1
|
Krantz A, Hanel AM, Strug I, Wilczynski A, Wolff JJ, Huang W, Huang LH, Settineri T, Holmes DL, Hardy MC, Bridon DP. Site-specific Labeling of a Protein Lysine Residue By Novel Kinetic Labeling Combinatorial Libraries. Comput Struct Biotechnol J 2014; 9:e201403001. [PMID: 24757504 PMCID: PMC3995232 DOI: 10.5936/csbj.201403001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 12/12/2022] Open
Abstract
The first example of a kinetic labeling library designed to enable the discovery of affinity labels is presented. Each library component (1) consists of a variable peptidyl component linked to a biotinyl moiety by a 4-mercaptobenzoyl linker in thioester format. We demonstrate that an affinity label can be uncovered by measuring reaction rates between library pools and the protein target, human serum albumin (HSA) and identifying significant outliers. By choosing peptide functionality compatible with a potentially reactive thioester labeling entity, libraries can be screened in pools. It is noteworthy that a limited subset of amino acids (R, S, E, F, Y, l, M, W, and Q) that compose the affinity moiety is sufficient to produce rate variances that guide the discovery process. After two rounds of deconvolution, J-FLYEE-NH2 (7-E) emerges as a bona fide affinity label of HSA. Unlike known affinity labels, the affinity moiety is not retained in the protein product, but is extruded upon acylation of the protein. This feature affords a method of introducing various payloads, without extraneous elements, onto protein frameworks.
Collapse
Affiliation(s)
- Allen Krantz
- Advanced Proteome Therapeutics Inc., 650 Albany Street, Suite 113, Boston, MA 02118, United States ; RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.)
| | - Arthur M Hanel
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.)
| | - Ivona Strug
- Advanced Proteome Therapeutics Inc., 650 Albany Street, Suite 113, Boston, MA 02118, United States ; Current address: EMD Millipore, 17 Cherry Hill Drive, Danvers, Massachusetts, 01923, United States
| | - Andrzej Wilczynski
- Advanced Proteome Therapeutics Inc., 650 Albany Street, Suite 113, Boston, MA 02118, United States
| | - Jeremy J Wolff
- Bruker Daltonics Inc., 40 Manning Road, Billerica, MA 01821, United States
| | - Wolin Huang
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.)
| | - Linda H Huang
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.)
| | - Tina Settineri
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.) ; Current address: Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, United States
| | - Darren L Holmes
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.)
| | - Margaret C Hardy
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.)
| | - Dominique P Bridon
- RedCell Inc., 270-B Littlefield Avenue, South San Francisco, CA, 94080, United States (Renamed ConjuChem LLC. Current address: 11755 Wilshire Blvd, Suite 2000, Los Angeles, CA 90025.) ; Current address: Optivia Biotechnology Inc., 115 Constitution Drive, Suite 7, Menlo Park, CA 94025, United States
| |
Collapse
|
2
|
Yang X, Xie Y, Pu J, Zhao H, Liao J, Yuan Y, Zhu S, Long G, Zhang C, Yuan H, Chen Y, Liao F. Estimation of affinities of ligands in mixtures via magnetic recovery of target-ligand complexes and chromatographic analyses: chemometrics and an experimental model. BMC Biotechnol 2011; 11:44. [PMID: 21545719 PMCID: PMC3096923 DOI: 10.1186/1472-6750-11-44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 05/05/2011] [Indexed: 11/22/2022] Open
Abstract
Abstract Conclusions This new method is robust and effective for each mixture possessing a limited number of candidate ligands whose molar quantities have moderate differences, and its integration with PCS has promise to routinely practice the mixture-based library strategy.
Collapse
Affiliation(s)
- Xiaolan Yang
- Unit for Analytical Probes and Protein Biotechnology, Key Laboratory of Medical Laboratory Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|