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Chang TH, Hsieh FL, Gu X, Smallwood PM, Kavran JM, Gabelli SB, Nathans J. Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae. Proc Natl Acad Sci U S A 2023; 120:e2221103120. [PMID: 36996108 PMCID: PMC10083539 DOI: 10.1073/pnas.2221103120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low-molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration-presumably a coiled coil-held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP-i.e., the long dimension of the pore-and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.
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Affiliation(s)
- Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Fu-Lien Hsieh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Xiaowu Gu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Philip M. Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jennifer M. Kavran
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD21205
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2
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Tan WL, Wong KH, Lei J, Sakai N, Tan HW, Hilgenfeld R, Tam JP. Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold. Sci Rep 2017; 7:5194. [PMID: 28701689 PMCID: PMC5507927 DOI: 10.1038/s41598-017-05037-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/22/2017] [Indexed: 12/27/2022] Open
Abstract
Cysteine-rich peptides (CRPs) of 2–6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.
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Affiliation(s)
- Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - Naoki Sakai
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Hong Wei Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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3
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Hegde RP, Fedorov AA, Sauder JM, Burley SK, Almo SC, Ramagopal UA. The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets. Acta Crystallogr F Struct Biol Commun 2017; 73:184-195. [PMID: 28368276 PMCID: PMC5379167 DOI: 10.1107/s2053230x17002680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/16/2017] [Indexed: 12/25/2022] Open
Abstract
Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98 Å wavelength in one case and at 1.74 Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ∼1.0 Å wavelength, where the f'' value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structure de novo or in accurately assigning surface-bound atoms.
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Affiliation(s)
- Raghurama P. Hegde
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, #4, 16th Cross, Sadashivnagar, Bangalore 560 080, India
| | - Alexander A. Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine, Ullmann Building, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
| | - J. Michael Sauder
- Lilly Biotechnology Center, Eli Lilly and Company, 10290 Campus Point Drive, San Diego, CA 92121, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers University, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Institute of Quantitative Biomedicine, Rutgers University, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, NJ 08903, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center, San Diego, California, USA
- Skaggs School of Pharmacy and Pharmceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Ullmann Building, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
| | - Udupi A. Ramagopal
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, #4, 16th Cross, Sadashivnagar, Bangalore 560 080, India
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4
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Storm SLS, Dall’Antonia F, Bourenkov G, Schneider TR. Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:19-28. [PMID: 28009543 PMCID: PMC5182018 DOI: 10.1107/s1600577516014764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/19/2016] [Indexed: 05/30/2023]
Abstract
High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified for the five crystals. A statistic σ{ΔF}D, calculated as the width σ of the normalized distribution of a set {ΔF} of anomalous differences collected at a dose D, is suggested as a measure of anomalous data quality as a function of dose. An empirical rule is proposed to identify the dose at which the gains in data quality due to increased multiplicity are outbalanced by the losses due to decreases in signal-to-noise as a consequence of radiation damage. Identifying this point of diminishing returns allows the optimization of the choice of data collection parameters and the selection of data to be used in subsequent crystal structure determination steps.
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Affiliation(s)
- Selina L. S. Storm
- Hamburg Outstation c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Fabio Dall’Antonia
- Hamburg Outstation c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Gleb Bourenkov
- Hamburg Outstation c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas R. Schneider
- Hamburg Outstation c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
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5
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Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nat Methods 2015; 12:127-30. [PMID: 25532136 PMCID: PMC4312553 DOI: 10.1038/nmeth.3212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/11/2014] [Indexed: 01/09/2023]
Abstract
We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.
