Folding of the SPKK Rich Peptide in the Presence of the Octa-Oligonucleotide

1997 ◽  
Vol 52 (1-2) ◽  
pp. 77-81 ◽  
Author(s):  
Igor Z. Zubrzycki ◽  
Lothar Bohm
Keyword(s):  
Thermal Denaturation ◽  
Helical Structure ◽  
Core Histone ◽  
Base Pairs ◽  
H1 Histone ◽  
Terminal Domain ◽  
Single Stranded Oligonucleotide

Abstract The nucleosome contains of 200 base pairs of DNA complexed with four core histone complex: H2A , H2B, H3, and H4. The fifth histone species, the H1 histone, interacts with linker DNA connecting neighbouring nucleosomes. We have studied the influence of the phosphorylation on the interactions of a repeating unit 15 residues long, containing the SPKK motif, the motif thought to induce turn along peptides sequences, enclosed within the trout testis H1 C-terminal domain with octanucleotide by means of the thermal denaturation and CD technique. The results indicate that the peptide preferentially binds to a single stranded oligonucleotide. It has been shown further that there is no β structure present but a distorted helical structure has been detected.

scholarly journals Ty3 Capsid Mutations Reveal Early and Late Functions of the Amino-Terminal Domain

2007 ◽  
Vol 81 (13) ◽  
pp. 6957-6972 ◽  
Author(s):  
Liza S. Z. Larsen ◽  
Min Zhang ◽  
Nadejda Beliakova-Bethell ◽  
Virginia Bilanchone ◽  
Anne Lamsa ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Helical Structure ◽  
Spherical Particles ◽  
P Bodies ◽  
Amino Terminal ◽  
Terminal Domain ◽  
Fluorescence And Electron Microscopy ◽  
Carboxyl Terminal ◽  
Rna Protection ◽  
Amino Terminal Domain

ABSTRACT The Ty3 retrotransposon assembles into 50-nm virus-like particles that occur in large intracellular clusters in the case of wild-type (wt) Ty3. Within these particles, maturation of the Gag3 and Gag3-Pol3 polyproteins by Ty3 protease produces the structural proteins capsid (CA), spacer, and nucleocapsid. Secondary and tertiary structure predictions showed that, like retroviral CA, Ty3 CA contains a large amount of helical structure arranged in amino-terminal and carboxyl-terminal bundles. Twenty-six mutants in which alanines were substituted for native residues were used to study CA subdomain functions. Transposition was measured, and particle morphogenesis and localization were characterized by analysis of protein processing, cDNA production, genomic RNA protection, and sedimentation and by fluorescence and electron microscopy. These measures defined five groups of mutants. Proteins from each group could be sedimented in a large complex. Mutations in the amino-terminal domain reduced the formation of fluorescent Ty3 protein foci. In at least one major homology region mutant, Ty3 protein concentrated in foci but no wt clusters of particles were observed. One mutation in the carboxyl-terminal domain shifted assembly from spherical particles to long filaments. Two mutants formed foci separate from P bodies, the proposed sites of assembly, and formed defective particles. P-body association was therefore found to be not necessary for assembly but correlated with the production of functional particles. One mutation in the amino terminus blocked transposition after cDNA synthesis. Our data suggest that Ty3 proteins are concentrated first, assembly associated with P bodies occurs, and particle morphogenesis concludes with a post-reverse transcription, CA-dependent step. Particle formation was generally resistant to localized substitutions, possibly indicating that multiple domains are involved.

scholarly journals The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

2020 ◽  
Vol 48 (4) ◽  
pp. 1748-1763 ◽  
Author(s):  
Jack W Shepherd ◽  
Robert J Greenall ◽  
Matt I J Probert ◽  
Agnes Noy ◽  
Mark C Leake
Keyword(s):  
Structural Changes ◽  
Periodic Structures ◽  
Helical Structure ◽  
Specific Response ◽  
Base Pairs ◽  
Structural Motifs ◽  
Double Helical Structure ◽  
Physiological Relevance ◽  
Stable Periodic ◽  
Dynamics Simulations

Abstract The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20–30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.

scholarly journals Effects of Stability of Base Pairs Containing an Oxazolone on DNA Elongation

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Masayo Suzuki ◽  
Kazuya Ohtsuki ◽  
Katsuhito Kino ◽  
Teruhiko Kobayashi ◽  
Masayuki Morikawa ◽  
...  
Keyword(s):  
Dna Replication ◽  
Oxidative Damage ◽  
Ab Initio ◽  
Base Pair ◽  
Thermal Denaturation ◽  
Primer Extension ◽  
Base Pairs ◽  
Nucleotide Incorporation ◽  
The Stability

