Brian Kuhlman

The Kuhlman lab uses a combination of computational and experimental tools to understand and redesign protein-protein interactions. Computer-based methods are being developed for identifying amino-acid mutations that will either enhance an interaction of interest or perturb binding specificity. The ability to manipulate protein binding events will allow the creation of biosensors, probes to study cell biology, and therapeutics with enhanced activity. The lab is currently focused on the following two projects:

1. Identifying E3 ubiquitin ligase substrates with redesigned E3s.
Tagging proteins with ubiquitin is one of the primary ways that cells get rid of unwanted proteins. Ubiquitin is attached to proteins by a cascade of enzymatic reactions that involve the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzymes, and the E3 ubiquitin ligases. The substrate specificity of the pathway is conveyed by the E3s, of which there are hundreds in the human genome. However, the substrates of most E3s are currently unknown. The Kuhlman lab is developing a new protocol for identifying E3 substrates in vivo that uses redesigned E3s to tag substrates with an epitope-tagged version of the ubiquitin-like molecule NEDD8. The primary step in this protocol is the computer-based redesign of a particular E3 to function with the conjugating enzyme for NEDD8 (UbcH12).

2. Using non-natural amino acids to design peptide-protein interfaces.
Peptide-protein interfaces are of great therapeutic interest since high-affinity peptides can modulate bioactivity when targeted toward binding sites normally occupied by other proteins. Evolution has probably selected for sequences that are relatively optimal for these interfaces; therefore, the Kuhlman lab plans to take advantage of amino acids that nature does not have at its disposal. Using non-natural amino acids, they hope to create novel geometries and packing configurations that will ultimately increase the affinity of peptide-protein interactions.

Selected Publications:
Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. (2007) Maintaining solvent accessible surface area under rotamer substitution for protein design. J Comput Chem. Feb 6; [Epub ahead of print]

Liu Y, Kuhlman B. (2006) RosettaDesign server for protein design. Nucleic Acids Res. 34(Web Server issue):W235-8.

Ambroggio XI, Kuhlman B. (2006) Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc. 128:1154-61.

Hu X, Kuhlman B. (2006) Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins. 62:739-48.

Eletr ZM, Huang DT, Duda DM, Schulman BA, Kuhlman B. (2005) E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nat Struct Mol Biol 12:933-4.

Jiang L, Kuhlman B, Kortemme T, Baker D. (2005) A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58:893-904.

Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL and Baker D. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-8.






		The Kuhlman lab uses a combination of computational and experimental tools to understand and redesign protein-protein interactions. Computer-based methods are being developed for identifying amino-acid mutations that will either enhance an interaction of interest or perturb binding specificity. The ability to manipulate protein binding events will allow the creation of biosensors, probes to study cell biology, and therapeutics with enhanced activity. The lab is currently focused on the following two projects: 1. Identifying E3 ubiquitin ligase substrates with redesigned E3s. Tagging proteins with ubiquitin is one of the primary ways that cells get rid of unwanted proteins. Ubiquitin is attached to proteins by a cascade of enzymatic reactions that involve the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzymes, and the E3 ubiquitin ligases. The substrate specificity of the pathway is conveyed by the E3s, of which there are hundreds in the human genome. However, the substrates of most E3s are currently unknown. The Kuhlman lab is developing a new protocol for identifying E3 substrates in vivo that uses redesigned E3s to tag substrates with an epitope-tagged version of the ubiquitin-like molecule NEDD8. The primary step in this protocol is the computer-based redesign of a particular E3 to function with the conjugating enzyme for NEDD8 (UbcH12). 2. Using non-natural amino acids to design peptide-protein interfaces. Peptide-protein interfaces are of great therapeutic interest since high-affinity peptides can modulate bioactivity when targeted toward binding sites normally occupied by other proteins. Evolution has probably selected for sequences that are relatively optimal for these interfaces; therefore, the Kuhlman lab plans to take advantage of amino acids that nature does not have at its disposal. Using non-natural amino acids, they hope to create novel geometries and packing configurations that will ultimately increase the affinity of peptide-protein interactions. Selected Publications: Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. (2007) Maintaining solvent accessible surface area under rotamer substitution for protein design. J Comput Chem. Feb 6; [Epub ahead of print] Liu Y, Kuhlman B. (2006) RosettaDesign server for protein design. Nucleic Acids Res. 34(Web Server issue):W235-8. Ambroggio XI, Kuhlman B. (2006) Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc. 128:1154-61. Hu X, Kuhlman B. (2006) Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins. 62:739-48. Eletr ZM, Huang DT, Duda DM, Schulman BA, Kuhlman B. (2005) E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nat Struct Mol Biol 12:933-4. Jiang L, Kuhlman B, Kortemme T, Baker D. (2005) A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58:893-904. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL and Baker D. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-8.


	contact information: [phone] (919) 843-0188 [email] [website]