Recent Facility Publications

• Srivastava Y, Blau ME, Jenkins JL, Wedekind JE. Full-Length NAD(+)-I Riboswitches Bind a Single Cofactor but Cannot Discriminate against Adenosine Triphosphate. Biochemistry. 2023 Dec 5;62(23):3396-3410. PubMed PMID: 37947391; PubMed Central PMCID: PMC10702441.
• Schroeder GM, Kiliushik D, Jenkins JL, Wedekind JE. Structure and function analysis of a type III preQ(1)-I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence. J Biol Chem. 2023 Oct;299(10):105208.  PubMed PMID: 37660906; PubMed Central PMCID: PMC10622847.
• Schroeder GM, Akinyemi O, Malik J, Focht CM, Pritchett EM, Baker CD, McSally JP, Jenkins JL, Mathews DH, Wedekind JE. A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic Acids Res. 2023 Mar 21;51(5):2464-2484. PubMed PMID: 36762498; PubMed Central PMCID: PMC10018353.
• Sparks RP, Arango AS, Starr ML, Aboff ZL, Hurst LR, Rivera-Kohr DA, Zhang C, Harnden KA, Jenkins JL, Guida WC, Tajkhorshid E, Fratti RA. Correction: A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion. J Biol Chem. 2022 Nov;298(11):102576.  PubMed PMID: 36257250; PubMed Central PMCID: PMC9579040.
• Galardi JW, Bela VN, Jeffery N, He X, Glasser E, Loerch S, Jenkins JL, Pulvino MJ, Boutz PL, Kielkopf CL. A UHM-ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing. J Biol Chem. 2022 Aug;298(8):102224.  PubMed PMID: 35780835; PubMed Central PMCID: PMC9364107.
• Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL. Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic Acids Res. 2022 May 20;50(9):5299-5312.  PubMed PMID: 35524551; PubMed Central PMCID: PMC9128377.
• Schroeder GM, Cavender CE, Blau ME, Jenkins JL, Mathews DH, Wedekind JE. A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nat Commun. 2022 Jan 11;13(1):199.  PubMed PMID: 35017488; PubMed Central PMCID: PMC8752633.
• Chatrikhi R, Feeney CF, Pulvino MJ, Alachouzos G, MacRae AJ, Falls Z, Rai S, Brennessel WW, Jenkins JL, Walter MJ, Graubert TA, Samudrala R, Jurica MS, Frontier AJ, Kielkopf CL. A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell Chem Biol. 2021 Aug 19;28(8):1145-1157.e6. doi: 10.1016/j.chembiol.2021.02.007. Epub 2021 Mar 8. PubMed PMID: 33689684; PubMed Central PMCID: PMC8380659.
• Srivastava Y, Bonn-Breach R, Chavali SS, Lippa GM, Jenkins JL, Wedekind JE. Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing. Crystals (Basel). 2021 Mar;11(3). doi: 10.3390/cryst11030273. Epub 2021 Mar 10. PubMed PMID: 33777416; PubMed Central PMCID: PMC7996396.
• Carminati DM, Moore EJ, Fasan R. Strategies for the expression and characterization of artificial myoglobin-based carbene transferases Methods Enzymol. 2020;644:35-61 doi: 10.1016/bs.mie.2020.07.007. Epub 2020 Aug 6. PMID: 32943150
• Swamy H, Glading AJ. Contribution of protein-protein interactions to the endothelial barrier-stabilizing function of KRIT1. J Cell Sci. 2021 Dec 17; doi: 10.1242/jcs.258816. PMID: 34918736
• Maji D, Glasser E, Henderson S, Galardi J, Pulvino MJ, Jenkins JL, Kielkopf CL (2020) Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing. J Biol Chem 295, 17148-17157 PubMed PMID: 33453965
• Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE (2020) Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors. J Biol Chem 295, 16470-16486 PubMed PMID: 33051202
• Sparks RP, Arango AS, Jenkins JL, Guida WC, Tajkhorshid E, Sparks CE, Sparks JD, Fratti RA (2020) An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9, and LDLR in Hepatocytes. Biochemistry 59, 4321-4335 PubMed PMID: 33153264; PubMed Central PMCID: PMC7674269
• Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE, (2020) Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation. Nucl Acids Res 48, 8146-8164 PubMed PMID: 32597951; PubMed Central PMCID: PMC7641330
• Sparks RP, Arango AS, Starr ML, Aboff ZL, Hurst LR, Rivera-Kohr DA, Zhang C, Harnden KA, Jenkins JL, Guida WC, Tajkhorshid E, Fratti RA. A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion. (2019) J Biol Chem. 5;294(46):17168-17185.PubMed PMID: 31515268; PubMed Central PMCID: PMC6873166.
