메뉴 건너뛰기




Volumn 41, Issue 1, 2012, Pages 41-61

Racemic protein crystallography

Author keywords

Centrosymmetric; Chemical protein synthesis; Crystallization; Phase problem; Space group

Indexed keywords

BACTERIAL PROTEIN; CHEMOKINE; CRAMBIN; GLYCOPROTEIN; KALIOTOXIN; MONELLIN; OMWAPRIN; PLECTASIN; PROTEIN; RUBREDOXIN; SCORPION VENOM; UNCLASSIFIED DRUG; VASCULOTROPIN;

EID: 84861378744     PISSN: 1936122X     EISSN: 19361238     Source Type: Book Series    
DOI: 10.1146/annurev-biophys-050511-102333     Document Type: Review
Times cited : (134)

References (65)
  • 2
    • 77957305360 scopus 로고    scopus 로고
    • Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography
    • Banigan JR, Mandal K, Sawaya MR, Thammavongsa V, Hendrickx AP, et al. 2010. Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography. Protein Sci. 19:1840-49
    • (2010) Protein Sci. , vol.19 , pp. 1840-1849
    • Banigan, J.R.1    Mandal, K.2    Sawaya, M.R.3    Thammavongsa, V.4    Hendrickx, A.P.5
  • 3
    • 0031045586 scopus 로고    scopus 로고
    • Centrosymmetric crystals of biomolecules: The racemate method
    • Berg JM, Goffeney NW. 1997. Centrosymmetric crystals of biomolecules: the racemate method. Methods Enzymol. 276:619-27
    • (1997) Methods Enzymol. , vol.276 , pp. 619-627
    • Berg, J.M.1    Goffeney, N.W.2
  • 4
    • 26744461416 scopus 로고
    • Towards a grammar of crystal packing
    • Brock CP, Dunitz JD. 1994. Towards a grammar of crystal packing. Chem. Mat. 6:1118-27
    • (1994) Chem. Mat. , vol.6 , pp. 1118-1127
    • Brock, C.P.1    Dunitz, J.D.2
  • 5
    • 0000602940 scopus 로고
    • On the validity of Wallach's rule: On the density and stability of racemic crystals compared with their chiral counterparts
    • Brock CP, Schweizer WB, Dunitz JD. 1991. On the validity of Wallach's rule: on the density and stability of racemic crystals compared with their chiral counterparts. J. Am. Chem. Soc. 113:9811-20
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 9811-9820
    • Brock, C.P.1    Schweizer, W.B.2    Dunitz, J.D.3
  • 6
    • 41649093175 scopus 로고    scopus 로고
    • Analysis of solvent content and oligomeric states in protein crystals\does symmetry matter?
    • Chruszcz M, Potrzebowski W, Zimmerman MD, Grabowski M, Zheng H, et al. 2008. Analysis of solvent content and oligomeric states in protein crystals\does symmetry matter? Protein Sci. 17:623-32
    • (2008) Protein Sci. , vol.17 , pp. 623-632
    • Chruszcz, M.1    Potrzebowski, W.2    Zimmerman, M.D.3    Grabowski, M.4    Zheng, H.5
  • 7
    • 34548153495 scopus 로고    scopus 로고
    • Native chemical ligation at phenylalanine
    • Crich D, Banerjee A. 2007. Native chemical ligation at phenylalanine. J. Am. Chem. Soc. 129:10064-65
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 10064-10065
    • Crich, D.1    Banerjee, A.2
  • 10
    • 84879505971 scopus 로고
    • Structural characteristics of enantiomorphic DNA: Crystal analysis of racemates of the d(CGCGCG) duplex
    • Doi M, Inoue M, Tomoo K, Ishida T, Ueda Y, et al. 1993. Structural characteristics of enantiomorphic DNA: crystal analysis of racemates of the d(CGCGCG) duplex. J. Am. Chem. Soc. 115:10432-33
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 10432-10433
    • Doi, M.1    Inoue, M.2    Tomoo, K.3    Ishida, T.4    Ueda, Y.5
  • 11
    • 34247569910 scopus 로고    scopus 로고
    • Convergent chemical synthesis and high-resolution X-ray structure of human lysozyme
    • Durek T, Torbeev VY, Kent SB. 2007. Convergent chemical synthesis and high-resolution X-ray structure of human lysozyme. Proc. Natl. Acad. Sci. USA 104:4846-51
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 4846-4851
