Evidence for pyrimidine-pyrimidine cyclobutane dimer formation in the covalent cross linking between transfer ribonucleic acid and 16S ribonucleic acid at the ribosomal P site

Biochemistry ◽  
1980 ◽  
Vol 19 (21) ◽  
pp. 4814-4822 ◽  
Author(s):  
James Ofengand ◽  
Richard Liou
Keyword(s):  
Ribonucleic Acid ◽  
Cross Linking ◽  
Dimer Formation ◽  
Cyclobutane Dimer ◽  
Ribosomal P

Covalent cross-linking of transfer ribonucleic acid to the ribosomal P site. Site of reaction in 16S ribonucleic acid

Biochemistry ◽  
1979 ◽  
Vol 18 (20) ◽  
pp. 4333-4339 ◽  
Author(s):  
Robert A. Zimmermann ◽  
Stephen M. Gates ◽  
Ira Schwartz ◽  
James Ofengand
Keyword(s):  
Ribonucleic Acid ◽  
Cross Linking ◽  
Ribosomal P

The Paradoxical Hemorrhagic and Thrombotic Nature of the Fibrinogen Aα R16C Mutation.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1047-1047
Author(s):  
Veronica H. Flood ◽  
Hamid A. Al-Mondhiry ◽  
David H. Farrell
Keyword(s):  
Factor Xiii ◽  
Biochemical Properties ◽  
Factor Xiiia ◽  
Cross Linking ◽  
Dimer Formation ◽  
Critical Position ◽  
Fibrin Polymerization ◽  
Dual Nature ◽  
Sds Page ◽  
Significant Difference

Abstract The Aα R16C mutation is a common cause of dysfibrinogenemia, but the complete implications of this mutation on the process of hemostasis have not been fully characterized. Because of its critical position at the fibrinopeptide A cleavage site, this mutation leads to delayed fibrinopeptide release and subsequent delayed fibrin polymerization. The point mutation responsible for this dysfibrinogen leads to a clinical paradox, however, with both hemorrhage and thrombosis as reported complications. Of previously identified patients with this dysfibrinogen, approximately 30% have experienced bleeding and 15% thrombosis, with the remainder asymptomatic. In this report, the biochemical properties of Aα R16C dysfibrinogens that contribute to either hemorrhage or thrombosis are characterized. Blood samples were obtained from two young siblings who presented with excessive trauma-induced bleeding. Functional fibrinogen levels were 46–55 mg/dL and fibrinogen antigen levels were 427–429 mg/dL, consistent with the diagnosis of dysfibrinogenemia (Fibrinogen Hershey III). DNA sequencing demonstrated both siblings to be heterozygous for the Aα R16C mutation. Fibrinogen was then purified from plasma by classical glycine precipitation. In order to determine if this dysfibrinogen has altered rates of factor XIIIa cross-linking, cross-linking kinetics were assessed by incubating normal or mutant fibrinogen with factor XIII and thrombin and quantifying band intensity at successive timepoints for the resultant γ-γ dimers and α multimers by SDS-PAGE. Analysis of factor XIIIa cross-linking showed a significant decrease in the amount of γ-γ dimer formation when compared to normal fibrinogen (p<0.05 for both siblings) but no significant difference in the rate or quantity of α multimer formation. After an initial lag, the rate of γ-γ dimer formation was not appreciably different from that of the control. This decreased amount of cross-linking, which may also reflect the delay in fibrin polymerization, likely contributes to the hemorrhagic phenotype sometimes seen with this dysfibrinogen. Fibrinolysis kinetics were next measured by monitoring the optical density of purified Fibrinogen Hershey III clotted with thrombin in the presence of factor XIII, tissue plasminogen activator, and Glu-plasminogen. For the propositus, fibrinolysis was significantly delayed, with t1/2 of 51 ± 3 minutes (mean ± SEM) compared to 38 ± 0.2 minutes for normal fibrinogen. Similar results were obtained for the second sibling. The decreased rate of fibrinolysis could explain the paradoxical thrombotic phenotype sometimes seen with this dysfibrinogen. Thus the dual nature of the Aα R16C mutation is demonstrated by the simultaneous presence of deficient fibrinolysis and deficient fibrin cross-linking. Slower clot formation results from the delays in fibrinopeptide cleavage and fibrin polymerization. The delay in fibrinolysis, however, represents a hypercoagulable state leading to potential thrombosis. For this particular dysfibrinogen, the balance of procoagulant versus fibrinolytic factors may be most important in determining its clinical phenotype.

