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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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Protein Crystallization in a Microfluidic Contactor with Nafion ®117 Membranes. MEMBRANES 2021; 11:membranes11080549. [PMID: 34436312 PMCID: PMC8398885 DOI: 10.3390/membranes11080549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/21/2022]
Abstract
Protein crystallization still remains mostly an empirical science, as the production of crystals with the required quality for X-ray analysis is dependent on the intensive screening of the best protein crystallization and crystal’s derivatization conditions. Herein, this demanding step was addressed by the development of a high-throughput and low-budget microfluidic platform consisting of an ion exchange membrane (117 Nafion® membrane) sandwiched between a channel layer (stripping phase compartment) and a wells layer (feed phase compartment) forming 75 independent micro-contactors. This microfluidic device allows for a simultaneous and independent screening of multiple protein crystallization and crystal derivatization conditions, using Hen Egg White Lysozyme (HEWL) as the model protein and Hg2+ as the derivatizing agent. This microdevice offers well-regulated crystallization and subsequent crystal derivatization processes based on the controlled transport of water and ions provided by the 117 Nafion® membrane. Diffusion coefficients of water and the derivatizing agent (Hg2+) were evaluated, showing the positive influence of the protein drop volume on the number of crystals and crystal size. This microfluidic system allowed for crystals with good structural stability and high X-ray diffraction quality and, thus, it is regarded as an efficient tool that may contribute to the enhancement of the proteins’ crystals structural resolution.
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Prieto-Castañeda A, Martínez-Caballero S, Agarrabeitia AR, García-Moreno I, Moya SDL, Ortiz MJ, Hermoso JA. First Lanthanide Complex for De Novo Phasing in Native Protein Crystallography at 1 Å Radiation. ACS APPLIED BIO MATERIALS 2021; 4:4575-4581. [DOI: 10.1021/acsabm.1c00305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alejandro Prieto-Castañeda
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Siseth Martínez-Caballero
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física “Rocasolano”, C.S.I.C., Serrano 119, 28006 Madrid, Spain
| | - Antonia R. Agarrabeitia
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Inmaculada García-Moreno
- Departamento de Sistemas de Baja Dimensionalidad, Superficies y Materia Condensada, Instituto de Química Física “Rocasolano”, C.S.I.C., Serrano 119, 28006 Madrid, Spain
| | - Santiago de la Moya
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - María J. Ortiz
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física “Rocasolano”, C.S.I.C., Serrano 119, 28006 Madrid, Spain
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4
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Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J, Aller P. High-throughput in situ experimental phasing. Acta Crystallogr D Struct Biol 2020; 76:790-801. [PMID: 32744261 PMCID: PMC7397491 DOI: 10.1107/s2059798320009109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Abstract
In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.
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Affiliation(s)
- Joshua M. Lawrence
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions (BF2i); Institut National des Sciences Appliquées de Lyon (INSA Lyon); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Lyon (Univ Lyon), F-69621 Villeurbanne, France
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - James Foadi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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5
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Huang X, Duddy OP, Silpe JE, Paczkowski JE, Cong J, Henke BR, Bassler BL. Mechanism underlying autoinducer recognition in the Vibrio cholerae DPO-VqmA quorum-sensing pathway. J Biol Chem 2020; 295:2916-2931. [PMID: 31964715 DOI: 10.1074/jbc.ra119.012104] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/15/2020] [Indexed: 11/06/2022] Open
Abstract
Quorum sensing is a bacterial communication process whereby bacteria produce, release, and detect extracellular signaling molecules called autoinducers to coordinate collective behaviors. In the pathogen Vibrio cholerae, the quorum-sensing autoinducer 3,5-dimethyl-pyrazin-2-ol (DPO) binds the receptor and transcription factor VqmA. The DPO-VqmA complex activates transcription of vqmR, encoding the VqmR small RNA, which represses genes required for biofilm formation and virulence factor production. Here, we show that VqmA is soluble and properly folded and activates basal-level transcription of its target vqmR in the absence of DPO. VqmA transcriptional activity is increased in response to increasing concentrations of DPO, allowing VqmA to drive the V. cholerae quorum-sensing transition at high cell densities. We solved the DPO-VqmA crystal structure to 2.0 Å resolution and compared it with existing structures to understand the conformational changes VqmA undergoes upon DNA binding. Analysis of DPO analogs showed that a hydroxyl or carbonyl group at the 2'-position is critical for binding to VqmA. The proposed DPO precursor, a linear molecule, N-alanyl-aminoacetone (Ala-AA), also bound and activated VqmA. Results from site-directed mutagenesis and competitive ligand-binding analyses revealed that DPO and Ala-AA occupy the same binding site. In summary, our structure-function analysis identifies key features required for VqmA activation and DNA binding and establishes that, whereas VqmA binds two different ligands, VqmA does not require a bound ligand for folding or basal transcriptional activity. However, bound ligand is required for maximal activity.
