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Photocrosslinking Approach to Investigate Protein Interactions in the BCL-2 Family

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BCL-2 Family Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1877))

Abstract

The Bcl-2 family of proteins regulates mitochondrial outer membrane permeability thereby making life or death decisions for cells. Most of Bcl-2 proteins contain hydrophobic regions that are embedded in intracellular membranes such as mitochondria. These membrane proteins are difficult to express and purify thereby preluding biochemical and biophysical characterizations. Here, we describe a photocrosslinking approach based on in vitro synthesis of Bcl-2 proteins with photoreactive amino acid analogs incorporated at specific locations. These photoreactive proteins are reconstituted into liposomal membranes with defined phospholipids or mitochondrial membranes isolated from animals, and their interactions with other Bcl-2 proteins are detected by photocrosslinking.

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References

  1. Leber B, Lin J, Andrews DW (2007) Embedded together: the life and death consequences of interaction of the Bcl-2 family with membranes. Apoptosis 12(5):897–911. https://doi.org/10.1007/s10495-007-0746-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Leber B, Lin J, Andrews DW (2010) Still embedded together binding to membranes regulates Bcl-2 protein interactions. Oncogene 29(38):5221–5230. https://doi.org/10.1038/onc.2010.283

    Article  CAS  PubMed  Google Scholar 

  3. Chi X, Kale J, Leber B, Andrews DW (2014) Regulating cell death at, on, and in membranes. Biochim Biophys Acta 1843(9):2100–2113. https://doi.org/10.1016/j.bbamcr.2014.06.002

    Article  CAS  PubMed  Google Scholar 

  4. Czabotar PE, Lessene G, Strasser A, Adams JM (2014) Control of apoptosis by the BCL-2 protein family: implications for physiology and therapy. Nat Rev Mol Cell Biol 15(1):49–63. https://doi.org/10.1038/nrm3722

    Article  CAS  PubMed  Google Scholar 

  5. Cosentino K, Garcia-Saez AJ (2017) Bax and Bak Pores: Are We Closing the Circle? Trends Cell Biol 27(4):266–275. https://doi.org/10.1016/j.tcb.2016.11.004

    Article  CAS  PubMed  Google Scholar 

  6. Zhang Z, Subramaniam S, Kale J, Liao C, Huang B, Brahmbhatt H, Condon SG, Lapolla SM, Hays FA, Ding J, He F, Zhang XC, Li J, Senes A, Andrews DW, Lin J (2016) BH3-in-groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes. EMBO J 35(2):208–236. https://doi.org/10.15252/embj.201591552

    Article  CAS  PubMed  Google Scholar 

  7. Kuwana T, Mackey MR, Perkins G, Ellisman MH, Latterich M, Schneiter R, Green DR, Newmeyer DD (2002) Bid, Bax, and lipids cooperate to form supramolecular openings in the outer mitochondrial membrane. Cell 111(3):331–342

    Article  CAS  PubMed  Google Scholar 

  8. Lovell JF, Billen LP, Bindner S, Shamas-Din A, Fradin C, Leber B, Andrews DW (2008) Membrane binding by tBid initiates an ordered series of events culminating in membrane permeabilization by Bax. Cell 135(6):1074–1084. https://doi.org/10.1016/j.cell.2008.11.010

    Article  CAS  PubMed  Google Scholar 

  9. Gavathiotis E, Reyna DE, Davis ML, Bird GH, Walensky LD (2010) BH3-triggered structural reorganization drives the activation of proapoptotic BAX. Mol Cell 40(3):481–492. https://doi.org/10.1016/j.molcel.2010.10.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ren D, Tu HC, Kim H, Wang GX, Bean GR, Takeuchi O, Jeffers JR, Zambetti GP, Hsieh JJ, Cheng EH (2010) BID, BIM, and PUMA are essential for activation of the BAX- and BAK-dependent cell death program. Science 330(6009):1390–1393. https://doi.org/10.1126/science.1190217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Czabotar PE, Westphal D, Dewson G, Ma S, Hockings C, Fairlie WD, Lee EF, Yao S, Robin AY, Smith BJ, Huang DC, Kluck RM, Adams JM, Colman PM (2013) Bax crystal structures reveal how BH3 domains activate Bax and nucleate its oligomerization to induce apoptosis. Cell 152(3):519–531. https://doi.org/10.1016/j.cell.2012.12.031

    Article  CAS  PubMed  Google Scholar 

  12. Moldoveanu T, Grace CR, Llambi F, Nourse A, Fitzgerald P, Gehring K, Kriwacki RW, Green DR (2013) BID-induced structural changes in BAK promote apoptosis. Nat Struct Mol Biol 20(5):589–597. https://doi.org/10.1038/nsmb.2563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sattler M, Liang H, Nettesheim D, Meadows RP, Harlan JE, Eberstadt M, Yoon HS, Shuker SB, Chang BS, Minn AJ, Thompson CB, Fesik SW (1997) Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis. Science 275(5302):983–986

