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Case M, Navaratna T, Vinh J, Thurber G. Rapid Evaluation of Staple Placement in Stabilized α Helices Using Bacterial Surface Display. ACS Chem Biol 2023; 18:905-914. [PMID: 37039514 PMCID: PMC10773984 DOI: 10.1021/acschembio.3c00048] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
There are a wealth of proteins involved in disease that cannot be targeted by current therapeutics because they are inside cells, inaccessible to most macromolecules, and lack small-molecule binding pockets. Stapled peptides, where two amino acids are covalently linked, form a class of macrocycles that have the potential to penetrate cell membranes and disrupt intracellular protein-protein interactions. However, their discovery relies on solid-phase synthesis, greatly limiting queries into their complex design space involving amino acid sequence, staple location, and staple chemistry. Here, we use stabilized peptide engineering by Escherichia coli display (SPEED), which utilizes noncanonical amino acids and click chemistry for stabilization, to rapidly screen staple location and linker structure to accelerate peptide design. After using SPEED to confirm hotspots in the mdm2-p53 interaction, we evaluated different staple locations and staple chemistry to identify several novel nanomolar and sub-nanomolar antagonists. Next, we evaluated SPEED in the B cell lymphoma 2 (Bcl-2) protein family, which is responsible for regulating apoptosis. We report that novel staple locations modified in the context of BIM, a high affinity but nonspecific naturally occurring peptide, improve its specificity against the highly homologous proteins in the Bcl-2 family. These compounds demonstrate the importance of screening linker location and chemistry in identifying high affinity and specific peptide antagonists. Therefore, SPEED can be used as a versatile platform to evaluate multiple design criteria for stabilized peptide engineering.
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2
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Li AJ, Lu M, Desta I, Sundar V, Grigoryan G, Keating AE. Neural network-derived Potts models for structure-based protein design using backbone atomic coordinates and tertiary motifs. Protein Sci 2023; 32:e4554. [PMID: 36564857 PMCID: PMC9854172 DOI: 10.1002/pro.4554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Designing novel proteins to perform desired functions, such as binding or catalysis, is a major goal in synthetic biology. A variety of computational approaches can aid in this task. An energy-based framework rooted in the sequence-structure statistics of tertiary motifs (TERMs) can be used for sequence design on predefined backbones. Neural network models that use backbone coordinate-derived features provide another way to design new proteins. In this work, we combine the two methods to make neural structure-based models more suitable for protein design. Specifically, we supplement backbone-coordinate features with TERM-derived data, as inputs, and we generate energy functions as outputs. We present two architectures that generate Potts models over the sequence space: TERMinator, which uses both TERM-based and coordinate-based information, and COORDinator, which uses only coordinate-based information. Using these two models, we demonstrate that TERMs can be utilized to improve native sequence recovery performance of neural models. Furthermore, we demonstrate that sequences designed by TERMinator are predicted to fold to their target structures by AlphaFold. Finally, we show that both TERMinator and COORDinator learn notions of energetics, and these methods can be fine-tuned on experimental data to improve predictions. Our results suggest that using TERM-based and coordinate-based features together may be beneficial for protein design and that structure-based neural models that produce Potts energy tables have utility for flexible applications in protein science.
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Affiliation(s)
- Alex J. Li
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mindren Lu
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Israel Desta
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Vikram Sundar
- Computational and Systems Biology ProgramMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Gevorg Grigoryan
- Department of Computer ScienceDartmouth CollegeHanoverNew HampshireUSA
| | - Amy E. Keating
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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3
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Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain. Biomolecules 2020; 10:biom10091308. [PMID: 32932757 PMCID: PMC7564285 DOI: 10.3390/biom10091308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 01/07/2023] Open
Abstract
Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 μs) of the murine γ-herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. We experimentally validate the role of these hydrophobic interactions by quantifying the impact of mutating these residues on binding to the Beclin1/BECN1 BH3D, demonstrating that these mutations adversely affect both protein stability and binding. To our knowledge, this is the first study detailing the binding-associated conformational changes and presence of long-range interactions within vBCL2s.
