Publications

2014
Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming. Nucleic Acids Res. 2014 Dec 24. pii: gku1323. [Epub ahead of print] PubMed PMID: 25539925.

Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc Natl Acad Sci U S A. 2014 Dec 22. pii: 201417910. [Epub ahead of print] PubMed PMID: 25535392.

Sandoval D, Hill S, Ziemba A, Lewis S, Kuhlman B, Kleiger G. Ubiquitin-conjugating enzyme Cdc34 and ubiquitin ligase SCF interact through
multiple conformations. J Biol Chem. 2014 Nov 25. pii: jbc.M114.615559. [Epub ahead of print] PubMed PMID: 25425648.

Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B. Computational de novo design of a four-helix bundle protein-DND_4HB. Protein Sci. 2014 Oct 6. doi: 10.1002/pro.2577. [Epub ahead of print] PubMed PMID: 25287625.

Strande NT, Carvajal-Garcia J, Hallett RA, Waters CA, Roberts SA, Strom C, Kuhlman B, Ramsden DA. Requirements for 5'dRP/AP lyase activity in Ku. Nucleic Acids Res. 2014;42(17):11136-43. doi: 10.1093/nar/gku796. Epub 2014 Sep 8. PubMed PMID: 25200085; PubMed Central PMCID: PMC4176175.

Carter CW Jr, Li L, Weinreb V, Collier M, Gonzalez-Rivera K, Jimenez-Rodriguez M, Erdogan O, Kuhlman B, Ambroggio X, Williams T, Chandrasekharan SN. The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed. Biol Direct. 2014 Jun 14;9:11. doi: 10.1186/1745-6150-9-11. PubMed PMID: 24927791; PubMed Central PMCID: PMC4082485.

Lewis SM, Wu X, Pustilnik A, Sereno A, Huang F, Rick HL, Guntas G, Leaver-Fay  A, Smith EM, Ho C, Hansen-Estruch C, Chamberlain AK, Truhlar SM, Conner EM, Atwell S, Kuhlman B, Demarest SJ. Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Nat Biotechnol. 2014 Feb;32(2):191-8. doi: 10.1038/nbt.2797. Epub 2014 Jan 26. PubMed PMID: 24463572.

2013


Jacobs TM, Kuhlman B.
"Using anchoring motifs for the computational design of protein-protein interactions" 
Biochem Soc Trans. 2013 Oct;41(5):1141-5.

Der BS, Kuhlman B. 
"Cages from coils" 
Nat Biotechnol. 2013 Sep;31(9):809-10.

Kamadurai HB, Qiu Y, Deng A, Harrison JS, Macdonald C, Actis M, Rodrigues P, Miller DJ, Souphron J, Lewis SM, Kurinov I, Fujii N, Hammel M, Piper R, Kuhlman B, Schulman BA. 
"Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3"
Elife. 2013 Aug 8;2:e00828.  

Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R. 
"Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design."
PLoS One. 2013 Jul 15;8(7):e67051. doi: 10.1371/journal.pone.0067051. Print 2013. 
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Harrison JS, Higgins CD, O'Meara MJ, Koellhoffer JF, Kuhlman BA, Lai JR.  
"Role of Electrostatic Repulsion in Controlling pH-Dependent Conformational Changes of Viral Fusion Proteins."
Structure. 2013 Jul 2;21(7):1085-96.
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Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B. 
"Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability." 
PLoS One. 2013 May 31;8(5):e64363. 
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Der BS, Kuhlman B. 
"Strategies to control the binding mode of de novo designed protein interactions." 
Curr Opin Struct Biol. 2013 May 31. [Epub ahead of print] 
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Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R. 
"Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)." 
PLoS One. 2013 May 22;8(5):e63906. 
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Der BS, Jha RK, Lewis SM, Thompson PM, Guntas G, Kuhlman B. 
"Combined computational design of a zinc-binding site and a protein-protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding." 
Proteins. 2013 Jul;81(7):1245-55. 
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Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B. 
"Scientific benchmarks for guiding macromolecular energy function improvement." 
Methods Enzymol. 2013;523:109-43. 
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Zhang J, Lewis SM, Kuhlman B, Lee AL. 
"Supertertiary structure of the MAGUK core from PSD-95." 
Structure. 2013 Mar 5;21(3):402-13. 

