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2024 |
57) |
Sedinkin, S.L., Roche, J. & Venditti, V.. (2024). Elucidation of the mechanisms of inter-domain coupling in the monomeric state of Enzyme I by high-pressure NMR. J. Mol. Biol. 436, 168553. |
2023 |
56) |
An, Y., Chatterjee, P., Naik, P., Banerjee, S., Huang, W., Slowing, I.I. & Venditti, V. (2023). Hydrogen spillover and substrate-support hydrogen bonding mediate hydrogenation of phenol catalyzed by palladium on reducible metal oxides. Chem. Sci. 14, 14166–14175. |
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55) |
Burns, D., Venditti, V., & Potoyan, D.A. (2023). Temperature-Sensitive Contact Modes Allosterically Gate TRPV3. PLoS Comput. Biol. 19, e1011545. |
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54) |
Sedinkin, S.L., Burns, D., Shukla, D. Potoyan, D.A., & Venditti, V. (2023). Solution structure ensembles of the open and closed forms of the ~130 kDa Enzyme I via AlphaFold modeling, Coarse Grained simulations and NMR. J. Am. Chem. Soc. 145, 13347-13356. |
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53) |
Singh, A., Burns, D., Sedinkin, S.L., VanVeller, B., Potoyan, D.A., & Venditti, V. (2023). Protein conformational dynamics underlie selective recognition of thermophilic over mesophilic Enzyme I by a substrate analogue. Biomolecules 13, 160. |
2022 |
52) |
Burns, D., Singh, A., Venditti, V., & Potoyan, D.A. (2022). Temperature-sensitive contacts in disordered loops tune Enzyme I activity. Proc. Natl. Acad. Sci. USA 119, e2210537119. |
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51) |
An, Y., Sedinkin, S.L., & Venditti, V. (2022). Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria. Nanoscale Adv. 4, 2583-2607. |
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50) |
Khatiwada, B., Nguyen, T.T., Purslow, J.A., & Venditti, V. (2022). Solution structure ensemble of human obesity-associated protein FTO reveals druggable surface pockets at the interface between the N- and C-terminal domain. J. Biol. Chem. 298, 101907. |
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49) |
Lisi, P.G., Rivalta, I., & Venditti, V. (2022). Editorial: structural and dynamic aspects of protein function and allostery. Front. Mol. Biosci. 9, 876499. |
2021 |
48) |
Naik, P.J., An, Y., Sedinkin, S., Mashing, H., Freppon, D., Smith, E.A., Venditti, V., & Slowing, I.I. (2021). Non-innocent role of the ceria support in Pd-catalyzed halophenol hydrodehalogenation. ACS Catal. 11, 10553-10564. |
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47) |
Purslow, J.A., Nguyen, T.T., Khatiwada, B., Singh, A., & Venditti, V. (2021). N6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5. Sci. Adv. 7, eabi8215. |
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46) |
Purslow, J.A., Thimmesch, J.N., Sivo, V., Nguyen, T.T., Khatiwada, B., Dotas, R.R., & Venditti, V. (2021). A single point mutation controls the rate of interconversion between the g+ and g- rotamers of the Histidine 189 Χ2 angle that activates bacterial Enzyme I for catalysis. Front. Mol. Biosci. 8, 699203. |
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45) |
Nguyen, T.T., Ghirlando, R., Roche, J., & Venditti, V. (2021). Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity. Proc. Natl. Acad. Sci. USA 118, e2100298118. |
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44) |
Singh, A., Purslow, A.J., & Venditti, V. (2021). 15N CPMG relaxation dispersion for the investigation of protein conformational dynamics on the µs-ms timescale. J. Vis. Exp. 170, e62395. |
2020 |
43) |
Sedinkin, S.L., An, Y., Naik, P., Slowing, I.I., & Venditti, V. (2020). An organogel library for solution NMR analysis of nanoparticle suspensions in non-aqueous samples. J. Magn. Reson. 321, 106874. |
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42) |
An, Y., Naik, P., Slowing, I.I., & Venditti, V. (2020). Substrate-support interactions mediate hydrogenation of phenolic compounds by Pd/CeO2 nanorods. ACS Appl. Nano Mater. 13, 11282–11288. |
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41) |
Ryan, V.H., Watters, S., Amaya, J., Khatiwada, B., Venditti, V., Naik, M.T., & Fawzi, N.L. (2020). Weak binding to the A2RE RNA rigidifies hnRNPA2 RRMs and reduces liquid-liquid phase separation and aggregation. Nucl. Acids Res. 48, 10542-10554. |
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40) |
Nguyen, T.T., & Venditti, V. (2020). An allosteric pocket for inhibition of bacterial Enzyme I identified by NMR-based fragment screening. J. Struct. Biol. X 4, 100034. |
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39) |
Dotas, R.R., Nguyen, T.T., Stewart Jr., C.E., Ghirlando, R., Potoyan, D.A., & Venditti, V. (2020). Hybrid thermophilic/mesophilic enzymes reveal a role for conformational disorder in regulation of bacterial Enzyme I. J. Mol. Biol. 432, 4481-4498. |
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38) |