    • Durek, T.1    Torbeev, V.Y.2    Kent, S.B.3
  • 12
    • 69049107757 scopus 로고    scopus 로고
    • Louis Pasteur's discovery of molecular chirality and spontaneous resolution in 1848, together with a complete review of his crystallographic and chemical work
    • Flack HD. 2009. Louis Pasteur's discovery of molecular chirality and spontaneous resolution in 1848, together with a complete review of his crystallographic and chemical work. Acta Crystallogr. A 65:371-89
    • (2009) Acta Crystallogr. A , vol.65 , pp. 371-389
    • Flack, H.D.1
  • 13
    • 0032963901 scopus 로고    scopus 로고
    • Ab initio structure solution of a dimeric cytochrome c3 from Desulfovibrio gigas containing disulfide bridges
    • Frazao C, Sieker L, Sheldrick G, Lamzin V, LeGall J, Carrondo MA. 1999. Ab initio structure solution of a dimeric cytochrome c3 from Desulfovibrio gigas containing disulfide bridges. J. Biol. Inorg. Chem. 4:162-65
    • (1999) J. Biol. Inorg. Chem. , vol.4 , pp. 162-165
    • Frazao, C.1    Sieker, L.2    Sheldrick, G.3    Lamzin, V.4    Legall, J.5    Carrondo, M.A.6
  • 14
    • 0001262916 scopus 로고
    • The structure of haemoglobin. IV. Sign determination by the isomorphous replacement method
    • Green DW, Ingram VM, Perutz MF. 1954. The structure of haemoglobin. IV. Sign determination by the isomorphous replacement method. Proc. R. Soc. Lond. A 225:287-307
    • (1954) Proc. R. Soc. Lond. A , vol.225 , pp. 287-307
    • Green, D.W.1    Ingram, V.M.2    Perutz, M.F.3
  • 16
    • 0002517916 scopus 로고
    • The determination of the phases of the structure factors of non-centrosymmetric crystals by the method of double isomorphous replacement
    • Harker D. 1956. The determination of the phases of the structure factors of non-centrosymmetric crystals by the method of double isomorphous replacement. Acta Crystallogr. 9:1-9
    • (1956) Acta Crystallogr. , vol.9 , pp. 1-9
    • Harker, D.1
  • 17
    • 0031058883 scopus 로고    scopus 로고
    • Phase determination from multiwavelength anomalous diffraction measurements
    • Hendrickson WA, Ogata CM. 1997. Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. 276:494-523
    • (1997) Methods Enzymol. , vol.276 , pp. 494-523
    • Hendrickson, W.A.1    Ogata, C.M.2
  • 19
    • 0033534374 scopus 로고    scopus 로고
    • Structural differences in D and L-monellin in the crystals of racemic mixture
    • Hung LW, Kohmura M, Ariyoshi Y, Kim SH. 1999. Structural differences in D and L-monellin in the crystals of racemic mixture. J. Mol. Biol. 285:311-21
    • (1999) J. Mol. Biol. , vol.285 , pp. 311-321
    • Hung, L.W.1    Kohmura, M.2    Ariyoshi, Y.3    Kim, S.H.4
  • 20
    • 0023889559 scopus 로고
    • Chemical synthesis of peptides and proteins
    • Kent SB. 1988. Chemical synthesis of peptides and proteins. Annu. Rev. Biochem. 57:957-89
    • (1988) Annu. Rev. Biochem. , vol.57 , pp. 957-989
    • Kent, S.B.1
  • 21
    • 62449282062 scopus 로고    scopus 로고
    • Total chemical synthesis of proteins
    • Kent SB. 2009. Total chemical synthesis of proteins. Chem. Soc. Rev. 38:338-51
    • (2009) Chem. Soc. Rev. , vol.38 , pp. 338-351
    • Kent, S.B.1
  • 23
    • 0035024436 scopus 로고    scopus 로고
    • Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI
    • Longenecker KL, Garrard SM, Sheffield PJ, Derewenda ZS. 2001. Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Acta Crystallogr. D Biol. Crystallogr. 57:679-88
    • (2001) Acta Crystallogr. D Biol. Crystallogr. , vol.57 , pp. 679-688
    • Longenecker, K.L.1    Garrard, S.M.2    Sheffield, P.J.3    Derewenda, Z.S.4
  • 24
    • 0035811061 scopus 로고    scopus 로고
