Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering

Швецов, А. В.; Лебедев, Д. В.; Chervyakova, Daria B.; Bakhlanova, Irina V.; Yung, Igor A.; Rădulescu, Aurel; Куклин, А. И.; Baitin, Dmitry; Isaev-Ivanov, V. V.

doi:10.1016/j.febslet.2014.01.053

Cited by 17 publications

(17 citation statements)

References 41 publications

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“…We use, to our knowledge, a novel approach-a combination of modern molecular modeling techniques (33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46) and atomic force microscopy (AFM) measurements-to add experimentally consistent models of these three new members to the family of atomistic structures of the nucleosome particles. …”

Section: Introductionmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

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The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A$H2B)$(H3$H4) 2 , the tetrasome (H3$H4) 2 , and the disome (H3$H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Fö rster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

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Section: Introductionmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

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“…Since RecX is a small protein inhibiting RecA in the absence of any co-factors, it provides a good basis to develop a new class of peptide inhibitors of the protein. Over the past decade, new insights on the structure and function of RecX have been published and several mechanisms of RecA inhibition by RecX have been proposed ( 11 , 13 – 16 ). However, details of the mechanism of RecX action still remain unclear.…”

Section: Introductionmentioning

confidence: 99%

“…Another model suggests that RecX interacts with RecA monomers randomly along the whole filament and provokes RecA dissociation at the site of interaction ( 11 ). It was earlier obtained the spatial model of the nucleoprotein complex, where the RecX protein interacts both with DNA and RecA protein ( 16 ). Available data show that spatial structure of the RecX protein from Escherichia coli contains nine α-helices, one or more of which presumably bind within the RecA filament groove.…”

Section: Introductionmentioning

confidence: 99%

Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide

Yakimov

Pobegalov

Bakhlanova

et al. 2017

Nucleic Acids Research

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The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance.

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“…The regulatory protein DinI modulates RecA filament stability and function after assembly [ 49 – 51 ]. When RecA function is no longer needed, RecA filament removal from the DNA is ensured by additional bacterial regulatory proteins such as RecX protein and DinD protein [ 50 , 52 – 58 ], as well as the UvrD, Rep, and PcrA helicases [ 59 – 65 ]. Genetic modulation or ablation of these different controls often has deleterious consequences for the cell [ 20 , 60 , 61 , 66 – 70 ].…”

Section: Introductionmentioning

confidence: 99%

DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype

et al. 2016

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The RecA recombinase of Escherichia coli has not evolved to optimally promote DNA pairing and strand exchange, the key processes of recombinational DNA repair. Instead, the recombinase function of RecA protein represents an evolutionary compromise between necessary levels of recombinational DNA repair and the potentially deleterious consequences of RecA functionality. A RecA variant, RecA D112R, promotes conjugational recombination at substantially enhanced levels. However, expression of the D112R RecA protein in E. coli results in a reduction in cell growth rates. This report documents the consequences of the substantial selective pressure associated with the RecA-mediated hyperrec phenotype. With continuous growth, the deleterious effects of RecA D112R, along with the observed enhancements in conjugational recombination, are lost over the course of 70 cell generations. The suppression reflects a decline in RecA D112R expression, associated primarily with a deletion in the gene promoter or chromosomal mutations that decrease plasmid copy number. The deleterious effects of RecA D112R on cell growth can also be negated by over-expression of the RecX protein from Neisseria gonorrhoeae. The effects of the RecX proteins in vivo parallel the effects of the same proteins on RecA D112R filaments in vitro. The results indicate that the toxicity of RecA D112R is due to its persistent binding to duplex genomic DNA, creating barriers for other processes in DNA metabolism. A substantial selective pressure is generated to suppress the resulting barrier to growth.

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Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering

Cited by 17 publications

References 41 publications

Partially Assembled Nucleosome Structures at Atomic Detail

Partially Assembled Nucleosome Structures at Atomic Detail

Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide

DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype

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