Egner, T.K., Naik, P., An, Y., Venkatesh, A., Rossini, A.J., Slowing, I.I., & Venditti, V. (2020). 'Surface Contrast' NMR reveals non-innocent role of support in Pd/CeO2 catalyzed phenol hydrogenation. ChemCatChem 12, 4160-4166. |
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37) |
Purslow, J.A., Khatiwada, B., Bayro, M.J., & Venditti, V. (2020). NMR Methods for Structural Characterization of Protein-Protein Complexes. Front. Mol. Biosci. 7, 9. |
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36) |
Khatiwada, B., Purslow, J.A., Underbakke, E.S., & Venditti, V. (2020). N-terminal fusion of the N-terminal domain of bacterial Enzyme I facilitates recombinant expression and purification of the human RNA demethylases FTO and Alkbh5. Protein Expr. Purif. 167, 105540. |
2019 |
35) |
Dotas, R.R., & Venditti, V. (2019). Resonance assignment of the 128 kDa Enzyme I dimer from Thermoanaerobacter tengcongensis. Biomol. NMR Assign. 13, 287-293. |
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34) |
Ma, L., Shi, Y., Siemianowski, O., Yuan, B., Egner, T.K., Mirnezami, S.V., Lind, K.R., Ganapathysubramaniam, B., Venditti, V., & Cademartiri, L. (2019). Hydrogel-based “transparent soils” for root phenotyping in vivo. Proc. Natl. Acad. Sci. USA 116, 11063-11068. |
2018 |
33) |
Purslow, J.A., Nguyen, T.T., Egner, T.K., Dotas, R.R., Khatiwada, B., & Venditti, V. (2018). Active site breathing of human Alkbh5 revealed by solution NMR and accelerated Molecular Dynamics. Biophys. J. 115, 1895-1905. |
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32) |
Yuan, B., Egner, T.K., Venditti, V., & Cademartiri, L. (2018). Sustainable scalable synthesis of sulfide nanocrystals at low cost with an ionic liquid sulfur precursor. Nat. Commun. 9, 4078. |
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31) |
Purslow, J.A., & Venditti, V. (2018). 1H, 15N, 13C backbone resonance assignment of human Alkbh5. Biomol. NMR Assign. 12, 297-301. |
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30) |
Evangelidis, T., Nerli, S., Novácek, J., Brereton, A.E., Karplus, P.A., Dotas, R.R., Venditti, V., Sgourakis, N.G., & Tripsianes, K. (2018). Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. Nat. Commun. 9, 384. |
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29) |
Nguyen, T.T., Ghirlando, R., & Venditti, V. (2018). The oligomerization state of bacterial enzyme I (EI) determines EI’s allosteric stimulation or competitive inhibition by α-ketoglutarate. J. Biol. Chem. 293, 2631-2639. |
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28) |
Venditti, V., & Fawzi, N.L. (2018). Probing the atomic structure of transient protein contacts by paramagnetic relaxation enhancement solution NMR. Methods Mol. Biol. 1688, 243-255. |
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27) |
Dotas, R.R., & Venditti, V. (2018). 1H, 15N, 13C backbone resonance assignment of the C-terminal domain of Enzyme I from Thermoanaerobacter Tengcongensis. Biomol. NMR Assign. 12, 103-106. |
2017 |
26) |
Egner, T.K., Naik, P., Nelson, N.C., Slowing, I.I., & Venditti, V. (2017). Mechanistic insights into nanoparticle surface adsorption by solution NMR spectroscopy in an aqueous gel. Angew. Chem. Int. Ed. 56, 9802-9806. |
Before ISU |
25) |
Venditti, V., Egner, T.K., & Clore, G.M. (2016). Hybrid approaches to structural characterization of conformational ensembles of complex macromolecular systems combining NMR residual dipolar couplings and solution X-ray scattering. Chem. Rev. 116, 6305-6322. |
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24) |
Venditti, V., Schwieters, C.D., Grishaev, A. & Clore, G.M. (2015). Dynamic equilibrium between closed and partially-closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Proc. Natl. Acad. Sci. USA 112, 11565-11570. |
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23) |
Venditti, V., Tugarinov, V., Schwieters, C.D., Grishaev, A. & Clore, G.M. (2015). Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I. Nat. Commun. 6, 5960. |
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22) |
Tugarinov, V., Venditti, V. & Clore, G.M. (2014). A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins. J. Biomol. NMR 58, 1-8. |
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21) |
Clore, G.M. & Venditti, V. (2013). Structure, dynamics and biophysics of the cytoplasmic protein complexes of the bacterial phosphoenolpyruvate:sugar phosphotransferase system. Trends Biochem. Sci. 38, 515-530. |
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20) |
Venditti, V., Ghirlando, R. & Clore, G.M. (2013). Structural basis for enzyme I inhibition by α-ketoglutarate. ACS Chem. Biol. 8, 1232-1240. |
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19) |
Venditti, V. & Clore, G.M. (2012). Conformational selection and substrate binding regulate the monomer/dimer equilibrium of the C-terminal domain of Escherichia coli enzyme I. J. Biol. Chem. 287, 26989-26998. |
