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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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Abstract
X-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, the methods of MAD (multiwavelength anomalous diffraction) and SAD (single-wavelength anomalous diffraction) now predominate for de novo determinations of atomic-level biological structures. This review describes the physical underpinnings of anomalous diffraction methods, the evolution of these methods to their current maturity, the elements, procedures and instrumentation used for effective implementation, and the realm of applications.
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Affiliation(s)
- Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, and Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032 USA. New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027 USA
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3
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Popov EM. Current advances in the X-ray crystallography of proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1995v064n12abeh000194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Inoue T, Suzuki S, Nishio N, Yamaguchi K, Kataoka K, Tobari J, Yong X, Hamanaka S, Matsumura H, Kai Y. The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J. J Mol Biol 2003; 333:117-24. [PMID: 14516747 DOI: 10.1016/j.jmb.2003.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The obligate methylotroph Methylomonas sp. strain J produces two azurins (Az-iso1 and Az-iso2) as candidates for electron acceptor from methylamine dehydrogenase (MADH) in the electron-transfer process involving the oxidation of methylamine to formaldehyde and ammonia. The X-ray crystallographic study indicated that Az-iso2 gives two types of crystals (form I and form II) with polyethylene glycol (PEG4000) and ammonium sulfate as the precipitants, respectively. Comparison between the two Az-iso2 structures in forms I and II reveals the remarkable structural changes at the top surface of the molecule around the copper atom. Az-iso2 possesses Gly43 instead of Val43 or Ala43, which is unique among all other azurins around the copper ligand His46, inducing the remarkable structural change in the loop region from Gly37 to Gly43. When the structure of Az-iso2 is superimposed on that of amicyanin in the ternary complex composed of MADH, amicyanin, and cytochrome c(551), the loop of Az-iso2 deeply overlaps with the light subunit of MADH. However, the Az-iso2 molecule is probably able to avoid any steric hindrance with the cognate MADH to form the complex for intermolecular electron-transfer reaction, since the loop containing Gly43 is flexible. We discuss why the electron-transfer activity of Az-iso2 is fivefold higher than that of Az-iso1.
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Affiliation(s)
- Tsuyoshi Inoue
- Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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5
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Abstract
The three-helix bundle is a common structural motif among natural proteins. It has been observed in numerous important proteins, such as fibrinogen, laminin, spectrin, dystrofin, hemagglutinin, and mannose binding proteins. The three-helix bundle is a simple structure in which three alpha-helices pack against each other, with a slight left-handed twist. Because of its simplicity relative to other structural motifs, the three-helix bundle can be conveniently used both to clarify the forces responsible for the protein folding and stability, and for the design of novel proteins. In this paper we describe the design, synthesis, and characterization of three peptides that self-assemble into antiparallel, heterotrimeric coiled coils. The experimental results, obtained from CD spectroscopy and ultracentrifugation equilibrium sedimentation, indicate that the mixture of the three peptides preferentially forms heterotrimers; moreover, these aggregates represent attractive systems for combinatorial design of libraries of pseudo C3 symmetric ligands or binding sites.