    • Total synthesis of cytochrome b562 by native chemical ligation using a removable auxiliary
    • Low DW, Hill MG, Carrasco MR, Kent SB, Botti P. 2001. Total synthesis of cytochrome b562 by native chemical ligation using a removable auxiliary. Proc. Natl. Acad. Sci. USA 98:6554-59
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 6554-6559
    • Low, D.W.1    Hill, M.G.2    Carrasco, M.R.3    Kent, S.B.4    Botti, P.5
  • 25
    • 0343747364 scopus 로고
    • Crystal enigma
    • Mackay A. 1989. Crystal enigma. Nature 342:133
    • (1989) Nature , vol.342 , pp. 133
    • MacKay, A.1
  • 26
    • 63149114770 scopus 로고    scopus 로고
    • X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods
    • Mandal K, Pentelute BL, Tereshko V, Kossiakoff AA, Kent SB. 2009. X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods. J. Am. Chem. Soc. 131:1362-63
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 1362-1363
    • Mandal, K.1    Pentelute, B.L.2    Tereshko, V.3    Kossiakoff, A.A.4    Kent, S.B.5
  • 27
    • 66349133644 scopus 로고    scopus 로고
    • Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods
    • Mandal K, Pentelute BL, Tereshko V, Thammavongsa V, Schneewind O, et al. 2009. Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods. Protein Sci. 18:1146-54
    • (2009) Protein Sci. , vol.18 , pp. 1146-1154
    • Mandal, K.1    Pentelute, B.L.2    Tereshko, V.3    Thammavongsa, V.4    Schneewind, O.5
  • 28
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews BW. 1968. Solvent content of protein crystals. J. Mol. Biol. 33:491-97
    • (1968) J. Mol. Biol. , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 29
    • 66349119864 scopus 로고    scopus 로고
    • Racemic crystallography\easy crystals and easy structures: What's not to like?
    • Matthews BW. 2009. Racemic crystallography\easy crystals and easy structures: What's not to like? Protein Sci. 18:1135-38
    • (2009) Protein Sci. , vol.18 , pp. 1135-1138
    • Matthews, B.W.1
  • 31
    • 0000727975 scopus 로고
    • Space-group frequencies for organic compounds
    • Mighell A, Himes V. 1983. Space-group frequencies for organic compounds. Acta Crystallogr. A 39:737-40
    • (1983) Acta Crystallogr. A , vol.39 , pp. 737-740
    • Mighell, A.1    Himes, V.2
  • 33
    • 0036570182 scopus 로고    scopus 로고
    • Extending synthetic access to proteins with a removable acyl transfer auxiliary
    • Offer J, Boddy CN, Dawson PE. 2002. Extending synthetic access to proteins with a removable acyl transfer auxiliary. J. Am. Chem. Soc. 124:4642-46
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4642-4646
    • Offer, J.1    Boddy, C.N.2    Dawson, P.E.3
  • 34
    • 84919227524 scopus 로고
    • Space group-frequencies of proteins and of organic compounds with more than one formular unit in the asymmetric unit
    • Padmaja N, Ramakurar S, Viswamitra M. 1990. Space group-frequencies of proteins and of organic compounds with more than one formular unit in the asymmetric unit. Acta Crystallogr. A 46:725-30
    • (1990) Acta Crystallogr. A , vol.46 , pp. 725-730
    • Padmaja, N.1    Ramakurar, S.2    Viswamitra, M.3
  • 35
    • 1642514905 scopus 로고    scopus 로고
    • Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS
    • Pantazatos D, Kim JS, Klock HE, Stevens RC, Wilson IA, et al. 2004. Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl. Acad. Sci. USA 101:751-56
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 751-756
    • Pantazatos, D.1    Kim, J.S.2    Klock, H.E.3    Stevens, R.C.4    Wilson, I.A.5
  • 36
    • 0000056775 scopus 로고
    • Mémoire sur la relation qui peut exister entre la forme cristalline et la composition chimique, et sur la cause de la polarisation rotatoire
