1301
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Tuukkanen AT, Svergun DI. Weak protein-ligand interactions studied by small-angle X-ray scattering. FEBS J 2014; 281:1974-87. [PMID: 24588935 DOI: 10.1111/febs.12772] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/22/2014] [Accepted: 02/28/2014] [Indexed: 12/20/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a powerful technique for studying weak interactions between proteins and their ligands (other proteins, DNA/RNA or small molecules) in solution. SAXS provides knowledge about the equilibrium state, the stoichiometry of binding and association-dissociation processes. The measurements are conducted in a solution environment that allows easy monitoring of modifications in protein-ligand association state upon environmental changes. Model-free parameters such as the molecular mass of a system and the radius of gyration can be obtained directly from the SAXS data and give indications about the association state. SAXS is also widely employed to build models of biological assemblies at a resolution of approximately 10-20 Å. Low-resolution shapes can be generated ab initio, although more detailed and biologically interpretable information can be obtained by hybrid modelling. In the latter approach, composite structures of protein-ligand complexes are constructed using atomic models of individual molecules. These may be predicted homology models or experimental structures from X-ray crystallography or NMR. This review focuses on using SAXS data to model structures of protein-ligand complexes and to study their dynamics. The combination of SAXS with other methods such as size exclusion chromatography and dynamic light scattering is discussed.
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1302
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Pijning T, Vujičić-Žagar A, Kralj S, Dijkhuizen L, Dijkstra BW. Flexibility of truncated and full-length glucansucrase GTF180 enzymes from Lactobacillus reuteri 180. FEBS J 2014; 281:2159-71. [PMID: 24597929 DOI: 10.1111/febs.12769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Glucansucrase enzymes synthesize high-molecular-mass extracellular α-glucan polysaccharides from sucrose. Previously, the crystal structure of truncated glucansucrase glucosyltransferase (GTF)180-ΔN from Lactobacillus reuteri 180 (lacking the N-terminal domain) revealed an elongated overall structure with two remote domains (IV and V) extending away from the core. By contrast, a new crystal form of the α-1,6/α-1,3 specific glucansucrase GTF180-ΔN shows an approximate 120(o) rotation of domain V about a hinge located between domains IV and V, giving a much more compact structure than before. Positional variability of domain V in solution is confirmed by small angle X-ray scattering experiments and rigid-body ensemble calculations. In addition, small angle X-ray scattering measurements of full-length GTF180 also provide the first structural data for a full-length glucansucrase, showing that the enzyme has an almost symmetric boomerang-like molecular shape, with a bend likely located between domains IV and V. The ~ 700-residue N-terminal domain, which is not present in the crystal structures, extends away from domain V and the catalytic core of the enzyme. We conclude that, as a result of the hinge region, in solution, GTF180-ΔN (and likely also the full-length GTF180) shows conformational flexibility; this may be a general feature of GH70 glucansucrases. DATABASE • Structural data for GTF180-ΔN II have been deposited in the Protein Data Bank under accession code 4AYG.
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Affiliation(s)
- Tjaard Pijning
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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1303
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Mansoorabadi SO, Wu M, Tao Z, Gao P, Pingali SV, Guo L, Liu HW. Conformational activation of poly(ADP-ribose) polymerase-1 upon DNA binding revealed by small-angle X-ray scattering. Biochemistry 2014; 53:1779-88. [PMID: 24588584 PMCID: PMC3971956 DOI: 10.1021/bi401439n] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear protein that plays key roles in several fundamental cellular processes. PARP-1 catalyzes the polymerization of nicotinamide adenine dinucleotide on itself and other acceptor proteins, forming long branched poly(ADP-ribose) polymers. The catalytic activity of PARP-1 is stimulated upon binding to damaged DNA, but how this signal is transmitted from the N-terminal DNA binding domain to the C-terminal catalytic domain in the context of the full-length enzyme is unknown. In this paper, small-angle X-ray scattering experiments and molecular dynamics simulations were used to gain insight into the conformational changes that occur during the catalytic activation of PARP-1 by an 8-mer DNA ligand. The data are consistent with a model in which binding of the DNA ligand establishes interdomain interactions between the DNA binding and catalytic domains, which induces an allosteric change in the active site that promotes catalysis. Moreover, the PARP-1-8-mer complex is seen to adopt a conformation that is poised to recruit DNA repair factors to the site of DNA damage. This study provides the first structural information about the DNA-induced conformational activation of full-length PARP-1.