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Affiliation(s)
- A Lombardi
- Centro Interdipartimentale di Ricerca su Peptidi Bioattivi, University of Napoli, Federico II, Italy
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6
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Mandal S, Das G, Singh R, Shukla R, Bharadwaj PK. Synthesis and studies of Cu(II)-thiolato complexes: bioinorganic perspectives. Coord Chem Rev 1997. [DOI: 10.1016/s0010-8545(96)01342-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Ramakrishnan V, Biou V. [31] Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. Methods Enzymol 1997; 276:538-557. [DOI: 10.1016/s0076-6879(97)76077-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Kofman V, Farver O, Pecht I, Goldfarb D. Two-Dimensional Pulsed EPR Spectroscopy of the Copper Protein Azurin. J Am Chem Soc 1996. [DOI: 10.1021/ja952704s] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. Kofman
- Contribution from the Departments of Chemical Physics and Chemical Immunology, The Weizmann Institute of Science, Rehovot, Israel, and Department of Analytical and Pharmaceutical Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark
| | - O. Farver
- Contribution from the Departments of Chemical Physics and Chemical Immunology, The Weizmann Institute of Science, Rehovot, Israel, and Department of Analytical and Pharmaceutical Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark
| | - I. Pecht
- Contribution from the Departments of Chemical Physics and Chemical Immunology, The Weizmann Institute of Science, Rehovot, Israel, and Department of Analytical and Pharmaceutical Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark
| | - D. Goldfarb
- Contribution from the Departments of Chemical Physics and Chemical Immunology, The Weizmann Institute of Science, Rehovot, Israel, and Department of Analytical and Pharmaceutical Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark
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10
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Mandal S, Shukla R, Bharadwaj PK. Modelling the blue protein active sites: Synthesis and characterization of CuN2S2 complexes showing rhombic EPR spectra and high CuII/CuI potential. Polyhedron 1995. [DOI: 10.1016/0277-5387(95)00028-q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Fourme R, Shepard W, Kahn R. Application of the anomalous dispersion of X-rays to macromolecular crystallography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1995; 64:167-99. [PMID: 8987383 DOI: 10.1016/s0079-6107(96)00002-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- R Fourme
- LURE (CNRS, CEA, MENSER), Université Paris-Sud, Orsay, France
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12
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Fattorusso R, Morelli G, Lombardi A, Nastri F, Maglio O, D'Auria G, Pedone C, Pavone V. Design of metal ion binding peptides. Biopolymers 1995; 37:401-10. [PMID: 8589245 DOI: 10.1002/bip.360370607] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two cyclic and branched peptides (PLA and AZU) were synthesized with the aim of reproducing the active site of the blue copper proteins plastocyanin and azurin. Both peptides, designed on the basis of the x-ray structures of Poplar plastocyanin and Alcaligenes denitrificans azurin, contain the same coordinating residues of the parent native proteins. The visible spectra of PLA in the presence of equimolar amount of Cu(II) strongly support the interaction between the peptide and copper(II) ion. The CD titration of AZU with the Hg(II) ion indicates for the formation of two species, [AZUHg]+ and [AZUHg2]3+ having binding constants (Keq) of 3.10(6) and 2.10(4) M-1, respectively.
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Affiliation(s)
- R Fattorusso
- Department of Chemistry, University of Naples Federico II, Italy
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13
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Abstract
Plastocyanin is one of the best characterized of the photosynthetic electron transfer proteins. Since the determination of the structure of poplar plastocyanin in 1978, the structure of algal (Scenedesmus, Enteromorpha, Chlamydomonas) and plant (French bean) plastocyanins has been determined either by crystallographic or NMR methods, and the poplar structure has been refined to 1.33 A resolution. Despite the sequence divergence among plastocyanins of algae and vascular plants (e.g., 62% sequence identity between the Chlamydomonas and poplar proteins), the three-dimensional structures are remarkably conserved (e.g., 0.76 A rms deviation in the C alpha positions between the Chlamydomonas and poplar proteins). Structural features include a distorted tetrahedral copper binding site at one end of an eight-stranded antiparallel beta-barrel, a pronounced negative patch, and a flat hydrophobic surface. The copper site is optimized for its electron transfer function, and the negative and hydrophobic patches are proposed to be involved in recognition of physiological reaction partners. Chemical modification, cross-linking, and site-directed mutagenesis experiments have confirmed the importance of the negative and hydrophobic patches in binding interactions with cytochrome f and Photosystem I, and validated the model of two functionally significant electron transfer paths in plastocyanin. One putative electron transfer path is relatively short (approximately 4 A) and involves the solvent-exposed copper ligand His-87 in the hydrophobic patch, while the other is more lengthy (approximately 12-15 A) and involves the nearly conserved residue Tyr-83 in the negative patch.
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Affiliation(s)
- M R Redinbo
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles 90024
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15
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Hoitink C, Canters G. The importance of Asn47 for structure and reactivity of azurin from Alcaligenes denitrificans as studied by site-directed mutagenesis and spectroscopy. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49644-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Smith JL. Determination of three-dimensional structure by multiwavelength anomalous diffraction. Curr Opin Struct Biol 1991. [DOI: 10.1016/0959-440x(91)90098-e] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Abstract
Recent studies on the structural and chemical properties of insulin have shown that the insulin hexamer is an allosteric protein capable of adopting three distinct conformations, designated T6, T3R3 and R6. Although the physiological consequences of this allostery are not established, new applications for the insulin hexamer as a model system for the study of allostery and for the study of zinc enzymes and copper proteins are emerging.