    Article  CAS  Google Scholar 

  14. Liu X, Dai S, Zhu Y, Marrack P, Kappler JW (2003) The structure of a Bcl-xL/Bim fragment complex: implications for Bim function. Immunity 19(3):341–352

    Article  CAS  PubMed  Google Scholar 

  15. Billen LP, Kokoski CL, Lovell JF, Leber B, Andrews DW (2008) Bcl-XL inhibits membrane permeabilization by competing with Bax. PLoS Biol 6(6):e147. https://doi.org/10.1371/journal.pbio.0060147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Aranovich A, Liu Q, Collins T, Geng F, Dixit S, Leber B, Andrews DW (2012) Differences in the mechanisms of proapoptotic BH3 proteins binding to Bcl-XL and Bcl-2 quantified in live MCF-7 cells. Mol Cell 45(6):754–763. https://doi.org/10.1016/j.molcel.2012.01.030

    Article  CAS  PubMed  Google Scholar 

  17. Ding J, Mooers BH, Zhang Z, Kale J, Falcone D, McNichol J, Huang B, Zhang XC, Xing C, Andrews DW, Lin J (2014) After embedding in membranes antiapoptotic Bcl-XL protein binds both Bcl-2 homology region 3 and helix 1 of proapoptotic Bax protein to inhibit apoptotic mitochondrial permeabilization. J Biol Chem 289(17):11873–11896. https://doi.org/10.1074/jbc.M114.552562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kim H, Rafiuddin-Shah M, Tu HC, Jeffers JR, Zambetti GP, Hsieh JJ, Cheng EH (2006) Hierarchical regulation of mitochondrion-dependent apoptosis by BCL-2 subfamilies. Nat Cell Biol 8(12):1348–1358. https://doi.org/10.1038/ncb1499

    Article  CAS  PubMed  Google Scholar 

  19. Willis SN, Fletcher JI, Kaufmann T, van Delft MF, Chen L, Czabotar PE, Ierino H, Lee EF, Fairlie WD, Bouillet P, Strasser A, Kluck RM, Adams JM, Huang DC (2007) Apoptosis initiated when BH3 ligands engage multiple Bcl-2 homologs, not Bax or Bak. Science 315(5813):856–859. https://doi.org/10.1126/science.1133289

    Article  CAS  PubMed  Google Scholar 

  20. Chou JJ, Li H, Salvesen GS, Yuan J, Wagner G (1999) Solution structure of Bid, an intracellular amplifier of apoptotic signaling. Cell 96:615–624

    Article  CAS  PubMed  Google Scholar 

  21. Suzuki M, Youle RJ, Tjandra N (2000) Structure of Bax: coregulation of dimer formation and intracellular localization. Cell 103(4):645–654

    Article  CAS  PubMed  Google Scholar 

  22. Kim PK, Annis MG, Dlugosz PJ, Leber B, Andrews DW (2004) During apoptosis Bcl-2 changes membrane topology at both the endoplasmic reticulum and mitochondria. Mol Cell 14(4):523–529

    Article  CAS  PubMed  Google Scholar 

  23. Annis MG, Soucie EL, Dlugosz PJ, Cruz-Aguado JA, Penn LZ, Leber B, Andrews DW (2005) Bax forms multispanning monomers that oligomerize to permeabilize membranes during apoptosis. EMBO J 24(12):2096–2103. https://doi.org/10.1038/sj.emboj.7600675

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Westphal D, Dewson G, Menard M, Frederick P, Iyer S, Bartolo R, Gibson L, Czabotar PE, Smith BJ, Adams JM, Kluck RM (2014) Apoptotic pore formation is associated with in-plane insertion of Bak or Bax central helices into the mitochondrial outer membrane. Proc Natl Acad Sci U S A 111(39):E4076–E4085. https://doi.org/10.1073/pnas.1415142111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Liao C, Zhang Z, Kale J, Andrews DW, Lin J, Li J (2016) Conformational heterogeneity of Bax Helix 9 dimer for apoptotic pore formation. Sci Rep 6:29502. https://doi.org/10.1038/srep29502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Oltersdorf T, Elmore SW, Shoemaker AR, Armstrong RC, Augeri DJ, Belli BA, Bruncko M, Deckwerth TL, Dinges J, Hajduk PJ, Joseph MK, Kitada S, Korsmeyer SJ, Kunzer AR, Letai A, Li C, Mitten MJ, Nettesheim DG, Ng S, Nimmer PM, O'Connor JM, Oleksijew A, Petros AM, Reed JC, Shen W, Tahir SK, Thompson CB, Tomaselli KJ, Wang B, Wendt MD, Zhang H, Fesik SW, Rosenberg SH (2005) An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 435(7042):677–681. https://doi.org/10.1038/nature03579

    Article  CAS  PubMed  Google Scholar 

  27. Gavathiotis E, Reyna DE, Bellairs JA, Leshchiner ES, Walensky LD (2012) Direct and selective small-molecule activation of proapoptotic BAX. Nat Chem Biol 8(7):639–645. https://doi.org/10.1038/nchembio.995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Cory S, Roberts AW, Colman PM, Adams JM (2016) Targeting BCL-2-like proteins to kill cancer cells. Trends Cancer 2(8):443–460. https://doi.org/10.1016/j.trecan.2016.07.001

