Recent Publications

Designer peptide-DNA cytoskeletons regulate the function of synthetic cells.
Daly ML, Nishi K, Klawa SJ, Hinton KY, Gao Y, Freeman R.
Nat Chem. 2024 Aug;16(8):1229-1239. doi: 10.1038/s41557-024-01509-w. Epub 2024 Apr 23.
PMID: 38654104 Free PMC article.

Contribution of Electrostatic CH3-π Interactions to Recognition of Histone Asymmetric Dimethylarginine by the SPIN1 Triple Tudor Domain.
Travis CR, Dumais RG, Treacy JW, Kean KM, Houk KN, Waters ML.
J Am Chem Soc. 2024 Jul 31;146(30):20678-20684. doi: 10.1021/jacs.4c03463. Epub 2024 Jul 18.
PMID: 39023428

Dynamic Implications of Noncovalent Interactions in Amphiphilic Single-Chain Polymer Nanoparticles.
Dykeman-Bermingham PA, Stingaciu LR, Do C, Knight AS.
ACS Macro Lett. 2024 Jul 16;13(7):889-895. doi: 10.1021/acsmacrolett.4c00269. Epub 2024 Jul 3.
PMID: 38959296

Leveraging Triphenylphosphine-Containing Polymers to Explore Design Principles for Protein-Mimetic Catalysts.
Sanders MA, Chittari SS, Foley JR, Swofford WM, Elder BM, Knight AS.
J Am Chem Soc. 2024 Jun 26;146(25):17404-17413. doi: 10.1021/jacs.4c05040. Epub 2024 Jun 11.
PMID: 38863219

Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics.
Simpson JB, Walker ME, Sekela JJ, Ivey SM, Jariwala PB, Storch CM, Kowalewski ME, Graboski AL, Lietzan AD, Walton WG, Davis KA, Cloer EW, Borlandelli V, Hsiao YC, Roberts LR, Perlman DH, Liang X, Overkleeft HS, Bhatt AP, Lu K, Redinbo MR.
Cell Host Microbe. 2024 Jun 12;32(6):925-944.e10. doi: 10.1016/j.chom.2024.04.018. Epub 2024 May 15.
PMID: 38754417

Stoichiometry for entry and binding properties of the Env protein of R5 T cell-tropic HIV-1 and its evolutionary variant of macrophage-tropic HIV-1.
Bonner X, Sondgeroth A, McCue A, Nicely N, Tripathy A, Spielvogel E, Moeser M, Ke R, Leiderman K, Joseph SB, Swanstrom R.
mBio. 2024 Apr 10;15(4):e0032124. doi: 10.1128/mbio.00321-24. Epub 2024 Mar 1.
PMID: 38426750 Free PMC article.

A divergent tumor overexpressed gene domain and oligomerization contribute to SPIRAL2 function in stabilizing microtubule minus ends.
Fan Y, Bilkey N, Bolhuis DL, Slep KC, Dixit R.
Plant Cell. 2024 Mar 29;36(4):1056-1071. doi: 10.1093/plcell/koad294.
PMID: 38011314 Free PMC article.

Tailoring Hierarchical Structure and Rare Earth Affinity of Compositionally Identical Polymers via Sequence Control.
Dykeman-Bermingham PA, Bogen MP, Chittari SS, Grizzard SF, Knight AS.
J Am Chem Soc. 2024 Mar 27;146(12):8607-8617. doi: 10.1021/jacs.4c00440. Epub 2024 Mar 12.
PMID: 38470430

Targeting Borrelia burgdorferi HtpG with a berserker molecule, a strategy for anti-microbial development.
Carlson DL, Kowalewski M, Bodoor K, Lietzan AD, Hughes PF, Gooden D, Loiselle DR, Alcorta D, Dingman Z, Mueller EA, Irnov I, Modla S, Chaya T, Caplan J, Embers M, Miller JC, Jacobs-Wagner C, Redinbo MR, Spector N, Haystead TAJ.
Cell Chem Biol. 2024 Mar 21;31(3):465-476.e12. doi: 10.1016/j.chembiol.2023.10.004. Epub 2023 Nov 1.
PMID: 37918401

The Dilute domain in Canoe is not essential for linking cell junctions to the cytoskeleton but supports morphogenesis robustness.
McParland ED, Butcher TA, Gurley NJ, Johnson RI, Slep KC, Peifer M.
J Cell Sci. 2024 Mar 15;137(6):jcs261734. doi: 10.1242/jcs.261734. Epub 2024 Mar 21.
PMID: 38323935 Free PMC article.

Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands.
Travis CR, Kean KM, Albanese KI, Henriksen HC, Treacy JW, Chao EY, Houk KN, Waters ML.
J Am Chem Soc. 2024 Feb 7;146(5):3086-3093. doi: 10.1021/jacs.3c10031. Epub 2024 Jan 24.
PMID: 38266163

Uncovering supramolecular chirality codes for the design of tunable biomaterials.
Klawa SJ, Lee M, Riker KD, Jian T, Wang Q, Gao Y, Daly ML, Bhonge S, Childers WS, Omosun TO, Mehta AK, Lynn DG, Freeman R.
Nat Commun. 2024 Jan 26;15(1):788. doi: 10.1038/s41467-024-45019-2.
PMID: 38278785 Free PMC article.

Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy.
McCue AC, Demarest SJ, Froning KJ, Hickey MJ, Antonysamy S, Kuhlman B.
MAbs. 2024 Jan-Dec;16(1):2373325. doi: 10.1080/19420862.2024.2373325. Epub 2024 Jul 4.
PMID: 38962811 Free PMC article.

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain.
Bolhuis DL, Dixit R, Slep KC.
PLoS One. 2023 Dec 29;18(12):e0290024. doi: 10.1371/journal.pone.0290024. eCollection 2023.
PMID: 38157339 Free PMC article.

In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models.
Goudy OJ, Nallathambi A, Kinjo T, Randolph NZ, Kuhlman B.
Proc Natl Acad Sci U S A. 2023 Dec 5;120(49):e2307371120. doi: 10.1073/pnas.2307371120. Epub 2023 Nov 30.
PMID: 38032933 Free PMC article.

Stepwise requirements for polymerases δ and θ in theta-mediated end joining.
Stroik S, Carvajal-Garcia J, Gupta D, Edwards A, Luthman A, Wyatt DW, Dannenberg RL, Feng W, Kunkel TA, Gupta GP, Hedglin M, Wood R, Doublié S, Rothenberg E, Ramsden DA.
Nature. 2023 Nov;623(7988):836-841. doi: 10.1038/s41586-023-06729-7. Epub 2023 Nov 15.
PMID: 37968395

Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen.
Shell DJ, Foley CA, Wang Q, Smith CM, Guduru SKR, Zeng H, Dong A, Norris-Drouin JL, Axtman M, Hardy PB, Gupta G, Halabelian L, Frye SV, James LI, Pearce KH.
J Med Chem. 2023 Oct 26;66(20):14133-14149. doi: 10.1021/acs.jmedchem.3c01192. Epub 2023 Oct 2.
PMID: 37782247 Free PMC article.

Analysis of the complex between MBD2 and the histone deacetylase core of NuRD reveals key interactions critical for gene silencing.
Leighton GO, Shang S, Hageman S, Ginder GD, Williams DC Jr.
Proc Natl Acad Sci U S A. 2023 Aug 15;120(33):e2307287120. doi: 10.1073/pnas.2307287120. Epub 2023 Aug 8.
PMID: 37552759 Free PMC article.

Trifluoroethanol and the behavior of a tardigrade desiccation-tolerance protein.
Wang S, Eicher J, Pielak GJ.
Protein Sci. 2023 Aug;32(8):e4716. doi: 10.1002/pro.4716.
PMID: 37401908 Free PMC article.

De novo design of stable proteins that efficaciously inhibit oncogenic G proteins.
Cummins MC, Tripathy A, Sondek J, Kuhlman B.
Protein Sci. 2023 Aug;32(8):e4713. doi: 10.1002/pro.4713.
PMID: 37368504 Free PMC article.

Polo-like kinase 4 homodimerization and condensate formation regulate its own protein levels but are not required for centriole assembly.
Ryniawec JM, Buster DW, Slevin LK, Boese CJ, Amoiroglou A, Dean SM, Slep KC, Rogers GC.
Mol Biol Cell. 2023 Jul 1;34(8):ar80. doi: 10.1091/mbc.E22-12-0572. Epub 2023 May 10.
PMID: 37163316 Free PMC article.

MBD2a-NuRD binds to the methylated γ-globin gene promoter and uniquely forms a complex required for silencing of HbF expression.
Shang S, Li X, Azzo A, Truong T, Dozmorov M, Lyons C, Manna AK, Williams DC Jr, Ginder GD.
Proc Natl Acad Sci U S A. 2023 Jun 20;120(25):e2302254120. doi: 10.1073/pnas.2302254120. Epub 2023 Jun 12.
PMID: 37307480 Free PMC article.

Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles.
Stingley KJ, Carpenter BA, Kean KM, Waters ML.
Chem Sci. 2023 Apr 3;14(18):4935-4944. doi: 10.1039/d3sc00231d. eCollection 2023 May 10.
PMID: 37181761 Free PMC article.

Microbial β-glucuronidases drive human periodontal disease etiology.
Lietzan AD, Simpson JB, Walton WG, Jariwala PB, Xu Y, Boynton MH, Liu J, Redinbo MR.
Sci Adv. 2023 May 5;9(18):eadg3390. doi: 10.1126/sciadv.adg3390. Epub 2023 May 5.
PMID: 37146137 Free PMC article.

Versatile Triphenylphosphine-Containing Polymeric Catalysts and Elucidation of Structure-Function Relationships.
Sanders MA, Chittari SS, Sherman N, Foley JR, Knight AS.
J Am Chem Soc. 2023 May 3;145(17):9686-9692. doi: 10.1021/jacs.3c01092. Epub 2023 Apr 20.
PMID: 37079910

SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx.
Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R.
Cell Rep Phys Sci. 2023 Apr 19;4(4):101346. doi: 10.1016/j.xcrp.2023.101346. Epub 2023 Apr 7.
PMID: 37077408 Free PMC article.

Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication.
Boerneke MA, Gokhale NS, Horner SM, Weeks KM.
Proc Natl Acad Sci U S A. 2023 Apr 11;120(15):e2217053120. doi: 10.1073/pnas.2217053120. Epub 2023 Apr 3.
PMID: 37011200 Free PMC article.

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut.
Foley MH, Walker ME, Stewart AK, O’Flaherty S, Gentry EC, Patel S, Beaty VV, Allen G, Pan M, Simpson JB, Perkins C, Vanhoy ME, Dougherty MK, McGill SK, Gulati AS, Dorrestein PC, Baker ES, Redinbo MR, Barrangou R, Theriot CM.
Nat Microbiol. 2023 Apr;8(4):611-628. doi: 10.1038/s41564-023-01337-7. Epub 2023 Mar 13.
PMID: 36914755 Free PMC article.

Designer installation of a substrate recruitment domain to tailor enzyme specificity.
Park R, Ongpipattanakul C, Nair SK, Bowers AA, Kuhlman B.
Nat Chem Biol. 2023 Apr;19(4):460-467. doi: 10.1038/s41589-022-01206-0. Epub 2022 Dec 12.
PMID: 36509904 Free PMC article.

De novo design of stable proteins that efficaciously inhibit oncogenic G proteins.
Cummins MC, Tripathy A, Sondek J, Kuhlman B.
bioRxiv [Preprint]. 2023 Mar 28:2023.03.28.534629. doi: 10.1101/2023.03.28.534629.
Update in:Protein Sci. 2023 Aug;32(8):e4713. doi: 10.1002/pro.4713.
PMID: 37034763 Free PMC article. Preprint.

Investigating Fundamental Principles of Nonequilibrium Assembly Using Temperature-Sensitive Copolymers.
Chittari SS, Obermeyer AC, Knight AS.
J Am Chem Soc. 2023 Mar 22;145(11):6554-6561. doi: 10.1021/jacs.3c00883. Epub 2023 Mar 13.
PMID: 36913711

32.

Macromolecular Crowding by Polyethylene Glycol Reduces Protein Breathing.
Chu IT, Hutcheson BO, Malsch HR, Pielak GJ.
J Phys Chem Lett. 2023 Mar 16;14(10):2599-2605. doi: 10.1021/acs.jpclett.3c00271. Epub 2023 Mar 7.
PMID: 36881386

Chiral-phonon-activated spin Seebeck effect.
Kim K, Vetter E, Yan L, Yang C, Wang Z, Sun R, Yang Y, Comstock AH, Li X, Zhou J, Zhang L, You W, Sun D, Liu J.
Nat Mater. 2023 Mar;22(3):322-328. doi: 10.1038/s41563-023-01473-9. Epub 2023 Feb 13.
PMID: 36781951

Disordered proteins mitigate the temperature dependence of site-specific binding free energies.
Thole JF, Waudby CA, Pielak GJ.
J Biol Chem. 2023 Mar;299(3):102984. doi: 10.1016/j.jbc.2023.102984. Epub 2023 Feb 3.
PMID: 36739945 Free PMC article.

