Promiscuity in protein‐RNA interactions: Conformational ensembles facilitate molecular recognition in the spliceosome

Boehr, David D.

doi:10.1002/bies.201100152

Cited by 13 publications

(11 citation statements)

References 78 publications

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“…Recent work suggests that conformational changes at the binding site are often responsible for the ability of proteins to bind different ligands (52,53). Using MD simulations, we determined the extent by which DBD-F is susceptible to conformational change (Figure 5).…”

Section: Resultsmentioning

confidence: 99%

A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A

Glanzer

Carnes

Soto

et al. 2012

Nucleic Acids Research

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Replication protein A (RPA), essential for DNA replication, repair and DNA damage signalling, possesses six ssDNA-binding domains (DBDs), including DBD-F on the N-terminus of the largest subunit, RPA70. This domain functions as a binding site for p53 and other DNA damage and repair proteins that contain amphipathic alpha helical domains. Here, we demonstrate direct binding of both ssDNA and the transactivation domain 2 of p53 (p53TAD2) to DBD-F, as well as DBD-F-directed dsDNA strand separation by RPA, all of which are inhibited by fumaropimaric acid (FPA). FPA binds directly to RPA, resulting in a conformational shift as determined through quenching of intrinsic tryptophan fluorescence in full length RPA. Structural analogues of FPA provide insight on chemical properties that are required for inhibition. Finally, we confirm the inability of RPA possessing R41E and R43E mutations to bind to p53, destabilize dsDNA and quench tryptophan fluorescence by FPA, suggesting that protein binding, DNA modulation and inhibitor binding all occur within the same site on DBD-F. The disruption of p53–RPA interactions by FPA may disturb the regulatory functions of p53 and RPA, thereby inhibiting cellular pathways that control the cell cycle and maintain the integrity of the human genome.

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Section: Resultsmentioning

confidence: 99%

A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A

Glanzer

Carnes

Soto

et al. 2012

Nucleic Acids Research

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“…One way viruses maximize the information content in their genomes is to encode multifunctional proteins like the 3C protease. One way to rationalize the multiple functions of 3C is to envision an ensemble of conformations, whose members are responsible for different functions (Boehr, 2012). For example, different conformations may be responsible for interacting with different RNA or protein binding partners; similar scenarios have been invoked for ubiquitin (Lange et al, 2008) and other proteins (Boehr et al, 2009) to help explain how these proteins interact with such divergent binding partners.…”

Section: Discussionmentioning

confidence: 99%

Long-Range Communication between Different Functional Sites in the Picornaviral 3C Protein

et al. 2016

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Summary The 3C protein is a master regulator of the picornaviral infection cycle, responsible for both cleaving viral and host proteins, and interacting with genomic RNA replication elements. Here we use nuclear magnetic resonance spectroscopy and molecular dynamics simulations to show that 3C is conformationally dynamic across multiple timescales. Binding of peptide and RNA lead to structural dynamics changes at both the protease active site and the RNA binding site, consistent with these sites being dynamically coupled. Indeed, binding of RNA influences protease activity, and likewise, interactions at the active site affect RNA binding. We propose that RNA and peptide binding reshapes the conformational energy landscape of 3C to regulate subsequent functions, including formation of complexes with other viral proteins. The observed channeling of the 3C energy landscape may be important for regulation of the viral infection cycle.

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“…Critically, the timing of the ligand interaction and the structural changes to the enzyme is not trivial; the processes of conformational selection and induced change have important biological consequences in terms of substrate promiscuity, enzyme regulation, protein evolution, and biological information storage 4. 42, 43…”

Section: Introductionmentioning

confidence: 99%

Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase

Weikl

Boehr

2012

Proteins

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Protein function often involves changes between different conformations. Central questions are how these conformational changes are coupled to the binding or catalytic processes during which they occur, and how they affect the catalytic rates of enzymes. An important model system is the enzyme dihydrofolate reductase (DHFR) from Escherichia coli, which exhibits characteristic conformational changes of the active-site loop during the catalytic step and during unbinding of the product. In this article, we present a general kinetic framework that can be used (1) to identify the ordering of events in the coupling of conformational changes, binding, and catalysis and (2) to determine the rates of the substeps of coupled processes from a combined analysis of nuclear magnetic resonance R(2) relaxation dispersion experiments and traditional enzyme kinetics measurements. We apply this framework to E. coli DHFR and find that the conformational change during product unbinding follows a conformational-selection mechanism, that is, the conformational change occurs predominantly prior to unbinding. The conformational change during the catalytic step, in contrast, is an induced change, that is, the change occurs after the chemical reaction. We propose that the reason for these conformational changes, which are absent in human and other vertebrate DHFRs, is robustness of the catalytic rate against large pH variations and changes to substrate/product concentrations in E. coli.

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Promiscuity in protein‐RNA interactions: Conformational ensembles facilitate molecular recognition in the spliceosome

Cited by 13 publications

References 78 publications

A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A

A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A

Long-Range Communication between Different Functional Sites in the Picornaviral 3C Protein

Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase

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