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Affiliation(s)
- Steven O Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry, and Institute of Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States
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1304
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Han S, Shin D, Choi H, Lee S. Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting. Biochem Biophys Res Commun 2014; 446:352-7. [PMID: 24607902 DOI: 10.1016/j.bbrc.2014.02.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 02/25/2014] [Indexed: 12/31/2022]
Abstract
Yeast Doa1/Ufd3 is an adaptor protein for Cdc48 (p97 in mammal), an AAA type ATPase associated with endoplasmic reticulum-associated protein degradation pathway and endosomal sorting into multivesicular bodies. Doa1 functions in the endosomal sorting by its association with Hse1, a component of endosomal sorting complex required for transport (ESCRT) system. The association of Doa1 with Hse1 was previously reported to be mediated between PFU domain of Doa1 and SH3 of Hse1. However, it remains unclear which residues are specifically involved in the interaction. Here we report that Doa1/PFU interacts with Hse1/SH3 with a moderate affinity of 5 μM. Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are found to be critical in the interaction while Phe-434, implicated in ubiquitin binding via a hydrophobic interaction, is not. Small-angle X-ray scattering measurements combined with molecular docking and biochemical analysis yield the solution structure of the Doa1/PFU:Hse1/SH3 complex. Taken together, our results suggest that hydrogen bonding is a major determinant in the interaction of Doa1/PFU with Hse1/SH3.
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Affiliation(s)
- Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Hoon Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, South Korea.
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1305
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Radically Different Thioredoxin Domain Arrangement of ERp46, an Efficient Disulfide Bond Introducer of the Mammalian PDI Family. Structure 2014; 22:431-43. [DOI: 10.1016/j.str.2013.12.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/25/2013] [Accepted: 12/28/2013] [Indexed: 11/20/2022]
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1306
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Gupta K, Contreras LM, Smith D, Qu G, Huang T, Spruce LA, Seeholzer SH, Belfort M, Van Duyne GD. Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering. Nucleic Acids Res 2014; 42:5347-60. [PMID: 24567547 PMCID: PMC4005650 DOI: 10.1093/nar/gku140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The stable ribonucleoprotein (RNP) complex formed between the Lactococcus lactis group II intron and its self-encoded LtrA protein is essential for the intron's genetic mobility. In this study, we report the biochemical, compositional, hydrodynamic and structural properties of active group II intron RNP particles (+A) isolated from its native host using a novel purification scheme. We employed small-angle X-ray scattering to determine the structural properties of these particles as they exist in solution. Using sucrose as a contrasting agent, we derived a two-phase quaternary model of the protein-RNA complex. This approach revealed that the spatial properties of the complex are largely defined by the RNA component, with the protein dimer located near the center of mass. A transfer RNA fusion engineered into domain II of the intron provided a distinct landmark consistent with this interpretation. Comparison of the derived +A RNP shape with that of the previously reported precursor intron (ΔA) particle extends previous findings that the loosely packed precursor RNP undergoes a dramatic conformational change as it compacts into its active form. Our results provide insights into the quaternary arrangement of these RNP complexes in solution, an important step to understanding the transition of the group II intron from the precursor to a species fully active for DNA invasion.
