1
|
Berman LE, Allaire M, Chance MR, Hendrickson WA, Héroux A, Jakoncic J, Liu Q, Orville AM, Robinson HH, Schneider DK, Shi W, Soares AS, Stojanoff V, Stoner-Ma D, Sweet RM. Optics Concept for a Pair of Undulator Beamlines for MX. Nucl Instrum Methods Phys Res A 2011; 649:131-135. [PMID: 21822346 PMCID: PMC3150574 DOI: 10.1016/j.nima.2010.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a concept for x-ray optics to feed a pair of macromolecular crystallography (MX) beamlines which view canted undulator radiation sources in the same storage ring straight section. It can be deployed at NSLS-II and at other low-emittance third-generation synchrotron radiation sources where canted undulators are permitted, and makes the most of these sources and beamline floor space, even when the horizontal angle between the two canted undulator emissions is as little as 1-2 mrad. The concept adopts the beam-separation principles employed at the 23-ID (GM/CA-CAT) beamlines at the Advanced Photon Source (APS), wherein tandem horizontally-deflecting mirrors separate one undulator beam from the other, following monochromatization by a double-crystal monochromator. The scheme described here would, in contrast, deliver the two tunable monochromatic undulator beams to separate endstations that address rather different and somewhat complementary purposes, with further beam conditioning imposed as required. A downstream microfocusing beamline would employ dual-stage focusing for work at the micron scale and, unique to this design, switch to single stage focusing for larger beams. On the other hand, the upstream, more highly automated beamline would only employ single stage focusing.
Collapse
Affiliation(s)
- L E Berman
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Evans-Lutterodt K, Qian K, Jakoncic J, Stojanoff V. The use of kinoform lenses as an option for microbeams in macromolecular crystallography. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311087824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
3
|
Schneider DK, Sweet RM, Sullivan M, Stoner-Ma D, Stojanoff V, Soares A, Shi W, Robinson H, Orville A, Liu Q, Lidestri J, Jakoncic J, Héroux A, Hendrickson WA, Chance M, Allaire M, Berman LE. Towards macromolecular crystallography beamlines at NSLS-II. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311093536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
4
|
|
5
|
Berman LE, Allaire M, Chance M, Hendrickson W, Héroux A, Jakoncic J, Liu Q, Orville A, Robinson H, Schneider D, Shi W, Soares A, Stojanoff V, Stoner-Ma D, Sullivan M, Sweet R. Pair of canted undulator MX beamlines proposed for NSLS-II. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311093615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
6
|
Wang J, Stojanoff V. Industrial applications at the National Synchrotron Light Source. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311082596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
|
7
|
Berman L, Allaire M, Chance M, Hendrickson W, Heroux A, Manjasetty B, Orville A, Robinson H, Saxena A, Schneider D, Shi W, Soares A, Stojanoff V, Sweet R. A proposed suite of macromolecular crystallography facilities for NSLS-II. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308094427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
8
|
Moreno A, Jakoncic J, Frontana-Uribe B, Stojanoff V. Electrochemically assisted protein crystallization. Applications to protein crystallography. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308088314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
9
|
Aslantas M, Stojanoff V, Kendi E. New aproaches to room-temperature synchrotron data collection in macromolecular crystallography. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308094348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
10
|
Jean J, Stojanoff V. A simple method to introduce anomalous scatterers in a wide number of proteins. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308098450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
11
|
Fuentes-Silva D, Mendoza-Hernández G, Stojanoff V, Palomares LA, Zenteno E, Torres-Larios A, Rodríguez-Romero A. Crystallization and identification of the glycosylated moieties of two isoforms of the main allergen Hev b 2 and preliminary X-ray analysis of two polymorphs of isoform II. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:787-91. [PMID: 17768356 PMCID: PMC2376315 DOI: 10.1107/s1744309107039838] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 08/10/2007] [Indexed: 11/10/2022]
Abstract
