Abstract
Deciphering the X-ray crystal structures of serine protease inhibitors (serpins) and serpin complexes has been an integral part of understanding serpin function and inhibitory mechanisms. In addition, high-resolution structural information of serpins derived from the three domains of life (bacteria, archaea, and eukaryotic) and viruses has provided valuable insights into the hereditary and evolutionary history of this unique superfamily of proteins. This chapter will provide an overview of the predominant biophysical method that has yielded this information, X-ray crystallography. In addition, details of up-and-coming methods, such as neutron crystallography, cryo-electron microscopy, and small- and wide-angle solution scattering, and their potential applications to serpin structural biology will be briefly discussed. As serpins remain important both biologically and medicinally, the information provided in this chapter will aid in future experiments to expand our knowledge of this family of proteins.
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References
Whisstock JC, Bird PI (eds) (2011) Serpin structure and evolution, Methods in enzymology, 1st edn. Elsevier, Acad. Press, Amsterdam
Belorgey D, Hägglöf P, Karlsson-Li S et al (2007) Protein misfolding and the serpinopathies. Prion 1:15–20
Ambadapadi S, Munuswamy-Ramanujam G, Zheng D et al (2016) Reactive center loop (RCL) peptides derived from serpins display independent coagulation and immune modulating activities. J Biol Chem 291:2874–2887
Lomas DA, Carrell RW (2002) Serpinopathies and the conformational dementias. Nat Rev Genet 3:759–768
Engh R, Löbermann H, Schneider M et al (1989) The S variant of human alpha 1-antitrypsin, structure and implications for function and metabolism. Protein Eng 2:407–415
Tucker HM, Mottonen J, Goldsmith EJ et al (1995) Engineering of plasminogen activator inhibitor-1 to reduce the rate of latency transition. Nat Struct Biol 2:442–445
Skinner R, Abrahams JP, Whisstock JC et al (1997) The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site. J Mol Biol 266:601–609
Gooptu B, Hazes B, Chang WS et al (2000) Inactive conformation of the serpin alpha(1)-antichymotrypsin indicates two-stage insertion of the reactive loop: implications for inhibitory function and conformational disease. Proc Natl Acad Sci U S A 97:67–72
Stein PE, Leslie AG, Finch JT et al (1991) Crystal structure of uncleaved ovalbumin at 1.95 A resolution. J Mol Biol 221:941–959
Mahon B, Ambadapadi S, Yaron J et al (2018) Crystal structure of cleaved Serp-1, a Myxomavirus-derived immune modulating serpin; structural design of serpin reactive center loop (RCL) peptides with improved therapeutic function. Biochemistry 57:1096–1107
Jin L, Abrahams JP, Skinner R et al (1997) The anticoagulant activation of antithrombin by heparin. Proc Natl Acad Sci U S A 94:14683–14688
Ye S, Cech AL, Belmares R et al (2001) The structure of a Michaelis serpin-protease complex. Nat Struct Biol 8:979–983
Huntington JA, Read RJ, Carrell RW (2000) Structure of a serpin-protease complex shows inhibition by deformation. Nature 407:923–926
Rose PW, Prlić A, Altunkaya A et al (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res 45:D271–D281
Rhodes G (2006) Crystallography made crystal clear: a guide for users of macromolecular models, Complementary science series, 3rd edn. Elsevier; Academic Press, Amsterdam; Boston
Wright HT, Qian HX, Huber R (1990) Crystal structure of plakalbumin, a proteolytically nicked form of ovalbumin. Its relationship to the structure of cleaved alpha-1-proteinase inhibitor. J Mol Biol 213:513–528
Baumann U, Huber R, Bode W et al (1991) Crystal structure of cleaved human alpha 1-antichymotrypsin at 2.7 A resolution and its comparison with other serpins. J Mol Biol 218:595–606
Johnson DJD, Langdown J, Huntington JA (2010) Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex. Proc Natl Acad Sci U S A 107:645–650
Xue Y, Björquist P, Inghardt T et al (1998) Interfering with the inhibitory mechanism of serpins: crystal structure of a complex formed between cleaved plasminogen activator inhibitor type 1 and a reactive-centre loop peptide. Structure 6:627–636
Huang X, Dementiev A, Olson ST et al (2010) Basis for the specificity and activation of the serpin protein Z-dependent proteinase inhibitor (ZPI) as an inhibitor of membrane-associated factor Xa. J Biol Chem 285:20399–20409
Beinrohr L, Harmat V, Dobó J et al (2007) C1 inhibitor serpin domain structure reveals the likely mechanism of heparin potentiation and conformational disease. J Biol Chem 282:21100–21109