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18) |
Bernini, A., Spiga, O., Venditti, V., Prischi, F., Botta, M., Croce, G., Tong, A.P., Wong, W.T. & Niccolai, N. (2012). The use of a ditopic Gd(III) paramagnetic probe for investigating α-bungarotoxin surface accessibility. J. Inorg. Biochem. 112, 25-31. |
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17) |
Venditti, V., Fawzi, N.L. & Clore, G.M. (2012). An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media. J. Biomol. NMR 52, 191-195. |
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16) |
Venditti, V., Fawzi, N.L. & Clore, G.M. (2011). Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy. J. Biomol. NMR 51, 319-328. |
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15) |
Spiga, O., Summa, D., Cirri, S., Bernini, A., Venditti, V., De Chiara, M., Priora, R., Frosali, S., Margaritis, A., Di Giuseppe, D., Di Simplicio, P. & Niccolai, N. (2011). A structurally driven analysis of thiol reactivity in mammalian albumins. Biopolymers 95, 278-285. |
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14) |
Venditti, V., Clos, L.II, Niccolai, N. & Butcher, S.E. (2009). Minimum energy path for a U6 RNA conformational change involving protonation, base pair rearrangement and base flipping. J. Mol. Biol. 391, 894-905. |
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13) |
Bernini, A., Venditti, V., Spiga, O. & Niccolai, N. (2009). Probing protein surface accessibility with solvent and paramagnetic molecules. Prog. Nucl. Mag. Res. Sp. 54, 278-289. |
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12) |
Bernini, A., Venditti, V., Spiga, O., Ciutti, A., Prischi, F., Consonni, R., Zetta, L., Arosio, I., Fusi, P., Guagliardi, A. & Niccolai, N. (2008). NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. Biophys. Chem. 137, 71-75. |
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11) |
Venditti, V., Niccolai, N. & Butcher, S.E. (2008). Measuring the surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Nucl. Acids Res., 36, e20. |
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10) |
Staple, D.W., Venditti, V., Niccolai, N., Elson-Schwab, L., Tor, Y. & Butcher, S.E. (2008). Structure of the HIV-1 frameshift site RNA in complex with the novel small molecule guanidinoneomycin B. ChemBioChem. 9, 93-102. |
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9) |
Summa, D., Spiga, O., Bernini, A., Venditti, V., Priora, R., Frosali, S., Margaritis, A., Di Giuseppe, D., Niccolai, N. & Di Simplicio, P. (2007). Protein-Thiol substitution or protein dethiolation by SH/SS exchange reactions: the albumin model. Proteins 69, 369-378. |
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8) |
Venditti, V., Bernini, A., De Simone, A., Spiga, O., Prischi, F. & Niccolai, N. (2007) MD and NMR studies of α-bungarotoxin surface accessibility. Biochem. Biophys. Res. Commun. 356, 114-117. |
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7) |
Sashital, D.G., Venditti, V., Angers, C., Cornilescu, G. & Butcher, S.E. (2007). Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. RNA 13, 328-338. |
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6) |
Spiga, O., Padula, M.G., Scarselli, M., Ciutti, A., Bernini, A., Venditti, V., Prischi, F., Falciani, C., Lozzi, L., Bracci, L., Valensin, P.E., Caudai, C. & Niccolai, N. (2006). Structurally driven selection of human hepatitis C virus mimotopes. Antivir. Ther. 11, 917-922. |
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5) |
Bernini, A., Spiga, O., Venditti, V., Prischi, F., Bracci, L., Tong, A.P., Wong, W.T. & Niccolai. N. (2006). NMR studies of lysozyme surface accessibility by using different paramagnetic relaxation probes. J. Am. Chem. Soc. 128, 9290-9291. |
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4) |
Bernini, A., Spiga, O., Ciutti, A., Venditti, V., Prischi, F., Governatori, M., Bracci, L., Lelli, B., Pileri, S., Botta, M., Barge, A., Laschi, F. & Niccolai, N. (2006). NMR studies of BPTI aggregation by using paramagnetic relaxation reagents. Biochim. Biophys. Acta. 1764, 856-862. |
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3) |
Bernini, A., Spiga, O., Venditti, V., Prischi, F., Bracci, L., Huang, J., Tanner, J.A. & Niccolai, N. (2006). Tertiary structure prediction of SARS coronavirus helicase. Biochem. Biophys. Res. Commun. 343, 1101-1104. |
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2) |
Varrazzo, D., Bernini, A., Spiga, O., Ciutti, A., Chiellini, S., Venditti, V., Bracci, L. & Niccolai, N. (2005). Three-dimensional computation of atom depth in complex molecular structures. Bioinformatics 12, 2856-2860. |
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1) |
Bernini, A., Spiga, O., Ciutti, A., Chiellini, S., Menciassi, N., Venditti, V. & Niccolai, N. (2004). On the dynamics of water molecules at the protein solute interfaces. Homeopathy 93, 199-202. |
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