Latex from Hevea brasiliensis contains several allergenic proteins that are involved in type I allergy. One of them is Hev b 2, which is a beta-1,3-glucanase enzyme that exists in different isoforms with variable glycosylation content. Two glucanase isoforms were isolated from trees of the GV-42 clone by gel filtration, affinity and ion-exchange chromatography. Isoform I had a carbohydrate content of about 20%, with N-linked N-acetyl-glucosamine, N-acetyl-galactosamine, fucose and galactose residues as the main sugars, while isoform II showed 6% carbohydrate content consisting of N-acetyl-glucosamine, fucose, mannose and xylose. Both isoforms were crystallized by the hanging-drop vapour-diffusion method. Isoform I crystals were grown using 0.2 M trisodium citrate dihydrate, 0.1 M Na HEPES pH 7.5 and 20%(v/v) 2-propanol, but these crystals were not appropriate for data collection. Isoform II crystals were obtained under two conditions and X-ray diffraction data were collected from both. In the first condition (0.2 M trisodium citrate, 0.1 M sodium cacodylate pH 6.5, 30% 2-propanol), crystals belonging to the tetragonal space group P4(1) with unit-cell parameters a = b = 150.17, c = 77.41 A were obtained. In the second condition [0.2 M ammonium acetate, 0.1 M trisodium citrate dihydrate pH 5.6, 30%(w/v) polyethylene glycol 4000] the isoform II crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 85.08, b = 89.67, c = 101.80 A, beta = 113.6 degrees. Preliminary analysis suggests that there are four molecules of isoform II in both asymmetric units.
Collapse
Affiliation(s)
- D. Fuentes-Silva
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510, Mexico
| | - G. Mendoza-Hernández
- Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510, Mexico
| | - V. Stojanoff
- Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY, USA
| | - L. A. Palomares
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510, Mexico
| | - E. Zenteno
- Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510, Mexico
| | - A. Torres-Larios
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510, Mexico
| | - A. Rodríguez-Romero
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510, Mexico
| |
Collapse
|
12
|
Moreno A, Quiroz-García B, Yokaichiya F, Stojanoff V, Rudolph P. Protein crystal growth in gels and stationary magnetic fields. Cryst Res Technol 2007. [DOI: 10.1002/crat.200610805] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
13
|
Aslantas M, Kendi E, Stojanoff V. Macromolecular crystallography at room temperature: wavelength dependence radiation sensitivity and damage. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305088653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
14
|
Stojanoff V, Vahedi-Faridi A, Yeh JI. Improvement of crystal quality by time controlled annealing. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305099629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
15
|
Teplitsky A, Feinberg H, Gilboa R, Lapidot A, Mechaly A, Stojanoff V, Capel M, Shoham Y, Shoham G. Crystallization and preliminary X-ray analysis of the thermostable alkaline-tolerant xylanase from Bacillus stearothermophilus T-6. Acta Crystallogr D Biol Crystallogr 2005; 53:608-11. [PMID: 15299894 DOI: 10.1107/s0907444997002734] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The extracellular thermostable xylanase (XT-6) produced by the thermophilic bacterium Bacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K, and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids with a calculated molecular weight of 43,808 and pI of 9.0. Crystallographic studies of XT-6 were initiated to study the mechanism of catalysis as well as to provide a structural basis for rational introduction of enhanced thermostability by site-specific mutagenesis. This report describes the crystallization and preliminary crystallographic characterization of the native XT-6 enzyme. The most suitable crystals were obtained by the vapor-diffusion method using ammonium sulfate and 2-methyl-2,4-pentanediol as an organic additive. The crystals belong to a primitive trigonal crystal system (space group P3(1) or P3(2)) with room-temperature cell dimensions of a = b = 114.9 and c = 122.6 A. At 103 K the volume of the unit cell decreased significantly with observed dimensions of a = b = 112.2 and c = 122.9 A. These crystals are mechanically strong and diffract X-rays to better than 2.2 A resolution. The crystals exhibit considerable radiation damage at room temperature even at relatively short exposures to X-rays. A full 2.3 A resolution diffraction data set (99.8% completeness) has recently been collected on flash-frozen crystals at 103 K using synchrotron radiation. Two derivatives of XT-6 were recently prepared. In the first derivative, a unique Cys residue replaced Glu265, the putative nucleophile in the active site. The second derivative was selenomethionyl xylanase which was produced biosynthetically. These derivatives have been crystallized and the resulting crystals were shown to be isomorphous to the native crystals and diffract X-rays to comparable resolutions.
