메뉴 건너뛰기




Volumn 169, Issue 2, 2010, Pages 135-144

Detailed assessment of X-ray induced structural perturbation in a crystalline state protein

Author keywords

Crystal structure; Electron transfer; High potential iron sulfur protein; Ultra high resolution; X ray damage

Indexed keywords

HIGH POTENTIAL IRON SULFUR PROTEIN; HYDROGEN; IRON SULFUR PROTEIN; UNCLASSIFIED DRUG;

EID: 74449084306     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2009.09.012     Document Type: Article
Times cited : (17)

References (56)
  • 4
    • 0034055545 scopus 로고    scopus 로고
    • Structural changes in a cryo-cooled protein crystal owing to radiation damage
    • Burmeister W.P. Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallogr. D56 (2000) 328-341
    • (2000) Acta Crystallogr. , vol.D56 , pp. 328-341
    • Burmeister, W.P.1
  • 5
    • 0010247881 scopus 로고    scopus 로고
    • High potential iron sulfur proteins
    • Messerschmidt A., Huber R., Poulos T.L., and Weighardt K. (Eds), Wiley, New York
    • Carter Jr. C.W. High potential iron sulfur proteins. In: Messerschmidt A., Huber R., Poulos T.L., and Weighardt K. (Eds). Handbook of Metalloproteins (2001), Wiley, New York 602-609
    • (2001) Handbook of Metalloproteins , pp. 602-609
    • Carter Jr., C.W.1
  • 7
    • 16244392086 scopus 로고    scopus 로고
    • When X-rays modify the protein structure: radiation damage at work
    • Carugo O., and Djinovic-Carugo K. When X-rays modify the protein structure: radiation damage at work. Trends. Biochem. Sci. 30 (2005) 213-219
    • (2005) Trends. Biochem. Sci. , vol.30 , pp. 213-219
    • Carugo, O.1    Djinovic-Carugo, K.2
  • 8
    • 0344665692 scopus 로고    scopus 로고
    • Protein structures at atomic resolution
    • Dauter Z. Protein structures at atomic resolution. Methods Enzymol. 368 (2003) 288-337
    • (2003) Methods Enzymol. , vol.368 , pp. 288-337
    • Dauter, Z.1
  • 11
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D60 (2004) 2126-2132
    • (2004) Acta Crystallogr. , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 12
    • 0000430313 scopus 로고    scopus 로고
    • Ferredoxins containing one [4Fe-4S] center
    • Messerschmidt A., Huber R., Poulos T.L., and Weighardt K. (Eds), Wiley, New York
    • Fukuyama K. Ferredoxins containing one [4Fe-4S] center. In: Messerschmidt A., Huber R., Poulos T.L., and Weighardt K. (Eds). Handbook of Metalloproteins (2001), Wiley, New York 543-552
    • (2001) Handbook of Metalloproteins , pp. 543-552
    • Fukuyama, K.1
  • 13
    • 0141987861 scopus 로고    scopus 로고
    • 'Cool' crystals: macromolecular cryocrystallography and radiation damage
    • Garman E. 'Cool' crystals: macromolecular cryocrystallography and radiation damage. Curr. Opin. Struct. Biol. 13 (2003) 545-551
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 545-551
    • Garman, E.1
  • 14
    • 33644877757 scopus 로고    scopus 로고
    • Cryocooling and radiation damage in macromolecular crystallography
    • Garman E.F., and Owen R.L. Cryocooling and radiation damage in macromolecular crystallography. Acta Crystallogr. D62 (2006) 32-47
    • (2006) Acta Crystallogr. , vol.D62 , pp. 32-47
    • Garman, E.F.1    Owen, R.L.2
  • 15
    • 0025071357 scopus 로고
    • Cryo-protection of protein crystals against radiation damage in electron and X-ray diffraction
    • Henderson R. Cryo-protection of protein crystals against radiation damage in electron and X-ray diffraction. Proc. R. Soc. Lond. B Biol. Sci. 241 (1990) 6-8
    • (1990) Proc. R. Soc. Lond. B Biol. Sci. , vol.241 , pp. 6-8
    • Henderson, R.1
  • 16
    • 0017202706 scopus 로고
    • Radiation damage in protein crystallography
    • Hendrickson W.A. Radiation damage in protein crystallography. J. Mol. Biol. 106 (1976) 889-893
    • (1976) J. Mol. Biol. , vol.106 , pp. 889-893
    • Hendrickson, W.A.1
  • 18
    • 10444252351 scopus 로고    scopus 로고
    • First results from the bio-crystallography beamline at SPring-8
    • Kamiya N., Kawano Y., and Kawamoto M. First results from the bio-crystallography beamline at SPring-8. RIKEN Rev. 18 (1998) 29-30