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA, Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA, Wadsworth Center, NYS Department of Health, Albany, NY 12201, USA, Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA, SUNY Downstate Medical Center, University Hospital, Brooklyn, NY 11203, USA and Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
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1307
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Lin CSH, Chao SY, Hammel M, Nix JC, Tseng HL, Tsou CC, Fei CH, Chiou HS, Jeng US, Lin YS, Chuang WJ, Wu JJ, Wang S. Distinct structural features of the peroxide response regulator from group A Streptococcus drive DNA binding. PLoS One 2014; 9:e89027. [PMID: 24586487 PMCID: PMC3931707 DOI: 10.1371/journal.pone.0089027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 01/19/2014] [Indexed: 11/23/2022] Open
Abstract
Group A streptococcus (GAS, Streptococcus pyogenes) is a strict human pathogen that causes severe, invasive diseases. GAS does not produce catalase, but has an ability to resist killing by reactive oxygen species (ROS) through novel mechanisms. The peroxide response regulator (PerR), a member of ferric uptake regulator (Fur) family, plays a key role for GAS to cope with oxidative stress by regulating the expression of multiple genes. Our previous studies have found that expression of an iron-binding protein, Dpr, is under the direct control of PerR. To elucidate the molecular interactions of PerR with its cognate promoter, we have carried out structural studies on PerR and PerR-DNA complex. By combining crystallography and small-angle X-ray scattering (SAXS), we confirmed that the determined PerR crystal structure reflects its conformation in solution. Through mutagenesis and biochemical analysis, we have identified DNA-binding residues suggesting that PerR binds to the dpr promoter at the per box through a winged-helix motif. Furthermore, we have performed SAXS analysis and resolved the molecular architecture of PerR-DNA complex, in which two 30 bp DNA fragments wrap around two PerR homodimers by interacting with the adjacent positively-charged winged-helix motifs. Overall, we provide structural insights into molecular recognition of DNA by PerR and define the hollow structural arrangement of PerR-30bpDNA complex, which displays a unique topology distinct from currently proposed DNA-binding models for Fur family regulators.
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Affiliation(s)
- Chang Sheng-Huei Lin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shi-Yu Chao
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hsiao-Ling Tseng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Cheng Tsou
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Chun-Hsien Fei
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Huo-Sheng Chiou
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Yee-Shin Lin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
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1308
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The structure of the N-terminal domain of the Legionella protein SidC. J Struct Biol 2014; 186:188-94. [PMID: 24556577 DOI: 10.1016/j.jsb.2014.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 01/15/2023]
Abstract
The Gram-negative bacterium Legionella pneumophila is the causative agent of Legionnaires' disease. During infection of eukaryotic cells, the bacterium releases about 300 different bacterial effector molecules that aid in the establishment of the Legionella-containing vacuole (LCV) among which SidC is one of these secreted proteins. However, apart from membrane lipid binding the function of SidC remains elusive. In order to characterize SidC further, we have determined the crystal structure of the N-terminal domain of SidC (amino acids 1-609, referred to as SidC-N) at 2.4Å resolution. SidC-N reveals a novel fold in which 4 potential subdomains (A-D) are arranged in a crescent-like structure. None of these subdomains currently has any known structural homologues, raising the question of how this fold has evolved. These domains are highly interconnected, with a low degree of flexibility towards each other. Due to the extended arrangement of the subdomains, SidC-N may contain multiple binding sites for potential interaction partners.
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1309
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Malecki PH, Vorgias CE, Petoukhov MV, Svergun DI, Rypniewski W. Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution. ACTA ACUST UNITED AC 2014; 70:676-84. [PMID: 24598737 DOI: 10.1107/s1399004713032264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 11/26/2013] [Indexed: 11/11/2022]
Abstract
The four-domain structure of chitinase 60 from Moritella marina (MmChi60) is outstanding in its complexity. Many glycoside hydrolases, such as chitinases and cellulases, have multi-domain structures, but only a few have been solved. The flexibility of the hinge regions between the domains apparently makes these proteins difficult to crystallize. The analysis of an active-site mutant of MmChi60 in an unliganded form and in complex with the substrates NAG4 and NAG5 revealed significant differences in the substrate-binding site compared with the previously determined complexes of most studied chitinases. A SAXS experiment demonstrated that in addition to the elongated state found in the crystal, the protein can adapt other conformations in solution ranging from fully extended to compact.