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Peptide design by optimization on a data-parameterized protein interaction landscape. Proc Natl Acad Sci U S A 2018; 115:E10342-E10351. [PMID: 30322927 DOI: 10.1073/pnas.1812939115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many applications in protein engineering require optimizing multiple protein properties simultaneously, such as binding one target but not others or binding a target while maintaining stability. Such multistate design problems require navigating a high-dimensional space to find proteins with desired characteristics. A model that relates protein sequence to functional attributes can guide design to solutions that would be hard to discover via screening. In this work, we measured thousands of protein-peptide binding affinities with the high-throughput interaction assay amped SORTCERY and used the data to parameterize a model of the alpha-helical peptide-binding landscape for three members of the Bcl-2 family of proteins: Bcl-xL, Mcl-1, and Bfl-1. We applied optimization protocols to explore extremes in this landscape to discover peptides with desired interaction profiles. Computational design generated 36 peptides, all of which bound with high affinity and specificity to just one of Bcl-xL, Mcl-1, or Bfl-1, as intended. We designed additional peptides that bound selectively to two out of three of these proteins. The designed peptides were dissimilar to known Bcl-2-binding peptides, and high-resolution crystal structures confirmed that they engaged their targets as expected. Excellent results on this challenging problem demonstrate the power of a landscape modeling approach, and the designed peptides have potential uses as diagnostic tools or cancer therapeutics.
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5
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Foight GW, Chen TS, Richman D, Keating AE. Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design. Methods Mol Biol 2018; 1561:213-232. [PMID: 28236241 DOI: 10.1007/978-1-4939-6798-8_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model.
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Affiliation(s)
- Glenna Wink Foight
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - T Scott Chen
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Daniel Richman
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA.
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Li X, Fu X, Gao Y, Li H, Wang W, Shen Y. Expression of tissue inhibitor of metalloproteinases-1 and B-cell lymphoma-2 in the synovial membrane in patients with knee osteoarthritis. Exp Ther Med 2018; 15:885-889. [PMID: 29399094 PMCID: PMC5772747 DOI: 10.3892/etm.2017.5462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/25/2017] [Indexed: 11/22/2022] Open
Abstract
The purpose of this study was to determine the expression and impact of tissue inhibitor of metalloproteinases-1 (TIMP-1) and B-cell lymphoma-2 (Bcl-2) in knee osteoarthritis (KOA). We collected synovial fluids from the knee joint of 70 KOA patients and 30 controls. The expression levels of TIMP-1 and Bcl-2 were significantly higher in KOA patients than those in the control group (P<0.01). We also found positive correlation between the severity of KOA and the expression level of TIMP-1 (r=0.8027, P<0.05) and and Bcl-2 (r=0.5336, P<0.05). However, we found no correlation between the expression levels of TIMP-1 and Bcl-2 in the synovial membranes of KOA patients (P>0.05). Both TIMP-1 and Bcl-2 are expressed at high levels in the synovial membrane with KOA, and are closely related to the occurrence and development of KOA. Thus, detection of TIMP-1 and Bcl-2 in KOA patients can be helpful in diagnosing the state of KOA.
