scholarly journals The effect of cross-links on the conformational dynamics of duplex DNA

1997 ◽  
Vol 25 (4) ◽  
pp. 836-842 ◽  
Author(s):  
R. J. Cain ◽  
G. D. Glick
Keyword(s):  
Conformational Dynamics ◽  
Duplex Dna ◽  
Cross Links

scholarly journals 4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA

2013 ◽  
Vol 41 (13) ◽  
pp. 6774-6781 ◽  
Author(s):  
Atsushi Nishimoto ◽  
Daichi Jitsuzaki ◽  
Kazumitsu Onizuka ◽  
Yosuke Taniguchi ◽  
Fumi Nagatsugi ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Pyrimidine Nucleosides ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
Selective Formation

scholarly journals Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA

2015 ◽  
Vol 43 (7) ◽  
pp. 3434-3441 ◽  
Author(s):  
Nathan E. Price ◽  
Michael J. Catalano ◽  
Shuo Liu ◽  
Yinsheng Wang ◽  
Kent S. Gates
Keyword(s):  
Structural Characterization ◽  
Duplex Dna ◽  
Abasic Sites ◽  
Interstrand Cross Links ◽  
Cross Links

Abstract 263: Isotopic Labeling and Chemical Cross-Linking Reveals Intermolecular Contacts and Dynamics of Apolipoprotein A-I Structure in Reconstituted HDL Particles

2012 ◽  
Vol 32 (suppl_1) ◽  
Author(s):  
Jamie Morris ◽  
Martin K Jones ◽  
Gang Ren ◽  
Jere Segrest ◽  
W Sean Davidson
Keyword(s):  
Conformational Dynamics ◽  
Density Lipoprotein ◽  
Isotopic Labeling ◽  
Peptide Fragmentation ◽  
Cross Linking ◽  
Naturally Occurring ◽  
Intermolecular Contacts ◽  
Cross Links ◽  
Mass Shifts ◽  
Chemical Cross Linking

Apolipoprotein (apo)A-I has been proposed to adopt a number of different, but related, structures when in contact with lipid. The technique of chemical cross-linking has recently been used to determine the spatial relationships between two molecules of apoA-I in reconstituted high density lipoprotein (rHDL) particles. However, this technique is limited in that it cannot unequivocally distinguish between intramolecular and intermolecular contacts. To address this issue, we have produced two forms of recombinant apoA-I that contain the naturally occurring isotope of nitrogen (N14) or a stable isotope (N15). These forms were mixed 1:1 and then used to produce reconstituted HDL particles with synthetic lipids. The resulting mass shifts (readily detectable in the mass spectrometer) were exploited to unambiguously distinguish between intramolecular (N14 to N14 or N15 to N15) and intermolecular (N14 to N15) cross-linked peptides. An additional benefit of this approach was the ability to identify cross-links with high certainty without the need for peptide fragmentation, allowing for dramatic increases in method sensitivity. We studied highly homogeneous rHDL particles made with the fully saturated phospholipid palmitoyl steroyl phosphatidylcholine (PSPC) to minimize apoA-I conformational dynamics. These particles were 98Å in diameter, contained two molecules of apoA-I, approximately 155 molecules of PC, and were discoidal in shape by cryo EM. We identified 30 cross-links (17 intramolecular, 13 intermolecular) that were overall consistent with the double belt model in which both apoA-I molecules wrap around a bilayer of lipids in an antiparallel orientation. Unambiguous intramolecular linkages between the N- and C-terminal regions of apoA-I were inconsistent with the ‘double super helix’ variant of the belt model. We identified several low abundance cross-links that suggest that the N-terminus may be conformationally dynamic and may spend some time folded back across the molecule as proposed for the ‘belt and buckle’ belt model.

scholarly journals High-density chemical cross-linking for modeling protein interactions

2019 ◽  
Vol 117 (1) ◽  
pp. 93-102 ◽  
Author(s):  
Julian Mintseris ◽  
Steven P. Gygi
Keyword(s):  
Mass Spectrometry ◽  
Method Development ◽  
Conformational Dynamics ◽  
Complex Function ◽  
Computational Cost ◽  
Dimensional Structure ◽  
Cross Linking ◽  
Proteasome Subunits ◽  
Cross Links ◽  
Chemical Cross Linking