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Affiliation(s)
- Piotr H Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Constantinos E Vorgias
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Zografou Campus, 157 01 Athens, Greece
| | - Maxim V Petoukhov
- Hamburg Unit, EMBL c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- Hamburg Unit, EMBL c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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1310
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Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae. mBio 2014; 5:e01120-13. [PMID: 24520066 PMCID: PMC3950521 DOI: 10.1128/mbio.01120-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The cytosolic N-acetylmuramoyl-l-alanine amidase LytA protein of Streptococcus pneumoniae, which is released by bacterial lysis, associates with the cell wall via its choline-binding motif. During exponential growth, LytA accesses its peptidoglycan substrate to cause lysis only when nascent peptidoglycan synthesis is stalled by nutrient starvation or β-lactam antibiotics. Here we present three-dimensional structures of LytA and establish the requirements for substrate binding and catalytic activity. The solution structure of the full-length LytA dimer reveals a peculiar fold, with the choline-binding domains forming a rigid V-shaped scaffold and the relatively more flexible amidase domains attached in a trans position. The 1.05-Å crystal structure of the amidase domain reveals a prominent Y-shaped binding crevice composed of three contiguous subregions, with a zinc-containing active site localized at the bottom of the branch point. Site-directed mutagenesis was employed to identify catalytic residues and to investigate the relative impact of potential substrate-interacting residues lining the binding crevice for the lytic activity of LytA. In vitro activity assays using defined muropeptide substrates reveal that LytA utilizes a large substrate recognition interface and requires large muropeptide substrates with several connected saccharides that interact with all subregions of the binding crevice for catalysis. We hypothesize that the substrate requirements restrict LytA to the sites on the cell wall where nascent peptidoglycan synthesis occurs. IMPORTANCE Streptococcus pneumoniae is a human respiratory tract pathogen responsible for millions of deaths annually. Its major pneumococcal autolysin, LytA, is required for autolysis and fratricidal lysis and functions as a virulence factor that facilitates the spread of toxins and factors involved in immune evasion. LytA is also activated by penicillin and vancomycin and is responsible for the lysis induced by these antibiotics. The factors that regulate the lytic activity of LytA are unclear, but it was recently demonstrated that control is at the level of substrate recognition and that LytA required access to the nascent peptidoglycan. The present study was undertaken to structurally and functionally investigate LytA and its substrate-interacting interface and to determine the requirements for substrate recognition and catalysis. Our results reveal that the amidase domain comprises a complex substrate-binding crevice and needs to interact with a large-motif epitope of peptidoglycan for catalysis.
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1311
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Vanwetswinkel S, Volkov AN, Sterckx YGJ, Garcia-Pino A, Buts L, Vranken WF, Bouckaert J, Roy R, Wyns L, van Nuland NAJ. Study of the structural and dynamic effects in the FimH adhesin upon α-d-heptyl mannose binding. J Med Chem 2014; 57:1416-27. [PMID: 24476493 DOI: 10.1021/jm401666c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Uropathogenic Escherichia coli cause urinary tract infections by adhering to mannosylated receptors on the human urothelium via the carbohydrate-binding domain of the FimH adhesin (FimHL). Numerous α-d-mannopyranosides, including α-d-heptyl mannose (HM), inhibit this process by interacting with FimHL. To establish the molecular basis of the high-affinity HM binding, we solved the solution structure of the apo form and the crystal structure of the FimHL-HM complex. NMR relaxation analysis revealed that protein dynamics were not affected by the sugar binding, yet HM addition promoted protein dimerization, which was further confirmed by small-angle X-ray scattering. Finally, to address the role of Y48, part of the "tyrosine gate" believed to govern the affinity and specificity of mannoside binding, we characterized the FimHL Y48A mutant, whose conformational, dynamical, and HM binding properties were found to be very similar to those of the wild-type protein.
