Search Results - "Wedekind, Joseph E."

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control by Schroeder, Griffin M., Cavender, Chapin E., Blau, Maya E., Jenkins, Jermaine L., Mathews, David H., Wedekind, Joseph E.

“…Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream…”
Get full text

Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations by Srivastava, Yoshita, Akinyemi, Olayinka, Rohe, Tiana C, Pritchett, Elizabeth M, Baker, Cameron D, Sharma, Akshara, Jenkins, Jermaine L, Mathews, David H, Wedekind, Joseph E

“…Riboswitches are structured RNAs that sense small molecules to control expression. Prequeuosine1 (preQ1)-sensing riboswitches comprise three classes (I, II and…”
Get full text

A riboswitch separated from its ribosome-binding site still regulates translation by Schroeder, Griffin M, Akinyemi, Olayinka, Malik, Jeffrey, Focht, Caroline M, Pritchett, Elizabeth M, Baker, Cameron D, McSally, James P, Jenkins, Jermaine L, Mathews, David H, Wedekind, Joseph E

“…Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to…”
Get full text

RNA target highlights in CASP15: Evaluation of predicted models by structure providers by Kretsch, Rachael C., Andersen, Ebbe S., Bujnicki, Janusz M., Chiu, Wah, Das, Rhiju, Luo, Bingnan, Masquida, Benoît, McRae, Ewan K. S., Schroeder, Griffin M., Su, Zhaoming, Wedekind, Joseph E., Xu, Lily, Zhang, Kaiming, Zheludev, Ivan N., Moult, John, Kryshtafovych, Andriy

“…The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who…”
Get full text

Structural analysis of a class III preQ₁ riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics by Liberman, Joseph A., Suddala, Krishna C., Aytenfisu, Asaminew, Chan, Dalen, Belashov, Ivan A., Salim, Mohammad, Mathews, David H., Spitale, Robert C., Walter, Nils G., Wedekind, Joseph E.

“…PreQ₁-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ₁ (7-aminomethyl-7-deazaguanine), a precursor to the…”
Get full text

The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain by Spitale, Robert C., Torelli, Andrew T., Krucinska, Jolanta, Bandarian, Vahe, Wedekind, Joseph E.

“…Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ1 riboswitch exhibits the smallest known ligand-binding domain…”
Get full text

RNA in the Loop: Probing T-loop/T-loop Receptor Interactions as Mediators of Long-range RNA Contacts that Influence Gene Regulation by Wedekind, Joseph E.

Get full text

A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis by Liberman, Joseph A, Guo, Man, Jenkins, Jermaine L, Krucinska, Jolanta, Chen, Yuanyuan, Carey, Paul R, Wedekind, Joseph E

“…One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman…”
Get full text

Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing by Srivastava, Yoshita, Bonn-Breach, Rachel, Chavali, Sai Shashank, Lippa, Geoffrey M, Jenkins, Jermaine L, Wedekind, Joseph E

“…RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires…”
Get full text

APOBEC3G Subunits Self-associate via the C-terminal Deaminase Domain by Bennett, Ryan P., Salter, Jason D., Liu, Xiang, Wedekind, Joseph E., Smith, Harold C.

“…Human APOBEC3G (hA3G) is a cytidine deaminase active on HIV single-stranded DNA. Small angle x-ray scattering and molecular envelope restorations predicted a…”
Get full text

Nanostructures of APOBEC3G Support a Hierarchical Assembly Model of High Molecular Mass Ribonucleoprotein Particles from Dimeric Subunits by Wedekind, Joseph E., Gillilan, Richard, Janda, Alena, Krucinska, Jolanta, Salter, Jason D., Bennett, Ryan P., Raina, Jay, Smith, Harold C.

“…Human APOBEC3G (hA3G) is a cytidine deaminase that restricts human immunodeficiency virus (HIV)-1 infection in a vif (the virion infectivity factor from…”
Get full text

Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation by Guo, Man, Spitale, Robert C, Volpini, Rosaria, Krucinska, Jolanta, Cristalli, Gloria, Carey, Paul R, Wedekind, Joseph E

“…Catalytic RNA molecules can achieve rate acceleration by shifting base pK(a) values toward neutrality. Prior evidence has suggested that base A38 of the…”
Get full text

Nucleobase mutants of a bacterial preQ1-II riboswitch that uncouple metabolite sensing from gene regulation by Dutta, Debapratim, Wedekind, Joseph E.

“…Riboswitches are a class of nonprotein-coding RNAs that directly sense cellular metabolites to regulate gene expression. They are model systems for analyzing…”
Get full text

Nuclear Exclusion of the HIV-1 Host Defense Factor APOBEC3G Requires a Novel Cytoplasmic Retention Signal and Is Not Dependent on RNA Binding by Bennett, Ryan P., Presnyak, Vladimir, Wedekind, Joseph E., Smith, Harold C.

“…Human APOBEC3G (hA3G) is a host factor that defends against HIV-1 as well as other exogenous retroviruses and endogenous retroelements. To this end, hA3G is…”
Get full text

Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery by Chavali, Sai Shashank, Bonn-Breach, Rachel, Wedekind, Joseph E.

“…Small molecules and short peptides that potently and selectively bind RNA are rare, making the molecular structures of these complexes highly exceptional…”
Get full text

Structure and function analysis of a type III preQ1-I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence by Schroeder, Griffin M., Kiliushik, Daniil, Jenkins, Jermaine L., Wedekind, Joseph E.

“…Riboswitches are small noncoding RNAs found primarily in the 5′ leader regions of bacterial messenger RNAs where they regulate expression of downstream genes…”
Get full text

Full-Length NAD + -I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate by Srivastava, Yoshita, Blau, Maya E, Jenkins, Jermaine L, Wedekind, Joseph E

“…Bacterial riboswitches are structured RNAs that bind small metabolites to control downstream gene expression. Two riboswitch classes have been reported to…”
Get full text

Crystal Structure of the Leadzyme at 1.8 Å Resolution:  Metal Ion Binding and the Implications for Catalytic Mechanism and Allo Site Ion Regulation by Wedekind, Joseph E, McKay, David B

“…The leadzyme is a small ribozyme, derived from in vitro selection, which catalyzes site specific, Pb2+-dependent RNA cleavage. Pb2+ is required for activity;…”
Get full text

Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove by Chavali, Sai Shashank, Cavender, Chapin E, Mathews, David H, Wedekind, Joseph E

“…RNA recognition by proteins is central to biology. Here we demonstrate the existence of a recurrent structural motif, the “arginine fork”, that codifies…”
Get full text

Knotty is nice: metabolite binding and RNA-mediated gene regulation by the preQ1 riboswitch family by Kiliushik, Daniil, Goenner, Coleman, Law, Matthew, Schroeder, Griffin M., Srivastava, Yoshita, Jenkins, Jermaine L., Wedekind, Joseph E.

“…Riboswitches sense specific cellular metabolites, leading to messenger RNA conformational changes that regulate downstream genes. Here we review the three…”
Get full text