The nucleoside 2,2,4-triamino-5(2H)-oxazolone (Oz) can result from oxidative damage to guanine residues in DNA. Despite differences among the three polymerases (Polβ, KF exo−, and Polη) regarding nucleotide incorporation patterns opposite Oz, all three polymerases can incorporate guanine opposite Oz. Based onab initiocalculations, we proposed a structure for a stable Oz:G base pair. Here, to assess the stability of each Oz-containing base pair (Oz:G, Oz:A, Oz:C, and Oz:T) upon DNA replication, we determined the efficiency of Polβ-, KF exo−-, or Polη-catalyzed primer extension beyond each base pair. With each polymerase, extension beyond Oz:G was more efficient than that beyond Oz:A, Oz:C, or Oz:T. Moreover, thermal denaturation studies revealed that theTmvalue for the duplex containing Oz:G was significantly higher than those obtained for duplexes containing Oz:A, Oz:C, or Oz:T. Therefore, the results fromab initiocalculations along with those from DNA replication assays and thermal denaturation experiments supported the conclusion that Oz:G is the most stable of the Oz-containing base pairs.

Rearrangements and reconstitution of mononucleosomes as monitored by thermal denaturation measurements

1980 ◽  
Vol 58 (1) ◽  
pp. 73-81 ◽  
Author(s):  
Susan S. Chiu ◽  
Kay P. Lee ◽  
Peter N. Lewis
Keyword(s):  
Freeze Drying ◽  
Thermal Denaturation ◽  
Guanidine Hydrochloride ◽  
Melting Transition ◽  
Melting Profile ◽  
Base Pairs ◽  
Structural Domains ◽  
Calf Thymus ◽  
Dna Size ◽  
Histone Core

Derivative melting profiles of calf thymus mononucleosomes have been examined for changes resulting from variations in solvent pH and ionic strength, histone H1 content, and DNA size. Samples of mononucleosomes were found to rearrange during freeze-drying to form an altered monomer and a series of noncovalent multimers. The derivative melting profiles of these particles differ significantly from those for the untreated monomer and dimer. The noncovalent dimer exhibited a new melting transition at 66 °C involving approximately 18 base pairs of DNA normally associated with the highest melting transition. Mononucleosomes were reconstituted from 6 M guanidine hydrochloride to give particles with physical properties including melting profile which were virtually indistinguishable from those of the starting material. This result confirms the notion that no structural domains exist in the histone core that can be irreversibly denatured by noncovalent perturbations.

scholarly journals ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain

Structure ◽  
2016 ◽  
Vol 24 (9) ◽  
pp. 1537-1549 ◽  
Author(s):  
Alexander E. Conicella ◽  
Gül H. Zerze ◽  
Jeetain Mittal ◽  
Nicolas L. Fawzi
Keyword(s):  
Phase Separation ◽  
Helical Structure ◽  
Low Complexity ◽  
Terminal Domain

scholarly journals Cloning and characterization of a core histone gene tandem repeat in Urechis caupo.

1988 ◽  
Vol 8 (10) ◽  
pp. 4425-4432 ◽  
Author(s):  
L D Ingham ◽  
F C Davis
Keyword(s):  
Sea Urchin ◽  
Tandem Repeat ◽  
Histone Gene ◽  
Core Histone ◽  
Histone Genes ◽  
S1 Nuclease ◽  
H1 Histone ◽  
The Core ◽  
Histone Mrnas ◽  
Urechis Caupo

A Urechis caupo histone gene tandem repeat has been isolated from a 5.0-kilobase EcoRI genomic library in lambda gtWES.lambda B. Genomic reconstruction experiments indicate that the cloned sequence is repeated approximately 100 times per haploid genome. Unique restriction fragments from the cloned sequence hybridize with individual core histone genes from a histone gene tandem repeat of the sea urchin, Strongylocentrotus purpuratus. No hybridization is detected when restriction digests are probed with a sea urchin H1 histone gene. Hybrid selection and in vitro translation of embryo mRNAs demonstrate that the clone contains sequences complementary to all four core histones; however, no H1 histone is detected among the translation products. Based on a restriction site map of the clone and the subcloned sequences which hybridize to the histone mRNAs, the order of the core histone genes in the clone is shown to be H3 H2A H2B H4. S1 nuclease hybrid protection mapping is used to locate the coding regions and to determine the transcript lengths of the core histone mRNAs. The transcript lengths of H2A, H2B, H3, and H4 mRNAs are approximately 464, 438, 494, and 397 bases, respectively. The S1 nuclease mapping also demonstrates that H2A and H4 are transcribed from one DNA strand while H2B and H3 are transcribed from the other strand. In the tandem repeat, the genes are organized so that transcription of the H2A-H2B and H3-H4 gene pairs is divergent.

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