Detailed mechanistic understanding of protein complex function is greatly enhanced by insights from its 3-dimensional structure. Traditional methods of protein structure elucidation remain expensive and labor-intensive and require highly purified starting material. Chemical cross-linking coupled with mass spectrometry offers an alternative that has seen increased use, especially in combination with other experimental approaches like cryo-electron microscopy. Here we report advances in method development, combining several orthogonal cross-linking chemistries as well as improvements in search algorithms, statistical analysis, and computational cost to achieve coverage of 1 unique cross-linked position pair for every 7 amino acids at a 1% false discovery rate. This is accomplished without any peptide-level fractionation or enrichment. We apply our methods to model the complex between a carbonic anhydrase (CA) and its protein inhibitor, showing that the cross-links are self-consistent and define the interaction interface at high resolution. The resulting model suggests a scaffold for development of a class of protein-based inhibitors of the CA family of enzymes. We next cross-link the yeast proteasome, identifying 3,893 unique cross-linked peptides in 3 mass spectrometry runs. The dataset includes 1,704 unique cross-linked position pairs for the proteasome subunits, more than half of them intersubunit. Using multiple recently solved cryo-EM structures, we show that observed cross-links reflect the conformational dynamics and disorder of some proteasome subunits. We further demonstrate that this level of cross-linking density is sufficient to model the architecture of the 19-subunit regulatory particle de novo.

scholarly journals Cho Endonuclease Functions during DNA Interstrand Cross-Link Repair in Escherichia coli

2016 ◽  
Vol 198 (22) ◽  
pp. 3099-3108 ◽  
Author(s):  
Anthonige Vidya Perera ◽  
James Brian Mendenhall ◽  
Charmain Tan Courcelle ◽  
Justin Courcelle
Keyword(s):  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Repair Process ◽  
Differential Sensitivity ◽  
Duplex Dna ◽  
Dna Lesion ◽  
Nucleotide Excision ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
Complex Lesions

ABSTRACTDNA interstrand cross-links are complex lesions that covalently link both strands of the duplex DNA. Lesion removal is proposed to be initiated via the UvrABC nucleotide excision repair complex; however, less is known about the subsequent steps of this complex repair pathway. In this study, we characterized the contribution of nucleotide excision repair mutants to survival in the presence of psoralen-induced damage. Unexpectedly, we observed that the nucleotide excision repair mutants exhibit differential sensitivity to psoralen-induced damage, withuvrCmutants being less sensitive than eitheruvrAoruvrB. We show that Cho, an alternative endonuclease, acts with UvrAB and is responsible for the reduced hypersensitivity ofuvrCmutants. We find that Cho's contribution to survival correlates with the presence of DNA interstrand cross-links, rather than monoadducts, and operates at a step after, or independently from, the initial incision during the global repair of psoralen DNA adducts from the genome.IMPORTANCEDNA interstrand cross-links are complex lesions that covalently bind to both strands of the duplex DNA and whose mechanism of repair remains poorly understood. In this study, we show that Cho, an alternative endonuclease, acts with UvrAB and participates in the repair of DNA interstrand cross-links formed in the presence of photoactivated psoralens. Cho's contribution to survival correlates with the presence of DNA interstrand cross-links and operates at a step after, or independently from, the initial incision during the repair process.

scholarly journals Nucleosomal embedding reshapes the dynamics of abasic sites

2020 ◽  
Author(s):  
Emmanuelle Bignon ◽  
Victor Claerbout ◽  
Tao Jiang ◽  
Christophe Morell ◽  
Natacha Gillet ◽  
...  
Keyword(s):  
Conformational Dynamics ◽  
Dna Lesions ◽  
Nucleosome Core ◽  
Abasic Sites ◽  
Nucleosomal Dna ◽  
Cross Links ◽  
Ap Sites ◽  
Base Excision ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTApurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the occurrence of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. This study paves the way towards an in silico mapping of DNA-protein cross-links.

Mechlorethamine cross-links deoxyguanosine residues at 5'-GNC sequences in duplex DNA fragments

1990 ◽  
Vol 112 (6) ◽  
pp. 2459-2460 ◽  
Author(s):  
Julie T. Millard ◽  
Stanley Raucher ◽  
Paul B. Hopkins
Keyword(s):  
Duplex Dna ◽  
Dna Fragments ◽  
Cross Links

scholarly journals Interstrand Cross-Links Generated by Abasic Sites in Duplex DNA

2007 ◽  
Vol 129 (7) ◽  
pp. 1852-1853 ◽  
Author(s):  
Sanjay Dutta ◽  
Goutam Chowdhury ◽  
Kent S. Gates
Keyword(s):  
Duplex Dna ◽  
Abasic Sites ◽  
Interstrand Cross Links ◽  
Cross Links
Sign in / Sign up

Export Citation Format

Share Document