    Article  PubMed  Google Scholar 

  29. Delbridge AR, Grabow S, Strasser A, Vaux DL (2016) Thirty years of BCL-2: translating cell death discoveries into novel cancer therapies. Nat Rev Cancer 16(2):99–109. https://doi.org/10.1038/nrc.2015.17

    Article  CAS  PubMed  Google Scholar 

  30. Niu X, Brahmbhatt H, Mergenthaler P, Zhang Z, Sang J, Daude M, Ehlert FGR, Diederich WE, Wong E, Zhu W, Pogmore J, Nandy JP, Satyanarayana M, Jimmidi RK, Arya P, Leber B, Lin J, Culmsee C, Yi J, Andrews DW (2017) A small-molecule inhibitor of bax and bak oligomerization prevents genotoxic cell death and promotes neuroprotection. Cell Chem Biol 24(4):493–506 e495. https://doi.org/10.1016/j.chembiol.2017.03.011

    Article  CAS  PubMed  Google Scholar 

  31. Zhang Z, Zhu W, Lapolla SM, Miao Y, Shao Y, Falcone M, Boreham D, McFarlane N, Ding J, Johnson AE, Zhang XC, Andrews DW, Lin J (2010) Bax forms an oligomer via separate, yet interdependent, surfaces. J Biol Chem 285(23):17614–17627. https://doi.org/10.1074/jbc.M110.113456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ding J, Zhang Z, Roberts GJ, Falcone M, Miao Y, Shao Y, Zhang XC, Andrews DW, Lin J (2010) Bcl-2 and Bax interact via the BH1-3 groove-BH3 motif interface and a novel interface involving the BH4 motif. J Biol Chem 285(37):28749–28763. https://doi.org/10.1074/jbc.M110.148361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Erickson AH, Blobel G (1983) Cell-free translation of messenger RNA in a wheat germ system. Methods Enzymol 96:38–50

    Article  CAS  PubMed  Google Scholar 

  34. Johnson AE, Woodward WR, Herbert E, Menninger JR (1976) Nepsilon-acetyllysine transfer ribonucleic acid: a biologically active analogue of aminoacyl transfer ribonucleic acids. Biochemistry 15(3):569–575

    Article  CAS  PubMed  Google Scholar 

  35. Krieg UC, Walter P, Johnson AE (1986) Photocrosslinking of the signal sequence of nascent preprolactin to the 54-kilodalton polypeptide of the signal recognition particle. Proc Natl Acad Sci U S A 83(22):8604–8608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Tan C, Dlugosz PJ, Peng J, Zhang Z, Lapolla SM, Plafker SM, Andrews DW, Lin J (2006) Auto-activation of the apoptosis protein Bax increases mitochondrial membrane permeability and is inhibited by Bcl-2. J Biol Chem 281(21):14764–14775. https://doi.org/10.1074/jbc.M602374200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Kale J, Chi X, Leber B, Andrews D (2014) Examining the molecular mechanism of bcl-2 family proteins at membranes by fluorescence spectroscopy. Methods Enzymol 544:1–23. https://doi.org/10.1016/B978-0-12-417158-9.00001-7

    Article  CAS  PubMed  Google Scholar 

  38. Gurevich VV, Pokrovskaya ID, Obukhova TA, Zozulya SA (1991) Preparative in vitro mRNA synthesis using SP6 and T7 RNA polymerases. Anal Biochem 195(2):207–213

    Article  CAS  PubMed  Google Scholar 

  39. Falcone D, Andrews DW (1991) Both the 5′ untranslated region and the sequences surrounding the start site contribute to efficient initiation of translation in vitro. Mol Cell Biol 11(5):2656–2664

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Brunner J (1993) New photolabeling and crosslinking methods. Annu Rev Biochem 62:483–514. https://doi.org/10.1146/annurev.bi.62.070193.002411

    Article  CAS  PubMed  Google Scholar 

  41. Johnson AE, Adkins HJ (1984) Glycerol, sucrose, and other diol-containing reagents are not inert components in in vitro incubations containing aminoacyl-tRNA. Anal Biochem 137(2):351–359

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the United States National Institutes of Health grants (R01GM062964, and P20GM103640), Oklahoma Center for the Advancement of Science and Technology grant (HR16-026), and Presbyterian Health Foundation grant (GRF00000125) to J.L.

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Correspondence to Jialing Lin .

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Lin, J., Johnson, A.E., Zhang, Z. (2019). Photocrosslinking Approach to Investigate Protein Interactions in the BCL-2 Family. In: Gavathiotis, E. (eds) BCL-2 Family Proteins. Methods in Molecular Biology, vol 1877. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8861-7_9

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  • DOI: https://doi.org/10.1007/978-1-4939-8861-7_9

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