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Suzuki R, Baba S, Mizuno N, Hasegawa K, Koizumi H, Kojima K, Kumasaka T, Tachibana M. Radiation-induced defects in protein crystals observed by X-ray topography. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:196-203. [DOI: 10.1107/s205979832101281x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022]
Abstract
The characterization of crystal defects induced by irradiation, such as X-rays, charged particles and neutrons, is important for understanding radiation damage and the associated generation of defects. Radiation damage to protein crystals has been measured using various methods. Until now, these methods have focused on decreased diffraction intensity, volume expansion of unit cells and specific damage to side chains. Here, the direct observation of specific crystal defects, such as dislocations, induced by X-ray irradiation of protein crystals at room temperature is reported. Dislocations are induced even by low absorbed doses of X-ray irradiation. This study revealed that for the same total absorbed dose, the formation of defects appears to critically depend on the dose rate. The relationship between dislocation energy and dose energy was analyzed based on dislocation theory associated with elasticity theory for crystalline materials. This demonstration of the crystal defects induced by X-ray irradiation could help to understand the underlying mechanisms of X-ray-induced radiation damage.
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Shen C, Julius EF, Tyree TJ, Moreau DW, Atakisi H, Thorne RE. Thermal contraction of aqueous glycerol and ethylene glycol solutions for optimized protein-crystal cryoprotection. Acta Crystallogr D Struct Biol 2016; 72:742-52. [PMID: 27303794 PMCID: PMC8493611 DOI: 10.1107/s2059798316005490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/01/2016] [Indexed: 11/10/2022] Open
Abstract
The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol at T = 77 K have been determined. Densities with accuracies of <0.5% to concentrations as low as 30%(w/v) were determined by rapidly cooling drops with volumes as small as 70 pl, assessing their optical clarity and measuring their buoyancy in liquid nitrogen-argon solutions. The use of these densities in contraction matching of internal solvent to the available solvent spaces is complicated by several factors, most notably the exclusion of cryoprotectants from protein hydration shells and the expected deviation of the contraction behavior of hydration water from bulk water. The present methods and results will assist in developing rational approaches to cryoprotection and an understanding of solvent behavior in protein crystals.
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Affiliation(s)
- Chen Shen
- Cornell University, Ithaca, NY 14853, USA
| | | | | | - David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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3
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Nave C, Sutton G, Evans G, Owen R, Rau C, Robinson I, Stuart DI. Imperfection and radiation damage in protein crystals studied with coherent radiation. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:228-37. [PMID: 26698068 PMCID: PMC4733927 DOI: 10.1107/s1600577515019700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/18/2015] [Indexed: 05/11/2023]
Abstract
Fringes and speckles occur within diffraction spots when a crystal is illuminated with coherent radiation during X-ray diffraction. The additional information in these features provides insight into the imperfections in the crystal at the sub-micrometre scale. In addition, these features can provide more accurate intensity measurements (e.g. by model-based profile fitting), detwinning (by distinguishing the various components), phasing (by exploiting sampling of the molecular transform) and refinement (by distinguishing regions with different unit-cell parameters). In order to exploit these potential benefits, the features due to coherent diffraction have to be recorded and any change due to radiation damage properly modelled. Initial results from recording coherent diffraction at cryotemperatures from polyhedrin crystals of approximately 2 µm in size are described. These measurements allowed information about the type of crystal imperfections to be obtained at the sub-micrometre level, together with the changes due to radiation damage.
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Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Geoff Sutton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robin Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Christoph Rau
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - David Ian Stuart
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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4
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Caleman C, Huldt G, Maia FRNC, Ortiz C, Parak FG, Hajdu J, van der Spoel D, Chapman HN, Timneanu N. On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. ACS NANO 2011; 5:139-46. [PMID: 21138321 DOI: 10.1021/nn1020693] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters, or nanoparticles. Coherent flash imaging will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single-shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain inaccessible using conventional X-ray sources.
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Affiliation(s)
- Carl Caleman
- Physik Department E17, Technische Universität München, James-Franck-Strasse, DE-85748 Garching, Germany
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5
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Fourme R, Girard E, Kahn R, Dhaussy AC, Mezouar M, Colloc'h N, Ascone I. High-pressure macromolecular crystallography (HPMX): status and prospects. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:384-90. [PMID: 16487756 DOI: 10.1016/j.bbapap.2006.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Revised: 01/09/2006] [Accepted: 01/10/2006] [Indexed: 11/30/2022]
Abstract
Recent technical developments, achievements and prospects of high-pressure (HP) macromolecular crystallography (MX) are reviewed. Technical difficulties associated with this technique have been essentially solved by combining synchrotron radiation of ultra-short wavelength, large-aperture diamond anvil cells and new sample-mounting techniques. The quality of diffraction data collected at HP can now meet standards of conventional MX. The exploitation of the potential of the combination of X-ray diffraction and high-pressure perturbation is progressing well. The ability of pressure to shift the population distribution of conformers in solution, which is exploited in particular by NMR, can also be used in the crystalline state with specific advantages. HPMX has indeed bright prospects, in particular to elucidate the structure of higher-energy conformers that are often of high biological significance. Furthermore, HPMX may be of interest for conventional crystallographic studies, as pressure is a fairly general tool to improve order in pre-existing crystals with minimal perturbation of the native structure.
