Publications
University of Denver

35. Miller JA, Khatib F, Hammond H, Cooper S, Horowitz S‡. Introducing Foldit Education Mode. Nature Structural & Molecular Biology. In press

34. Son A, Horowitz S‡, Seong B‡. Chaperna: Linking the Ancient RNA and Protein Worlds. RNA Biology In press

33. Begeman A*, Son A*, Litberg TJ, Wroblewski TH, Gehring T, Huizar Cabral V, Bourne J, Xuan Z, Horowitz S‡. G-Quadruplexes Act as Sequence Dependent Protein Chaperones. EMBO Reports In Press

32. Koehler Leman J, [et al, including Horowitz S]. Macromolecular modeling and design in Rosetta: new methods and frameworks. Nature Methods Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2 (2020)

31. Litberg TJ, Docter B, Hughes MP, Bourne J, Horowitz S‡. DNA facilitates oligomerization and prevents aggregation via DNA networks. Biophysical Journal Nov 23. pii: S0006-3495(19)30945-2. doi: 10.1016/j.bpj.2019.11.022. (2019)

30. Rocchio S, Duman R, El Omarib K, Mykhaylyk, Yan Z, Wagner A‡, Bardwell JCA‡, Horowitz S‡. Identifying dynamic, partially occupied residues using anomalous scattering. Acta Cryst D Dec 1;75(Pt 12):1084-1095. doi: 10.1107/S2059798319014475. Epub 2019 Nov 19. (2019)

 

29. Khatib F‡, Desfosses A, Players F, Koepnick B, Flatten J, Popovic Z, Baker D, Cooper S, Gutsche I, Horowitz S‡. Building Denovo Cryo-EM Structures Collaboratively with Video Gamers. PLoS Biol Nov 12;17(11):e3000472. doi: 10.1371/journal.pbio.3000472 (2019)

-Recommended on F1000

 

28. Fick RJ, Horowitz S, McDole BG, Clay MC, Mehl RA, Al-Hashimi HM, Scheiner S, Trievel, RC. Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Biochemistry Apr 23;58(16):2152-2159. doi: 10.1021/acs.biochem.8b01141. (2019)

 

27. Dsilva L, Mittal S, Koepnick B, Flatten J, Cooper S‡, Horowitz S‡. Creating custom Foldit puzzles for teaching biochemistry. Biochem Mol Biol Educ. 47(2):133-139. doi: 10.1002/bmb.21208. (2019)

26. Salmon L‡, Ahlstrom LS, Afonine P, Bardwell JCA, Horowitz S‡. Selecting conformational ensembles using residual electron and anomalous density (READ). Methods Mol Biol. 1764:491-504. doi: 10.1007/978-1-4939-7759-8_31 (2018)

25. Horowitz S‡, Koldewey P, Stull F, Bardwell JCA‡. Folding while bound to chaperones. Curr. Opin. Struct. Biol. Feb;48:1-5. doi: 10.1016/j.sbi.2017.06.009 Feb (2018)

24. Salmon L‡, Stull F, Sayle S, Cato C, Akgül Ş, Foit L, Ahlstrom LS, Eisenmesser EZ, Al-Hashimi HM, Bardwell JCA‡, Horowitz S‡. The Mechanism of HdeA Unfolding and Chaperone Activation. J. Molecular Biology. pii: S0022-2836(17)30540-5 (2018)

 

23. Koldewey P*, Horowitz S*, Bardwell JCA. Chaperone-client interactions: non-specificity engenders multi-functionality. J. Biol. Chem. Jul 21;292(29):12010-12017 (2017)

Previous Publications

22. Horowitz S, Bardwell JCA. RNAs as chaperones. RNA Biol. 13(12):1228-1231 (2016)

 

21. Johansson KE, Johansen NT, Christensen S, Horowitz S, Bardwell JCA, Olsen JG, Willemoes M, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T, Winther RJ. Computational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template. J. Mol. Biology. Sep 19. pii: S0022-2836(16)30378-3. doi: 10.1016/j.jmb.2016.09.013 (2016).

 

20. Horowitz, S‡*, Koepnick, B*, Martin, R*, Tymieniecki, A, Winburn, AA, Cooper, S, Flatten, JF, Rogawski DS, Koropatkin, NM, Hailu, TT, Jain, N, Koldewey, P, Ahlstrom, LS, Chapman, MR, Sikkema, AP, Skiba, MA, Maloney, FP, Beinlich, FRM, Players, F, Students, UM, Popovic, Z, Baker, D, Khatib, F‡ and Bardwell, JCA‡. Determining crystal structures through crowdsourcing and coursework. Nature Communications. Sep 16;7:12549. doi: 10.1038/ncomms12549 (2016).