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Affiliation(s)
- Xiuliang Huang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Jon E Paczkowski
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
| | - Jianping Cong
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Brad R Henke
- Opti-Mol Consulting, LLC, Cary, North Carolina 27513
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815.
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6
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Abstract
Due to the availability of many macromolecular models in the Protein Data Bank, the majority of crystal structures are currently solved by molecular replacement. However, truly novel structures can only be solved by one of the versions of the special-atom method. The special atoms such as sulfur, phosphorus or metals could be naturally present in the macromolecules, or could be intentionally introduced in a derivatization process. The isomorphous and/or anomalous scattering of X-rays by these special atoms is then utilized for phasing. There are many ways to obtain potentially useful derivatives, ranging from the introduction of special atoms to proteins or nucleic acids by genetic engineering or by chemical synthesis, to soaking native crystals in solutions of appropriate compounds with heavy and/or anomalously scattering atoms. No approach guarantees the ultimate success and derivatization remains largely a trial-and-error process. In practice, however, there is a very good chance that one of a wide variety of the available procedures will lead to successful structure solution.
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7
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Pike ACW, Garman EF, Krojer T, von Delft F, Carpenter EP. An overview of heavy-atom derivatization of protein crystals. Acta Crystallogr D Struct Biol 2016; 72:303-18. [PMID: 26960118 PMCID: PMC4784662 DOI: 10.1107/s2059798316000401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/08/2016] [Indexed: 11/11/2022] Open
Abstract
Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.
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Affiliation(s)
- Ashley C. W. Pike
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Aukland Park 2006, South Africa
| | - Elisabeth P. Carpenter
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
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8
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Lu J, Sun PD. A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives. FEBS J 2014; 281:4021-8. [PMID: 25040395 DOI: 10.1111/febs.12910] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/26/2014] [Accepted: 07/03/2014] [Indexed: 11/29/2022]
Abstract
In attempts to replace the conventional trial-and-error heavy-atom derivative search method with a rational approach, we previously defined heavy metal compound reactivity against peptide ligands. Here, we assembled a composite pH- and buffer-dependent peptide reactivity profile for each heavy metal compound to guide rational heavy-atom derivative search. When knowledge of the best-reacting heavy-atom compound is combined with mass spectrometry assisted derivatization, and with a quick-soak method to optimize phasing, it is likely that the traditional heavy-atom compounds could meet the demand of modern high-throughput X-ray crystallography. As an example, we applied this rational heavy-atom phasing approach to determine a previously unknown mouse serum amyloid A2 crystal structure.
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Affiliation(s)
- Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
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9
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El Omari K, Iourin O, Kadlec J, Fearn R, Hall DR, Harlos K, Grimes JM, Stuart DI. Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1. ACTA ACUST UNITED AC 2014; 70:2197-203. [PMID: 25084338 PMCID: PMC4118829 DOI: 10.1107/s139900471401339x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/08/2014] [Indexed: 11/21/2022]
Abstract
The sulfur SAD phasing method was successfully used to determine the structure of the N-terminal domain of HCV E1 from low-resolution diffracting crystals by combining data from 32 crystals. Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.
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Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Oleg Iourin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Jan Kadlec
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Richard Fearn
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - David R Hall
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - David I Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
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10
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Mizutani R, Shimizu Y, Saiga R, Ueno G, Nakamura Y, Takeuchi A, Uesugi K, Suzuki Y. Spatiotemporal development of soaked protein crystal. Sci Rep 2014; 4:5731. [PMID: 25043871 PMCID: PMC5375977 DOI: 10.1038/srep05731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/30/2014] [Indexed: 11/28/2022] Open
Abstract
Crystal soaking is widely performed in biological crystallography. This paper reports time-resolved X-ray crystallographic and microtomographic analyses of tetragonal crystals of chicken egg-white lysozyme soaked in mother liquor containing potassium hexachloroplatinate. The microtomographic analysis showed that X-ray attenuation spread from the superficial layer of the crystal and then to the crystal core. The crystallographic analyses indicated that platinum sites can be classified into two groups from the temporal development of the electron densities. A soaking process consisting of binding-rate-driven and equilibrium-driven layers is proposed to describe these results. This study suggests that the composition of chemical and structural species resulting from the soaking process varies depending on the position in the crystal.
