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Zhang S, De Leon Rodriguez LM, Li FF, Brimble MA. Recent developments in the cleavage, functionalization, and conjugation of proteins and peptides at tyrosine residues. Chem Sci 2023; 14:7782-7817. [PMID: 37502317 PMCID: PMC10370606 DOI: 10.1039/d3sc02543h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Peptide and protein selective modification at tyrosine residues has become an exploding field of research as tyrosine constitutes a robust alternative to lysine and cysteine-targeted traditional peptide/protein modification protocols. This review offers a comprehensive summary of the latest advances in tyrosine-selective cleavage, functionalization, and conjugation of peptides and proteins from the past three years. This updated overview complements the extensive body of work on site-selective modification of peptides and proteins, which holds significant relevance across various disciplines, including chemical, biological, medical, and material sciences.
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Affiliation(s)
- Shengping Zhang
- Center for Translational Medicine, Shenzhen Bay Laboratory New Zealand
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
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2
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Ramesh B, Abnouf S, Mali S, Moree WJ, Patil U, Bark SJ, Varadarajan N. Engineered ChymotrypsiN for Mass Spectrometry-Based Detection of Protein Glycosylation. ACS Chem Biol 2019; 14:2616-2628. [PMID: 31710461 DOI: 10.1021/acschembio.9b00506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have engineered the substrate specificity of chymotrypsin to cleave after Asn by high-throughput screening of large libraries created by comprehensive remodeling of the substrate binding pocket. The engineered variant (chymotrypsiN, ChyB-Asn) demonstrated an altered substrate specificity with an expanded preference for Asn-containing substrates. We confirmed that protein engineering did not compromise the stability of the enzyme by biophysical characterization. Comparison of wild-type ChyB and ChyB-Asn in profiling lysates of HEK293 cells demonstrated both qualitative and quantitative differences in the nature of the peptides and proteins identified by liquid chromatography and tandem mass spectrometry. ChyB-Asn enabled the identification of partially glycosylated Asn sites within a model glycoprotein and in the extracellular proteome of Jurkat T cells. ChymotrypsiN is a valuable addition to the toolkit of proteases to aid the mapping of N-linked glycosylation sites within proteins and proteomes.
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Affiliation(s)
- Balakrishnan Ramesh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, United States
| | - Shaza Abnouf
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, United States
| | - Sujina Mali
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Wilna J. Moree
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Steven J. Bark
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, United States
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3
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Urmey AR, Zondlo NJ. Design of a Protein Motif Responsive to Tyrosine Nitration and an Encoded Turn-Off Sensor of Tyrosine Nitration. Biochemistry 2019; 58:2822-2833. [PMID: 31140788 PMCID: PMC6688601 DOI: 10.1021/acs.biochem.9b00334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine nitration is a protein post-translational modification that is predominantly non-enzymatic and is observed to be increased under conditions of nitrosative stress and in numerous disease states. A small protein motif (14-18 amino acids) responsive to tyrosine nitration has been developed. In this design, nitrotyrosine replaced the conserved Glu12 of an EF-hand metal-binding motif. Thus, the non-nitrated peptide bound terbium weakly. In contrast, tyrosine nitration resulted in a 45-fold increase in terbium affinity. Nuclear magnetic resonance spectroscopy indicated direct binding of nitrotyrosine to the metal and EF-hand-like metal contacts in this designed peptide. Nitrotyrosine is an efficient quencher of fluorescence. To develop a sensor of tyrosine nitration, the initial design was modified to incorporate Glu residues at EF-hand positions 9 and 16 as additional metal-binding residues, to increase the terbium affinity of the peptide with unmodified tyrosine. This peptide with a tyrosine at residue 12 bound terbium and effectively sensitized terbium luminescence. Tyrosine nitration resulted in a 180-fold increase in terbium affinity ( Kd = 1.6 μM) and quenching of terbium luminescence. This sequence was incorporated as an encoded protein tag and applied as a turn-off fluorescent protein sensor of tyrosine nitration. The sensor was responsive to nitration by peroxynitrite, with fluorescence quenched upon nitration. The greater terbium affinity upon tyrosine nitration resulted in a large dynamic range and sensitivity to substoichiometric nitration. An improved approach for the synthesis of peptides containing nitrotyrosine was also developed, via the in situ silyl protection of nitrotyrosine. This work represents the first designed, encodable protein motif that is responsive to tyrosine nitration.