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Affiliation(s)
- M L Brader
- Department of Biochemistry, University of California, Riverside 92521-0129
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18
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Nar H, Messerschmidt A, Huber R, van de Kamp M, Canters GW. X-ray crystal structure of the two site-specific mutants His35Gln and His35Leu of azurin from Pseudomonas aeruginosa. J Mol Biol 1991; 218:427-47. [PMID: 1901363 DOI: 10.1016/0022-2836(91)90723-j] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The three-dimensional structures of two site-specific mutants of the blue copper protein azurin from Pseudomonas aeruginosa have been solved by a combination of isomorphous replacement and Patterson search techniques, and refined by energy-restrained least-squares methods. The mutations introduced by recombinant DNA techniques involve residue His35, which was exchanged for glutamine and leucine, to probe for its suggested role in electron transfer. The two mutants, His35Gln (H35Q) and His35Leu (H35L), crystallize non-isomorphously in the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 109.74 A, b = 99.15 A, c = 47.82 A for H35Q, a = 57.82 A, b = 81.06 A, c = 110.03 A for H35L. In each crystal form, there are four molecules in the asymmetric unit. They are arranged as a dimer of dimers in the H35Q case and are distorted from ideal C2 symmetry in H35L. The final crystallographic R-value is 16.3% for 20.747 reflections to a resolution of 2.1 A for H35Q and 17.0% for 32,548 reflections to 1.9 A for H35L. The crystal structures reported here represent the first crystallographically refined structures for azurin from P. aeruginosa. The structure is very similar to that of azurin from Alcaligenes denitrificans. The copper atom is located about 7 A below a hydrophobic surface region and is ligated by five donor groups in a distorted trigonal bipyramidal fashion. The implications for electron transfer properties of the protein are discussed in terms of the mutation site and the packing of the molecules within the tetramer.
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Affiliation(s)
- H Nar
- Max Planck Institut für Biochemie, Abteilung Strukturforschung Martinsried b. München, Germany
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20
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Meyer TE, Cusanovich MA. Structure, function and distribution of soluble bacterial redox proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 975:1-28. [PMID: 2660909 DOI: 10.1016/s0005-2728(89)80196-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- T E Meyer
- Department of Biochemistry, University of Arizona, Tucson 85721
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21
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Hendrickson WA, Pähler A, Smith JL, Satow Y, Merritt EA, Phizackerley RP. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. Proc Natl Acad Sci U S A 1989; 86:2190-4. [PMID: 2928324 PMCID: PMC286877 DOI: 10.1073/pnas.86.7.2190] [Citation(s) in RCA: 428] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A three-dimensional crystal structure of the biotin-binding core of streptavidin has been determined at 3.1-A resolution. The structure was analyzed from diffraction data measured at three wavelengths from a single crystal of the selenobiotinyl complex with streptavidin. Streptavidin is a tetramer with subunits arrayed in D2 symmetry. Each protomer is an 8-stranded beta-barrel with simple up-down topology. Biotin molecules are bound at one end of each barrel. This study demonstrates the effectiveness of multiwavelength anomalous diffraction (MAD) procedures for macromolecular crystallography and provides a basis for detailed study of biotin-avidin interactions.