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Affiliation(s)
- Xiaomiao Li
- Department of Orthopedics, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Xiaodong Fu
- Department of Orthopedics, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yingjian Gao
- Department of Orthopedics, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Hao Li
- Department of Orthopedics, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Weili Wang
- Department of Orthopedics, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yi Shen
- Department of Orthopedics, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
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7
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Lapelosa M. Conformational dynamics and free energy of BHRF1 binding to Bim BH3. Biophys Chem 2018; 232:22-28. [DOI: 10.1016/j.bpc.2017.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 01/10/2023]
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8
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胡 司, 李 辉, 康 品, 陈 天, 李 妙, 朱 建, 高 大, 张 恒, 王 洪. [Effects of simvastatin on aortic vascular endothelial cell apoptosis and Bcl-2 protein expression in a rat model of atherosclerosis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:1456-1460. [PMID: 29180324 PMCID: PMC6779642 DOI: 10.3969/j.issn.1673-4254.2017.11.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Indexed: 05/21/2023]
Abstract
OBJECTIVE To explore the effects of simvastatin on vascular endothelial cell apoptosis and Bcl-2 protein expression in the aorta in a rat model of atherosclerosis. METHODS Thirty-six rats were randomized into control group (n=10), atherosclerosis model group (n=13) and simvastatin intervention group (n=13). In the latter two groups, rat models of atherosclerosis were established by intraperitoneal injection of vitamin D3 combined with high-fat feeding for 6 weeks, and the control rats were fed with regular diet. In the intervention group, the rats were further fed with high-fat diet with daily simvastatin treatment for 4 weeks. After the treatments, the pathological changes and plaque in the thoracic aorta were observed, and the expression of Bcl-2 protein was detected with immunohistochemistry. TUNEL assay was used to determine the apoptosis index (AI) of the vascular endothelial cells. RESULTS Compared with that in the control group, Bcl-2 protein expression in the aorta of atherosclerotic rats was significantly decreased (P<0.05); simvastatin treatment obviously increased the expression of Bcl-2 protein in atherosclerotic rats (P<0.05) to a level similar to that in the control group. The AI was the highest in the model group (P<0.05) and comparable between the control and simvastatin treatment group. CONCLUSION The therapeutic effect of simvastatin against atherosclerosis is probably mediated by up-regulation of Bcl-2 protein, which inhibits vascular endothelial cell apoptosis in rats with aortic atherosclerosis.
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Affiliation(s)
- 司淦 胡
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 辉 李
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 品方 康
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 天平 陈
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 妙男 李
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 建 朱
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 大胜 高
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 恒 张
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
| | - 洪巨 王
- />蚌埠医学院第一附属医院 心血管科,安徽 蚌埠 233004Department of Cardiovascular Medicine, First Affiliated Hospital, Bengbu Medical College, Bengbu 233004, China
- 王洪巨,博士,教授,E-mail:
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9
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Fitzsimmons L, Kelly GL. EBV and Apoptosis: The Viral Master Regulator of Cell Fate? Viruses 2017; 9:E339. [PMID: 29137176 PMCID: PMC5707546 DOI: 10.3390/v9110339] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) was first discovered in cells from a patient with Burkitt lymphoma (BL), and is now known to be a contributory factor in 1-2% of all cancers, for which there are as yet, no EBV-targeted therapies available. Like other herpesviruses, EBV adopts a persistent latent infection in vivo and only rarely reactivates into replicative lytic cycle. Although latency is associated with restricted patterns of gene expression, genes are never expressed in isolation; always in groups. Here, we discuss (1) the ways in which the latent genes of EBV are known to modulate cell death, (2) how these mechanisms relate to growth transformation and lymphomagenesis, and (3) how EBV genes cooperate to coordinately regulate key cell death pathways in BL and lymphoblastoid cell lines (LCLs). Since manipulation of the cell death machinery is critical in EBV pathogenesis, understanding the mechanisms that underpin EBV regulation of apoptosis therefore provides opportunities for novel therapeutic interventions.
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Affiliation(s)
- Leah Fitzsimmons
- Institute of Cancer and Genomic Sciences and Centre for Human Virology, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Gemma L Kelly
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, Melbourne, VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Melbourne, VIC 3052, Australia.
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10
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Jenson JM, Ryan JA, Grant RA, Letai A, Keating AE. Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1. eLife 2017; 6:e25541. [PMID: 28594323 PMCID: PMC5464773 DOI: 10.7554/elife.25541] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.
