2012
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.
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.
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.
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, PMID 22510088.
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.
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.
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.
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. Biochemistry. From computational design to a protein that binds. Science. 2011 May 13;332(6031):801-2.
PubMed PMID: 21566181.
Lewis SM, Kuhlman B. Anchored design of protein-protein interfaces. PLoS One. 2011 Jun 17; 6(6)e20872.
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. PubMed PMID: 21474069; PubMed Central PMCID: PMC3091889.
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. Epub 2011 Mar 9. PubMed PMID: 21388199;
PubMed Central PMCID: PMC3081598.
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. PubMed PMID: 21187238.
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.
Epub 2010 Nov 29. PubMed PMID: 21115486; PubMed Central PMCID: PMC3030341.
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. Epub 2010 Oct 25. PubMed PMID: 20974935;
PubMed Central PMCID: PMC2984139.
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.
Epub 2010 Sep 23. PubMed PMID: 20864539; PubMed Central PMCID: PMC2992291.
Hahn KM, Kuhlman B. "Hold me tightly LOV". Nat Methods. 2010 Aug;7(8):595, 597. PubMed PMID: 20676078.
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. Epub 2010 May 10. PubMed PMID: 204601.
Purbeck C, Eletr ZM, Kuhlman B. Kinetics of the transfer of ubiquitin from UbcH7 to E6AP.
Biochemistry. 2010 Feb 23;49(7):1361-3. PubMed PMID: 20039703.
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. Epub 2009 Dec 23. PubMed PMID: 20080561
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. Epub 2009 Aug 19. PubMed PMID: 19693014;
PubMed Central PMCID: PMC2766670.
[view]
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. PubMed PMID: 19945379
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. PubMed PMID: 19919145.
Kuhlman B, DeGrado WF. "Engineering and design: editorial overview". Curr Opin Struct Biol. 2009 Aug;19(4):440-1.
Epub 2009 Aug 13. PubMed PMID: 19683427.
Karanicolas J, Kuhlman B. "Computational design of affinity and specificity at protein-protein interfaces".
Curr Opin Struct Biol. 2009 Aug;19(4):458-63. Epub 2009 Jul 29. PubMed PMID: 19646858.
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. Epub 2009 Jan 27.
PubMed PMID: 19176477; PubMed Central PMCID: PMC2659251.
Leaver-Fay, A; Snoeyink, J; Kuhlman, B
"On-the-fly rotamer pair energy evaluation in protein design ".
BIOINFORMATICS RESEARCH AND APPLICATIONS.
4983343-354 2008
[view]
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 ".<\br>
STRUCTURE.
2008 Dec 10;16(12):1799-805.
PMID: 19081056 [PubMed - indexed for MEDLINE]
[view\]
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.
PMID: 18076032 [PubMed - in process]
[view]
2007
Hu X, Wang H, Ke H, Kuhlman B.
"High-resolution design of a protein loop. ".
Proc Natl Acad Sci U S A..
Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17668-73. Epub 2007 Oct 30.
PMID: 17971437 [PubMed - indexed for MEDLINE]
[view]
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. Epub 2007 Jun 8.
PMID: 17603074 [PubMed - indexed for MEDLINE]
[view]
Eletr ZM, Kuhlman B. "Sequence Determinants of E2-E6AP Binding Affinity and
Specificity".
J Mol Biol.
2007 Jun 1;369(2):419-28. Epub 2007 Mar 19.
PMID: 17433363 [PubMed - in process]
[view]
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. PMID: 17386262 [PubMed -
indexed for MEDLINE]
[view]
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. PMID:
17285560 [PubMed - indexed for MEDLINE]
[view]
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. Epub 2006 Aug 4.
PMID: 16949611 [PubMed - indexed for MEDLINE]
[view]
Ambroggio XI, Kuhlman B."Design
of protein conformational switches."
Curr Opin Struct
Biol. 2006 Aug;16(4):525-30. Epub 2006 Jun 12. PMID:
16765587 [PubMed - indexed for
MEDLINE]
[view]
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.PMID: 16317667 [PubMed -
- indexed for MEDLINE]
[view]
Liu Y, Kuhlman B."RosettaDesign
server for protein design."
Nucleic Acids Res.
2006 Jul 1;34(Web Server issue):W235-8.PMID: 16845000 [PubMed
- indexed for MEDLINE]
[view]
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. PMID: 16433531 [PubMed -
- indexed for MEDLINE]
[view]
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. PMID: 15651050 [PubMed
- indexed for MEDLINE]
[view]
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. Epub 2005 Sep 4. PMID: 16142244 [PubMed
- indexed for MEDLINE]
[view]
Leaver-Fay A, Kuhlman B,
Snoeyink J. "An adaptive dynamic programming
algorithm for the side chain placement problem "
Pac Symp
Biocomput.2005;:16-27. PMID: 15759610 [PubMed - indexed
for MEDLINE]
[view]
Butterfoss GL, Kuhlman B.
"Computer-Based Design of Novel Protein Structures."
Annu Rev Biophys
Biomol Struct. 2005 Dec 7; [Epub ahead of print] PMID:
16336082 [PubMed - as supplied by publisher]
[view]
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. PMID: 15102454 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 14631033 PMID: 14631033 [PubMed
- indexed for MEDLINE]
[view]
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. PMID: 12948494 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 12945051 [PubMed
- indexed for MEDLINE]>
[view]
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.PMID: 12875852 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 12441390 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 11786026 [PubMed
- indexed for MEDLINE]
[view]
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. PMID: 11526208 [PubMed -
indexed for MEDLINE]
[view]
Nauli S, Kuhlman B, Baker
D., "Computer-based redesign of a protein folding
pathway."
Nat Struct Biol. 2001 Jul;8(7):602-5.PMID: 11427890 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 10984534 [PubMed - indexed for
MEDLINE]
[view]
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.PMID: 10339414 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 10220353
[PubMed - indexed for MEDLINE]
[view]
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.PMID: 10200179
[PubMed - indexed for MEDLINE]
[view]
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.PMID: 9878377 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 9828007 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 9761480 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 9512717 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 9454593 [PubMed
- indexed for MEDLINE]
[view]
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.PMID: 9245593
[PubMed - indexed for MEDLINE]
[view]
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.PMID: 9109670
[PubMed - indexed for MEDLINE]
[view]