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Affiliation(s)
- Sophie Vanwetswinkel
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
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1312
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De D, Jeong MH, Leem YE, Svergun DI, Wemmer DE, Kang JS, Kim KK, Kim SH. Inhibition of master transcription factors in pluripotent cells induces early stage differentiation. Proc Natl Acad Sci U S A 2014; 111:1778-83. [PMID: 24434556 PMCID: PMC3918783 DOI: 10.1073/pnas.1323386111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The potential for pluripotent cells to differentiate into diverse specialized cell types has given much hope to the field of regenerative medicine. Nevertheless, the low efficiency of cell commitment has been a major bottleneck in this field. Here we provide a strategy to enhance the efficiency of early differentiation of pluripotent cells. We hypothesized that the initial phase of differentiation can be enhanced if the transcriptional activity of master regulators of stemness is suppressed, blocking the formation of functional transcriptomes. However, an obstacle is the lack of an efficient strategy to block protein-protein interactions. In this work, we take advantage of the biochemical property of seventeen kilodalton protein (Skp), a bacterial molecular chaperone that binds directly to sex determining region Y-box 2 (Sox2). The small angle X-ray scattering analyses provided a low resolution model of the complex and suggested that the transactivation domain of Sox2 is probably wrapped in a cleft on Skp trimer. Upon the transduction of Skp into pluripotent cells, the transcriptional activity of Sox2 was inhibited and the expression of Sox2 and octamer-binding transcription factor 4 was reduced, which resulted in the expression of early differentiation markers and appearance of early neuronal and cardiac progenitors. These results suggest that the initial stage of differentiation can be accelerated by inhibiting master transcription factors of stemness. This strategy can possibly be applied to increase the efficiency of stem cell differentiation into various cell types and also provides a clue to understanding the mechanism of early differentiation.
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Affiliation(s)
- Debojyoti De
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Myong-Ho Jeong
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Young-Eun Leem
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany; and
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Jong-Sun Kang
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Sung-Hou Kim
- Department of Chemistry, University of California, Berkeley, CA 94720
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1313
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Lansky S, Alalouf O, Solomon HV, Alhassid A, Govada L, Chayen NE, Belrhali H, Shoham Y, Shoham G. A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus. ACTA ACUST UNITED AC 2014; 70:261-78. [PMID: 24531461 DOI: 10.1107/s139900471302840x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/15/2013] [Indexed: 08/26/2023]
Abstract
Geobacillus stearothermophilus T6 is a thermophilic, Gram-positive soil bacterium that possesses an extensive and highly regulated hemicellulolytic system, allowing the bacterium to efficiently degrade high-molecular-weight polysaccharides such as xylan, arabinan and galactan. As part of the xylan-degradation system, the bacterium uses a number of side-chain-cleaving enzymes, one of which is Axe2, a 219-amino-acid intracellular serine acetylxylan esterase that removes acetyl side groups from xylooligosaccharides. Bioinformatic analyses suggest that Axe2 belongs to the lipase GDSL family and represents a new family of carbohydrate esterases. In the current study, the detailed three-dimensional structure of Axe2 is reported, as determined by X-ray crystallography. The structure of the selenomethionine derivative Axe2-Se was initially determined by single-wavelength anomalous diffraction techniques at 1.70 Å resolution and was used for the structure determination of wild-type Axe2 (Axe2-WT) and the catalytic mutant Axe2-S15A at 1.85 and 1.90 Å resolution, respectively. These structures demonstrate that the three-dimensional structure of the Axe2 monomer generally corresponds to the SGNH hydrolase fold, consisting of five central parallel β-sheets flanked by two layers of helices (eight α-helices and five 310-helices). The catalytic triad residues, Ser15, His194 and Asp191, are lined up along a substrate channel situated on the concave surface of the monomer. Interestingly, the Axe2 monomers are assembled as a `doughnut-shaped' homo-octamer, presenting a unique quaternary structure built of two staggered tetrameric rings. The eight active sites are organized in four closely situated pairs, which face the relatively wide internal cavity. The biological relevance of this octameric structure is supported by independent results obtained from gel-filtration, TEM and SAXS experiments. These data and their comparison to the structural data of related hydrolases are used for a more general discussion focusing on the structure-function relationships of enzymes of this category.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Onit Alalouf
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Hodaya Vered Solomon