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Affiliation(s)
- Andrew R. Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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4
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Tran DT. Engineering Proteases for Mass Spectrometry‐Based Post Translational Modification Analyses. Proteomics 2018; 19:e1700471. [DOI: 10.1002/pmic.201700471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/23/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Duc T. Tran
- School of BiotechnologyInternational University—Vietnam National University in HCMC Ho Chi Minh City 720351 Vietnam
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5
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Li Q, Yi L, Hoi KH, Marek P, Georgiou G, Iverson BL. Profiling Protease Specificity: Combining Yeast ER Sequestration Screening (YESS) with Next Generation Sequencing. ACS Chem Biol 2017; 12:510-518. [PMID: 27977123 DOI: 10.1021/acschembio.6b00547] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An enzyme engineering technology involving yeast endoplasmic reticulum (ER) sequestration screening (YESS) has been recently developed. Here, a new method is established, in which the YESS platform is combined with NextGen sequencing (NGS) to enable a comprehensive survey of protease specificity. In this approach, a combinatorial substrate library is targeted to the yeast ER and transported through the secretory pathway, interacting with any protease(s) residing in the ER. Multicolor FACS screening is used to isolate cells labeled with fluorophore-conjugated antibodies, followed by NGS to profile the cleaved substrates. The YESS-NGS method was successfully applied to profile the sequence specificity of the wild-type and an engineered variant of the tobacco etch mosaic virus protease. Proteolysis in the yeast secretory pathway was also mapped for the first time in vivo revealing a major cleavage pattern of Ali/Leu-X-Lys/Arg-Arg. Here Ali is any small aliphatic residue, but especially Leu. This pattern was verified to be due to the well-known endogenous protease Kex2 after comparison to a newly generated Kex2 knockout strain as well as cleavage of peptides with recombinant Kex2 in vitro. This information is particularly important for those using yeast display technology, as library members with Ali/Leu-X-Lys/Arg-Arg patterns are likely being removed from screens via Kex2 cleavage without the researcher's knowledge.
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Affiliation(s)
- Qing Li
- Department of Chemistry, ‡Department of Biomedical
Engineering, §Department of Chemical Engineering, and ∥Section of Molecular Genetics and
Microbiology, University of Texas, Austin, Texas 78712, United States
| | - Li Yi
- Department of Chemistry, ‡Department of Biomedical
Engineering, §Department of Chemical Engineering, and ∥Section of Molecular Genetics and
Microbiology, University of Texas, Austin, Texas 78712, United States
| | - Kam Hon Hoi
- Department of Chemistry, ‡Department of Biomedical
Engineering, §Department of Chemical Engineering, and ∥Section of Molecular Genetics and
Microbiology, University of Texas, Austin, Texas 78712, United States
| | - Peter Marek
- Department of Chemistry, ‡Department of Biomedical
Engineering, §Department of Chemical Engineering, and ∥Section of Molecular Genetics and
Microbiology, University of Texas, Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemistry, ‡Department of Biomedical
Engineering, §Department of Chemical Engineering, and ∥Section of Molecular Genetics and
Microbiology, University of Texas, Austin, Texas 78712, United States
| | - Brent L. Iverson
- Department of Chemistry, ‡Department of Biomedical
Engineering, §Department of Chemical Engineering, and ∥Section of Molecular Genetics and
Microbiology, University of Texas, Austin, Texas 78712, United States
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6
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Evolution of a mass spectrometry-grade protease with PTM-directed specificity. Proc Natl Acad Sci U S A 2016; 113:14686-14691. [PMID: 27940920 DOI: 10.1073/pnas.1609925113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mapping posttranslational modifications (PTMs), which diversely modulate biological functions, represents a significant analytical challenge. The centerpiece technology for PTM site identification, mass spectrometry (MS), requires proteolytic cleavage in the vicinity of a PTM to yield peptides for sequencing. This requirement catalyzed our efforts to evolve MS-grade mutant PTM-directed proteases. Citrulline, a PTM implicated in epigenetic and immunological function, made an ideal first target, because citrullination eliminates arginyl tryptic sites. Bead-displayed trypsin mutant genes were translated in droplets, the mutant proteases were challenged to cleave bead-bound fluorogenic probes of citrulline-dependent proteolysis, and the resultant beads (1.3 million) were screened. The most promising mutant efficiently catalyzed citrulline-dependent peptide bond cleavage (kcat/KM = 6.9 × 105 M-1⋅s-1). The resulting C-terminally citrullinated peptides generated characteristic isotopic patterns in MALDI-TOF MS, and both a fragmentation product y1 ion corresponding to citrulline (176.1030 m/z) and diagnostic peak pairs in the extracted ion chromatograms of LC-MS/MS analysis. Using these signatures, we identified citrullination sites in protein arginine deiminase 4 (12 sites) and in fibrinogen (25 sites, two previously unknown). The unique mass spectral features of PTM-dependent proteolytic digest products promise a generalized PTM site-mapping strategy based on a toolbox of such mutant proteases, which are now accessible by laboratory evolution.