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Affiliation(s)
- Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Ralf W. Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - James M. Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
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6
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Botha S, Nass K, Barends TRM, Kabsch W, Latz B, Dworkowski F, Foucar L, Panepucci E, Wang M, Shoeman RL, Schlichting I, Doak RB. Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. ACTA ACUST UNITED AC 2015; 71:387-97. [DOI: 10.1107/s1399004714026327] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/30/2014] [Indexed: 11/10/2022]
Abstract
Recent advances in synchrotron sources, beamline optics and detectors are driving a renaissance in room-temperature data collection. The underlying impetus is the recognition that conformational differences are observed in functionally important regions of structures determined using crystals kept at ambient as opposed to cryogenic temperature during data collection. In addition, room-temperature measurements enable time-resolved studies and eliminate the need to find suitable cryoprotectants. Since radiation damage limits the high-resolution data that can be obtained from a single crystal, especially at room temperature, data are typically collected in a serial fashion using a number of crystals to spread the total dose over the entire ensemble. Several approaches have been developed over the years to efficiently exchange crystals for room-temperature data collection. These includein situcollection in trays, chips and capillary mounts. Here, the use of a slowly flowing microscopic stream for crystal delivery is demonstrated, resulting in extremely high-throughput delivery of crystals into the X-ray beam. This free-stream technology, which was originally developed for serial femtosecond crystallography at X-ray free-electron lasers, is here adapted to serial crystallography at synchrotrons. By embedding the crystals in a high-viscosity carrier stream, high-resolution room-temperature studies can be conducted at atmospheric pressure using the unattenuated X-ray beam, thus permitting the analysis of small or weakly scattering crystals. The high-viscosity extrusion injector is described, as is its use to collect high-resolution serial data from native and heavy-atom-derivatized lysozyme crystals at the Swiss Light Source using less than half a milligram of protein crystals. The room-temperature serial data allowde novostructure determination. The crystal size used in this proof-of-principle experiment was dictated by the available flux density. However, upcoming developments in beamline optics, detectors and synchrotron sources will enable the use of true microcrystals. This high-throughput, high-dose-rate methodology provides a new route to investigating the structure and dynamics of macromolecules at ambient temperature.
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7
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Liu Q, Guo Y, Chang Y, Cai Z, Assur Z, Mancia F, Greene MI, Hendrickson WA. Multi-crystal native SAD analysis at 6 keV. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2544-57. [PMID: 25286840 PMCID: PMC4188002 DOI: 10.1107/s1399004714013376] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/08/2014] [Indexed: 11/10/2022]
Abstract
Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.
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Affiliation(s)
- Qun Liu
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Youzhong Guo
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yanqi Chang
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
| | - Zheng Cai
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zahra Assur
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Mark I. Greene
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wayne A. Hendrickson
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
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8
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De novo protein crystal structure determination from X-ray free-electron laser data. Nature 2013; 505:244-7. [PMID: 24270807 DOI: 10.1038/nature12773] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/14/2013] [Indexed: 11/08/2022]
Abstract
The determination of protein crystal structures is hampered by the need for macroscopic crystals. X-ray free-electron lasers (FELs) provide extremely intense pulses of femtosecond duration, which allow data collection from nanometre- to micrometre-sized crystals in a 'diffraction-before-destruction' approach. So far, all protein structure determinations carried out using FELs have been based on previous knowledge of related, known structures. Here we show that X-ray FEL data can be used for de novo protein structure determination, that is, without previous knowledge about the structure. Using the emerging technique of serial femtosecond crystallography, we performed single-wavelength anomalous scattering measurements on microcrystals of the well-established model system lysozyme, in complex with a lanthanide compound. Using Monte-Carlo integration, we obtained high-quality diffraction intensities from which experimental phases could be determined, resulting in an experimental electron density map good enough for automated building of the protein structure. This demonstrates the feasibility of determining novel protein structures using FELs. We anticipate that serial femtosecond crystallography will become an important tool for the structure determination of proteins that are difficult to crystallize, such as membrane proteins.
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9
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Liu Q, Liu Q, Hendrickson WA. Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1314-32. [PMID: 23793158 PMCID: PMC3689535 DOI: 10.1107/s0907444913001479] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 01/15/2013] [Indexed: 11/24/2022]
Abstract
Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms (Zmax ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers (Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f'' scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct structural analysis.
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Affiliation(s)
- Qun Liu
- New York Structural Biology Center, NSLS X4, Building 725, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Wayne A. Hendrickson
- New York Structural Biology Center, NSLS X4, Building 725, Brookhaven National Laboratory, Upton, NY 11973, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
- Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
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10
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Vijayakumar B, Velmurugan D. Use of europium ions for SAD phasing of lysozyme at the Cu Kα wavelength. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:20-4. [PMID: 23295480 PMCID: PMC3539697 DOI: 10.1107/s1744309112047562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 11/19/2012] [Indexed: 11/10/2022]
Abstract
Europium is shown to be a good anomalous scatterer in SAD phasing for solving the structure of biological macromolecules. The large value of the anomalous contribution of europium, f'' = 11.17 e(-), at the Cu Kα wavelength is an advantage in de novo phasing and automated model building. Tetragonal crystals of hen egg-white lysozyme (HEWL) incorporating europium(III) chloride (50 mM) were obtained which diffracted to a resolution of 2.3 Å at a wavelength of 1.54 Å (Cu Kα). The master data set (360° frames) was split and analyzed for anomalous signal-to-noise ratio, multiplicity, completeness, SAD phasing and automated building. The structure solution and model building of the split data sets were carried out using phenix.autosol and phenix.autobuild. The contributions of the Eu ions to SAD phasing using in-house data collection are discussed. This study revealed successful lysozyme phasing by SAD using laboratory-source data involving Eu ions, which are mainly coordinated by the side chains of Asn46, Asp52 and Asp101 together with some water molecules.