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Anat Alhassid
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lata Govada
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, England
| | - Naomi E Chayen
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, England
| | - Hassan Belrhali
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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1314
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Ptak CP, Hsieh CL, Weiland GA, Oswald RE. Role of stoichiometry in the dimer-stabilizing effect of AMPA receptor allosteric modulators. ACS Chem Biol 2014; 9:128-33. [PMID: 24152170 PMCID: PMC3947009 DOI: 10.1021/cb4007166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Protein dimerization provides a mechanism for the modulation of cellular signaling events. In α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors, the rapidly desensitizing, activated state has been correlated with a weakly dimeric, glutamate-binding domain conformation. Allosteric modulators can form bridging interactions that stabilize the dimer interface. While most modulators can only bind to one position with a one modulator per dimer ratio, some thiazide-based modulators can bind to the interface in two symmetrical positions with a two modulator per dimer ratio. Based on small-angle X-ray scattering (SAXS) experiments, dimerization curves for the isolated glutamate-binding domain show that a second modulator binding site produces both an increase in positive cooperativity and a decrease in the EC50 for dimerization. Four body binding equilibrium models that incorporate a second dimer-stabilizing ligand were developed to fit the experimental data. The work illustrates why stoichiometry should be an important consideration during the rational design of dimerizing modulators.
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Affiliation(s)
- Christopher P. Ptak
- Department of Molecular
Medicine and ‡Department of Population Medicine
and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Ching-Lin Hsieh
- Department of Molecular
Medicine and ‡Department of Population Medicine
and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Gregory A. Weiland
- Department of Molecular
Medicine and ‡Department of Population Medicine
and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Robert E. Oswald
- Department of Molecular
Medicine and ‡Department of Population Medicine
and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
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1315
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Schulte T, Löfling J, Mikaelsson C, Kikhney A, Hentrich K, Diamante A, Ebel C, Normark S, Svergun D, Henriques-Normark B, Achour A. The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold. Open Biol 2014; 4:130090. [PMID: 24430336 PMCID: PMC3909270 DOI: 10.1098/rsob.130090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187–385) determined to 2.0 Å resolution. BR187–385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.
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Affiliation(s)
- Tim Schulte
- Science for Life Laboratory, Center for Infectious Medicine (CIM), Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet Science Park, Tomtebodavägen 23A Solna, Stockholm 17165, Sweden
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1316
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Wong JEMM, Alsarraf HMAB, Kaspersen JD, Pedersen JS, Stougaard J, Thirup S, Blaise M. Cooperative binding of LysM domains determines the carbohydrate affinity of a bacterial endopeptidase protein. FEBS J 2014; 281:1196-208. [PMID: 24355088 DOI: 10.1111/febs.12698] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 12/12/2013] [Accepted: 12/17/2013] [Indexed: 01/01/2023]
Abstract
Cellulose, chitin and peptidoglycan are major long-chain carbohydrates in living organisms, and constitute a substantial fraction of the biomass. Characterization of the biochemical basis of dynamic changes and degradation of these β,1-4-linked carbohydrates is therefore important for both functional studies of biological polymers and biotechnology. Here, we investigated the functional role of multiplicity of the carbohydrate-binding lysin motif (LysM) domain that is found in proteins involved in bacterial peptidoglycan synthesis and remodelling. The Bacillus subtilis peptidoglycan-hydrolysing NlpC/P60 D,L-endopeptidase, cell wall-lytic enzyme associated with cell separation, possesses four LysM domains. The contribution of each LysM domain was determined by direct carbohydrate-binding studies in aqueous solution with microscale thermophoresis. We found that bacterial LysM domains have affinity for N-acetylglucosamine (GlcNac) polymers in the lower-micromolar range. Moreover, we demonstrated that a single LysM domain is able to bind carbohydrate ligands, and that LysM domains act additively to increase the binding affinity. Our study reveals that affinity for GlcNAc polymers correlates with the chain length of the carbohydrate, and suggests that binding of long carbohydrates is mediated by LysM domain cooperativity. We also show that bacterial LysM domains, in contrast to plant LysM domains, do not discriminate between GlcNAc polymers, and recognize both peptidoglycan fragments and chitin polymers with similar affinity. Finally, an Ala replacement study suggested that the carbohydrate-binding site in LysM-containing proteins is conserved across phyla.