• Bonn-Breach R, Gu Y, Jenkins JL, Fasan R, Wedekind JE (2019) Structure of Sonic Hedgehog protein in complex with zinc(II) and magnesium(II) reveals ion-coordination plasticity relevant to peptide drug design. Acta Cryst D 75, 969-979. PubMed PMID: 31692471; PubMed Central PMCID: PMC6834079
• Talkish J, Igel H, Hunter O, Horner SW, Jeffery NN, Leach JR, Jenkins JL, Kielkopf CL, Ares M Jr. Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction. RNA. 2019 May 20;. doi: 10.1261/rna.070649.119.
• Hilt ZT, Pariser DN, Ture SK, Mohan A, Quijada P, Asante AA, Cameron SJ, Sterling JA, Merkel AR, Johanson AL, Jenkins JL, Small EM, McGrath KE, Palis J, Elliott MR, Morrell CN. Platelet-derived β2M regulates monocyte inflammatory responses. JCI Insight. 2019 Mar 7;4(5). pii: 122943. doi: 10.1172/jci.insight.122943. eCollection 2019 Mar 7.
• Starr ML, Sparks RP, Arango AS, Hurst LR, Zhao Z, Lihan M, Jenkins JL, Tajkhorshid E, Fratti RA. Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming. J Biol Chem. 2019 Mar 1;294(9):3100-3116. doi: 10.1074/jbc.RA118.006552. Epub 2019 Jan 7.
• Loerch S, Leach JR, Horner SW, Maji D, Jenkins JL, Pulvino MJ, Kielkopf CL. The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface. J Biol Chem. 2019 Feb 22;294(8):2892-2902. doi: 10.1074/jbc.RA118.006764. Epub 2018 Dec 19.
• Sparks RP, Jenkins JL, Fratti R. Use of Surface Plasmon Resonance (SPR) to Determine Binding Affinities and Kinetic Parameters Between Components Important in Fusion Machinery. Methods Mol Biol. 2019;1860:199-210. doi: 10.1007/978-1-4939-8760-3_12.
• Nogales A, Piepenbrink MS, Wang J, Ortega S, Basu M, Fucile CF, Treanor JJ, Rosenberg AF, Zand MS, Keefer MC, Martinez-Sobrido L, Kobie JJ. A Highly Potent and Broadly Neutralizing H1 Influenza-Specific Human Monoclonal Antibody. Sci Rep. 2018 Mar 12;8(1):4374. doi: 10.1038/s41598-018-22307-8.
• Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.Nucleic acids research. 2018 Jun 29.
• Wedekind JE, Dutta D, Belashov IA, Jenkins JL. Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes.The Journal of biological chemistry. 2017; 292(23):9441-9450.  PMID: 28455443 PMCID: PMC5465474
• Maureen R. Newman, Steven G. Russell, Christopher S. Schmitt, Ian A. Marozas, Tzong-Jen Sheu, J. Edward Puzas, and Danielle S. W. Benoit. Multivalent Presentation of Peptide Targeting Groups Alters Polymer Biodistribution to Target Tissues.  Biomacromolecules. 2018 Jan 8; 19(1):71-84.  
• Moore EJ, Zorine D, Hansen WA, Khare SD, Fasan R. Enzyme stabilization via computationally guided protein stapling. Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12472-12477.
• Chatrikhi R., Wang W., Gupta A., Loerch S., Maucuer A., Kielkopf CL  (2016) SF1 Phosphorylation Enhances Specific Binding to U2AF65 and Reduces Binding to 3´-Splice-Site RNA. Biophys J. 111, 2570-2586.
• Clark, KM, Jenkins JL, Fedoriw, N, and Dumont, ME. Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors. Protein Sci. 2017; 26, 242-257.
• Jade J. Welch, Ria J. Swanekamp, Christiaan King, David A. Dean, and Bradley L. Nilsson. Functional Delivery of siRNA by Disulfide-Constrained Cyclic Amphipathic Peptides. ACS Med. Chem. Lett. 2016, 7(6), 584−589.
• Sparks RP, Jenkins JL, Miner GE, Wang Y, Guida WC, Sparks CE, Fratti RA, Sparks JD. Phosphatidylinositol (3,4,5)-trisphosphate binds to sortilin and competes with neurotensin: Implications for very low density lipoprotein binding. Biochem Biophys Res Commun. 2016 Oct 21;479(3):551-556.
• Jenkins JL, Wedekind JE. The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures. Methods Mol Biol. 2016;1490:265-80.