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Affiliation(s)
- Roger Fourme
- Synchrotron-SOLEIL, BP48 Saint Aubin, 91192 Gif sur Yvette, France.
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Stojanoff V, Cappelle B, Epelboin Y, Hartwig J, Moradela AB, Otalora F. High Resolution Imaging as a Characterization Tool for Biological Crystals. Ann N Y Acad Sci 2004; 1027:48-55. [PMID: 15644344 DOI: 10.1196/annals.1324.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Biomolecular crystals consist of large unit cells that form a rather flexible medium that is able to accommodate a certain degree of lattice distortion, leading to several interesting issues ranging from structural to physical properties. Several techniques, from X-ray diffraction to microscopy, have been adapted to study the structural and physical properties of biomolecular crystals systematically. The use of synchrotron-based monochromatic X-ray diffraction topography, with triple axis diffractometry and rocking curve measurements, to characterize biomolecular crystals is reviewed. Recent X-ray diffraction images from gel and solution grown lysozyme crystals are presented. Defect structures in these crystals are discussed, together with reciprocal space mapping, and compared with results obtained from crystals grown in a low gravity environment.
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Affiliation(s)
- Vivian Stojanoff
- National Synchrotron Light Source, Brookhaven National Laboratories, Upton, NY 11973, USA.
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7
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Jacquamet L, Ohana J, Joly J, Borel F, Pirocchi M, Charrault P, Bertoni A, Israel-Gouy P, Carpentier P, Kozielski F, Blot D, Ferrer JL. Automated Analysis of Vapor Diffusion Crystallization Drops with an X-Ray Beam. Structure 2004; 12:1219-25. [PMID: 15242598 DOI: 10.1016/j.str.2004.04.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Revised: 04/29/2004] [Accepted: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Crystallogenesis, usually based on the vapor diffusion method, is currently considered one of the most difficult steps in macromolecular X-ray crystallography. Due to the increasing number of crystallization assays performed by protein crystallographers, several automated analysis methods are under development. Most of these methods are based on microscope images and shape recognition. We propose an alternative method of identifying protein crystals: by directly exposing the crystallization drops to an X-ray beam. The resulting diffraction provides far more information than classical microscope images. Not only is the presence of diffracting crystals revealed, but also a first estimation of the space group, cell parameters, and mosaicity is obtained. In certain cases, it is also possible to collect enough data to verify the presence of a specific substrate or a heavy atom. All these steps are performed without the sometimes tedious necessity of removing crystals from their crystallization drop.
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Affiliation(s)
- Lilian Jacquamet
- IBS J.-P. Ebel CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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8
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Affiliation(s)
- Edward H Snell
- NASA Laboratory for Structural Biology, Huntsville, Alabama 35812, USA
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical Engineering, University of Houston, Houston, Texas 77204, USA
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Yau ST, Thomas BR, Galkin O, Gliko O, Vekilov PG. Molecular mechanisms of microheterogeneity-induced defect formation in ferritin crystallization. Proteins 2001. [DOI: 10.1002/prot.1047] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Vekilov PG, Alexander JID. Dynamics of Layer Growth in Protein Crystallization. Chem Rev 2000; 100:2061-2090. [PMID: 11749284 DOI: 10.1021/cr9800558] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter G. Vekilov
- Department of Chemistry and Center for Microgravity and Materials Research, University of Alabama-Huntsville, RI Building D-29, Huntsville, Alabama 35899, and Department of Mechanical and Aerospace Engineering and National Center for Microgravity Research on Fluids and Combustion, Glennan 416, Case Western Reserve University, Cleveland, Ohio 44106-7222
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12
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Caylor C, Dobrianov I, Lemay S, Kimmer C, Kriminski S, Finkelstein K, Zipfel W, Webb W, Thomas B, Chernov A, Thorne R. Macromolecular impurities and disorder in protein crystals. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990815)36:3<270::aid-prot2>3.0.co;2-n] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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13
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Ng JD, Kuznetsov YG, Malkin AJ, Keith G, Giegé R, McPherson A. Visualization of RNA crystal growth by atomic force microscopy. Nucleic Acids Res 1997; 25:2582-8. [PMID: 9185567 PMCID: PMC146776 DOI: 10.1093/nar/25.13.2582] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The crystallization of transfer RNA (tRNA) was investigated using atomic force microscopy (AFM) over the temperature range from 4 to 16 degrees C, and this produced the first in situ AFM images of developing nucleic acid crystals. The growth of the (110) face of hexagonal yeast tRNAPhe crystals was observed to occur at steps on vicinal hillocks generated by multiple screw dislocation sources in the temperature range of 13.5-16 degrees C. Two-dimensional nucleation begins to dominate at 13.5 degrees C, with the appearance of three-dimensional nuclei at 12 degrees C. The changes in growth mechanisms are correlated with variations in supersaturation which is higher in the low temperature range. Growth of tRNA crystals was characterized by a strong anisotropy in the tangential step movement and transformation of growth modes on single crystals were directly observed by AFM over the narrow temperature range utilized. Finally, lattice resolution images of the molecular structure of surface layers were recorded. The implications of the strong temperature dependence of tRNAPhe crystal growth are discussed in view of improving and better controlling crystallization of nucleic acids.