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Affiliation(s)
- W A Hendrickson
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
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Hendrickson WA, Horton JR, Murthy HM, Pahler A, Smith JL. Multiwavelength anomalous diffraction as a direct phasing vehicle in macromolecular crystallography. BASIC LIFE SCIENCES 1989; 51:317-24. [PMID: 2818433 DOI: 10.1007/978-1-4684-8041-2_28] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- W A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032
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Baker EN. Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules. J Mol Biol 1988; 203:1071-95. [PMID: 3210236 DOI: 10.1016/0022-2836(88)90129-5] [Citation(s) in RCA: 279] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The structure of the blue copper protein azurin, from Alcaligenes denitrificans, has been refined crystallographically by restrained least-squares methods. The final crystallographic R value for 21,980 observed reflections to 1.8 A (1 A = 0.1 nm) resolution is 0.157. The asymmetric unit of the crystal contains two independent azurin molecules, the model for which comprises 1973 protein atoms, together with three SO2-4 ions, and 281 water molecules. Comparison of the two molecules shows very high correspondence. For 125 out of 129 residues (excluding only the chain termini, residues 1 to 2 and 128 to 129) the root-mean-square (r.m.s.) deviation in main-chain atom positions is 0.27 A. For other structural parameters r.m.s. deviations are also low; torsion angles 6.5 degrees, hydrogen bond lengths 0.12 A, bonds to copper 0.04 A and bond angles at the copper 3.9 degrees. The only significant differences are at the chain termini and in several loops. Some of these can be attributed to crystal packing effects, others to genuine structural microheterogeneity. Refinement has confirmed that the copper co-ordination is best described as distorted trigonal planar, with strong in-plane bonds to His46 N delta 1, His117 N delta 1 and Cys112 S gamma, and much weaker axial interactions with Met121 S delta and Gly45 C = O. Two N-H...S hydrogen bonds characterize Cys112 S gamma as a thiolate (S-) sulphur and may influence the visible absorption maximum. Atoms in and around the copper site have very low mobility, whereas the most mobile regions of the molecule are the chain termini and some of the connecting loops between secondary structure elements, especially those at the "southern" end, remote from the copper site. Main-chain to side-chain hydrogen bonds supply important stabilizing interactions at the "northern" end. Surface features include the hydrophobic patch around His117, probably important for electron transfer, the SO2-4 site at His83, and the general absence of ion pairs, despite the presence of many charged amino acid residues. The 281 water molecules include 182 that occur as approximately twofold-related pairs. There are no internal water molecules. The water sites common to both azurin molecules include those in surface pockets and some in intermolecular contact regions. They are characterized by relatively low thermal parameters and numerous protein contacts.
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Affiliation(s)
- E N Baker
- Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand
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25
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Guss JM, Merritt EA, Phizackerley RP, Hedman B, Murata M, Hodgson KO, Freeman HC. Phase determination by multiple-wavelength x-ray diffraction: crystal structure of a basic "blue" copper protein from cucumbers. Science 1988; 241:806-11. [PMID: 3406739 DOI: 10.1126/science.3406739] [Citation(s) in RCA: 161] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A novel x-ray diffraction technique, multiple-wavelength anomalous dispersion (MAD) phasing, has been applied to the de novo determination of an unknown protein structure, that of the "blue" copper protein isolated from cucumber seedlings. This method makes use of crystallographic phases determined from measurements made at several wavelengths and has recently been made technically feasible through the use of intense, polychromatic synchrotron radiation together with accurate data collection from multiwire electronic area detectors. In contrast with all of the conventional methods of solving protein structures, which require either multiple isomorphous derivatives or coordinates of a similar structure for molecular replacement, this technique allows direct solution of the classical "phase problem" in x-ray crystallography. MAD phase assignment should be particularly useful for determining structures of small to medium-sized metalloproteins for which isomorphous derivatives are difficult or impossible to make. The structure of this particular protein provides new insights into the spectroscopic and redox properties of blue copper proteins, an important class of metalloproteins widely distributed in nature.
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Affiliation(s)
- J M Guss
- Department of Inorganic Chemistry, University of Sydney, New South Wales, Australia
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Hendrickson WA, Smith JL, Phizackerley RP, Merritt EA. Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. Proteins 1988; 4:77-88. [PMID: 3227016 DOI: 10.1002/prot.340040202] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The molecular structure of lamprey hemoglobin was previously determined and refined by conventional crystallographic analysis. In this study, the structural analysis has been repeated in the course of developing the method of multiwavelength anomalous diffraction (MAD) for phase determination. New experimental and analytical procedures that were devised to perform this determination should have general applicability. These include an experimental design to optimize signal strength and reduce systematic errors, experimental evaluation of anomalous scattering factors, and a least-squares procedure for analyzing the MAD data. MAD phases for the structure at 3 A resolution are as accurate overall as the multiple isomorphous replacement (MIR) phases determined previously.
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Affiliation(s)
- W A Hendrickson
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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