter H. von Hippel
Keyword(s):  
Crystal Structure ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Site ◽  
Crystal Structures ◽  
Base Pair ◽  
Biochemical Properties ◽  
Functional Coupling ◽  
Hexameric Helicases ◽  
Base Pair Opening

1. Mechanisms of nucleic acid (NA) unwinding by helicases 4322. Helicases may take advantage of ‘breathing’ fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs 4342.2 dsNAs ‘breathe’ in isolation 4352.3 Thermodynamics of terminal base pairs of dsNA 4382.4 Thermal fluctuations may be responsible for sequential base-pair opening at replication forks 4392.5 Helicases may capture single base-pair opening events sequentially 4403. Biochemical properties of helicases 4433.1 Binding of NAs 4433.2 Binding and hydrolysis of NTP 4453.3 Coordination between NA binding and NTP binding and hydrolysis activities 4464. Helicase structures and mechanistic consequences 4474.1 Amino-acid sequence analysis reveals conserved motifs that constitute the NTP-binding pocket and a portion of the NA-binding site 4474.2 Organization of hepatitis virus C NS3 RNA helicase 4494.2.1 Biochemical properties of HCV NS3 4494.2.2 Crystal structures of HCV NS3 helicase 4504.2.2.1 The apoprotein 4504.2.2.2 The protein–dU8 complex 4504.2.3 A possible unwinding mechanism 4524.2.4 What is the functional oligomeric state of HCV NS3? 4524.3 Organization of the PcrA helicase 4534.3.1 The apoenzyme and ADP–PcrA complex 4544.3.2 The protein–DNA–sulfate complex 4564.3.3 The PcrA–DNA–ADPNP complex 4564.3.4 A closer look at the NTP-binding site in the crystal structure of PcrA–ADPNP–DNA 4574.3.5 Communication between domains A and B 4574.3.6 How might ssDNA stimulate the ATPase activity of PcrA? 4574.3.7 A possible helicase translocation mechanism 4584.3.8 A possible unwinding mechanism 4584.4 Organization of the Rep helicase 4594.4.1 Biochemical properties 4594.4.2 Crystal structure of Rep bound to ssDNA 4624.5 Organization of the RecG helicase 4624.6 Hexameric helicases 4664.6.1 Insights from crystal structures of hexameric helicases 4674.6.2 Possible translocation and unwinding mechanisms 4685. Conclusions 4696. Acknowledgments 4727. References 472Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven ‘breathing’ of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.

scholarly journals The C Terminus of the Major Yeast Telomere Binding Protein Rap1p Enhances Telomere Formation

1998 ◽  
Vol 18 (3) ◽  
pp. 1284-1295 ◽  
Author(s):  
Alo Ray ◽  
Kurt W. Runge
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Reverse Transcriptase ◽  
Binding Site ◽  
Binding Protein ◽  
Telomerase Activity ◽  
Telomerase Rna ◽  
Constant Length ◽  
C Terminus ◽  
Telomere Binding Protein ◽  
Yeast Telomere

ABSTRACT The telomeres of most organisms consist of short repeated sequences that can be elongated by telomerase, a reverse transcriptase complex that contains its own RNA template for the synthesis of telomere repeats. In Saccharomyces cerevisiae, the RAP1gene encodes the major telomere binding protein Rap1p. Here we use a quantitative telomere formation assay to demonstrate that Rap1p C termini can enhance telomere formation more than 30-fold when they are located at internal sites. This stimulation is distinct from protection from degradation. Enhancement of formation required the gene for telomerase RNA but not Sir1p, Sir2p, Sir3p, Sir4p, Tel1p, or the Rif1p binding site in the Rap1p C terminus. Our data suggest that Rap1p C termini enhance telomere formation by attracting or increasing the activity of telomerase near telomeres. Earlier work suggests that Rap1p molecules at the chromosome terminus inhibit the elongation of long telomeres by blocking the access of telomerase. Our results suggest a model where a balance between internal Rap1p increasing telomerase activity and Rap1p at the termini of long telomeres controlling telomerase access maintains telomeres at a constant length.

scholarly journals A novel transcriptional regulatory region within the core promoter of the hepatocyte growth factor gene is responsible for its inducibility by cytokines via the C/EBP family of transcription factors.

1997 ◽  
Vol 17 (10) ◽  
pp. 5758-5770 ◽  
Author(s):  
J G Jiang ◽  
R Zarnegar
Keyword(s):  
Transcription Factors ◽  
Growth Factor ◽  
Hepatocyte Growth Factor ◽  
Binding Site ◽  
Promoter Region ◽  
Binding Protein ◽  
Tissue Growth ◽  
Transcriptional Level ◽  
The Core ◽  
Hepatocyte Growth

Hepatocyte growth factor (HGF) is an inducible cytokine that is essential for the normal growth and development of various tissues, such as the liver. To decipher the molecular mechanisms that regulate HGF gene induction at the transcriptional level, we carried out in vitro and in vivo studies on the mouse HGF gene promoter. We have identified a novel regulatory element, located between -6 and +7 bp (from the transcription start site) in the HGF basal promoter region, which binds to inducible transcription factors and dictates responsiveness to extracellular stimuli that activate this gene. The core binding sequence for the inducible cis-acting factors was determined to be TTTGCAA (-4 to +3 bp) within the HGF promoter. Competition and gel mobility supershift assays showed that these binding complexes are composed of C/EBPbeta (CCAAT/enhancer-binding protein beta) and C/EBPdelta. DNA binding analysis also revealed that the binding site for the C/EBP family of transcription factors in the HGF promoter region overlaps that of another binding protein (complex C1), which binds specifically to a novel sequence with a core binding site of ACCGGT located adjacent to the C/EBP site (-9 to -4 bp). C1 binds to this region of the promoter and represses the inducible upregulation by C/EBP through direct competition for their individual binding sites. Partial hepatectomy, which is known to activate HGF gene expression in the liver, increased C/EBP (especially C/EBPbeta) binding activity to this region of the HGF promoter. Thus, our present results provide a mechanistic explanation for the transcriptional induction of the HGF gene by extracellular signals (i.e., cytokines) that induce tissue growth and regeneration.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

ASSOCIATION BEHAVIOUR OF THE OESTRADIOL-BINDING PROTEIN COMPLEX WITH THE NUCLEAR FRACTION

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S420-S438 ◽  
Author(s):  
David L. Williams ◽  
Jack Gorski
Keyword(s):  
Binding Site ◽  
Protein Complex ◽  
Binding Protein ◽  
Nuclear Fraction ◽  
Site Saturation ◽  
Total Binding

ABSTRACT A number of studies have been carried out to examine the distribution of the oestradiol-binding protein complex between cytosol and nuclear fractions as a function of total binding site saturation. The results of these studies suggest that each binding protein has one binding site for the hormone. In addition, these studies suggest that the interaction of the oestradiol-binding protein complex with the nucleus involves a large number of low affinity association sites.

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