    • (1998) RIKEN Rev. , vol.18 , pp. 29-30
    • Kamiya, N.1    Kawano, Y.2    Kawamoto, M.3
  • 19
    • 0012478439 scopus 로고    scopus 로고
    • The bio-crystallography beamline (BL41XU) at SPring-8
    • Kawamoto M., Kawano Y., and Kamiya N. The bio-crystallography beamline (BL41XU) at SPring-8. Nucl. Instr. Meth. A 467-468 (2001) 1375-1379
    • (2001) Nucl. Instr. Meth. A , vol.467-468 , pp. 1375-1379
    • Kawamoto, M.1    Kawano, Y.2    Kamiya, N.3
  • 20
    • 33748353816 scopus 로고    scopus 로고
    • Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures
    • Kmetko J., Husseini N.S., Naides M., Kalinin Y., and Thorne R.E. Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures. Acta Crystallogr. D62 (2006) 1030-1038
    • (2006) Acta Crystallogr. , vol.D62 , pp. 1030-1038
    • Kmetko, J.1    Husseini, N.S.2    Naides, M.3    Kalinin, Y.4    Thorne, R.E.5
  • 21
    • 0035177316 scopus 로고    scopus 로고
    • X-ray beam/biomaterial thermal interactions in third-generation synchrotron sources
    • Kuzay T.M., Kazmierczak M., and Hsieh B.J. X-ray beam/biomaterial thermal interactions in third-generation synchrotron sources. Acta Crystallogr. D57 (2001) 69-81
    • (2001) Acta Crystallogr. , vol.D57 , pp. 69-81
    • Kuzay, T.M.1    Kazmierczak, M.2    Hsieh, B.J.3
  • 22
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Thornton, J.M.3
  • 23
    • 0035073965 scopus 로고    scopus 로고
    • Atomic resolution structures of trypsin provide insight into structural radiation damage
    • Leiros H.K., McSweeney S.M., and Smalås A.O. Atomic resolution structures of trypsin provide insight into structural radiation damage. Acta Crystallogr. D57 (2001) 488-497
    • (2001) Acta Crystallogr. , vol.D57 , pp. 488-497
    • Leiros, H.K.1    McSweeney, S.M.2    Smalås, A.O.3
  • 24
    • 33644870851 scopus 로고    scopus 로고
    • Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?
    • Leiros H.K., Timmins J., Ravelli R.B., and McSweeney S.M. Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?. Acta Crystallogr. D62 (2006) 125-132
    • (2006) Acta Crystallogr. , vol.D62 , pp. 125-132
    • Leiros, H.K.1    Timmins, J.2    Ravelli, R.B.3    McSweeney, S.M.4
  • 25
    • 0035997116 scopus 로고    scopus 로고
    • Ultrahigh-resolution structure of high-potential iron-sulfur protein from Thermochromatium tepidum
    • Liu L., Nogi T., Kobayashi M., Nozawa T., and Miki K. Ultrahigh-resolution structure of high-potential iron-sulfur protein from Thermochromatium tepidum. Acta Crystallogr. D58 (2002) 1085-1091
    • (2002) Acta Crystallogr. , vol.D58 , pp. 1085-1091
    • Liu, L.1    Nogi, T.2    Kobayashi, M.3    Nozawa, T.4    Miki, K.5
  • 26
  • 27
    • 0036452022 scopus 로고    scopus 로고
    • Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin
    • Matsui Y., Sakai K., Murakami M., Shiro Y., Adachi S., Okumura H., and Kouyama T. Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin. J. Mol. Biol. 324 (2002) 469-481
    • (2002) J. Mol. Biol. , vol.324 , pp. 469-481
    • Matsui, Y.1    Sakai, K.2    Murakami, M.3    Shiro, Y.4    Adachi, S.5    Okumura, H.6    Kouyama, T.7
  • 28
    • 33947321097 scopus 로고    scopus 로고
    • Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study
    • Meents A., Wagner A., Schneider R., Pradervand C., Pohl E., and Schulze-Briese C. Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study. Acta Crystallogr. D63 (2007) 302-309
    • (2007) Acta Crystallogr. , vol.D63 , pp. 302-309
    • Meents, A.1    Wagner, A.2    Schneider, R.3    Pradervand, C.4    Pohl, E.5    Schulze-Briese, C.6
  • 29
    • 61449115935 scopus 로고    scopus 로고
    • A new aspect of specific radiation damage: hydrogen abstraction from organic molecules
    • Meents A., Dittrich B., and Gutmann S. A new aspect of specific radiation damage: hydrogen abstraction from organic molecules. J. Synchrotron Radiat. 16 (2009) 183-190
    • (2009) J. Synchrotron Radiat. , vol.16 , pp. 183-190
    • Meents, A.1    Dittrich, B.2    Gutmann, S.3
  • 30
    • 0033152783 scopus 로고    scopus 로고
    • Expanding the model: anisotropic displacement parameters in protein structure refinement