• Sparks RP, Guida WC, Sowden MP, Jenkins JL, Starr ML, Fratti RA, Sparks CE, Sparks JD. Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells. Biochem Biophys Res Commun. 2016 Sep 16;478(2):546-52. Epub 2016 Aug 2.
• Miralem T, Lerner-Marmarosh N, Gibbs PE, Jenkins JL, Heimiller C, Maines MD (2016). Interaction of human biliverdin reductase with Akt/protein kinase B and phosphatidylinositol-dependent kinase 1 regulates glycogen synthase kinase 3 activity: a novel mechanism of Akt activation. FASEB J. 2016 May 10. pii: fj.201600330RR. [Epub ahead of print].
• Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL(2016). An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal. Nat Commun. 2016 Mar 8;7:10950. doi: 10.1038/ncomms10950.
• Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE (2015). Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3485-94.
• Liberman JA, Bogue JT, Jenkins JL, Salim M, Wedekind JE (2014). ITC analysis of ligand binding to preQ₁ riboswitches. Methods Enzymol. 2014;549:435-50.
• Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf CL (2014). Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA. Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17420-5.
• Loerch S, Maucuer A, Manceau V, Green MR, Kielkopf CL (2014). Cancer-relevant splicing factor CAPERα engages the essential splicing factor SF3b155 in a specific ternary complex. J Biol Chem. 2014 Jun 289(25):17325-37.
• Smith JM, Frost JR, Fasan R (2014). Designer macrocyclic organo-peptide hybrids inhibit the interaction between p53 and HDM2/X by accommodating a functional α-helix. Chem Commun (Camb). 2014 May 21;50(39):5027-30.
• Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL 3rd, Walter NG (2013). Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res. 2013 Dec;41(22):10462-75.
• Griffiths AE, Rydkin I, Fay PJ (2013). Factor VIIIa A2 Subunit Shows a High Affinity Interaction with Factor IXa: CONTRIBUTION OF A2 SUBUNIT RESIDUES 707-714 TO THE INTERACTION WITH FACTOR IXa J. Biol Chem. 288(21).
• Liberman JA, Salim M, Krucinska J, Wedekind JE (2013). Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nature Chem. Biol. 10.1038/NChemBio.1231.
• Gleghorn ML, Gong C, Kielkopf CL, Maquat LE (2013). Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay. Nat Struct Mol Biol. 20, 515-24.
• Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013). U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res. 41, 3859-73.
• Wang W, Maucuer A, Gupta A, Manceau V, Thickman KR, Bauer WJ, Kennedy SD, Wedekind JE, Green MR, Kielkopf CL (2013). Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure 21, 197-208.
• Daddacha W, Noble E, Nguyen LA, Kennedy EM, Kim B (2013). Effect of Ribonucleotides Embedded in DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity. J. Biol. Chem. Epub 2013 Mar 11.
• Jenkins JL, Agarwal AA, Gupta A, Green MR, Kielkopf CL (2013). U2AF⁶⁵ adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucl. Acids. Res. 41(6), 3859-3873.
• Takeyama M, Wakabayashi H, Fay PJ (2012). Factor VIII light chain contains a binding site for factor X that contributes to the catalytic efficiency of factor Xase. Biochemistry 51(3), 820-828.
• Salter JD, Lippa GM, Belashov IA, Wedekind JE (2012). Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry 51(44) 8702-8704
• Bauer WJ, Heath J, Jenkins JL, Kielkopf CL (2012). Three RNA Recognition Motifs Participate in RNA Recognition and Structural Organization by the Pro-apoptotic Splicing Factor TIA-1. J. Mol. Biol. 415(4), 727-740.
• Jenkins JL, Krucinska J, McCarty RM, Bandarian V, Wedekind JE (2011). Comparison of a preQ1 riboswitch aptamer in the metabolite-bound and free states with implications for gene regulation. J. Biol. Chem. 286(28), 24626-24637.
• Williams KJ, Jenkins JL, Kielkopf CL (2011). Large Favorable Enthalpy Changes Drive Specific RNA Recognition by RNA Recognition Motif Proteins. Biochemistry. 50(9), 1429-1431.
• Gupta A, Jenkins JL, Kielkopf CL (2011). RNA induces conformational changes in SF1/U2AF⁶⁵ splicing factor complex. J. Mol. Biol. 405(5), 1128-1138.
• Jenkins JL, Shen H, Green MR, Kielkopf CL (2008). Solution Conformation and Thermodynamic Characteristics of RNA binding by Splicing Factor U2AF⁶⁵. J. Biol. Chem. 283(48), 33641-33649.