Collapse
Affiliation(s)
- A Teplitsky
- Department of Inorganic Chemistry, Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Israel
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Vekilov PG, Monaco BR, Thomas BR, Stojanoff V, Rosenberger F. Repartitioning of NaCl and protein impurities in lysozyme crystallization. Acta Crystallogr D Biol Crystallogr 2005; 52:785-98. [PMID: 15299643 DOI: 10.1107/s0907444996003265] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonuniform precipitant and impurity incorporation in protein crystals can cause lattice strain and, thus, possibly decrease the X-ray diffraction resolution. To address this issue, a series of crystallization experiments were carried out, in which initial supersaturation, NaCl concentration, protein purity level and crystallized fraction were varied. Lysozyme and protein impurities, as well as sodium and chloride were independently determined in the initial solution, supernatant and crystals. The segregation coefficients for Na(+) and Cl(-) were found to be independent of supersaturation and NaCl concentration, and decreased with crystallized fraction/crystal size. Numerical evaluation of the extensive body of data, based on a nucleation-growth-repartitioning model, suggests a core of approximately 40 micro m in which salt is incorporated in much greater concentrations than during later growth. Small crystals containing higher amounts of incorporated NaCl also had higher protein impurity contents. This suggests that the excess salt is associated with the protein impurities in the core. X-ray topography revealed strain fields in the center of the crystals comparable in size to the inferred core. The growth rates of crystals smaller than 30-40 micro m in size were consistently 1.5-2 times lower than those of larger crystals, presumably due to higher chemical potentials in the core.
Collapse
Affiliation(s)
- P G Vekilov
- Center for Microgravity and Materials Research, University of Alabama in Huntsville, Alabama 35899, USA.
| | | | | | | | | |
Collapse
|
17
|
Moraleda Merlo AB, Gavira JA, Otálora F, Stojanoff V. The effect of the low magnetic field on the quality of tetragonal lysozyme crystals grown with paramagnetic salts. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304094395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
18
|
Teplitsky A, Mechaly A, Stojanoff V, Sainz G, Golan G, Feinberg H, Gilboa R, Reiland V, Zolotnitsky G, Shallom D, Thompson A, Shoham Y, Shoham G. Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing. Acta Crystallogr D Biol Crystallogr 2004; 60:836-48. [PMID: 15103129 DOI: 10.1107/s0907444904004123] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Accepted: 02/20/2004] [Indexed: 11/10/2022]
Abstract
Xylanases are hemicellulases that hydrolyze the internal beta-1,4-glycoside bonds of xylan. The extracellular thermostable endo-1,4-beta-xylanase (EC 3.2.1.8; XT6) produced by the thermophilic bacterium Geobacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids, with a calculated molecular weight of 43 808 Da and a pI of 9.0. Crystallographic studies of XT6 were performed in order to study the mechanism of catalysis and to provide a structural basis for the rational introduction of enhanced thermostability by site-specific mutagenesis. XT6 was crystallized in the primitive trigonal space group P3(2)21, with unit-cell parameters a = b = 112.9, c = 122.7 A. A full diffraction data set for wild-type XT6 has been measured to 2.4 A resolution on flash-frozen crystals using synchrotron radiation. A fully exchanged selenomethionyl XT6 derivative (containing eight Se atoms per XT6 molecule) was also prepared and crystallized in an isomorphous crystal form, providing full selenium MAD data at three wavelengths and enabling phase solution and structure determination. The structure of wild-type XT6 was refined at 2.4 A resolution to a final R factor of 15.6% and an R(free) of 18.6%. The structure demonstrates that XT6 is made up of an eightfold TIM-barrel containing a deep active-site groove, consistent with its 'endo' mode of action. The two essential catalytic carboxylic residues (Glu159 and Glu265) are located at the active site within 5.5 A of each other, as expected for 'retaining' glycoside hydrolases. A unique subdomain was identified in the carboxy-terminal part of the enzyme and was suggested to have a role in xylan binding. The three-dimensional structure of XT6 is of great interest since it provides a favourable starting point for the rational improvement of its already high thermal and pH stabilities, which are required for a number of biotechnological and industrial applications.