Choi EJ, Jacak R, Kuhlman B. 
"A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins."
Protein Eng Des Sel. 2013 Apr;26(4):283-9.
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Stranges PB, Kuhlman B. 
"A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds."
Protein Science. 2013 22(1):74-82.
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2012


Baker R, Lewis SM, Sasaki AT, Wilkerson EM, Locasale JW, Cantley LC, Kuhlman B, Dohlman HG, Campbell SL. 
"Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function."
Nat Struct Mol Biol. 2013 Jan;20(1):46-52.
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Murphy GS, Mills JL, Miley MJ, Machius M, Szyperski T, Kuhlman B. 
"Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core."
Structure. 2012 Jun 6;20(6):1086-96.

Guntas G, Kuhlman B. 
"Redesigning the NEDD8 pathway with a bacterial genetic screen for ubiquitin-like molecule transfer."
J Mol Biol. 2012 May 4; 18(3-4):161-166. 
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Lungu OI, Hallett RA, Choi EJ, Aiken MJ, Hahn KM, Kuhlman B. 
"Designing photoswitchable peptides using the AsLOV2 domain."  
Chemistry & Biology. 2012 April 20; 19(4):507-517.
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Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR,
Zacharko MA, Carney JP, Gray JJ, Georgiou G, Kuhlman B, Ellington AD. 
"Structure-based design of supercharged, highly thermoresistant antibodies."
Chemistry & Biology. 2012 April 20; 19(4):449-455.
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Der BS, Edwards DR, Kuhlman B.
"Catalysis by a de novo zinc-mediated protein interface: implications for natural enzyme evolution and rational enzyme engineering." 
Biochemistry. 2012 April 17.
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Der BS, Machius M, Miley MJ, Mills JL, Szyperski TA, Kuhlman B. 
"Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer." 
J Am Chem Soc. 2012, 134 (1), pp 375–385.
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Renfrew PD, Choi EJ, Bonneau R, Kuhlman B. 
"Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design." 
PLoS One. 2012 Mar 14; 7(3):e32637. 

Jacak R, Leaver-Fay A, Kuhlman B. 
"Computational protein design with explicit consideration of surface hydrophobic patches." 
Proteins. 2012, 80(3):825-38.
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2011


Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B. 
"Computational design of a symmetric homodimer using β-strand assembly." 
Proc Natl Acad Sci USA. 2011 December 20; 108: 20562-20567.
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Jha RK, Wu YI, Zawistowski JS, Macnevin C, Hahn KM, Kuhlman B. 
"Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications." 
J Mol Biol. 2011 Oct 21;413(2):513-22.

Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B. 
"A generic program for multistate protein design." 
PLoS One. 2011;6(7):e20937.

Der BS, Kuhlman B. 
"Perspective. From computational design to a protein that binds." 
Science. 2011 May 13;332(6031):801-2. 

Lewis SM, Kuhlman B. 
"Anchored design of protein-protein interfaces." 
PLoS One. 2011 Jun 17; 6(6)e20872.
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Gulyani A, Vitriol E, Allen R, Wu J, Gremyachinskiy D, Lewis S, Dewar B, Graves LM, Kay BK, Kuhlman B, Elston T, Hahn KM. 
"A biosensor generated via high-throughput screening quantifies cell edge Src dynamics." 
Nat Chem Biol. 2011 Jun 12;7(7):437-44. 

Saha A, Lewis S, Kleiger G, Kuhlman B, Deshaies RJ. 
"Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate." 
Mol Cell. 2011 Apr 8;42(1):75-83.
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Sammond DW, Bosch DE, Butterfoss GL, Purbeck C, Machius M, Siderovski DP, Kuhlman B. 
"Computational design of the sequence and structure of a protein-binding peptide." 
J Am Chem Soc. 2011 Mar 30;133(12):4190-2.
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Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S,
Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ,
Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. 
"ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules." 
Methods Enzymol. 2011;487:545-74. 
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2010


Bosch DE, Kimple AJ, Sammond DW, Muller RE, Miley MJ, Machius M, Kuhlman B, Willard FS, Siderovski DP. 
"Structural determinants of affinity enhancement between GoLoco motifs and G-protein alpha subunit mutants." 
J Biol Chem. 2011 Feb 4;286(5):3351-8.

Guntas G, Purbeck C, Kuhlman B. 
"Engineering a protein-protein interface using a computationally designed library." 
Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19296-301.

Pham Y, Kuhlman B, Butterfoss GL, Hu H, Weinreb V, Carter CW Jr. 
"Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation." 
J Biol Chem. 2010 Dec 3;285(49):38590-601.