Design of a protease-activated PD-L1 inhibitor.
Goudy OJ, Peng A, Tripathy A, Kuhlman B.
Protein Sci. 2023 Mar;32(3):e4578. doi: 10.1002/pro.4578.
PMID: 36705186 Free PMC article.

Curvature sensing as an emergent property of multiscale assembly of septins.
Shi W, Cannon KS, Curtis BN, Edelmaier C, Gladfelter AS, Nazockdast E.
Proc Natl Acad Sci U S A. 2023 Feb 7;120(6):e2208253120. doi: 10.1073/pnas.2208253120. Epub 2023 Jan 30.
PMID: 36716363 Free PMC article.

Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones.
Guffy SL, Pulavarti SVSRK, Harrison J, Fleming D, Szyperski T, Kuhlman B.
Biochemistry. 2023 Feb 7;62(3):770-781. doi: 10.1021/acs.biochem.2c00595. Epub 2023 Jan 12.
PMID: 36634348 Free PMC article.

Diverse but desolate landscape of gut microbial azoreductases: A rationale for idiopathic IBD drug response.
Simpson JB, Sekela JJ, Carry BS, Beaty V, Patel S, Redinbo MR.
Gut Microbes. 2023 Jan-Dec;15(1):2203963. doi: 10.1080/19490976.2023.2203963.
PMID: 37122075 Free PMC article.

Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain.
Travis CR, Francis DY, Williams DC Jr, Waters ML.
Protein Sci. 2023 Jan;32(1):e4533. doi: 10.1002/pro.4533.
PMID: 36482045 Free PMC article.

Discovery of hit compounds for methyl-lysine reader proteins from a target class DNA-encoded library.
Shell DJ, Rectenwald JM, Buttery PH, Johnson RL, Foley CA, Guduru SKR, Uguen M, Rubiano JS, Zhang X, Li F, Norris-Drouin JL, Axtman M, Brian Hardy P, Vedadi M, Frye SV, James LI, Pearce KH.
SLAS Discov. 2022 Dec;27(8):428-439. doi: 10.1016/j.slasd.2022.10.003. Epub 2022 Oct 19.
PMID: 36272689

High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression.
Veggiani G, Villaseñor R, Martyn GD, Tang JQ, Krone MW, Gu J, Chen C, Waters ML, Pearce KH, Baubec T, Sidhu SS.
Nat Commun. 2022 Nov 15;13(1):6975. doi: 10.1038/s41467-022-34269-7.
PMID: 36379931 Free PMC article.

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.
Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL.
Nat Microbiol. 2022 Nov;7(11):1817-1833. doi: 10.1038/s41564-022-01244-3. Epub 2022 Oct 20.
PMID: 36266335 Free PMC article.

Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3.
Leighton GO, Irvin EM, Kaur P, Liu M, You C, Bhattaram D, Piehler J, Riehn R, Wang H, Pan H, Williams DC Jr.
J Biol Chem. 2022 Oct;298(10):102428. doi: 10.1016/j.jbc.2022.102428. Epub 2022 Aug 28.
PMID: 36037972 Free PMC article.

RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction.
Arney JW, Weeks KM.
Biochemistry. 2022 Aug 2;61(15):1625-1632. doi: 10.1021/acs.biochem.2c00177. Epub 2022 Jul 8.
PMID: 35802500 Free PMC article.

AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein.
Cummins MC, Jacobs TM, Teets FD, DiMaio F, Tripathy A, Kuhlman B.
Protein Sci. 2022 Jul;31(7):e4368. doi: 10.1002/pro.4368.
PMID: 35762713 Free PMC article.

A conserved set of mutations for stabilizing soluble envelope protein dimers from dengue and Zika viruses to advance the development of subunit vaccines.
Phan TTN, Hvasta MG, Kudlacek ST, Thiono DJ, Tripathy A, Nicely NI, de Silva AM, Kuhlman B.
J Biol Chem. 2022 Jul;298(7):102079. doi: 10.1016/j.jbc.2022.102079. Epub 2022 May 26.
PMID: 35643320 Free PMC article.

SHAPE-enabled fragment-based ligand discovery for RNA.
Zeller MJ, Favorov O, Li K, Nuthanakanti A, Hussein D, Michaud A, Lafontaine DA, Busan S, Serganov A, Aubé J, Weeks KM.
Proc Natl Acad Sci U S A. 2022 May 17;119(20):e2122660119. doi: 10.1073/pnas.2122660119. Epub 2022 May 13.
PMID: 35561226 Free PMC article.