Collapse
Affiliation(s)
- A Teplitsky
- Department of Inorganic Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Capelle B, Epelboin Y, Härtwig J, Moraleda AB, Otálora F, Stojanoff V. Characterization of dislocations in protein crystals by means of synchrotron double-crystal topography. J Appl Crystallogr 2004. [DOI: 10.1107/s0021889803024415] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Hen egg-white lysozyme (HEWL) crystals have been studied by means of double-crystal synchrotron topography. The crystals reveal a number of features that are quite well known in hydrothermally grown inorganic crystals: dislocations, growth bands and growth sector boundaries. Dislocations in the 〈110〉 sectors have been characterized as edge dislocations with Burgers vector parallel to thecaxis. They are distinguishable only under weak beam conditions. The presence of edge dislocations shown in this paper is consistent with the spiral growth steps previously reported. This spiral growth on protein crystals has been observed many times by surface techniques.
Collapse
|
20
|
Allaire M, Aslantas M, Berntson A, Berman L, Cheung S, Clay B, Greene R, Jakoncic J, Johnson E, Kao CC, Lenhard A, Pjerov S, Siddons DP, Stober W, Venkatagiriyappa V, Yin Z, Stojanoff V. The NIGMS structural biology facility at the NSLS. ACTA ACUST UNITED AC 2003. [DOI: 10.1080/08940880308603063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
21
|
Berntson A, Stojanoff V, Takai H. Application of a neural network in high-throughput protein crystallography. J Synchrotron Radiat 2003; 10:445-449. [PMID: 14551445 DOI: 10.1107/s0909049503020855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2003] [Accepted: 09/22/2003] [Indexed: 05/24/2023]
Abstract
High-throughput protein crystallography requires the automation of multiple steps used in the protein structure determination. One crucial step is to find and monitor the crystal quality on the basis of its diffraction pattern. It is often time-consuming to scan protein crystals when selecting a good candidate for exposure. The use of neural networks for this purpose is explored. A dynamic neural network algorithm to achieve a fast convergence and high-speed image recognition has been developed. On the test set a 96% success rate in identifying properly the quality of the crystal has been achieved.
Collapse
Affiliation(s)
- A Berntson
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | |
Collapse
|
22
|
Allaire M, Berman LE, Johnson ED, Siddons DP, Yin Z, Stojanoff V. A NIGMS East Coast structural biology facility. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302087809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
23
|
Stojanoff V. Biomolecular crystals: from X-ray diffraction topography to reciprocal space mapping. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302086865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
24
|
Andreoletti P, Gambarelli S, Sainz G, Stojanoff V, White C, Desfonds G, Gagnon J, Gaillard J, Jouve HM. Formation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity. Biochemistry 2001; 40:13734-43. [PMID: 11695923 DOI: 10.1021/bi010687f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteus mirabilis catalase (PMC) belongs to the family of NADPH binding catalases. The function of NADPH in these enzymes is still a matter of debate. This study presents the effects of two independent phenylalanine mutations (F194 and F215), located between NADPH and heme in the PMC structure. The phenylalanines were replaced with tyrosines which we predicted could carry radicals in a NADPH-heme electron transfer. The X-ray crystal structures of the two mutants indicated that neither the binding site of NADPH nor the immediate environment of the residues was affected by the mutations. Measurements using H2O2 as a substrate confirmed that the variants were as active as the native enzyme. With equivalent amounts of peroxoacetic acid, wild-type PMC, F215Y PMC, and beef liver catalase (BLC) formed a stable compound I, while the F194Y PMC variant produced a compound I which was rapidly transformed into compound II and a tyrosyl radical. EPR studies showed that this radical, generated by the oxidation of Y194, was not related to the previously observed radical in BLC, located on Y369. In the presence of excess NADPH, compound I was reduced to a resting enzyme (k(obs) = 1.7 min(-1)) in a two-electron process. This was independent of the enzyme's origin and did not require any thus far identified tyrosyl radicals. Conversely, the presence of a tyrosyl radical in F194Y PMC greatly enhanced the oxidation of reduced beta-nicotinamide mononucleotide under a steady-state H2O2 flow with observable compound II. This process could involve a one-electron reduction of compound I via Y194.
