The structural basis for the self-inhibition of DNA binding by apo-σ70
Joron, K.; Zamel, J.; Dvir, S.; Kalisman, N.; Lerner, E.
Show abstract
The initiation of transcription in Escherichia coli (E. coli) is facilitated by promoter specificity factors, also known as {sigma} factors, which may bind a promoter only as part of a complex with RNA polymerase (RNAP). By performing in vitro cross-linking mass spectrometry (CL-MS) of apo-{sigma}70, we reveal structural features suggesting a compact conformation compared to the known RNAP-bound extended conformation. Then, we validate the existence of the compact conformation using in vivo CL-MS by identifying cross-links similar to those found in vitro, which deviate from the extended conformation only during the stationary phase of bacterial growth. Conclusively, we provide information in support of a compact conformation of apo-{sigma}70 that exists in live cells, which might represent a transcriptionally-inactive form that can be activated upon binding to RNAP.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET 96%
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein 95%
- Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides 95%
Similar papers in this journal
- A small cationic probe for accurate, punctate discovery of RNA tertiary structure 93%
- Conformational modulation of a mobile loop controls catalysis in the (βα)8-barrel enzyme of histidine biosynthesis HisF 93%
- Substrate dynamics contribute to enzymatic specificity in human and bacterial methionine adenosyltransferases 93%
Similar papers in this journal
- DNA modulates structural transitions and oligomerization kinetics of the functional amyloid CRES 96%
- Rational design of protein-specific folding modifiers 95%
- Mass spectrometry of RNA-binding proteins during liquid-liquid phase separation reveals distinct assembly mechanisms and droplet architectures 94%
Similar papers in this journal
- Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine 93%
- Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage 93%
- Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.