Reprogramming CBX8-PRC1 function with a positive allosteric modulator.
Suh JL, Bsteh D, Hart B, Si Y, Weaver TM, Pribitzer C, Lau R, Soni S, Ogana H, Rectenwald JM, Norris JL, Cholensky SH, Sagum C, Umana JD, Li D, Hardy B, Bedford MT, Mumenthaler SM, Lenz HJ, Kim YM, Wang GG, Pearce KH, James LI, Kireev DB, Musselman CA, Frye SV, Bell O.
Cell Chem Biol. 2022 Apr 21;29(4):555-571.e11. doi: 10.1016/j.chembiol.2021.10.003. Epub 2021 Oct 28.
PMID: 34715055 Free PMC article.

Cdyl Deficiency Brakes Neuronal Excitability and Nociception through Promoting Kcnb1 Transcription in Peripheral Sensory Neurons.
Sun ZW, Waybright JM, Beldar S, Chen L, Foley CA, Norris-Drouin JL, Lyu TJ, Dong A, Min J, Wang YP, James LI, Wang Y.
Adv Sci (Weinh). 2022 Apr;9(10):e2104317. doi: 10.1002/advs.202104317. Epub 2022 Feb 4.
PMID: 35119221 Free PMC article.

Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles.
Allen BP, Wright ZM, Taylor HF, Oweida TJ, Kader-Pinky S, Patteson EF, Bucci KM, Cox CA, Senthilvel AS, Yingling YG, Knight AS.
Angew Chem Int Ed Engl. 2022 Mar 28;61(14):e202115547. doi: 10.1002/anie.202115547. Epub 2022 Jan 27.
PMID: 35037351 Free PMC article.

Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.
Zeller MJ, Nuthanakanti A, Li K, Aubé J, Serganov A, Weeks KM.
ACS Chem Biol. 2022 Feb 18;17(2):438-448. doi: 10.1021/acschembio.1c00880. Epub 2022 Jan 21.
PMID: 35060698 Free PMC article.

Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases.
Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML.
J Am Chem Soc. 2022 Feb 16;144(6):2535-2545. doi: 10.1021/jacs.1c09902. Epub 2022 Feb 2.
PMID: 35108000 Free PMC article.

Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding.
Kean KM, Baril SA, Lamb KN, Dishman SN, Treacy JW, Houk KN, Brustad EM, James LI, Waters ML.
J Med Chem. 2022 Feb 10;65(3):2646-2655. doi: 10.1021/acs.jmedchem.1c02049. Epub 2022 Jan 11.
PMID: 35014255 Free PMC article.

Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes.
Welsh KA, Bolhuis DL, Nederstigt AE, Boyer J, Temple BRS, Bonacci T, Gu L, Ordureau A, Harper JW, Steimel JP, Zhang Q, Emanuele MJ, Harrison JS, Brown NG.
EMBO J. 2022 Feb 1;41(3):e108823. doi: 10.15252/embj.2021108823. Epub 2021 Dec 23.
PMID: 34942047 Free PMC article.

Discovery of Potent Peptidomimetic Antagonists for Heterochromatin Protein 1 Family Proteins.
Lamb KN, Dishman SN, Waybright JM, Engelberg IA, Rectenwald JM, Norris-Drouin JL, Cholensky SH, Pearce KH, James LI, Frye SV.
ACS Omega. 2021 Dec 22;7(1):716-732. doi: 10.1021/acsomega.1c05381. eCollection 2022 Jan 11.
PMID: 35036738 Free PMC article.

Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract.
Zhang J, Walker ME, Sanidad KZ, Zhang H, Liang Y, Zhao E, Chacon-Vargas K, Yeliseyev V, Parsonnet J, Haggerty TD, Wang G, Simpson JB, Jariwala PB, Beaty VV, Yang J, Yang H, Panigrahy A, Minter LM, Kim D, Gibbons JG, Liu L, Li Z, Xiao H, Borlandelli V, Overkleeft HS, Cloer EW, Major MB, Goldfarb D, Cai Z, Redinbo MR, Zhang G.
Nat Commun. 2022 Jan 10;13(1):136. doi: 10.1038/s41467-021-27762-y.
PMID: 35013263 Free PMC article.

Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate.
Simpson JB, Sekela JJ, Graboski AL, Borlandelli VB, Bivins MM, Barker NK, Sorgen AA, Mordant AL, Johnson RL, Bhatt AP, Fodor AA, Herring LE, Overkleeft H, Lee JR, Redinbo MR.
Gut Microbes. 2022 Jan-Dec;14(1):2107289. doi: 10.1080/19490976.2022.2107289.
PMID: 35953888 Free PMC article.