    • Merritt E.A. Expanding the model: anisotropic displacement parameters in protein structure refinement. Acta Crystallogr. D55 (1999) 1109-1117
    • (1999) Acta Crystallogr. , vol.D55 , pp. 1109-1117
    • Merritt, E.A.1
  • 31
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: photorealistic molecular graphics
    • Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 32
    • 20644462974 scopus 로고    scopus 로고
    • Three-dimensional numerical analysis of convection and conduction cooling of spherical biocrystals with localized heating from synchrotron X-ray beams
    • Mhaisekar A., Kazmierczak M.J., and Banerjee R. Three-dimensional numerical analysis of convection and conduction cooling of spherical biocrystals with localized heating from synchrotron X-ray beams. J. Synchrotron Radiat. 12 (2005) 318-328
    • (2005) J. Synchrotron Radiat. , vol.12 , pp. 318-328
    • Mhaisekar, A.1    Kazmierczak, M.J.2    Banerjee, R.3
  • 33
    • 0027179573 scopus 로고
    • Primary structure of Chromatium tepidum high-potential iron-sulfur protein in relation to thermal denaturation
    • Moulis J.M., Scherrer N., Gagnon J., Forest E., Petillot Y., and Garcia D. Primary structure of Chromatium tepidum high-potential iron-sulfur protein in relation to thermal denaturation. Arch. Biochem. Biophys. 305 (1993) 186-192
    • (1993) Arch. Biochem. Biophys. , vol.305 , pp. 186-192
    • Moulis, J.M.1    Scherrer, N.2    Gagnon, J.3    Forest, E.4    Petillot, Y.5    Garcia, D.6
  • 34
    • 4043099008 scopus 로고    scopus 로고
    • X-ray absorption by macromolecular crystals: the effects of wavelength and crystal composition on absorbed dose
    • Murray J.W., Garman E.F., and Ravelli R.B. X-ray absorption by macromolecular crystals: the effects of wavelength and crystal composition on absorbed dose. J. Appl. Cryst. 37 (2004) 513-522
    • (2004) J. Appl. Cryst. , vol.37 , pp. 513-522
    • Murray, J.W.1    Garman, E.F.2    Ravelli, R.B.3
  • 36
    • 20644441110 scopus 로고    scopus 로고
    • Towards an understanding of radiation damage in cryocooled macromolecular crystals
    • Nave C., and Garman E.F. Towards an understanding of radiation damage in cryocooled macromolecular crystals. J. Synchrotron Radiat. 12 (2005) 257-260
    • (2005) J. Synchrotron Radiat. , vol.12 , pp. 257-260
    • Nave, C.1    Garman, E.F.2
  • 37
    • 0034113441 scopus 로고    scopus 로고
    • Crystallization and preliminary crystallographic analysis of the high-potential iron-sulfur protein from Thermochromatium tepidum
    • Nogi T., Kobayashi M., Nozawa T., and Miki K. Crystallization and preliminary crystallographic analysis of the high-potential iron-sulfur protein from Thermochromatium tepidum. Acta Crystallogr. D56 (2000) 656-658
    • (2000) Acta Crystallogr. , vol.D56 , pp. 656-658
    • Nogi, T.1    Kobayashi, M.2    Nozawa, T.3    Miki, K.4
  • 38
    • 0034610266 scopus 로고    scopus 로고
    • Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer
    • Nogi T., Fathir I., Kobayashi M., Nozawa T., and Miki K. Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer. Proc. Natl. Acad. Sci. USA 97 (2000) 13561-13566
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 13561-13566
    • Nogi, T.1    Fathir, I.2    Kobayashi, M.3    Nozawa, T.4    Miki, K.5
  • 39
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 40
    • 33645498518 scopus 로고    scopus 로고
    • Experimental determination of the radiation dose limit for cryocooled protein crystals
    • Owen R.L., Rudiño-Piñera E., and Garman E.F. Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc. Natl. Acad. Sci. USA 103 (2006) 4912-4917
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 4912-4917
    • Owen, R.L.1    Rudiño-Piñera, E.2    Garman, E.F.3
  • 41
    • 0034654346 scopus 로고    scopus 로고
    • The 'fingerprint' that X-rays can leave on structures
    • Ravelli R.B., and McSweeney S.M. The 'fingerprint' that X-rays can leave on structures. Structure 8 (2002) 315-328
    • (2002) Structure , vol.8 , pp. 315-328
    • Ravelli, R.B.1    McSweeney, S.M.2
  • 42