Walls D, Loughran ST (2011) Tagging recombinant proteins to enhance solubility and aid purification. Methods Mol Biol 681:151–175
Kimple ME, Brill AL, Pasker RL (2013) Overview of affinity tags for protein purification: affinity tags for protein purification. In: Coligan JE, Dunn BM, Speicher DW, Wingfield PT (eds) Current protocols in protein science. Wiley, Hoboken, NJ, pp 9.9.1–9.9.23. https://doi.org/10.1002/0471140864.ps0909s73
Al-Ayyoubi M, Gettins PGW, Volz K (2004) Crystal structure of human maspin, a serpin with antitumor properties: reactive center loop of Maspin is exposed but constrained. J Biol Chem 279:55540–55544
Wingfield PT (2015) Overview of the purification of recombinant proteins: purification of recombinant proteins. In: Coligan JE, Dunn BM, Speicher DW, Wingfield PT (eds) Current protocols in protein science. Wiley, Hoboken, NJ, pp 6.1.1–6.1.35. https://doi.org/10.1002/0471140864.ps0601s80
McCoy AJ, Pei XY, Skinner R et al (2003) Structure of beta-antithrombin and the effect of glycosylation on antithrombin’s heparin affinity and activity. J Mol Biol 326:823–833
Hopkins FG, Pinkus SN (1898) Observations on the crystallization of animal Proteids. J Physiol 23:130–136
Weber PC (1997) [2] Overview of protein crystallization methods, Methods in Enzymology, vol 276. Elsevier, Amsterdam, pp 13–22
Bunker RD, Dickson JMJ, Caradoc-Davies TT et al (2012) Use of a repetitive seeding protocol to obtain diffraction-quality crystals of a putative human D-xylulokinase. Acta Crystallograph Sect F Struct Biol Cryst Commun 68:1259–1262
Bergfors T (2009) Protein crystallization, 2nd edn. International University Line, San Diego
Manuel Garcıa-Ruiz J (2003) Nucleation of protein crystals. J Struct Biol 142:22–31
Elton LRB, Jackson DF (1966) X-ray diffraction and the Bragg law. Am J Phys 34:1036–1038
Leslie AGW, Powell HR, Winter G et al (2002) Automation of the collection and processing of X-ray diffraction data – a generic approach. Acta Crystallogr D Biol Crystallogr 58:1924–1928
Skarzynski T (2013) Collecting data in the home laboratory: evolution of X-ray sources, detectors and working practices. Acta Crystallogr D Biol Crystallogr 69:1283–1288
Sliz P, Harrison SC, Rosenbaum G (2003) How does radiation damage in protein crystals depend on X-ray dose? Structure 11:13–19
International Union of Crystallography (2006) International tables for crystallography. Wiley, Hoboken, NJ
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326
Battye TGG, Kontogiannis L, Johnson O et al (2011) iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr D Biol Crystallogr 67:271–281
Taylor G (2003) The phase problem. Acta Crystallogr D Biol Crystallogr 59:1881–1890
Perutz MF, Rossmann MG, Cullis AF et al (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis. Nature 185:416–422
Kendrew JC, Dickerson RE, Strandberg BE et al (1960) Structure of myoglobin: a three-dimensional Fourier synthesis at 2 A. resolution. Nature 185:422–427
Cowtan K (2003) Phase problem in X-ray crystallography, and its solution. In: Encyclopedia of life sciences. Wiley, Chichester. https://doi.org/10.1038/npg.els.0002722
Rossmann MG (1990) The molecular replacement method. Acta Crystallogr A 46(Pt 2):73–82
Kim S-J, Woo J-R, Seo EJ et al (2001) A 2.1 Å resolution structure of an uncleaved α1-antitrypsin shows variability of the reactive center and other loops. J Mol Biol 306:109–119
Messerschmidt A (2007) X-ray crystallography of biomacromolecules. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. https://doi.org/10.1002/9783527610129
Trapani S, Navaza J (2008) AMoRe: classical and modern. Acta Crystallogr D Biol Crystallogr 64:11–16
Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66:22–25
McCoy AJ (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr 63:32–41
Kissinger CR, Gehlhaar DK, Fogel DB (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr D Biol Crystallogr 55:484–491
Glykos NM, Kokkinidis M (2000) A stochastic approach to molecular replacement. Acta Crystallogr D Biol Crystallogr 56:169–174
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Gasteiger E, Gattiker A, Hoogland C et al (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788
Dodson E (2008) The befores and afters of molecular replacement. Acta Crystallogr D Biol Crystallogr 64:17–24
Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132
Adams PD, Afonine PV, Bunkóczi G et al (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221