Hahn KM, Kuhlman B. 
"Hold me tightly LOV". 
Nat Methods. 2010 Aug;7(8):595, 597. 

Jha RK, Leaver-Fay A, Yin S, Wu Y, Butterfoss GL, Szyperski T, Dokholyan NV, Kuhlman B. 
"Computational design of a PAK1 binding protein." 
J Mol Biol. 2010 Jul9;400(2):257-70.

Purbeck C, Eletr ZM, Kuhlman B. 
"Kinetics of the transfer of ubiquitin from UbcH7 to E6AP." 
Biochemistry. 2010 Feb 23;49(7):1361-3. 
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2009


Salgado EN, Ambroggio XI, Brodin JD, Lewis RA, Kuhlman B, Tezcan FA. 
"Metal templated design of protein interfaces." 
Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1827-32.

Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM. 
"A genetically encoded photoactivatable Rac controls the motility of living cells."
Nature. 2009 Sep 3;461(7260):104-8.
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Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. 
"Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates." 
Cell. 2009 Nov 25;139(5):957-68. 

Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R. 
"A preliminary survey of the peptoid folding landscape." 
J Am Chem Soc. 2009 Nov 25;131(46):16798-807. 

Kuhlman B, DeGrado WF. 
"Engineering and design: editorial overview."
Curr Opin Struct Biol. 2009 Aug;19(4):440-1.

Karanicolas J, Kuhlman B. 
"Computational design of affinity and specificity at protein-protein interfaces." 
Curr Opin Struct Biol. 2009 Aug;19(4):458-63.

Torres MP, Lee MJ, Ding F, Purbeck C, Kuhlman B, Dokholyan NV, Dohlman HG. 
"G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase." 
J Biol Chem. 2009 Mar 27;284(13):8940-50.
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Leaver-Fay, A; Snoeyink, J; Kuhlman, B. 
"On-the-fly rotamer pair energy evaluation in protein design."
Bioinformatics Research and Applications. 4983343-354 2008
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2008


Hu, XZ; Wang, HC; Ke, HM; Kuhlman, B. 
"Computer-Based Redesign of a beta Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo beta Sheet Design." 
Structure. 2008 Dec 10;16(12):1799-805.
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Renfrew PD, Butterfoss GL, Kuhlman B. 
"Using quantum mechanics to improve estimates of amino acid side chain rotamer energies."
Proteins. 2008 Jun;71(4):1637-46.
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2007


Hu X, Wang H, Ke H, Kuhlman B. 
"High-resolution design of a protein loop."
Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17668-73.
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Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, Kuhlman B. 
"Structure-based protocol for identifying mutations that enhance protein-protein binding affinities."
J Mol Biol. 2007 Aug 31;371(5):1392-404.
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Eletr ZM, Kuhlman B. 
"Sequence Determinants of E2-E6AP Binding Affinity and Specificity".
J Mol Biol. 2007 Jun 1;369(2):419-28.
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Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss GL, Kuhlman B, Carter CW Jr.
"A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases."
Mol Cell. 2007 Mar 23;25(6):851-62. 
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Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. 
"Maintaining solvent accessible surface area under rotamer substitution for protein design."
J Comput Chem. 2007 Jun;28(8):1336-41. 
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2006


Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. 
"Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution."
J Mol Biol. 2006 Oct 6;362(5):1004-24.
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Ambroggio XI, Kuhlman B. 
"Design of protein conformational switches."
Curr Opin Struct Biol. 2006 Aug;16(4):525-30.
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Hu X, Kuhlman B. 
"Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences."
Proteins. 2006 Mar 15;62(3):739-48.
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Liu Y, Kuhlman B. 
"RosettaDesign server for protein design."
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W235-8.
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Ambroggio XI, Kuhlman B. 
"Computational design of a single amino acid sequence that can switch between two distinct protein folds."
J Am Chem Soc. 2006 Feb 1;128(4):1154-61. 
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2005


Jiang L, Kuhlman B, Kortemme T, Baker D. 
"A solvated rotamer approach to modeling water-mediated hydrogen bonds at protein-protein interfaces."
Proteins. 2005 Mar 1;58(4):893-904. 
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Eletr ZM, Huang DT, Duda DM, Schulman BA, Kuhlman B. 
"E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer."
Nat Struct Mol Biol. 2005 Oct;12(10):933-4.
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Leaver-Fay A, Kuhlman B, Snoeyink J. 
"An adaptive dynamic programming algorithm for the side chain placement problem."
Pac Symp Biocomput. 2005;16-27. 
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Butterfoss GL, Kuhlman B. 
"Computer-Based Design of Novel Protein Structures."
Annu Rev Biophys Biomol Struct. 2006;35:49-65.
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2004


Kuhlman B, Baker D. 
"Exploring folding free energy landscapes using computational protein design."
Curr Opin Struct Biol. 2004 Feb;14(1):89-95. Review. 