    • Pasteur L. 1848. Mémoire sur la relation qui peut exister entre la forme cristalline et la composition chimique, et sur la cause de la polarisation rotatoire. C. R. Acad. Sci. Paris 26:535-38
    • (1848) C. R. Acad. Sci. Paris , vol.26 , pp. 535-538
    • Pasteur, L.1
  • 37
    • 0032789938 scopus 로고    scopus 로고
    • Centrosymmetric bilayers in the 0.75 A° resolution structure of a designed alpha-helical peptide, d, l-alpha-1
    • Patterson WR, Anderson DH, DeGrado WF, Cascio D, Eisenberg D. 1999. Centrosymmetric bilayers in the 0.75 A° resolution structure of a designed alpha-helical peptide, d, l-alpha-1. Protein Sci. 8:1410-22
    • (1999) Protein Sci. , vol.8 , pp. 1410-1422
    • Patterson, W.R.1    Anderson, D.H.2    Degrado, W.F.3    Cascio, D.4    Eisenberg, D.5
  • 38
    • 48249090027 scopus 로고    scopus 로고
    • Mirror image forms of snow flea antifreeze protein prepared by total chemical synthesis have identical antifreeze activities
    • Pentelute BL, Gates ZP, Dashnau JL, Vanderkooi JM, Kent SB. 2008. Mirror image forms of snow flea antifreeze protein prepared by total chemical synthesis have identical antifreeze activities. J. Am. Chem. Soc. 130:9702-7
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 9702-9707
    • Pentelute, B.L.1    Gates, Z.P.2    Dashnau, J.L.3    Vanderkooi, J.M.4    Kent, S.B.5
  • 39
    • 48249101260 scopus 로고    scopus 로고
    • X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers
    • Pentelute BL, Gates ZP, Tereshko V, Dashnau JL, Vanderkooi JM, et al. 2008. X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers. J. Am. Chem. Soc. 130:9695-701
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 9695-9701
    • Pentelute, B.L.1    Gates, Z.P.2    Tereshko, V.3    Dashnau, J.L.4    Vanderkooi, J.M.5
  • 40
    • 77958469851 scopus 로고    scopus 로고
    • Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography
    • Pentelute BL, Mandal K, Gates ZP, Sawaya MR, Yeates TO, Kent SB. 2010. Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Chem. Commun. 46:8174-76
    • (2010) Chem. Commun. , vol.46 , pp. 8174-8176
    • Pentelute, B.L.1    Mandal, K.2    Gates, Z.P.3    Sawaya, M.R.4    Yeates, T.O.5    Kent, S.B.6
  • 41
    • 0026742584 scopus 로고
    • On the other hand
    • Petsko GA. 1992. On the other hand. Science 256:1403-4
    • (1992) Science , vol.256 , pp. 1403-1404
    • Petsko, G.A.1
  • 46
    • 0027482860 scopus 로고
    • Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: An X-ray analysis at 1.8-A° resolution
    • Rypniewski WR, Holden HM, Rayment I. 1993. Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an X-ray analysis at 1.8-A° resolution. Biochemistry 32:9851-58
    • (1993) Biochemistry , vol.32 , pp. 9851-9858
    • Rypniewski, W.R.1    Holden, H.M.2    Rayment, I.3
  • 47
    • 84857802722 scopus 로고    scopus 로고
    • Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data
    • Sawaya MR, Pentelute BL, Kent SBH, Yeates TO. 2012. Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data. Acta Crystallogr. D 68:62-68
    • (2012) Acta Crystallogr. D , vol.68 , pp. 62-68
    • Sawaya, M.R.1    Pentelute, B.L.2    Kent, S.B.H.3    Yeates, T.O.4
  • 48
    • 0026525457 scopus 로고
    • Constructing proteins by dovetailing unprotected synthetic peptides: Backbone-engineered HIV protease
    • Schnolzer M, Kent SB. 1992. Constructing proteins by dovetailing unprotected synthetic peptides: backbone-engineered HIV protease. Science 256:221-25
    • (1992) Science , vol.256 , pp. 221-225
    • Schnolzer, M.1    Kent, S.B.2
  • 50
    • 37549039510 scopus 로고    scopus 로고