Collapse
Affiliation(s)
- P Andreoletti
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA/CNRS/UJF, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Sainz G, Leonard G, Stojanoff V, Thompson A. Different 'ways' in multiwavelength anomalous dispersion (MAD) data collection. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300026313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
26
|
Boggon TJ, Helliwell JR, Judge RA, Olczak A, Siddons DP, Snell EH, Stojanoff V. Synchrotron X-ray reciprocal-space mapping, topography and diffraction resolution studies of macromolecular crystal quality. Acta Crystallogr D Biol Crystallogr 2000; 56:868-80. [PMID: 10930833 DOI: 10.1107/s0907444900005837] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/1999] [Accepted: 04/17/2000] [Indexed: 11/10/2022]
Abstract
A comprehensive study of microgravity and ground-grown chicken egg-white lysozyme crystals is presented using synchrotron X-ray reciprocal-space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed reduced intrinsic mosaicities on average, but no differences in terms of strain over their ground-grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the ground-control case only a small volume of the crystal contributed to the intensity at the diffraction peak. The techniques prove to be highly complementary, with the reciprocal-space mapping providing a quantitative measure of the crystal mosaicity and strain (or variation in lattice spacing) and the topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out at the synchrotron.
Collapse
Affiliation(s)
- T J Boggon
- Chemistry Department, University of Manchester, Oxford Road, Manchester M13 9PL, England
| | | | | | | | | | | | | |
Collapse
|
27
|
Choudhury D, Thompson A, Stojanoff V, Langermann S, Pinkner J, Hultgren SJ, Knight SD. X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli. Science 1999; 285:1061-6. [PMID: 10446051 DOI: 10.1126/science.285.5430.1061] [Citation(s) in RCA: 465] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Type 1 pili-adhesive fibers expressed in most members of the Enterobacteriaceae family-mediate binding to mannose receptors on host cells through the FimH adhesin. Pilus biogenesis proceeds by way of the chaperone/usher pathway. The x-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli at 2.5 angstrom resolution reveals the basis for carbohydrate recognition and for pilus assembly. The carboxyl-terminal pilin domain of FimH has an immunoglobulin-like fold, except that the seventh strand is missing, leaving part of the hydrophobic core exposed. A donor strand complementation mechanism in which the chaperone donates a strand to complete the pilin domain explains the basis for both chaperone function and pilus biogenesis.
Collapse
Affiliation(s)
- D Choudhury
- Department of Molecular Biology, Uppsala Biomedical Center, Swedish University of Agricultural Sciences, Box 590, S-753 24 Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
28
|
Stojanoff V, Siddons DP, Monaco LA, Vekilov P, Rosenberger F. X-ray Topography of Tetragonal Lysozyme Grown by the Temperature-Controlled Technique. Acta Crystallogr D Biol Crystallogr 1997; 53:588-95. [PMID: 15299890 DOI: 10.1107/s0907444997005763] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Growth-induced defects in lysozyme crystals were observed by white-beam and monochromatic X-ray topography at the National Synchrotron Light Source (NSLS) at the Brookhaven National Laboratory (BNL). The topographic methods were non-destructive to the extent that traditional diffraction data collection could be performed to high resolution after topography. It was found that changes in growth parameters, defect concentration as detected by X-ray topography, and the diffraction quality obtainable from the crystals were all strongly correlated. In addition, crystals with fewer defects showed lower mosaicity and higher diffraction resolution as expected.
