The disordered C-terminus of the RNA Polymerase II phosphatase FCP1 is partially helical in the unbound state

Lawrence, Chad W.; Bonny, Alain R; Showalter, Scott A.

doi:10.1016/j.bbrc.2011.05.160

Cited by 21 publications

(34 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interaction between the winged helix domain of RAP74, a component of the general transcription factor IIF (TFIIF), and the C‐terminus of the TFIIF‐associating CTD phosphatase (FCP1) is responsible for recycling of RNA polymerase II after transcription [110]. The formation of this recycling complex is driven by the partially structured sub‐region of the intrinsically disordered C‐terminal domain of FCP1 that forms an α‐helix in the complex and that possesses nascent α‐helical structure in the unbound state [110].…”

Section: Functional Repertoire Of Flexible Tailsmentioning

confidence: 99%

The most important thing is the tail: Multitudinous functionalities of intrinsically disordered protein termini

2013

View full text Add to dashboard Cite

a b s t r a c tMany functional proteins do not have well-folded structures in their substantial parts, representing hybrids that possess both ordered and disordered regions. Disorder is unevenly distributed within these hybrid proteins and is typically more common at protein termini. Disordered tails are engaged in a wide range of functions, some of which are unique for termini and cannot be found in other disordered parts of a protein. This review covers some of the key functions of disordered protein termini and emphasizes that these tails are not simple flexible protrusions but are evolved to serve.

show abstract

Section: Functional Repertoire Of Flexible Tailsmentioning

confidence: 99%

The most important thing is the tail: Multitudinous functionalities of intrinsically disordered protein termini

2013

View full text Add to dashboard Cite

show abstract

“… 39 The phosphorylation of an SPN element in the CTD of RNA polymerase has been shown to enhance the cis-state of the proline. 40 Our data indicate that phosphorylation of the linker could destabilize the bound-state conformation and thus alter the regulatory role of the AT-L-BD in BAF function. 29 , 30 Further studies will be required to fully elucidate how this region is regulating BAF activity.…”

Section: Discussionmentioning

confidence: 74%

Evolutionary Conservation of Structural and Functional Coupling between the BRM AT-Hook and Bromodomain

Lupo

Chu

Harms

et al. 2021

Journal of Molecular Biology

View full text Add to dashboard Cite

The BAF chromatin remodeling complex is critical for genome regulation. The central ATPase of BAF is either BRM or BRG1, both of which contain a C-terminal bromodomain, known to associate with acetylated lysines. We have recently demonstrated that in addition to acetyl-lysine binding, the BRG1/BRM bromodomain can associate with DNA through a lysine/arginine rich patch that is adjacent to the acetyl-lysine binding pocket. Flanking the bromodomain is an AT-hook separated by a short, proline-rich linker. We previously found that the AT-hook and bromodomain can associate with DNA in a multivalent manner. Here, we investigate the conservation of this composite module and find that the AT-hook, linker, and lysine/arginine rich bromodomain patch are ancient, conserved over ~1 billion years. We utilize extensive mutagenesis, NMR spectroscopy, and fluorescence anisotropy to dissect the contribution of each of these conserved elements in association of this module with DNA. Our results reveal a structural and functional coupling of the AT-hook and bromodomain mediated by the linker. The lysine/arginine rich patch on the bromodomain and the conserved elements of the AT-hook are critical for robust affinity for DNA, while the conserved elements of the linker are dispensable for overall DNA affinity but critical for maintaining the relative conformation of the AT-hook and bromodomain in binding to DNA. This supports that the coupled action of the AT-hook and bromodomain are important for BAF activity.

show abstract

“…The C‐terminus of the TFIIF‐associating CTD phosphatase exhibits a 16‐residue‐long helical region in its bound form, whereas it is disordered in the unbound state. Lawrence et al 31 show that also in the disordered state residues 945–955 form a nascent α‐helical structure. Our HMM detects a strong α‐helical signal in the same region [Fig.…”

Section: Resultsmentioning

confidence: 99%

A probabilistic model for secondary structure prediction from protein chemical shifts

Mechelke

Habeck

2013

Proteins

View full text Add to dashboard Cite

Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts.

show abstract

The disordered C-terminus of the RNA Polymerase II phosphatase FCP1 is partially helical in the unbound state

Cited by 21 publications

References 28 publications

The most important thing is the tail: Multitudinous functionalities of intrinsically disordered protein termini

The most important thing is the tail: Multitudinous functionalities of intrinsically disordered protein termini

Evolutionary Conservation of Structural and Functional Coupling between the BRM AT-Hook and Bromodomain

A probabilistic model for secondary structure prediction from protein chemical shifts

Contact Info

Product

Resources

About