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Items: 1 to 50 of 139

1.

Advances in protein structure prediction and design.

Kuhlman B, Bradley P.

Nat Rev Mol Cell Biol. 2019 Aug 15. doi: 10.1038/s41580-019-0163-x. [Epub ahead of print] Review.

PMID:
31417196
2.

Evolution of a highly active and enantiospecific metalloenzyme from short peptides.

Studer S, Hansen DA, Pianowski ZL, Mittl PRE, Debon A, Guffy SL, Der BS, Kuhlman B, Hilvert D.

Science. 2018 Dec 14;362(6420):1285-1288. doi: 10.1126/science.aau3744.

PMID:
30545884
3.

Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution.

Lerner AM, Yumerefendi H, Goudy OJ, Strahl BD, Kuhlman B.

ACS Synth Biol. 2018 Dec 21;7(12):2898-2907. doi: 10.1021/acssynbio.8b00368. Epub 2018 Nov 29.

4.

A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation.

DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, Kuhlman B, Klevit RE.

Mol Cell. 2018 Nov 15;72(4):753-765.e6. doi: 10.1016/j.molcel.2018.09.029. Epub 2018 Nov 1.

PMID:
30392931
5.

Correction to Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

Maguire JB, Boyken SE, Baker D, Kuhlman B.

J Chem Theory Comput. 2018 Oct 9;14(10):5434. doi: 10.1021/acs.jctc.8b00883. Epub 2018 Sep 17. No abstract available.

PMID:
30221938
6.

Engineering a Protein Binder Specific for p38α with Interface Expansion.

Hussain M, Angus SP, Kuhlman B.

Biochemistry. 2018 Jul 31;57(30):4526-4535. doi: 10.1021/acs.biochem.8b00408. Epub 2018 Jul 19.

PMID:
29975520
7.

Microgravity Impairs DNA Damage Repair in Human Hematopoietic Stem/Progenitor Cells and Inhibits Their Differentiation into Dendritic Cells.

Low EK, Brudvik E, Kuhlman B, Wilson PF, Almeida-Porada G, Porada CD.

Stem Cells Dev. 2018 Sep 15;27(18):1257-1267. doi: 10.1089/scd.2018.0052. Epub 2018 Jul 16.

PMID:
29901426
8.

Exposure of the Bone Marrow Microenvironment to Simulated Solar and Galactic Cosmic Radiation Induces Biological Bystander Effects on Human Hematopoiesis.

Almeida-Porada G, Rodman C, Kuhlman B, Brudvik E, Moon J, George S, Guida P, Sajuthi SP, Langefeld CD, Walker SJ, Wilson PF, Porada CD.

Stem Cells Dev. 2018 Sep 15;27(18):1237-1256. doi: 10.1089/scd.2018.0005. Epub 2018 Apr 26.

PMID:
29698131
9.

Physiological temperatures reduce dimerization of dengue and Zika virus recombinant envelope proteins.

Kudlacek ST, Premkumar L, Metz SW, Tripathy A, Bobkov AA, Payne AM, Graham S, Brackbill JA, Miley MJ, de Silva AM, Kuhlman B.

J Biol Chem. 2018 Jun 8;293(23):8922-8933. doi: 10.1074/jbc.RA118.002658. Epub 2018 Apr 20.

10.

Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program.

Guffy SL, Teets FD, Langlois MI, Kuhlman B.

J Chem Inf Model. 2018 May 29;58(5):895-901. doi: 10.1021/acs.jcim.8b00060. Epub 2018 Apr 23.

11.

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

Maguire JB, Boyken SE, Baker D, Kuhlman B.

J Chem Theory Comput. 2018 May 8;14(5):2751-2760. doi: 10.1021/acs.jctc.8b00033. Epub 2018 Apr 20. Erratum in: J Chem Theory Comput. 2018 Oct 9;14(10):5434.

12.

Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB.

Nucleic Acids Res. 2018 May 18;46(9):4405-4416. doi: 10.1093/nar/gky151.