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7
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Slusky JS. Outer membrane protein design. Curr Opin Struct Biol 2016; 45:45-52. [PMID: 27894013 DOI: 10.1016/j.sbi.2016.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/02/2016] [Indexed: 01/23/2023]
Abstract
Membrane proteins are the gateway to the cell. These proteins are also a control center of the cell, as information from the outside is passed through membrane proteins as signals to the cellular machinery. The design of membrane proteins seeks to harness the power of these gateways and signal carriers. This review will focus on the design of the membrane proteins that are in the outer membrane, a membrane which only exists for gram negative bacteria, mitochondria, and chloroplasts. Unlike other membrane proteins, outer membrane proteins are uniquely shaped as β-barrels. Herein, I describe most known examples of membrane β-barrel design to date, focusing particularly on categorizing designs as: Firstly, structural deconstruction; secondly, structural changes; thirdly, chemical function design; and finally, the creation of new folds.
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Affiliation(s)
- Joanna Sg Slusky
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 4010 Haworth Hall, 1200 Sunnyside Ave., Lawrence, KS 66045, United States.
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Urbach C, Gordon NC, Strickland I, Lowne D, Joberty-Candotti C, May R, Herath A, Hijnen D, Thijs JL, Bruijnzeel-Koomen CA, Minter RR, Hollfelder F, Jermutus L. Combinatorial Screening Identifies Novel Promiscuous Matrix Metalloproteinase Activities that Lead to Inhibition of the Therapeutic Target IL-13. ACTA ACUST UNITED AC 2015; 22:1442-1452. [PMID: 26548614 DOI: 10.1016/j.chembiol.2015.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/10/2015] [Accepted: 09/28/2015] [Indexed: 12/20/2022]
Abstract
The practical realization of disease modulation by catalytic degradation of a therapeutic target protein suffers from the difficulty to identify candidate proteases, or to engineer their specificity. We identified 23 measurable, specific, and new protease activities using combinatorial screening of 27 human proteases against 24 therapeutic protein targets. We investigate the cleavage of monocyte chemoattractant protein 1, interleukin-6 (IL-6), and IL-13 by matrix metalloproteinases (MMPs) and serine proteases, and demonstrate that cleavage of IL-13 leads to potent inhibition of its biological activity in vitro. MMP-8 degraded human IL-13 most efficiently in vitro and ex vivo in human IL-13 transgenic mouse bronchoalveolar lavage. Hence, MMP-8 is a therapeutic protease lead against IL-13 for inflammatory conditions whereby reported genetic and genomics data suggest an involvement of MMP-8. This work describes the first exploitation of human enzyme promiscuity for therapeutic applications, and reveals both starting points for protease-based therapies and potential new regulatory networks in inflammatory disease.
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Affiliation(s)
- Carole Urbach
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.
| | - Nathaniel C Gordon
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Ian Strickland
- Department of Respiratory, Inflammation and Autoimmunity, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - David Lowne
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | | | - Richard May
- Department of Respiratory, Inflammation and Autoimmunity, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - Athula Herath
- Non Clinical Biostatistics, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - DirkJan Hijnen
- Department of Dermatology, University Medical Center, 3508 GA Utrecht, the Netherlands
| | - Judith L Thijs
- Department of Dermatology, University Medical Center, 3508 GA Utrecht, the Netherlands
| | | | - Ralph R Minter
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Lutz Jermutus
- Department of Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK
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9
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Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc Natl Acad Sci U S A 2013; 110:7229-34. [PMID: 23589865 DOI: 10.1073/pnas.1215994110] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Myriad new applications of proteases would be enabled by an ability to fine-tune substrate specificity and activity. Herein we present a general strategy for engineering protease selectivity and activity by capitalizing on sequestration of the protease to be engineered within the yeast endoplasmic reticulum (ER). A substrate fusion protein composed of yeast adhesion receptor subunit Aga2, selection and counterselection substrate sequences, multiple intervening epitope tag sequences, and a C-terminal ER retention sequence is coexpressed with a protease library. Cleavage of the substrate fusion protein by the protease eliminates the ER retention sequence, facilitating transport to the yeast surface. Yeast cells that display Aga2 fusions in which only the selection substrate is cleaved are isolated by multicolor FACS with fluorescently labeled antiepitope tag antibodies. Using this system, the Tobacco Etch Virus protease (TEV-P), which strongly prefers Gln at P1 of its canonical ENLYFQ↓S substrate, was engineered to recognize selectively Glu or His at P1. Kinetic analysis indicated an overall 5,000-fold and 1,100-fold change in selectivity, respectively, for the Glu- and His-specific TEV variants, both of which retained high catalytic turnover. Human granzyme K and the hepatitis C virus protease were also shown to be amenable to this unique approach. Further, by adjusting the signaling strategy to identify phosphorylated as opposed to cleaved sequences, this unique system was shown to be compatible with the human Abelson tyrosine kinase.