2003


Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. 
"Design of a novel globular protein fold with atomic-level accuracy."
Science. 2003 Nov 21;302(5649):1364-8.
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Dantas G, Kuhlman B, Callender D, Wong M, Baker D.
"A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins."
J Mol Biol. 2003 Sep 12;332(2):449-60. 
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Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. 
"An improved protein decoy set for testing energy functions for protein structure prediction."
Proteins. 2003 Oct 1;53(1):76-87.
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Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. 
"Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations."
J Mol Biol. 2003 Aug 1;331(1):281-99.
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2002


Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D. 
"Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2."
Protein Sci. 2002 Dec;11(12):2924-31.
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Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. 
"Accurate computer-based design of a new backbone conformation in the second turn of protein L."  
J Mol Biol. 2002 Jan 18;315(3):471-7.
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2001


Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. 
"Conversion of monomeric protein L to an obligate dimer by computational protein design."  
Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10687-91. Epub 2001 Aug 28. 
Erratum in: Proc Natl Acad Sci U S A 2002 May 28;99(11):7809. 
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Nauli S, Kuhlman B, Baker D. 
"Computer-based redesign of a protein folding pathway."
Nat Struct Biol. 2001 Jul;8(7):602-5.
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2000


Kuhlman B, Baker D. 
"Native protein sequences are close to optimal for their structures."
Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10383-8. 
Erratum in: Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13460.



1999


Luisi DL, Kuhlman B, Sideras K, Evans PA, Raleigh DP. 
"Effects of varying the local propensity to form secondary structure on the stability and folding kinetics of a rapid folding mixed alpha/beta protein: characterization of a truncation mutant of the N-terminal domain of the ribosomal protein L9."
J Mol Biol. 1999 May 28;289(1):167-74.
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Sato S, Kuhlman B, Wu WJ, Raleigh DP. 
"Folding of the multidomain ribosomal protein L9: the two domains fold independently with remarkably different rates."
Biochemistry. 1999 Apr 27;38(17):5643-50.
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Kuhlman B, Luisi DL, Young P, Raleigh DP. 
"pKa values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions."
Biochemistry. 1999 Apr 13;38(15):4896-903.
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1998


Kuhlman B, Luisi DL, Evans PA, Raleigh DP. 
"Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9." 
J Mol Biol. 1998 Dec 18;284(5):1661-70.
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Kuhlman B, Raleigh DP. 
"Global analysis of the thermal and chemical denaturation of the N-terminal domain of the ribosomal protein L9 in H2O and D2O. Determination of the thermodynamic parameters, deltaH(o), deltaS(o), and deltaC(o)p and evaluation of solvent isotope effects."  
Protein Sci. 1998 Nov;7(11):2405-12.
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Vugmeyster L, Kuhlman B, Raleigh DP. 
"Amide proton exchange measurements as a probe of the stability and dynamics of the N-terminal domain of the ribosomal protein L9: comparison with the intact protein."  
Protein Sci. 1998 Sep;7(9):1994-7.
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Spector S, Kuhlman B, Fairman R, Wong E, Boice JA, Raleigh DP. 
"Cooperative folding of a protein mini domain: the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex."
J Mol Biol. 1998 Feb 20;276(2):479-89.
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Kuhlman B, Boice JA, Fairman R, Raleigh DP. 
"Structure and stability of the N-terminal domain of the ribosomal protein L9: evidence for rapid two-state folding."
Biochemistry. 1998 Jan 27;37(4):1025-32.
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1997


Kuhlman B, Yang HY, Boice JA, Fairman R, Raleigh DP. 
"An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability."  
J Mol Biol. 1997 Aug 1;270(5):640-7.
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Kuhlman B, Boice JA, Wu WJ, Fairman R, Raleigh DP. 
"Calcium binding peptides from alpha-lactalbumin: implications for protein folding and stability."  
Biochemistry. 1997 Apr 15;36(15):4607-15.
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