13.

Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch.

Yumerefendi H, Wang H, Dickinson DJ, Lerner AM, Malkus P, Goldstein B, Hahn K, Kuhlman B.

Chembiochem. 2018 Jun 18;19(12):1319-1325. doi: 10.1002/cbic.201700681. Epub 2018 Apr 6.

14.

We FRET so You Don't Have To: New Models of the Lipoprotein Lipase Dimer.

Hayne CK, Yumerefendi H, Cao L, Gauer JW, Lafferty MJ, Kuhlman B, Erie DA, Neher SB.

Biochemistry. 2018 Jan 16;57(2):241-254. doi: 10.1021/acs.biochem.7b01009. Epub 2018 Jan 5.

15.

Control of microtubule dynamics using an optogenetic microtubule plus end-F-actin cross-linker.

Adikes RC, Hallett RA, Saway BF, Kuhlman B, Slep KC.

J Cell Biol. 2018 Feb 5;217(2):779-793. doi: 10.1083/jcb.201705190. Epub 2017 Dec 19.

16.

Cells lay their own tracks - optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration.

Zimmerman SP, Asokan SB, Kuhlman B, Bear JE.

J Cell Sci. 2017 Sep 15;130(18):2971-2983. doi: 10.1242/jcs.205948. Epub 2017 Jul 28.

17.

Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies.

Froning KJ, Leaver-Fay A, Wu X, Phan S, Gao L, Huang F, Pustilnik A, Bacica M, Houlihan K, Chai Q, Fitchett JR, Hendle J, Kuhlman B, Demarest SJ.

Protein Sci. 2017 Oct;26(10):2021-2038. doi: 10.1002/pro.3240. Epub 2017 Jul 31.

18.

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides.

Grove TL, Himes PM, Hwang S, Yumerefendi H, Bonanno JB, Kuhlman B, Almo SC, Bowers AA.

J Am Chem Soc. 2017 Aug 30;139(34):11734-11744. doi: 10.1021/jacs.7b01283. Epub 2017 Aug 21.

19.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ.

J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

20.

Functional Class I and II amino acid-activating enzymes can be coded by opposite strands of the same gene.

Martinez-Rodriguez L, Erdogan O, Jimenez-Rodriguez M, Gonzalez-Rivera K, Williams T, Li L, Weinreb V, Collier M, Chandrasekaran SN, Ambroggio X, Kuhlman B, Carter CW Jr.

J Biol Chem. 2016 Nov 4;291(45):23830-23831. No abstract available.

21.

Computational Repacking of HIF-2α Cavity Replaces Water-Based Stabilized Core.

Corrêa F, Key J, Kuhlman B, Gardner KH.

Structure. 2016 Nov 1;24(11):1918-1927. doi: 10.1016/j.str.2016.08.014. Epub 2016 Sep 22.

22.

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.

Harrison JS, Cornett EM, Goldfarb D, DaRosa PA, Li ZM, Yan F, Dickson BM, Guo AH, Cantu DV, Kaustov L, Brown PJ, Arrowsmith CH, Erie DA, Major MB, Klevit RE, Krajewski K, Kuhlman B, Strahl BD, Rothbart SB.

Elife. 2016 Sep 6;5. pii: e17101. doi: 10.7554/eLife.17101.

23.

Engineering and Application of LOV2-Based Photoswitches.

Zimmerman SP, Kuhlman B, Yumerefendi H.

Methods Enzymol. 2016;580:169-90. doi: 10.1016/bs.mie.2016.05.058. Epub 2016 Jul 1.

24.

Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.

Zimmerman SP, Hallett RA, Bourke AM, Bear JE, Kennedy MJ, Kuhlman B.

Biochemistry. 2016 Sep 20;55(37):5264-71. doi: 10.1021/acs.biochem.6b00529. Epub 2016 Sep 8.

25.

LOVTRAP: an optogenetic system for photoinduced protein dissociation.

Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM.

Nat Methods. 2016 Sep;13(9):755-8. doi: 10.1038/nmeth.3926. Epub 2016 Jul 18.

26.

Go in! Go out! Inducible control of nuclear localization.

Di Ventura B, Kuhlman B.

Curr Opin Chem Biol. 2016 Oct;34:62-71. doi: 10.1016/j.cbpa.2016.06.009. Epub 2016 Jun 30. Review.

27.

Probing the minimal determinants of zinc binding with computational protein design.

Guffy SL, Der BS, Kuhlman B.

Protein Eng Des Sel. 2016 Aug;29(8):327-338. doi: 10.1093/protein/gzw026. Epub 2016 Jun 29.

28.

Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C.

Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA.

Cell. 2016 Jun 2;165(6):1440-1453. doi: 10.1016/j.cell.2016.05.037.

29.

Lamellipodia are crucial for haptotactic sensing and response.

King SJ, Asokan SB, Haynes EM, Zimmerman SP, Rotty JD, Alb JG Jr, Tagliatela A, Blake DR, Lebedeva IP, Marston D, Johnson HE, Parsons M, Sharpless NE, Kuhlman B, Haugh JM, Bear JE.

J Cell Sci. 2016 Jun 15;129(12):2329-42. doi: 10.1242/jcs.184507. Epub 2016 May 12.

30.

Design of structurally distinct proteins using strategies inspired by evolution.

Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T, Kuhlman B.

Science. 2016 May 6;352(6286):687-90. doi: 10.1126/science.aad8036.

31.

Computational Design of Protein Linkers.

Kuhlman B, Jacobs T, Linskey T.

Methods Mol Biol. 2016;1414:341-51. doi: 10.1007/978-1-4939-3569-7_20.

PMID:
27094301
32.

Light-induced nuclear export reveals rapid dynamics of epigenetic modifications.

Yumerefendi H, Lerner AM, Zimmerman SP, Hahn K, Bear JE, Strahl BD, Kuhlman B.

Nat Chem Biol. 2016 Jun;12(6):399-401. doi: 10.1038/nchembio.2068. Epub 2016 Apr 18.

33.

Mechanism of Lysine 48 Selectivity during Polyubiquitin Chain Formation by the Ube2R1/2 Ubiquitin-Conjugating Enzyme.

Hill S, Harrison JS, Lewis SM, Kuhlman B, Kleiger G.

Mol Cell Biol. 2016 May 16;36(11):1720-32. doi: 10.1128/MCB.00097-16. Print 2016 Jun 1.

34.

Computationally Designed Bispecific Antibodies using Negative State Repertoires.

Leaver-Fay A, Froning KJ, Atwell S, Aldaz H, Pustilnik A, Lu F, Huang F, Yuan R, Hassanali S, Chamberlain AK, Fitchett JR, Demarest SJ, Kuhlman B.

Structure. 2016 Apr 5;24(4):641-651. doi: 10.1016/j.str.2016.02.013. Epub 2016 Mar 17.

35.

Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon.

Nguyen TV, Lee JE, Sweredoski MJ, Yang SJ, Jeon SJ, Harrison JS, Yim JH, Lee SG, Handa H, Kuhlman B, Jeong JS, Reitsma JM, Park CS, Hess S, Deshaies RJ.

Mol Cell. 2016 Mar 17;61(6):809-20. doi: 10.1016/j.molcel.2016.02.032.

36.

Data in support of UbSRD: The Ubiquitin Structural Relational Database.

Harrison JS, Jacobs TM, Houlihan K, Van Doorslaer K, Kuhlman B.

Data Brief. 2015 Oct 19;5:605-15. doi: 10.1016/j.dib.2015.10.007. eCollection 2015 Dec.

37.

Boosting protein stability with the computational design of β-sheet surfaces.

Kim DN, Jacobs TM, Kuhlman B.

Protein Sci. 2016 Mar;25(3):702-10. doi: 10.1002/pro.2869. Epub 2016 Jan 13.