Substitution of the γ-chain Asn308 disturbs the D:D interface affecting fibrin polymerization, fibrinopeptide B release, and FXIIIa-catalyzed cross-linking

Blood ◽  
2004 ◽  
Vol 103 (11) ◽  
pp. 4157-4163 ◽  
Author(s):  
Nobuo Okumura ◽  
Oleg V. Gorkun ◽  
Fumiko Terasawa ◽  
Susan T. Lord
Keyword(s):  
High Performance ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Factor Xiiia ◽  
Cross Linking ◽  
Dimer Formation ◽  
Polymer Formation ◽  
Crystallographic Structures ◽  
Link Formation

Abstract Crystallographic structures indicate that γ-chain residue Asn308 participates in D:D interactions and indeed substitutions of γAsn308 with lysine or isoleucine have been identified in dysfibrinogens with impaired polymerization. To probe the role of Asn308 in polymerization, we synthesized 3 variant fibrinogens: γAsn308 changed to lysine (γN308K), isoleucine (γN308I), and alanine (γN308A). We measured thrombin-catalyzed polymerization by turbidity, fibrinopeptide release by high-performance liquid chromatography, and factor XIIIa–catalyzed cross-linking by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. In the absence of added calcium, polymerization was clearly impaired with all 3 variants. In contrast, at 0.1 mM calcium, only polymerization of γN308K remained markedly abnormal. The release of thrombin-catalyzed fibrinopeptide B (FpB) was delayed in the absence of calcium, whereas at 1 mM calcium FpB release was delayed only with γN308K. Factor XIIIa–catalyzed γ-γ dimer formation was delayed with fibrinogen (in absence of thrombin), whereas with fibrin (in presence of thrombin) γ-γ dimer formation of only γN308K was delayed. These data corroborate the recognized link between FpB release and polymerization. They show fibrin cross-link formation likely depends on the structure of protofibrils. Together, our results show substitution of Asn308 with a hydrophobic residue altered neither polymer formation nor polymer structure at physiologic calcium concentrations, whereas substitution with lysine altered both.

Photochemical behavior of some α, β-unsaturated lactams. Dependence of reaction path on multiplicity

1969 ◽  
Vol 47 (15) ◽  
pp. 2781-2786 ◽  
Author(s):  
E. Cavalieri ◽  
S. Horoupian
Keyword(s):  
Excited State ◽  
Spectral Properties ◽  
Reaction Path ◽  
Triplet Excited State ◽  
Excited Singlet ◽  
Cleavage Reaction ◽  
Dimer Formation ◽  
Cyclobutane Dimer ◽  
Direct Irradiation ◽  
Cyclobutane Dimers

Whereas direct irradiation (2537 Å) of 5,6-dihydro-4,6,6-trimethyl-2(1H)-pyridone 1 (1a) produced almost exclusively the cleavage products 2 and 3, the acetophenone sensitized reaction (3500 Å) gave a single cyclobutane dimer. In contrast, direct (2537 Å) or sensitized (acetophenone, 3500 Å) irradiation of the homo derivative 7 of compound 1 gave approximately the same mixture of two cyclobutane dimers. It was thus demonstrated that dimer formation proceeded by way of a triplet excited state and that the cleavage reaction most probably occurred via an excited singlet state.A structure for each cyclobutane dimer in the seven-membered series was proposed on the basis of its spectral properties.

scholarly journals Fibrinogen variant BβD432A has normal polymerization but does not bind knob “B”

Blood ◽  
2009 ◽  
Vol 113 (18) ◽  
pp. 4425-4430 ◽  
Author(s):  
Sheryl R. Bowley ◽  
Susan T. Lord
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Cross Linking ◽  
Dimer Formation ◽  
Fibrin Polymerization ◽  
Per Se ◽  
Clot Structure ◽  
Scanning Electron

AbstractFibrinogen residue Bβ432Asp is part of hole “b” that interacts with knob “B,” whose sequence starts with Gly-His-Arg-Pro-amide (GHRP). Because previous studies showed BβD432A has normal polymerization, we hypothesized that Bβ432Asp is not critical for knob “B” binding and that new knob-hole interactions would compensate for the loss of this Asp residue. To test this hypothesis, we solved the crystal structure of fragment D from BβD432A. Surprisingly, the structure (rfD-BβD432A+GH) showed the peptide GHRP was not bound to hole “b.” We then re-evaluated the polymerization of this variant by examining clot turbidity, clot structure, and the rate of FXIIIa cross-linking. The turbidity and the rate of γ-γ dimer formation for BβD432A were indistinguishable compared with normal fibrinogen. Scanning electron microscopy showed no significant differences between the clots of BβD432A and normal, but the thrombin-derived clots had thicker fibers than clots obtained from batroxobin, suggesting that cleavage of FpB is more important than “B:b” interactions. We conclude that hole “b” and “B:b” knob-hole binding per se have no influence on fibrin polymerization.