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Affiliation(s)
- Balakrishnan Vijayakumar
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai 600 025, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai 600 025, India
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11
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Liu Q, Dahmane T, Zhang Z, Assur Z, Brasch J, Shapiro L, Mancia F, Hendrickson WA. Structures from anomalous diffraction of native biological macromolecules. Science 2012; 336:1033-7. [PMID: 22628655 DOI: 10.1126/science.1218753] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.
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Affiliation(s)
- Qun Liu
- New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA
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12
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Doutch J, Hough MA, Hasnain SS, Strange RW. Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:19-29. [PMID: 22186640 DOI: 10.1107/s0909049511049004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 11/17/2011] [Indexed: 05/31/2023]
Abstract
The sulfur SAD phasing method allows the determination of protein structures de novo without reference to derivatives such as Se-methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimeric Achromobacter cycloclastes nitrite reductase (AcNiR), which contains a near average proportion of sulfur-containing residues and two Cu atoms per subunit. Experiments using X-ray wavelengths in the range 1.9-2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful for automated structure solution and model building using existing beamlines and current software tools. On the other hand, experiments using the shortest X-ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long-wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ~1.25% at ~2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ~0.75 Å) for AcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.
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Affiliation(s)
- James Doutch
- Barkla X-ray Laboratory of Biophysics, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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13
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Unge J, Mueller-Dieckmann C, Panjikar S, Tucker PA, Lamzin VS, Weiss MS. On the routine use of soft X-rays in macromolecular crystallography. Part V. Molecular replacement and anomalous scattering. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:729-38. [DOI: 10.1107/s0907444911024887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/24/2011] [Indexed: 11/10/2022]
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14
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Kitago Y, Watanabe N, Tanaka I. Semi-automated protein crystal mounting device for the sulfur single-wavelength anomalous diffraction method. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889809054272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Use of longer-wavelength X-rays has advantages for the detection of small anomalous signals from light atoms, such as sulfur, in protein molecules. However, the accuracy of the measured diffraction data decreases at longer wavelengths because of the greater X-ray absorption. The capillary-top mounting method (formerly the loopless mounting method) makes it possible to eliminate frozen solution around the protein crystal and reduces systematic errors in the evaluation of small anomalous differences. However, use of this method requires custom-made tools and a large amount of skill. Here, the development of a device that can freeze the protein crystal semi-automatically using the capillary-top mounting method is described. This device can pick up the protein crystal from the crystallization drop using a micro-manipulator, and further procedures, such as withdrawal of the solution around the crystal by suction and subsequent flash freezing of the protein crystal, are carried out automatically. This device makes it easy for structural biologists to use the capillary-top mounting method for sulfur single-wavelength anomalous diffraction phasing using longer-wavelength X-rays.
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15
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Abendroth J, Mitchell DD, Korotkov KV, Johnson TL, Kreger A, Sandkvist M, Hol WGJ. The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of Vibrio cholerae. J Struct Biol 2009; 166:303-15. [PMID: 19324092 DOI: 10.1016/j.jsb.2009.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/04/2009] [Accepted: 03/18/2009] [Indexed: 12/30/2022]
Abstract
The type 2 secretion system (T2SS), a multi-protein machinery that spans both the inner and the outer membranes of Gram-negative bacteria, is used for the secretion of several critically important proteins across the outer membrane. Here we report the crystal structure of the N-terminal cytoplasmic domain of EpsF, an inner membrane spanning T2SS protein from Vibrio cholerae. This domain consists of a bundle of six anti-parallel helices and adopts a fold that has not been described before. The long C-terminal helix alpha6 protrudes from the body of the domain and most likely continues as the first transmembrane helix of EpsF. Two N-terminal EpsF domains form a tight dimer with a conserved interface, suggesting that the observed dimer occurs in the T2SS of many bacteria. Two calcium binding sites are present in the dimer interface with ligands provided for each site by both subunits. Based on this new structure, sequence comparisons of EpsF homologs and localization studies of GFP fused with EpsF, we propose that the second cytoplasmic domain of EpsF adopts a similar fold as the first cytoplasmic domain and that full-length EpsF, and its T2SS homologs, have a three-transmembrane helix topology.
