scholarly journals Structural and thermodynamic analyses of the β-to-α transformation in RfaH reveal principles of fold-switching proteins

2022 ◽  
Author(s):  
Philipp K Zuber ◽  
Tina Daviter ◽  
Ramona Heissmann ◽  
Ulrike Persau ◽  
Kristian Schweimer ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Structural Biology ◽  
Structural Dynamics ◽  
Thermodynamic Stability ◽  
Conformational Switch ◽  
Domain Protein

The two-domain protein RfaH, a paralog of the universally conserved NusG/Spt5 transcription factors, is regulated by autoinhibition coupled to the reversible conformational switch of its 60- residue C-terminal KOW domain between an α-hairpin and a β-barrel. In contrast, NusG/Spt5-KOW domains only occur in the β-barrel state. To understand the principles underlying the drastic fold switch in RfaH, we elucidated the thermodynamic stability and the structural dynamics of two RfaH- and four NusG/Spt5-KOW domains by combining biophysical and structural biology methods. We find that the RfaH-KOW β-barrel is thermodynamically less stable than that of most NusG/Spt5-KOWs and we show that it is in equilibrium with a globally unfolded species, which, strikingly, contains two helical regions that prime the transition towards the α-hairpin. Our results suggest that transiently structured elements in the unfolded form might drive the global folding transition in metamorphic proteins in general.

scholarly journals Structural Dynamics of the Heterodimerization Between the DNA-Binding Domains from Human FoxP1 and FoP2 Transcription Factors

2021 ◽  
Vol 120 (3) ◽  
pp. 127a
Author(s):  
Exequiel Medina ◽  
Ricardo Coñuecar ◽  
Cesar A. Ramirez-Sarmiento ◽  
Hugo Sanabria ◽  
Jorge Babul
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Structural Dynamics ◽  
Dna Binding Domains ◽  
Binding Domains

scholarly journals Multiplexed, bioorthogonal labeling of multicomponent, biomolecular complexes using genomically encoded, non-canonical amino acids

2019 ◽  
Author(s):  
Bijoy J. Desai ◽  
Ruben L. Gonzalez
Keyword(s):  
Amino Acids ◽  
Structural Biology ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Functional Studies ◽  
Bioorthogonal Labeling ◽  
Biomolecular Complexes ◽  
And Function

Stunning advances in the structural biology of multicomponent biomolecular complexes (MBCs) have ushered in an era of intense, structure-guided mechanistic and functional studies of these complexes. Nonetheless, existing methods to site-specifically conjugate MBCs with biochemical and biophysical labels are notoriously impracticable and/or significantly perturb MBC assembly and function. To overcome these limitations, we have developed a general, multiplexed method in which we genomically encode non-canonical amino acids (ncAAs) into multiple, structure-informed, individual sites within a target MBC; select for ncAA-containing MBC variants that assemble and function like the wildtype MBC; and site-specifically conjugate biochemical or biophysical labels to these ncAAs. As a proof-of-principle, we have used this method to generate unique single-molecule fluorescence resonance energy transfer (smFRET) signals reporting on ribosome structural dynamics that have thus far remained inaccessible to smFRET studies of translation.

scholarly journals Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

2014 ◽  
Vol 55 (5) ◽  
pp. 708-722 ◽  
Author(s):  
Andrew J. Oldfield ◽  
Pengyi Yang ◽  
Amanda E. Conway ◽  
Senthilkumar Cinghu ◽  
Johannes M. Freudenberg ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Chromatin Accessibility ◽  
Cell Type ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
Cell Type Specific ◽  
Domain Protein

scholarly journals Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermodynamic Stability

Biochemistry ◽  
2014 ◽  
Vol 53 (9) ◽  
pp. 1456-1465 ◽  
Author(s):  
Hari Bhaskaran ◽  
Takaaki Taniguchi ◽  
Takeo Suzuki ◽  
Tsutomu Suzuki ◽  
John J. Perona
Keyword(s):  
Structural Dynamics ◽  
Thermodynamic Stability ◽  
Mitochondrial Trna

scholarly journals Auxin Response Factors — output control in auxin biology

2017 ◽  
Author(s):  
Mark Roosjen ◽  
Sébastien Paque ◽  
Dolf Weijers
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Structural Biology ◽  
Auxin Signaling ◽  
Auxin Response ◽  
Response Factors ◽  
Output Control ◽  
Auxin Response Factors ◽  
Almost All ◽  
Near Future

AbstractThe phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal to the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family likely contributes to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics and structural biology have helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.

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