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Affiliation(s)
- Jaslyn E M M Wong
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Denmark
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1317
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Thestrup T, Litzlbauer J, Bartholomäus I, Mues M, Russo L, Dana H, Kovalchuk Y, Liang Y, Kalamakis G, Laukat Y, Becker S, Witte G, Geiger A, Allen T, Rome LC, Chen TW, Kim DS, Garaschuk O, Griesinger C, Griesbeck O. Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes. Nat Methods 2014; 11:175-82. [DOI: 10.1038/nmeth.2773] [Citation(s) in RCA: 253] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/29/2013] [Indexed: 01/20/2023]
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1318
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Linke-Winnebeck C, Paterson NG, Young PG, Middleditch MJ, Greenwood DR, Witte G, Baker EN. Structural model for covalent adhesion of the Streptococcus pyogenes pilus through a thioester bond. J Biol Chem 2014; 289:177-89. [PMID: 24220033 PMCID: PMC3879542 DOI: 10.1074/jbc.m113.523761] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/11/2013] [Indexed: 11/06/2022] Open
Abstract
The human pathogen Streptococcus pyogenes produces pili that are essential for adhesion to host surface receptors. Cpa, the adhesin at the pilus tip, was recently shown to have a thioester-containing domain. The thioester bond is believed to be important in adhesion, implying a mechanism of covalent attachment analogous to that used by human complement factors. Here, we have characterized a second active thioester-containing domain on Cpa, the N-terminal domain of Cpa (CpaN). Expression of CpaN in Escherichia coli gave covalently linked dimers. These were shown by x-ray crystallography and mass spectrometry to comprise two CpaN molecules cross-linked by the polyamine spermidine following reaction with the thioester bonds. This cross-linked CpaN dimer provides a model for the covalent attachment of Cpa to target receptors and thus the streptococcal pilus to host cells. Similar thioester domains were identified in cell wall proteins of other Gram-positive pathogens, suggesting that thioester domains are more widely used and provide a mechanism of adhesion by covalent bonding to target molecules on host cells that mimics that used by the human complement system to eliminate pathogens.
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MESH Headings
- Adhesins, Bacterial/chemistry
- Adhesins, Bacterial/genetics
- Adhesins, Bacterial/metabolism
- Base Sequence
- Complement System Proteins/chemistry
- Complement System Proteins/genetics
- Complement System Proteins/metabolism
- Crystallography, X-Ray
- Escherichia coli
- Fimbriae, Bacterial/chemistry
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/metabolism
- Humans
- Models, Molecular
- Molecular Sequence Data
- Protein Multimerization
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Streptococcus pyogenes/chemistry
- Streptococcus pyogenes/genetics
- Streptococcus pyogenes/pathogenicity
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Affiliation(s)
- Christian Linke-Winnebeck
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 921019, Auckland 1142, New Zealand and
| | - Neil G. Paterson
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 921019, Auckland 1142, New Zealand and
| | - Paul G. Young
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 921019, Auckland 1142, New Zealand and
| | - Martin J. Middleditch
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 921019, Auckland 1142, New Zealand and
| | - David R. Greenwood
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 921019, Auckland 1142, New Zealand and
| | - Gregor Witte
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Edward N. Baker
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 921019, Auckland 1142, New Zealand and
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1319
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Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure 2014; 21:875-81. [PMID: 23747111 DOI: 10.1016/j.str.2013.04.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/24/2013] [Accepted: 04/18/2013] [Indexed: 12/13/2022]
Abstract
This report presents the conclusions of the July 12-13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding.