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Affiliation(s)
- Jan Abendroth
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, 1959 Pacific Ave. NE, Box 357742, Seattle, WA 98195, USA
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16
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Hooft RWW, Straver LH, Spek AL. Determination of absolute structure using Bayesian statistics on Bijvoet differences. J Appl Crystallogr 2008; 41:96-103. [PMID: 19461838 PMCID: PMC2467520 DOI: 10.1107/s0021889807059870] [Citation(s) in RCA: 583] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 11/16/2007] [Indexed: 11/10/2022] Open
Abstract
A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The outcome of this type of analysis can also be cast in the form of a new value, along with associated standard uncertainty, that resembles the value of the well known Flack x parameter. The standard uncertainty we obtain is often about half of the standard uncertainty in the value of the Flack x parameter. The proposed formalism is suited in particular to absolute configuration determination from diffraction data of biologically active (pharmaceutical) compounds where the strongest resonant scattering signal often comes from oxygen. It is shown that a reliable absolute configuration assignment in such cases can be made on the basis of Cu Kalpha data, and in some cases even with carefully measured Mo Kalpha data.
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18
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Nanao MH, Ravelli RBG. Phasing macromolecular structures with UV-induced structural changes. Structure 2006; 14:791-800. [PMID: 16615919 DOI: 10.1016/j.str.2006.02.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 01/29/2006] [Accepted: 02/14/2006] [Indexed: 10/24/2022]
Abstract
Experimental phasing of macromolecular crystal structures relies on the accurate measurement of two or more sets of reflections from isomorphous crystals, where the scattering power of a few atoms is different for each set. Recently, it was demonstrated that X-ray-induced intensity differences can also contain phasing information, exploiting specific structural changes characteristic of X-ray damage. This method (radiation damage-induced phasing; RIP) has the advantage that it can be performed on a single crystal of the native macromolecule. However, a drawback is that X-rays introduce many small changes to both solvent and macromolecule. In this study, ultraviolet (UV) radiation has been used to induce specific changes in the macromolecule alone, leading to a larger contrast between radiation-susceptible and nonsusceptible sites. Unlike X-ray RIP, UV RIP does not require the use of a synchrotron. The method has been demonstrated for a series of macromolecules.
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Affiliation(s)
- Max H Nanao
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, B.P. 181, 38042 Grenoble Cedex 9, France
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19
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Santos-Silva T, Trincão J, Carvalho AL, Bonifácio C, Auchère F, Raleiras P, Moura I, Moura JJG, Romão MJ. The first crystal structure of class III superoxide reductase from Treponema pallidum. J Biol Inorg Chem 2006; 11:548-58. [PMID: 16791639 DOI: 10.1007/s00775-006-0104-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 03/20/2006] [Indexed: 12/01/2022]
Abstract
Superoxide reductase (SOR) is a metalloprotein containing a non-heme iron centre, responsible for the scavenging of superoxide radicals in the cell. The crystal structure of Treponema pallidum (Tp) SOR was determined using soft X-rays and synchrotron radiation. Crystals of the oxidized form were obtained using poly(ethylene glycol) and MgCl2 and diffracted beyond 1.55 A resolution. The overall architecture is very similar to that of other known SORs but TpSOR contains an N-terminal domain in which the desulforedoxin-type Fe centre, found in other SORs, is absent. This domain conserves the beta-barrel topology with an overall arrangement very similar to that of other SOR proteins where the centre is present. The absence of the iron ion and its ligands, however, causes a decrease in the cohesion of the domain and some disorder is observed, particularly in the region where the metal would be harboured. The C-terminal domain exhibits the characteristic immunoglobulin-like fold and harbours the Fe(His)4(Cys) active site. The five ligands of the iron centre are well conserved despite some disorder observed for one of the four molecules in the asymmetric unit. The participation of a glutamate as the sixth ligand of some of the iron centres in Pyrococcus furiosus SOR was not observed in TpSOR. A possible explanation is that either X-ray photoreduction occurred or there was a mixture of redox states at the start of data collection. In agreement with earlier proposals, details in the TpSOR structure also suggest that Lys49 might be involved in attraction of superoxide to the active site.