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Affiliation(s)
- Ryuta Mizutani
- Department of Applied Biochemistry, School of Engineering, Tokai University, Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan
| | - Yusuke Shimizu
- Department of Applied Biochemistry, School of Engineering, Tokai University, Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan
| | - Rino Saiga
- Department of Applied Biochemistry, School of Engineering, Tokai University, Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Yuki Nakamura
- Rigaku Corporation, 14-8, Akaoji-cho, Takatsuki-Shi, Osaka 569-1146, Japan
| | - Akihisa Takeuchi
- Research and Utilization Division, JASRI/SPring-8, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Kentaro Uesugi
- Research and Utilization Division, JASRI/SPring-8, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Yoshio Suzuki
- Research and Utilization Division, JASRI/SPring-8, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
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Liu M, Imamura K, Averill AM, Wallace SS, Doublié S. Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNA. Structure 2013; 21:247-56. [PMID: 23313161 DOI: 10.1016/j.str.2012.12.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 12/21/2022]
Abstract
Endonuclease VIII-like 3 (Neil3) is a DNA glycosylase of the base excision repair pathway that protects cells from oxidative DNA damage by excising a broad spectrum of cytotoxic and mutagenic base lesions. Interestingly, Neil3 exhibits an unusual preference for DNA with single-stranded regions. Here, we report the 2.0 Å crystal structure of a Neil3 enzyme. Although the glycosylase region of mouse Neil3 (MmuNeil3Δ324) exhibits the same overall fold as that of other Fpg/Nei proteins, it presents distinct structural features. First, MmuNeil3Δ324 lacks the αF-β9/10 loop that caps the flipped-out 8-oxoG in bacterial Fpg, which is consistent with its inability to cleave 8-oxoguanine. Second, Neil3 not only lacks two of the three void-filling residues that stabilize the opposite strand, but it also harbors negatively charged residues that create an unfavorable electrostatic environment for the phosphate backbone of that strand. These structural features provide insight into the substrate specificity and marked preference of Neil3 for ssDNA.
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Affiliation(s)
- Minmin Liu
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
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12
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Dumont E, Pompidor G, D'Aléo A, Vicat J, Toupet L, Kahn R, Girard E, Maury O, Giraud N. Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study. Phys Chem Chem Phys 2013; 15:18235-42. [DOI: 10.1039/c3cp53671h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Paczkowski JE, Richardson BC, Strassner AM, Fromme JC. The exomer cargo adaptor structure reveals a novel GTPase-binding domain. EMBO J 2012; 31:4191-203. [PMID: 23000721 DOI: 10.1038/emboj.2012.268] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 08/30/2012] [Indexed: 11/09/2022] Open
Abstract
Cargo adaptors control intracellular trafficking of transmembrane proteins by sorting them into membrane transport carriers. The COPI, COPII, and clathrin cargo adaptors are structurally well characterized, but other cargo adaptors remain poorly understood. Exomer is a specialized cargo adaptor that sorts specific proteins into trans-Golgi network (TGN)-derived vesicles in response to cellular signals. Exomer is recruited to the TGN by the Arf1 GTPase, a universally conserved trafficking regulator. Here, we report the crystal structure of a tetrameric exomer complex composed of two copies each of the Chs5 and Chs6 subunits. The structure reveals the FN3 and BRCT domains of Chs5, which together we refer to as the FBE domain (FN3-BRCT of exomer), project from the exomer core complex. The overall architecture of the FBE domain is reminiscent of the appendage domains of other cargo adaptors, although it exhibits a distinct topology. In contrast to appendage domains, which bind accessory factors, we show that the primary role of the FBE domain is to bind Arf1 for recruitment of exomer to membranes.
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Affiliation(s)
- Jon E Paczkowski
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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14
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Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE. SAD phasing using iodide ions in a high-throughput structural genomics environment. ACTA ACUST UNITED AC 2011; 12:83-95. [PMID: 21359836 PMCID: PMC3123459 DOI: 10.1007/s10969-011-9101-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 02/14/2011] [Indexed: 03/16/2023]
Abstract
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.
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