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Li Q, Yi L, Marek P, Iverson BL. Commercial proteases: present and future. FEBS Lett 2013; 587:1155-63. [PMID: 23318711 DOI: 10.1016/j.febslet.2012.12.019] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 12/23/2022]
Abstract
This review presents a brief overview of the general categories of commercially used proteases, and critically surveys the successful strategies currently being used to improve the properties of proteases for various commercial purposes. We describe the broad application of proteases in laundry detergents, food processing, and the leather industry. The review also introduces the expanding development of proteases as a class of therapeutic agents, as well as highlighting recent progress in the field of protease engineering. The potential commercial applications of proteases are rapidly growing as recent technological advances are producing proteases with novel properties and substrate specificities.
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Affiliation(s)
- Qing Li
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
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12
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Goldsmith M, Tawfik DS. Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 2012; 22:406-12. [DOI: 10.1016/j.sbi.2012.03.010] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 12/26/2022]
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Yoo TH, Pogson M, Iverson BL, Georgiou G. Directed evolution of highly selective proteases by using a novel FACS-based screen that capitalizes on the p53 regulator MDM2. Chembiochem 2012; 13:649-53. [PMID: 22334509 DOI: 10.1002/cbic.201100718] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Tae Hyeon Yoo
- Department of Molecular Science and Technology, Division of Applied Chemistry and Biological Engineering, Ajou University, Suwon 443-749, South Korea
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Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol 2010; 398:747-62. [PMID: 20363230 DOI: 10.1016/j.jmb.2010.03.058] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 03/22/2010] [Accepted: 03/26/2010] [Indexed: 11/22/2022]
Abstract
Interactions among Bcl-2 family proteins are important for regulating apoptosis. Prosurvival members of the family interact with proapoptotic BH3 (Bcl-2-homology-3)-only members, inhibiting execution of cell death through the mitochondrial pathway. Structurally, this interaction is mediated by binding of the alpha-helical BH3 region of the proapoptotic proteins to a conserved hydrophobic groove on the prosurvival proteins. Native BH3-only proteins exhibit selectivity in binding prosurvival members, as do small molecules that block these interactions. Understanding the sequence and structural basis of interaction specificity in this family is important, as it may allow the prediction of new Bcl-2 family associations and/or the design of new classes of selective inhibitors to serve as reagents or therapeutics. In this work, we used two complementary techniques--yeast surface display screening from combinatorial peptide libraries and SPOT peptide array analysis--to elucidate specificity determinants for binding to Bcl-x(L)versus Mcl-1, two prominent prosurvival proteins. We screened a randomized library and identified BH3 peptides that bound to either Mcl-1 or Bcl-x(L) selectively or to both with high affinity. The peptides competed with native ligands for binding into the conserved hydrophobic groove, as illustrated in detail by a crystal structure of a specific peptide bound to Mcl-1. Mcl-1-selective peptides from the screen were highly specific for binding Mcl-1 in preference to Bcl-x(L), Bcl-2, Bcl-w, and Bfl-1, whereas Bcl-x(L)-selective peptides showed some cross-interaction with related proteins Bcl-2 and Bcl-w. Mutational analyses using SPOT arrays revealed the effects of 170 point mutations made in the background of a peptide derived from the BH3 region of Bim, and a simple predictive model constructed using these data explained much of the specificity observed in our Mcl-1 versus Bcl-x(L) binders.
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