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Affiliation(s)
- Teresa Santos-Silva
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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20
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Agarwal R, Bonanno JB, Burley SK, Swaminathan S. Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2006; 62:383-91. [PMID: 16552139 PMCID: PMC1431508 DOI: 10.1107/s0907444906001600] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Accepted: 01/13/2006] [Indexed: 05/07/2023]
Abstract
The availability of high-intensity synchrotron facilities, technological advances in data-collection techniques and improved data-reduction and crystallographic software have ushered in a new era in high-throughput macromolecular crystallography. Here, the de novo automated crystal structure determination at 1.28 A resolution of an NAD(P)H-dependent FMN reductase flavoprotein from Pseudomonas aeruginosa PA01-derived protein Q9I4D4 using the anomalous signal from an unusually small number of S atoms is reported. Although this protein lacks the flavodoxin key fingerprint motif [(T/S)XTGXT], it has been confirmed to bind flavin mononucleotide and the binding site was identified via X-ray crystallography. This protein contains a novel flavin mononucleotide-binding site GSLRSGSYN, which has not been previously reported. Detailed statistics pertaining to sulfur phasing and other factors contributing to structure determination are discussed. Structural comparisons of the apoenzyme and the protein complexed with flavin mononucleotide show conformational changes on cofactor binding. NADPH-dependent activity has been confirmed with biochemical assays.
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Affiliation(s)
- Rakhi Agarwal
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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21
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Santos-Silva T, Trincão J, Carvalho AL, Bonifácio C, Auchère F, Moura I, Moura JJG, Romão MJ. Superoxide reductase from the syphilis spirochete Treponema pallidum: crystallization and structure determination using soft X-rays. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:967-70. [PMID: 16511209 PMCID: PMC1978137 DOI: 10.1107/s174430910502885x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Accepted: 09/12/2005] [Indexed: 11/10/2022]
Abstract
Superoxide reductase is a 14 kDa metalloprotein containing a catalytic non-haem iron centre [Fe(His)4Cys]. It is involved in defence mechanisms against oxygen toxicity, scavenging superoxide radicals from the cell. The oxidized form of Treponema pallidum superoxide reductase was crystallized in the presence of polyethylene glycol and magnesium chloride. Two crystal forms were obtained depending on the oxidizing agents used after purification: crystals grown in the presence of K3Fe(CN)6 belonged to space group P2(1) (unit-cell parameters a = 60.3, b = 59.9, c = 64.8 A, beta = 106.9 degrees) and diffracted beyond 1.60 A resolution, while crystals grown in the presence of Na2IrCl6 belonged to space group C2 (a = 119.4, b = 60.1, c = 65.6 A, beta = 104.9 degrees) and diffracted beyond 1.55 A. A highly redundant X-ray diffraction data set from the C2 crystal form collected on a copper rotating-anode generator (lambda = 1.542 A) clearly defined the positions of the four Fe atoms present in the asymmetric unit by SAD methods. A MAD experiment at the iron absorption edge confirmed the positions of the previously determined iron sites and provided better phases for model building and refinement. Molecular replacement using the P2(1) data set was successful using a preliminary trace as a search model. A similar arrangement of the four protein molecules could be observed.
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Affiliation(s)
- Teresa Santos-Silva
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José Trincão
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana L. Carvalho
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cecília Bonifácio
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Françoise Auchère
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Isabel Moura
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria J. Romão
- REQUIMTE Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Choe J, Suresh S, Wisedchaisri G, Kennedy KJ, Gelb MH, Hol WGJ. Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase. CHEMISTRY & BIOLOGY 2002; 9:1189-97. [PMID: 12445769 DOI: 10.1016/s1074-5521(02)00243-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pathogenic protozoa such as Trypanosome and Leishmania species cause tremendous suffering worldwide. Because of their dependence on glycolysis for energy, the glycolytic enzymes of these organisms, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. Using the adenine part of NAD as a lead compound, several 2,6-disubstituted purines were synthesized as inhibitors of Leishmania mexicana GPDH (LmGPDH). The electron densities for the inhibitor 2-bromo-6-chloro-purine bound to LmGPDH using a "conventional" wavelength around 1 A displayed a quasisymmetric shape. The anomalous signals from data collected at 1.77 A clearly indicated the positions of the halogen atoms and revealed the multiple binding modes of this inhibitor. Intriguing differences in the observed binding modes of the inhibitor between very similarly prepared crystals illustrate the possibility of crystal-to-crystal variations in protein-ligand complex structures.
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Affiliation(s)
- Jungwoo Choe
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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