Collapse
Affiliation(s)
- V Stojanoff
- NSLS, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | | | | | |
Collapse
|
29
|
Lobb L, Stec B, Kantrowitz EK, Yamano A, Stojanoff V, Markman O, Teeter MM. Expression, purification and characterization of recombinant crambin. Protein Eng 1996; 9:1233-9. [PMID: 9010938 DOI: 10.1093/protein/9.12.1233] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Crambin, a small hydrophobic protein (4.7 kDa and 46 residues), has been successfully expressed in Escherichia coli from an artificial, synthetic gene. Several expression systems were investigated. Ultimately, crambin was successfully expressed as a fusion protein with the maltose binding protein, which was purified by affinity chromatography. Crambin expressed as a C-terminal domain was then cleaved from the fusion protein with Factor Xa protease and purified. Circular dichroism spectroscopy and amino acid analysis suggested that the purified material was identical to crambin isolated from seed. For positive identification the protein was crystallized from an ethanol-water solution, by a novel method involving the inclusion of phospholipids in the crystallization buffer, and then subjected to crystallographic analysis. Diffraction data were collected at the Brookhaven synchrotron (beamline-X12C) to a resolution of 1.32 A at 150 K. The structure, refined to an R value of 9.6%, confirmed that the cloned protein was crambin. The availability of cloned crambin will allow site-specific mutagenesis studies to be performed on the protein known to the highest resolution.
Collapse
Affiliation(s)
- L Lobb
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02167, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Snell EH, Helliwell JR, Cassetta A, Boggon TJ, Chayen NE, Weckert E, Holzer K, Schroer K, Stojanoff V, Siddons DP. Protein crystal perfection and the crystal growth process. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396078920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
31
|
Chayen NE, Boggon TJ, Cassetta A, Deacon A, Gleichmann T, Habash J, Harrop SJ, Helliwell JR, Nieh YP, Peterson MR, Raftery J, Snell EH, Hädener A, Niemann AC, Siddons DP, Stojanoff V, Thompson AW, Ursby T, Wulff M. Trends and challenges in experimental macromolecular crystallography. Q Rev Biophys 1996; 29:227-78. [PMID: 8968112 DOI: 10.1017/s0033583500005837] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Macromolecular X-ray crystallography underpins the vigorous field of structural molecular biology having yielded many protein, nucleic acid and virus structures in fine detail. The understanding of the recognition by these macromolecules, as receptors, of their cognate ligands involves the detailed study of the structural chemistry of their molecular interactions. Also these structural details underpin the rational design of novel inhibitors in modern drug discovery in the pharmaceutical industry. Moreover, from such structures the functional details can be inferred, such as the biological chemistry of enzyme reactivity. There is then a vast number and range of types of biological macromolecules that potentially could be studied. The completion of the protein primary sequencing of the yeast genome, and the human genome sequencing project comprising some 105proteins that is underway, raises expectations for equivalent three dimensional structural databases.
Collapse
Affiliation(s)
- N E Chayen
- Biophysics Section, Blackett Laboratory, Imperial College of Science, Technology and Medicine, London, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
|
33
|
Siddons D, Stojanoff V, Snell E, Helliwell J, Scott J, Abela R, Hirt W, Joho W, Rivkin L, Weyer H, Barr S. News and views. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/08940889608602860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
34
|
Abstract
Soybean lipoxygenase-3 has been crystallized by the vapor diffusion method in 16-20% polyethylene glycol (average M(r), 3,400), 0.2 M sodium acetate buffer, pH 5.7, at 21 degrees C, at a protein concentration of 8-15 mg/mL. The crystals, which diffract to 3-A spacings, belong to the monoclinic space group C2. Cell constants are a = 111.9, b = 136.4, and c = 61.6 A and beta = 95.7 degrees. The calculated value of Matthews's constant, Vm = 2.48 A3/kDa, is consistent with the presence of one molecule of lipoxygenase per crystallographic asymmetric unit (Z = 4).
Collapse
Affiliation(s)
- J Steczko
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | |
Collapse
|
35
|
Hämäläinen K, Kao C, Hastings JB, Siddons DP, Berman LE, Stojanoff V, Cramer SP. Spin-dependent x-ray absorption of MnO and MnF2. Phys Rev B Condens Matter 1992; 46:14274-14277. [PMID: 10003517 DOI: 10.1103/physrevb.46.14274] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
36
|
|