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Affiliation(s)
- Justin M Jenson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jeremy A Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States,Department of Biology, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States,
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11
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Foight GW, Keating AE. Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5. Protein Sci 2016; 25:1273-89. [PMID: 26779844 PMCID: PMC4918428 DOI: 10.1002/pro.2881] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/17/2022]
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs) constitute a family of adapter proteins that act in numerous signaling pathways important in human biology and disease. The MATH domain of TRAF proteins binds peptides found in the cytoplasmic domains of signaling receptors, thereby connecting extracellular signals to downstream effectors. Beyond several very general motifs, the peptide binding preferences of TRAFs have not been extensively characterized, and differences between the binding preferences of TRAF paralogs are poorly understood. Here we report a screening system that we established to explore TRAF peptide-binding specificity using deep mutational scanning of TRAF-peptide ligands. We displayed single- and double-mutant peptide libraries based on the TRAF-binding sites of CD40 or TANK on the surface of Escherichia coli and screened them for binding to TRAF2, TRAF3, and TRAF5. Enrichment analysis of the library sequencing results showed differences in the permitted substitution patterns in the TANK versus CD40 backgrounds. The three TRAF proteins also demonstrated different preferences for binding to members of the CD40 library, and three peptides from that library that were analyzed individually showed striking differences in affinity for the three TRAFs. These results illustrate a previously unappreciated level of binding specificity between these close paralogs and demonstrate that established motifs are overly simplistic. The results from this work begin to outline differences between TRAF family members, and the experimental approach established herein will enable future efforts to investigate and redesign TRAF peptide-binding specificity.
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Affiliation(s)
- Glenna Wink Foight
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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12
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Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 2016; 39:27-38. [PMID: 27123812 DOI: 10.1016/j.sbi.2016.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 04/03/2016] [Indexed: 02/04/2023]
Abstract
Short helical peptides combine characteristics of small molecules and large proteins and provide an exciting area of opportunity in protein design. A growing number of studies report novel helical peptide inhibitors of protein-protein interactions. New techniques have been developed for peptide design and for chemically stabilizing peptides in a helical conformation, which frequently improves protease resistance and cell permeability. We summarize advances in peptide crosslinking chemistry and give examples of peptide design studies targeting coiled-coil transcription factors, Bcl-2 family proteins, MDM2/MDMX, and HIV gp41, among other targets.
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Affiliation(s)
- Raheleh Rezaei Araghi
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Amy E Keating
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; MIT Department of Biological Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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13
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Rosenfeld L, Heyne M, Shifman JM, Papo N. Protein Engineering by Combined Computational and In Vitro Evolution Approaches. Trends Biochem Sci 2016; 41:421-433. [PMID: 27061494 DOI: 10.1016/j.tibs.2016.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/29/2016] [Accepted: 03/09/2016] [Indexed: 12/30/2022]
Abstract
Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs.
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Affiliation(s)
- Lior Rosenfeld
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael Heyne
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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14
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Burrer CM, Foight GW, Keating AE, Chan GC. Selective peptide inhibitors of antiapoptotic cellular and viral Bcl-2 proteins lead to cytochrome c release during latent Kaposi's sarcoma-associated herpesvirus infection. Virus Res 2015; 211:86-8. [PMID: 26456186 DOI: 10.1016/j.virusres.2015.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 11/18/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with B-cell lymphomas including primary effusion lymphoma and multicentric Castleman's disease. KSHV establishes latency within B cells by modulating or mimicking the antiapoptotic Bcl-2 family of proteins to promote cell survival. Our previous BH3 profiling analysis, a functional assay that assesses the contribution of Bcl-2 proteins towards cellular survival, identified two Bcl-2 proteins, cellular Mcl-1 and viral KsBcl-2, as potential regulators of mitochondria polarization within a latently infected B-cell line, Bcbl-1. In this study, we used two novel peptide inhibitors identified in a peptide library screen that selectively bind KsBcl-2 (KL6-7_Y4eK) or KsBcl-2 and Mcl-1 (MS1) in order to decipher the relative contribution of Mcl-1 and KsBcl-2 in maintaining mitochondrial membrane potential. We found treatment with KL6-7_Y4eK and MS1 stimulated a similar amount of cytochrome c release from mitochondria isolated from Bcbl-1 cells, indicating that inhibition of KsBcl-2 alone is sufficient for mitochondrial outer membrane permiabilzation (MOMP) and thus apoptosis during a latent B cell infection. In turn, this study also identified and provides a proof-of-concept for the further development of novel KsBcl-2 inhibitors for the treatment of KSHV-associated B-cell lymphomas via the targeting of latently infected B cells.
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Affiliation(s)
- Christine M Burrer
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Glenna W Foight
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Gary C Chan
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, United States.
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