38.

Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display.

Guntas G, Lewis SM, Mulvaney KM, Cloer EW, Tripathy A, Lane TR, Major MB, Kuhlman B.

Protein Eng Des Sel. 2016 Jan;29(1):1-9. doi: 10.1093/protein/gzv055. Epub 2015 Oct 20.

39.

Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide.

Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B.

ACS Synth Biol. 2016 Jan 15;5(1):53-64. doi: 10.1021/acssynbio.5b00119. Epub 2015 Oct 30.

40.

UbSRD: The Ubiquitin Structural Relational Database.

Harrison JS, Jacobs TM, Houlihan K, Van Doorslaer K, Kuhlman B.

J Mol Biol. 2016 Feb 22;428(4):679-687. doi: 10.1016/j.jmb.2015.09.011. Epub 2015 Sep 25.

41.

Labelling and optical erasure of synaptic memory traces in the motor cortex.

Hayashi-Takagi A, Yagishita S, Nakamura M, Shirai F, Wu YI, Loshbaugh AL, Kuhlman B, Hahn KM, Kasai H.

Nature. 2015 Sep 17;525(7569):333-8. doi: 10.1038/nature15257. Epub 2015 Sep 9.

42.

Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene.

Martinez-Rodriguez L, Erdogan O, Jimenez-Rodriguez M, Gonzalez-Rivera K, Williams T, Li L, Weinreb V, Collier M, Chandrasekaran SN, Ambroggio X, Kuhlman B, Carter CW Jr.

J Biol Chem. 2015 Aug 7;290(32):19710-25. doi: 10.1074/jbc.M115.642876. Epub 2015 Jun 18. Erratum in: J Biol Chem. 2016 Nov 4;291(45):23830-23831.

43.

Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation.

Yumerefendi H, Dickinson DJ, Wang H, Zimmerman SP, Bear JE, Goldstein B, Hahn K, Kuhlman B.

PLoS One. 2015 Jun 17;10(6):e0128443. doi: 10.1371/journal.pone.0128443. eCollection 2015.

44.

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B.

J Chem Theory Comput. 2015 Feb 10;11(2):609-22. doi: 10.1021/ct500864r.

45.

Fab-based bispecific antibody formats with robust biophysical properties and biological activity.

Wu X, Sereno AJ, Huang F, Lewis SM, Lieu RL, Weldon C, Torres C, Fine C, Batt MA, Fitchett JR, Glasebrook AL, Kuhlman B, Demarest SJ.

MAbs. 2015;7(3):470-82. doi: 10.1080/19420862.2015.1022694.

46.

SwiftLib: rapid degenerate-codon-library optimization through dynamic programming.

Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A.

Nucleic Acids Res. 2015 Mar 11;43(5):e34. doi: 10.1093/nar/gku1323. Epub 2014 Dec 24.

47.

Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins.

Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):112-7. doi: 10.1073/pnas.1417910112. Epub 2014 Dec 22.

48.

Ubiquitin-conjugating enzyme Cdc34 and ubiquitin ligase Skp1-cullin-F-box ligase (SCF) interact through multiple conformations.

Sandoval D, Hill S, Ziemba A, Lewis S, Kuhlman B, Kleiger G.

J Biol Chem. 2015 Jan 9;290(2):1106-18. doi: 10.1074/jbc.M114.615559. Epub 2014 Nov 25.

49.

Computational de novo design of a four-helix bundle protein--DND_4HB.

Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B.

Protein Sci. 2015 Apr;24(4):434-45. doi: 10.1002/pro.2577. Epub 2014 Nov 6.

50.

Requirements for 5'dRP/AP lyase activity in Ku.

Strande NT, Carvajal-Garcia J, Hallett RA, Waters CA, Roberts SA, Strom C, Kuhlman B, Ramsden DA.

Nucleic Acids Res. 2014;42(17):11136-43. doi: 10.1093/nar/gku796. Epub 2014 Sep 8.

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