Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite
| dc.contributor.author | Clingman, Carina C. | |
| dc.contributor.author | Deveau, Laura M. | |
| dc.contributor.author | Hay, Samantha A. | |
| dc.contributor.author | Genga, Ryan M. J. | |
| dc.contributor.author | Shandilya, Shivender | |
| dc.contributor.author | Massi, Francesca | |
| dc.contributor.author | Ryder, Sean P. | |
| dc.date | 2022-08-11T08:09:43.000 | |
| dc.date.accessioned | 2022-08-23T16:40:49Z | |
| dc.date.available | 2022-08-23T16:40:49Z | |
| dc.date.issued | 2014-06-16 | |
| dc.date.submitted | 2015-09-02 | |
| dc.identifier.citation | Elife. 2014 Jun 16;3:e02848. doi: 10.7554/eLife.02848. <a href="http://dx.doi.org/10.7554/eLife.02848">Link to article on publisher's site</a> | |
| dc.identifier.issn | 2050-084X (Linking) | |
| dc.identifier.doi | 10.7554/eLife.02848 | |
| dc.identifier.pmid | 24935936 | |
| dc.identifier.uri | http://hdl.handle.net/20.500.14038/39757 | |
| dc.description | <p>First author Carina C. Clingman is a doctoral student in the Biochemistry and Molecular Pharmacology Program in the Graduate School of Biomedical Sciences (GSBS) at UMass Medical School.</p> | |
| dc.description.abstract | Gene expression and metabolism are coupled at numerous levels. Cells must sense and respond to nutrients in their environment, and specialized cells must synthesize metabolic products required for their function. Pluripotent stem cells have the ability to differentiate into a wide variety of specialized cells. How metabolic state contributes to stem cell differentiation is not understood. In this study, we show that RNA-binding by the stem cell translation regulator Musashi-1 (MSI1) is allosterically inhibited by 18-22 carbon omega-9 monounsaturated fatty acids. The fatty acid binds to the N-terminal RNA Recognition Motif (RRM) and induces a conformational change that prevents RNA association. Musashi proteins are critical for development of the brain, blood, and epithelium. We identify stearoyl-CoA desaturase-1 as a MSI1 target, revealing a feedback loop between omega-9 fatty acid biosynthesis and MSI1 activity. We propose that other RRM proteins could act as metabolite sensors to couple gene expression changes to physiological state. | |
| dc.language.iso | en_US | |
| dc.relation | <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=24935936&dopt=Abstract">Link to Article in PubMed</a> | |
| dc.relation.url | http://dx.doi.org/10.7554/eLife.02848 | |
| dc.rights | <p>© 2014, Clingman et al. This article is distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a>, which permits unrestricted use and redistribution provided that the original author and source are credited.</p> | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
| dc.subject | Allosteric Site | |
| dc.subject | Amino Acid Motifs | |
| dc.subject | Animals | |
| dc.subject | Cell Differentiation | |
| dc.subject | Cell Line, Tumor | |
| dc.subject | Gene Expression Profiling | |
| dc.subject | Gene Expression Regulation | |
| dc.subject | Mice | |
| dc.subject | Molecular Dynamics Simulation | |
| dc.subject | Nerve Tissue Proteins | |
| dc.subject | Oleic Acid | |
| dc.subject | Pluripotent Stem Cells | |
| dc.subject | Protein Structure, Tertiary | |
| dc.subject | RNA-Binding Proteins | |
| dc.subject | Recombinant Proteins | |
| dc.subject | Stearoyl-CoA Desaturase | |
| dc.subject | Stem Cells | |
| dc.subject | Structure-Activity Relationship | |
| dc.subject | RNA-binding protein | |
| dc.subject | biochemistry | |
| dc.subject | biophysics | |
| dc.subject | gene expression | |
| dc.subject | metabolism | |
| dc.subject | oligodendrocyte | |
| dc.subject | post-transcriptional regulation | |
| dc.subject | structural biology | |
| dc.subject | Biochemistry | |
| dc.subject | Biochemistry, Biophysics, and Structural Biology | |
| dc.subject | Biophysics | |
| dc.subject | Genetics and Genomics | |
| dc.subject | Genomics | |
| dc.subject | Structural Biology | |
| dc.title | Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite | |
| dc.type | Journal Article | |
| dc.source.journaltitle | eLife | |
| dc.source.volume | 3 | |
| dc.identifier.legacyfulltext | https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=3557&context=oapubs&unstamped=1 | |
| dc.identifier.legacycoverpage | https://escholarship.umassmed.edu/oapubs/2553 | |