Triplet Excited Fluoroquinolones as Mediators for Thymine Cyclobutane Dimer Formation in DNA

2007 ◽  
Vol 111 (25) ◽  
pp. 7409-7414 ◽  
Author(s):  
Virginie Lhiaubet-Vallet ◽  
M. Consuelo Cuquerella ◽  
Jose V. Castell ◽  
Francisco Bosca ◽  
Miguel A. Miranda
Keyword(s):  
Dimer Formation ◽  
Cyclobutane Dimer

scholarly journals The action of mono- and di-functional sulphur mustards on the ribonucleic acid-containing bacteriophage μ2

1971 ◽  
Vol 125 (3) ◽  
pp. 829-840 ◽  
Author(s):  
K. V. Shooter ◽  
P. A. Edwards ◽  
P. D. Lawley
Keyword(s):  
Ribonucleic Acid ◽  
Cross Linking ◽  
Single Event ◽  
Reaction Products ◽  
Minor Contribution ◽  
The Mean ◽  
A Minor ◽  
Lethal Doses ◽  
Rna Bases

Bacteriophage μ2 is inactivated by both mono- and di-functional sulphur mustards at relatively low extents of alkylation. No degradation of alkylated RNA was detected. Cross-linking of RNA to protein was observed with the difunctional agent, but this reaction was only a minor contribution to the inactivation. Analyses of the reaction products in bacteriophage RNA showed that, at the mean lethal doses, more than one mono-alkylation of guanine had occurred but the sum total of other types of RNA alkylation was close to a single event. The results therefore suggest that inactivation results from the mono-alkylation of adenine or cytosine. In experiments with the difunctional agent cross-linking of RNA bases or of RNA to protein also prevented replication, the existence of these reactions accounting for the greater sensitivity of the bacteriophage to this agent.

scholarly journals The Aer Protein of Escherichia coli Forms a Homodimer Independent of the Signaling Domain and Flavin Adenine Dinucleotide Binding

2004 ◽  
Vol 186 (21) ◽  
pp. 7456-7459 ◽  
Author(s):  
Qinhong Ma ◽  
Francis Roy ◽  
Sarah Herrmann ◽  
Barry L. Taylor ◽  
Mark S. Johnson
Keyword(s):  
Escherichia Coli ◽  
Flavin Adenine Dinucleotide ◽  
Cross Linking ◽  
Membrane Anchor ◽  
Dimer Formation ◽  
Signaling Domain ◽  
Aer Receptor

ABSTRACT In vivo cross-linking between native cysteines in the Aer receptor of Escherichia coli showed dimer formation at the membrane anchor and in the putative HAMP domain. Dimers also formed in mutants that did not bind flavin adenine dinucleotide and in truncated peptides without a signaling domain and part of the HAMP domain.

scholarly journals Alpha-actinin of the chlorarchiniophyte Bigelowiella natans

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4288 ◽  
Author(s):  
Lars Backman
Keyword(s):  
Domain Structure ◽  
Calcium Binding ◽  
Actin Filaments ◽  
Actin Binding ◽  
Cross Linking ◽  
Primary Sequence ◽  
Dimer Formation ◽  
Spectrin Repeat ◽  
Actin Binding Domain ◽  
Ef Hand

The genome of the chlorarchiniophyte Bigelowiella natans codes for a protein annotated as an α-actinin-like protein. Analysis of the primary sequence indicate that this protein has the same domain structure as other α-actinins, a N-terminal actin-binding domain and a C-terminal calmodulin-like domain. These two domains are connected by a short rod domain, albeit long enough to form a single spectrin repeat. To analyse the functional properties of this protein, the full-length protein as well as the separate domains were cloned and isolated. Characerisation showed that the protein is capable of cross-linking actin filaments into dense bundles, probably due to dimer formation. Similar to human α-actinin, calcium-binding occurs to the most N-terminal EF-hand motif in the calmodulin-like C-terminal domain. The results indicate that this Bigelowiella protein is a proper α-actinin, with all common characteristics of a typical α-actinin.

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