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Affiliation(s)
- J D Ng
- Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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14
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Neutze R, Hajdu J. Femtosecond time resolution in x-ray diffraction experiments. Proc Natl Acad Sci U S A 1997; 94:5651-5. [PMID: 9159127 PMCID: PMC20833 DOI: 10.1073/pnas.94.11.5651] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This paper presents the theoretical background for a synthesis of femtosecond spectroscopy and x-ray diffraction. When a diffraction quality crystal with 0.1-0.3 mm overall dimensions is photoactivated by a femtosecond laser pulse (physical length = 0.3 microm), the evolution of molecules at separated points in the crystal will not be simultaneous because a finite time is required for the laser pulse to propagate through the body of the crystal. Utilizing this lack of global crystal synchronization, topographic x-ray diffraction may enable femtosecond temporal resolution to be achieved from reflection profiles in the diffraction pattern with x-ray exposures of picosecond or longer duration. Such x-ray pulses are currently available, and could be used to study femtosecond reaction dynamics at atomic resolution on crystals of both small- and macromolecules. A general treatment of excitation and diffraction geometries in relation to spatial and temporal resolution is presented.
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Affiliation(s)
- R Neutze
- Department of Biochemistry, Biomedical Centre, Uppsala University, Box 576, S-75123 Uppsala, Sweden.
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15
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Abstract
Crystallization is necessary to obtain the three-dimensional structure of proteins and nucleic acids; it often represents the bottleneck in structure determination. Our understanding of crystallization mechanisms is still incomplete. In this review, we emphasize fundamental aspects of the crystallization process. Protein-protein contacts in crystals are complex, involving a delicate balance of specific and nonspecific interactions. Depending on solution conditions, these interactions can lead to nucleation of crystals or to amorphous aggregation; this stage of crystallization has been successfully studied by light scattering. Post-nucleation crystal growth may proceed by mechanisms involving crystal defects or two-dimensional nucleation, as observed by atomic force and interference microscopy. Cessation of growth has been observed but remains incompletely understood. Impurities may play important roles during all stages of crystallization. Phase diagrams can guide optimization of conditions for nucleation and subsequent crystal growth; a theoretical understanding relating these to the intermolecular interactions is beginning to develop.
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Affiliation(s)
- S D Durbin
- Department of Physics and Astronomy, Carleton College, Northfield, Minnesota 55057, USA
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16
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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] [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.
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Affiliation(s)
- N E Chayen
- Biophysics Section, Blackett Laboratory, Imperial College of Science, Technology and Medicine, London, UK.
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17
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Williams PA, Fülöp V, Leung YC, Chan C, Moir JW, Howlett G, Ferguson SJ, Radford SE, Hajdu J. Pseudospecific docking surfaces on electron transfer proteins as illustrated by pseudoazurin, cytochrome c550 and cytochrome cd1 nitrite reductase. NATURE STRUCTURAL BIOLOGY 1995; 2:975-82. [PMID: 7583671 DOI: 10.1038/nsb1195-975] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The structure of pseudoazurin from Thiosphaera pantotropha has been determined and compared to structures of both soluble and membrane-bound periplasmic redox proteins. The results show a matching set of unipolar, but promiscuous, docking motifs based on a positive hydrophobic surface patch on the electron shuttle proteins pseudoazurin and cytochrome c550 and a negative hydrophobic patch on the surface of their known redox partners. The observed electrostatic handedness is argued to be associated with the charge-asymmetry of the membrane-bound components of the redox chain due to von Heijne's 'positives-inside' principle. We propose a 'positives-in-between' rule for electron shuttle proteins, and expect a negative hydrophobic patch to be present on both the highest and lowest redox potential species in a series of electron carriers.
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Affiliation(s)
- P A Williams
- Laboratory of Molecular Biophysics, University of Oxford, UK
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