| dc.identifier.contextkey | 7548583 | |
| refterms.dateFOA | 2022-08-23T16:40:49Z | |
| html.description.abstract | <p>Gene expression and metabolism are coupled at numerous levels. Cells must sense and respond to nutrients in their environment, and specialized cells must synthesize metabolic products required for their function. Pluripotent stem cells have the ability to differentiate into a wide variety of specialized cells. How metabolic state contributes to stem cell differentiation is not understood. In this study, we show that RNA-binding by the stem cell translation regulator Musashi-1 (MSI1) is allosterically inhibited by 18-22 carbon omega-9 monounsaturated fatty acids. The fatty acid binds to the N-terminal RNA Recognition Motif (RRM) and induces a conformational change that prevents RNA association. Musashi proteins are critical for development of the brain, blood, and epithelium. We identify stearoyl-CoA desaturase-1 as a MSI1 target, revealing a feedback loop between omega-9 fatty acid biosynthesis and MSI1 activity. We propose that other RRM proteins could act as metabolite sensors to couple gene expression changes to physiological state.</p> | |
| dc.identifier.submissionpath | oapubs/2553 | |
| dc.contributor.department | Department of Biochemistry and Molecular Pharmacology | |
| dc.source.pages | e02848 |
Files in this item
This item appears in the following Collection(s)
Except where otherwise noted, this item's license is described as <p>© 2014, Clingman et al. This article is distributed under the terms of the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</a>, which permits unrestricted use and redistribution provided that the original author and source are credited.</p>
Related items
Showing items related by title, author, creator and subject.
-
Modulation of frustration in folding by sequence permutationFolding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.
-
The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanismGTPase activating proteins (GAPs) from pathogenic bacteria and eukaryotic host organisms deactivate Rab GTPases by supplying catalytic arginine and glutamine fingers in trans and utilizing the cis-glutamine in the DXXGQ motif of the GTPase for binding rather than catalysis. Here, we report the transition state mimetic structure of the Legionella pneumophila GAP LepB in complex with Rab1 and describe a comprehensive structure-based mutational analysis of potential catalytic and recognition determinants. The results demonstrate that LepB does not simply mimic other GAPs but instead deploys an expected arginine finger in conjunction with a novel glutamic acid finger, which forms a salt bridge with an indispensible switch II arginine that effectively locks the cis-glutamine in the DXXGQ motif of Rab1 in a catalytically competent though unprecedented transition state configuration. Surprisingly, a heretofore universal transition state interaction with the cis-glutamine is supplanted by an elaborate polar network involving critical P-loop and switch I serines. LepB further employs an unusual tandem domain architecture to clamp a switch I tyrosine in an open conformation that facilitates access of the arginine finger to the hydrolytic site. Intriguingly, the critical P-loop serine corresponds to an oncogenic substitution in Ras and replaces a conserved glycine essential for the canonical transition state stereochemistry. In addition to expanding GTP hydrolytic paradigms, these observations reveal the unconventional dual finger and non-canonical catalytic network mechanisms of Rab GAPs as necessary alternative solutions to a major impediment imposed by substitution of the conserved P-loop glycine.
-
Protein-protein docking benchmark version 4.0We updated our protein-protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high-resolution complex structures that are nonredundant at the family-family pair level, for which the X-ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound-unbound cases that can be used for protein-protein docking method development and assessment. Seventeen of the newly added cases are enzyme-inhibitor complexes, and we found no new antigen-antibody complexes. Classifying the new cases according to expected difficulty for protein-protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/.