Podjarny AD, Rees B, Urzhumtsev AG (1996) Density modification in X-ray crystallography, Crystallographic methods and protocols, vol 56. Humana Press, New Jersey, pp 205–226
Read RJ, Zhou A, Stein PE (2011) Solving serpin crystal structures, Methods in enzymology, vol 501. Elsevier, Amsterdam, pp 49–61
DiMaio F, Terwilliger TC, Read RJ et al (2011) Improved molecular replacement by density- and energy-guided protein structure optimization. Nature 473:540–543
Laskowski RA, MacArthur MW, Moss DS et al (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291
Levantino M, Yorke BA, Monteiro DC et al (2015) Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules. Curr Opin Struct Biol 35:41–48
Spence JCH (2017) XFELs for structure and dynamics in biology. IUCrJ 4:322–339
Crowther RA (2016) The resolution revolution: recent advances in cryoEM. Elsevier, Amsterdam
Frank J (2017) Advances in the field of single-particle cryo-electron microscopy over the last decade. Nat Protoc 12:209–212
Gupta S, Feng J, Chance M et al (2016) Recent advances and applications in synchrotron X-ray protein footprinting for protein structure and dynamics elucidation. Protein Pept Lett 23:309–322
Blakeley MP (2009) Neutron macromolecular crystallography. Crystallogr Rev 15:157–218
Myles DAA (2006) Neutron protein crystallography: current status and a brighter future. Curr Opin Struct Biol 16:630–637
Tuukkanen AT, Spilotros A, Svergun DI (2017) Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons. IUCrJ 4:518–528
Spilotros A, Svergun DI (2014) Advances in small- and wide-angle X-ray scattering SAXS and WAXS of proteins. In: Meyers RA (ed) Encyclopedia of analytical chemistry. Wiley, Chichester, pp 1–34
Khan MS, Singh P, Azhar A et al (2011) Serpin inhibition mechanism: a delicate balance between native metastable state and polymerization. J Amino Acids 2011:1–10
Schreuder HA, de Boer B, Dijkema R et al (1994) The intact and cleaved human antithrombin III complex as a model for serpin–proteinase interactions. Nat Struct Biol 1:48–54
Perry SL, Guha S, Pawate AS et al (2014) In situ serial Laue diffraction on a microfluidic crystallization device. J Appl Crystallogr 47:1975–1982
Graber T, Anderson S, Brewer H et al (2011) BioCARS: a synchrotron resource for time-resolved X-ray science. J Synchrotron Radiat 18:658–670
Martin-Garcia JM, Conrad CE, Nelson G et al (2017) Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. IUCrJ 4:439–454
Kinjo R, Bizen T, Tanaka T (2015) Undulator development for SPring-8-II. Synchrotron radiat. News 28:45–49
Hatsui T, Graafsma H (2015) X-ray imaging detectors for synchrotron and XFEL sources. IUCrJ 2:371–383
Schroer CG, Falkenberg G (2014) Hard X-ray nanofocusing at low-emittance synchrotron radiation sources. J Synchrotron Radiat 21:996–1005
Matsuyama S, Nakamori H, Goto T et al (2016) Nearly diffraction-limited X-ray focusing with variable-numerical-aperture focusing optical system based on four deformable mirrors. Sci Rep 6. https://doi.org/10.1038/srep24801
Mahon BP, Kurian JJ, Lomelino CL et al (2016) Microbatch mixing: “shaken not stirred”, a method for macromolecular microcrystal production for serial crystallography. Cryst Growth Des 16:6214. https://doi.org/10.1021/acs.cgd.6b00643
Heymann M, Opthalage A, Wierman JL et al (2014) Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction. IUCrJ 1:349–360
Pawate AS, Šrajer V, Schieferstein J et al (2015) Towards time-resolved serial crystallography in a microfluidic device. Acta Crystallogr Sect F Struct Biol Commun 71:823–830
Cazzolli G, Wang F, a Beccara S et al (2014) Serpin latency transition at atomic resolution. Proc Natl Acad Sci 111:15414–15419
Baker EN (2006) Hydrogen bonding in biological macromolecules. In: Rossmann MG, Arnold E (eds) International tables for crystallography, 1st edn. International Union of Crystallography, Chester, England, pp 546–552
Wade RC, Goodford PJ (1989) The role of hydrogen-bonds in drug binding. Prog Clin Biol Res 289:433–444
Woinska M, Grabowsky S, Dominiak PM et al (2016) Hydrogen atoms can be located accurately and precisely by x-ray crystallography. Sci Adv 2:e1600192–e1600192
Kovalevsky AY, Liu F, Leshchenko S et al (2006) Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114. J Mol Biol 363:161–173
Blakeley MP, Langan P, Niimura N et al (2008) Neutron crystallography: opportunities, challenges, and limitations. Curr Opin Struct Biol 18:593–600
Blakeley MP, Hasnain SS, Antonyuk SV (2015) Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential. IUCrJ 2:464–474