    • A short history of SHELX
    • Sheldrick GM. 2008. A short history of SHELX. Acta Crystallogr. A 64:112-22
    • (2008) Acta Crystallogr. A , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 57
    • 34248230589 scopus 로고    scopus 로고
    • Convergent chemical synthesis and crystal structure of a 203 amino acid "covalent dimer" HIV-1 protease enzyme molecule
    • Torbeev VY, Kent SB. 2007. Convergent chemical synthesis and crystal structure of a 203 amino acid "covalent dimer" HIV-1 protease enzyme molecule. Angew. Chem. Int. Ed. Engl. 46:1667-70
    • (2007) Angew. Chem. Int. Ed. Engl. , vol.46 , pp. 1667-1670
    • Torbeev, V.Y.1    Kent, S.B.2
  • 58
    • 37349094422 scopus 로고    scopus 로고
    • Free-radical-based, specific desulfurization of cysteine: A powerful advance in the synthesis of polypeptides and glycopolypeptides
    • Wan Q, Danishefsky SJ. 2007. Free-radical-based, specific desulfurization of cysteine: a powerful advance in the synthesis of polypeptides and glycopolypeptides. Angew. Chem. Int. Ed. Engl. 46:9248-52
    • (2007) Angew. Chem. Int. Ed. Engl. , vol.46 , pp. 9248-9252
    • Wan, Q.1    Danishefsky, S.J.2
  • 59
    • 0028787430 scopus 로고
    • Why protein crystals favour some space-groups over others
    • Wukovitz SW, Yeates TO. 1995. Why protein crystals favour some space-groups over others. Nat. Struct. Biol. 2:1062-67
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 1062-1067
    • Wukovitz, S.W.1    Yeates, T.O.2
  • 60
    • 34250860262 scopus 로고    scopus 로고
    • 'Crystal lattice engineering, ' an approach to engineer protein crystal contacts by creating intermolecular symmetry: Crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines
    • Yamada H, Tamada T, Kosaka M, Miyata K, Fujiki S, et al. 2007. 'Crystal lattice engineering, ' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines. Protein Sci. 16:1389-97
    • (2007) Protein Sci. , vol.16 , pp. 1389-1397
    • Yamada, H.1    Tamada, T.2    Kosaka, M.3    Miyata, K.4    Fujiki, S.5
  • 61
    • 0035977638 scopus 로고    scopus 로고
    • Synthesis of peptides and proteins without cysteine residues by native chemical ligation combined with desulfurization
    • Yan LZ, Dawson PE. 2001. Synthesis of peptides and proteins without cysteine residues by native chemical ligation combined with desulfurization. J. Am. Chem. Soc. 123:526-33
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 526-533
    • Yan, L.Z.1    Dawson, P.E.2
  • 62
    • 77950915587 scopus 로고    scopus 로고
    • Solution structure of proinsulin: Connecting domain flexibility and prohormone processing
    • Yang Y, Hua QX, Liu J, Shimizu EH, Choquette MH, et al. 2010. Solution structure of proinsulin: connecting domain flexibility and prohormone processing. J. Biol. Chem. 285:7847-51
    • (2010) J. Biol. Chem. , vol.285 , pp. 7847-7851
    • Yang, Y.1    Hua, Q.X.2    Liu, J.3    Shimizu, E.H.4    Choquette, M.H.5
  • 64
    • 0027238026 scopus 로고
    • The structure of a centrosymmetric protein crystal
    • Zawadzke LE, Berg JM. 1993. The structure of a centrosymmetric protein crystal. Proteins 16:301-5
    • (1993) Proteins , vol.16 , pp. 301-305
    • Zawadzke, L.E.1    Berg, J.M.2
  • 65
    • 84856507104 scopus 로고    scopus 로고
    • Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology
    • Mandal K, Pentelute BL, Bang D, Gates ZP, Torbeev VY, Kent SBH. 2012. Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angew. Chem. 51:1481-86
    • (2012) Angew. Chem. , vol.51 , pp. 1481-1486
    • Mandal, K.1    Pentelute, B.L.2    Bang, D.3    Gates, Z.P.4    Torbeev, V.Y.5    Kent, S.B.H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.