    • 0036849851 scopus 로고    scopus 로고
    • Unit-cell volume change as a metric of radiation damage in crystals of macromolecules
    • Ravelli R.B., Theveneau P., McSweeney S., and Caffrey M. Unit-cell volume change as a metric of radiation damage in crystals of macromolecules. J. Synchrotron Radiat. 9 (2002) 355-360
    • (2002) J. Synchrotron Radiat. , vol.9 , pp. 355-360
    • Ravelli, R.B.1    Theveneau, P.2    McSweeney, S.3    Caffrey, M.4
  • 43
    • 0036913881 scopus 로고    scopus 로고
    • Veni, vidi, vici - atomic resolution unravelling the mysteries of protein function
    • Schmidt A., and Lamzin V.S. Veni, vidi, vici - atomic resolution unravelling the mysteries of protein function. Curr. Opin. Struct. Biol. 12 (2002) 698-703
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 698-703
    • Schmidt, A.1    Lamzin, V.S.2
  • 45
  • 46
    • 33846117949 scopus 로고    scopus 로고
    • Dose dependence of radiation damage for protein crystals studied at various X-ray energies
    • Shimizu N., Hirata K., Hasegawa K., Ueno G., and Yamamoto M. Dose dependence of radiation damage for protein crystals studied at various X-ray energies. J. Synchrotron Radiat. 14 (2007) 4-10
    • (2007) J. Synchrotron Radiat. , vol.14 , pp. 4-10
    • Shimizu, N.1    Hirata, K.2    Hasegawa, K.3    Ueno, G.4    Yamamoto, M.5
  • 47
    • 0037227747 scopus 로고    scopus 로고
    • How does radiation damage in protein crystals depend on X-ray dose?
    • Sliz P., Harrison S.C., and Rosenbaum G. How does radiation damage in protein crystals depend on X-ray dose?. Structure 11 (2003) 13-19
    • (2003) Structure , vol.11 , pp. 13-19
    • Sliz, P.1    Harrison, S.C.2    Rosenbaum, G.3
  • 49
    • 36749071554 scopus 로고    scopus 로고
    • Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography
    • Southworth-Davies R.J., Medina M.A., Carmichael I., and Garman E.F. Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography. Structure 15 (2007) 1531-1541
    • (2007) Structure , vol.15 , pp. 1531-1541
    • Southworth-Davies, R.J.1    Medina, M.A.2    Carmichael, I.3    Garman, E.F.4
  • 50
    • 12944249846 scopus 로고
    • Sequential radiation damage in protein crystallography
    • Sygusch J., and Allaire M. Sequential radiation damage in protein crystallography. Acta Crystallogr. A44 (1988) 443-448
    • (1988) Acta Crystallogr. , vol.A44 , pp. 443-448
    • Sygusch, J.1    Allaire, M.2
  • 51
    • 3843096037 scopus 로고    scopus 로고
    • Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix
    • Takeda K., Matsui Y., Kamiya N., Adachi S., Okumura H., and Kouyama T. Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix. J. Mol. Biol. 341 (2004) 1023-1037
    • (2004) J. Mol. Biol. , vol.341 , pp. 1023-1037
    • Takeda, K.1    Matsui, Y.2    Kamiya, N.3    Adachi, S.4    Okumura, H.5    Kouyama, T.6
  • 52
    • 0034345359 scopus 로고    scopus 로고
    • Primary radiation damage of protein crystals by an intense synchrotron X-ray beam
    • Teng T.Y., and Moffat K. Primary radiation damage of protein crystals by an intense synchrotron X-ray beam. J. Synchrotron Radiat. 7 (2000) 313-317
    • (2000) J. Synchrotron Radiat. , vol.7 , pp. 313-317
    • Teng, T.Y.1    Moffat, K.2
  • 53
    • 0348111557 scopus 로고    scopus 로고
    • Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
    • Vrielink A., and Sampson N. Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?. Curr. Opin. Struct. Biol. 13 (2003) 709-715
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 709-715
    • Vrielink, A.1    Sampson, N.2
  • 56
    • 20644465999 scopus 로고    scopus 로고
    • On the influence of the incident photon energy on the radiation damage in crystalline biological samples
    • Weiss M.S., Panjikar S., Mueller-Dieckmann C., and Tucker P.A. On the influence of the incident photon energy on the radiation damage in crystalline biological samples. J. Synchrotron Radiat. 12 (2005) 304-309
    • (2005) J. Synchrotron Radiat. , vol.12 , pp. 304-309
    • Weiss, M.S.1    Panjikar, S.2    Mueller-Dieckmann, C.3    Tucker, P.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.