Gerlits O, Keen DA, Blakeley MP et al (2017) Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100 K. J Med Chem 60:2018–2025
Press Release: The Nobel Prize in Chemistry 2017 (2017) Nobelprize.org
Henderson R, Baldwin JM, Ceska TA et al (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213:899–929
Thompson RF, Walker M, Siebert CA et al (2016) An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods 100:3–15
Milne JLS, Borgnia MJ, Bartesaghi A et al (2013) Cryo-electron microscopy - a primer for the non-microscopist. FEBS J 280:28–45
Banerjee S, Bartesaghi A, Merk A et al (2016) 2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 351:871–875
Lomas DA, Belorgey D, Mallya M et al (2005) Molecular mousetraps and the serpinopathies. Biochem Soc Trans 33:321–330
Lucas AR, Ambadapadi S, Mahon BP et al (2017) The serpentine solution. J. Clin. Exp. Cardiolog. 8:e150. https://doi.org/10.4172/2155-9880.1000e150
Guineir A, Fournet G (1955) Small-angle scattering of X-rays (structure of matter series). Wiley, New York
Feigin LA, Svergun DI (1987) In: Taylor GW (ed) Structure analysis by small-angle X-ray and neutron scattering. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-6624-0
Jacques DA, Trewhella J (2010) Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls. Protein Sci 19:642–657
Cho HS, Schotte F, Dashdorj N et al (2016) Picosecond photobiology: watching a signaling protein function in real time via time-resolved small- and wide-angle X-ray scattering. J Am Chem Soc 138:8815–8823
Behrens MA, Sendall TJ, Pedersen JS et al (2014) The shapes of Z-α1-antitrypsin polymers in solution support the C-terminal domain-swap mechanism of polymerization. Biophys J 107:1905–1912
Li D, Boland C, Walsh K et al (2012) Use of a robot for high-throughput crystallization of membrane proteins in lipidic mesophases. J Vis Exp. https://doi.org/10.3791/4000
Moraes I, Archer M (2015) Methods for the successful crystallization of membrane proteins. In: Owens RJ (ed) Structural proteomics, vol 1261. Springer, New York, pp 211–230
Rayment I (2002) Small-scale batch crystallization of proteins revisited. Structure 10:147–151
Dong A, Xu X, Edwards AM et al (2007) In situ proteolysis for protein crystallization and structure determination. Nat Methods 4:1019–1021
Berejnov V, Husseini NS, Alsaied OA et al (2006) Effects of cryoprotectant concentration and cooling rate on vitrification of aqueous solutions. J Appl Crystallogr 39:244–251
Dunstone MA, Whisstock JC (2011) Crystallography of serpins and serpin complexes, Methods in enzymology, vol 501. Elsevier, Amsterdam, pp 63–87
Law RHP, Irving JA, Buckle AM et al (2005) The high resolution crystal structure of the human tumor suppressor maspin reveals a novel conformational switch in the G-helix. J Biol Chem 280:22356–22364
Zhou A, Carrell RW, Murphy MP et al (2010) A redox switch in angiotensinogen modulates angiotensin release. Nature 468:108–111
Whisstock JC, Pike RN, Jin L et al (2000) Conformational changes in serpins: II. The mechanism of activation of antithrombin by heparin. J Mol Biol 301:1287–1305
Mottonen J, Strand A, Symersky J et al (1992) Structural basis of latency in plasminogen activator inhibitor-1. Nature 355:270–273
Sharp AM, Stein PE, Pannu NS et al (1999) The active conformation of plasminogen activator inhibitor 1, a target for drugs to control fibrinolysis and cell adhesion. Structure 7:111–118
Kmiecik S, Gront D, Kolinski M et al (2016) Coarse-grained protein models and their applications. Chem Rev 116:7898–7936
Xu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80:1715–1735
Ó Conchúir S, Barlow KA, Pache RA et al (2015) A web resource for standardized benchmark datasets, metrics, and Rosetta protocols for macromolecular modeling and design. PLoS One 10:e0130433
Rigden DJ, Keegan RM, Winn MD (2008) Molecular replacement using ab initio polyalanine models generated with ROSETTA. Acta Crystallogr D Biol Crystallogr 64:1288–1291
Briand C, Kozlov SV, Sonderegger P et al (2001) Crystal structure of neuroserpin: a neuronal serpin involved in a conformational disease. FEBS Lett 505:18–22
Terwilliger TC, Grosse-Kunstleve RW, Afonine PV et al (2008) Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr 64:61–69
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Mahon, B.P., McKenna, R. (2018). Methods for Determining and Understanding Serpin Structure and Function: X-Ray Crystallography. In: Lucas, A. (eds) Serpins. Methods in Molecular Biology, vol 1826. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8645-3_2
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