19. Salmon L, Ahlstrom LS, Horowitz S, Dickson A, Brooks III CL, Bardwell JCA. Capturing a dynamic chaperone-substrate interaction using NMR-optimized molecular modeling. Journal of the American Chemical Society. Aug 10;138(31):9826-39. (2016)

 

18. Koldewey P, Stull F, Horowitz S, Martin R, Bardwell JCA. Forces driving chaperone action. Cell, Jun 9. pii: S0092-8674(16)30657-2 (2016)

 

17. Horowitz S‡*, Salmon L*, Koldewey P*, Ahlstrom LS, Martin M, Quan S, Afonine PV, Bedem H, Wang L, Xu Q, Trievel RC, Brooks III CL, Bardwell JCA‡. Visualizing chaperone-assisted protein folding. Nature Structural & Molecular Biology, Jul;23(7):691-7. doi: 10.1038/nsmb.3237. Epub 2016 May 30. (2016)

16. Docter BE, Horowitz S, Gray MJ, Jakob U, Bardwell JCA. Do nucleic acids moonlight as molecular chaperones? Nucleic Acids Research, Jun 2;44(10):4835-45 (2016)

 

15. Fick RJ, Kroner GM, Nepal B, Magnani R, Horowitz S, Houtz RL, Scheiner S, Trievel RC. Sulfur - Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9. ACS Chemical Biology, 11(3), 748-54 (2016)

 

14. Groitl B, Horowitz S‡, Makepeace K, Petrotchenko EV, Reichmann D, Bardwell JCA, Jakob U‡. Protein unfolding as a switch from self-recognition to high affinity client binding? Nature Communications, 7:10357 (2016)

13. Vander Meulen KA, Horowitz S, Trievel RC, Butcher SE. Measuring the Kinetics of Molecular Association by Isothermal Titration Calorimetry. Methods in Enzymology, 567, 181-213 (2016)

 

12. Dahl JU, Koldewey P, Salmon L, Horowitz S, Bardwell JCA, Jakob U. HdeB has a protective role in response to acid stress at pH 4 in Escherichia coli. Journal of Biological Chemistry 290 (1), 65-75 (2015)

 

11. Yesselman JD*, Horowitz S*, Brooks CL, Trievel RC. Frequent Side Chain Methyl Carbon-Oxygen Hydrogen Bonding in Proteins Revealed by Computational and Stereochemical Analysis of Neutron Structures. Proteins: Structure, Function, and Bioinformatics 83 (3), 403-410 (2015)

 

10.  Horowitz S‡, Koldewey P, Bardwell, JC. Undergraduates Improve upon Published Crystal Structure in Class Assignment. Biochemistry and Molecular Biology Education doi:10.1002/bmb.20811 (2014)

 

9.  Horowitz S, Adhikari U, Dirk, L.M.A., Del Rizzo PA, Mehl RA, Houtz RL, Al-Hashimi HM, Scheiner S, Trievel RC Manipulating Unconventional CH-based Hydrogen Bonding in a Methyltransferase via Non-Canonical Amino Acid Mutagenesis. ACS chemical biology 9 (8), 1692-1697 (2014)

 

8.  Quan S, Wang L, Petrotchenko EV, Makepeace KAT, Horowitz S, Yang J, Zhang Y, Borchers CH, Bardwell JCA. Super Spy Variants Implicate Flexibility in Chaperone Action. eLife 3:e01584 (2014)

 

7.  Horowitz S, Dirk LMA, Yesselman JD, Nimtz J, Adhikari, U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. Conservation and Functional Importance of Carbon-Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases. J. Am. Chem. Soc, 135(41); 15536-15548 (2013)

 

6. Frank AT, Horowitz S, Andricioaei I, Al-Hashimi HM. Utility of 1H NMR Chemical Shifts in Determining RNA Structure and Dynamics. J. Phys. Chem. B, 117(7):2045-2052 (2013)

 

5.  Horowitz S, Trievel RC. Carbon-Oxygen Hydrogen Bonds in Biology. J. Biol. Chem, 287; 41576-41582 (2012)

 

4.  Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC. Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9. J. Biol. Chem, 286(21):18658-63 (2011)

 

3.  Krishnan S*, Horowitz S*, Trievel RC. Structure and Function of Histone H3 Lysine 9 Methyltransferases and Demethylases. Chembiochem 12(2):254-263 (2011)

2.  Horowitz S, Binion DG, Nelson VM, Kanaa Y, Javadi P, Lazarova Z, Andrekopoulos C, Kalyanaraman B, Otterson MF, Rafiee P. Increased Arginase Activity and Endothelial Dysfunction in Human Inflammatory Bowel Disease, Am. J. Physiol Gastrointest Liver Physiol, 292(5)G1323-G1336 (2007)

 

1. Rafiee P, Theriot ME, Nelson VM, Heidemann J, Kanaa Y, Horowitz SA, Rogaczewski A, Johnson CP, Ali I, Shaker R, Binion DG. Human Esophageal Microvascular Endothelial Cells Respond to Acidic pH Stress by PI3K/AKT and p38 MAPK-regulated Induction of Hsp70 and Hsp27. Am J Physiol Cell Physiol, 291(5) C931-945 (2006)