Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Structural biology of RNA polymerase II transcription: 20 years on
S Osman, P Cramer - Annual Review of Cell and …, 2020 - annualreviews.org
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the
eukaryotic genome and a focal point for cellular regulation during development …
eukaryotic genome and a focal point for cellular regulation during development …
RNA polymerase II transcription: structure and mechanism
X Liu, DA Bushnell, RD Kornberg - Biochimica et Biophysica Acta (BBA) …, 2013 - Elsevier
A minimal RNA polymerase II (pol II) transcription system comprises the polymerase and five
general transcription factors (GTFs) TFIIB,-D,-E,-F, and-H. The addition of Mediator enables …
general transcription factors (GTFs) TFIIB,-D,-E,-F, and-H. The addition of Mediator enables …
Widespread backtracking by RNA Pol II is a major effector of gene activation, 5′ pause release, termination, and transcription elongation rate
In addition to phosphodiester bond formation, RNA polymerase II has an RNA
endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and …
endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and …
Enzyme dynamics point to stepwise conformational selection in catalysis
B Ma, R Nussinov - Current opinion in chemical biology, 2010 - Elsevier
Recent data increasingly reveal that conformational dynamics are indispensable to enzyme
function throughout the catalytic cycle, in substrate recruiting, chemical transformation, and …
function throughout the catalytic cycle, in substrate recruiting, chemical transformation, and …
RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases
(RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the …
(RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the …
A two-way street: regulatory interplay between RNA polymerase and nascent RNA structure
J Zhang, R Landick - Trends in biochemical sciences, 2016 - cell.com
The vectorial (5′-to-3′ at varying velocity) synthesis of RNA by cellular RNA polymerases
(RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long …
(RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long …
Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA
DksA and ppGpp are the central players in the stringent response and mediate a complete
reprogramming of the transcriptome. A major component of the response is a reduction in …
reprogramming of the transcriptome. A major component of the response is a reduction in …
Transcription elongation of the plant RNA polymerase IV is prone to backtracking
C Fang, K Huang, X Wu, H Zhang, Z Gu, J Wang… - Science …, 2024 - science.org
RNA polymerase IV (Pol IV) forms a complex with RNA-directed RNA polymerase 2 (RDR2)
to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In …
to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In …
Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II
During transcription, RNA polymerase II (RNAPII) must select the correct nucleotide,
catalyze its addition to the growing RNA transcript, and move stepwise along the DNA until a …
catalyze its addition to the growing RNA transcript, and move stepwise along the DNA until a …