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Affiliation(s)
- Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.
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1320
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Moglianetti M, Ong QK, Reguera J, Harkness KM, Mameli M, Radulescu A, Kohlbrecher J, Jud C, Svergun DI, Stellacci F. Scanning tunneling microscopy and small angle neutron scattering study of mixed monolayer protected gold nanoparticles in organic solvents. Chem Sci 2014. [DOI: 10.1039/c3sc52595c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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1321
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Casey LW, Mark AE, Kobe B. Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer. Aust J Chem 2014. [DOI: 10.1071/ch14396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The role of small-angle X-ray scattering (SAXS) in structural biology is now well established, and its usefulness in combination with macromolecular crystallography is clear. However, the highly averaged SAXS data present a significant risk of over-interpretation to the unwary practitioner, and it can be challenging to frame SAXS results in a manner that maximises the reliability of the conclusions drawn. In this review, a series of recent examples are used to illustrate both the challenges for interpretation and approaches through which these can be overcome.
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1322
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Small-angle X-ray scattering to obtain models of multivalent lectin-glycan complexes. Methods Mol Biol 2014; 1200:511-26. [PMID: 25117261 DOI: 10.1007/978-1-4939-1292-6_42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recent advances in small-angle X-ray scattering (SAXS) have led to the ability to model the glycans on glycoproteins and to obtain the low-resolution solution structures of complexes of lectins bound to multivalent glycan-presenting scaffolds. This progress in SAXS can respond to the increasing interest in the biological action of glycoproteins and lectins and in the design of multivalent glycan-based antagonists. Carbohydrates make up a significant part of the X-ray scattering content in SAXS and should be included in the model together with the protein, whose structure is most often based on a crystal structure or NMR ensemble, to give a far-improved fit with the experimental data. The modeling of the spatial positioning of glycans on proteins or in the architecture of lectin-glycan complexes delivers low-resolution structural information hitherto unmatched by any other method. SAXS data on the bacterial lectin FimH, strongly bound to heptyl α-D-mannose on a sevenfold derivatized β-cyclodextrin, permitted determination of the stoichiometry of the complex and the geometry of the lectin deposition on the multivalent β-cyclodextrin. The SAXS methods can be applied to larger complexes as the technique imposes no limit on the size of the macromolecular assembly in solution.
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1323
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High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol 2014; 1091:245-58. [PMID: 24203338 DOI: 10.1007/978-1-62703-691-7_18] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The recent innovation of collecting X-ray scattering from solutions containing purified macromolecules in high-throughput has yet to be truly exploited by the biological community. Yet, this capability is becoming critical given that the growth of sequence and genomics data is significantly outpacing structural biology results. Given the huge mismatch in information growth rates between sequence and structural methods, their combined high-throughput and high success rate make high-throughput small angle X-ray scattering (HT-SAXS) analyses increasingly valuable. HT-SAXS connects sequence as well as NMR and crystallographic results to biological outcomes by defining the flexible and dynamic complexes controlling cell biology. Commonly falling under the umbrella of bio-SAXS, HT-SAXS data collection pipelines have or are being developed at most synchrotrons. How investigators practically get their biomolecules of interest into these pipelines, balance sample requirements and manage HT-SAXS data output format varies from facility to facility. While these features are unlikely to be standardized across synchrotron beamlines, a detailed description of HT-SAXS issues for one pipeline provides investigators with a practical guide to the general procedures they will encounter. One of the longest running and generally accessible HT-SAXS endstations is the SIBYLS beamline at the Advanced Light Source in Berkeley CA. Here we describe the current state of the SIBYLS HT-SAXS pipeline, what is necessary for investigators to integrate into it, the output format and a summary of results from 2 years of operation. Assessment of accumulated data informs issues of concentration, background, buffers, sample handling, sample shipping, homogeneity requirements, error sources, aggregation, radiation sensitivity, interpretation, and flags for concern. By quantitatively examining success and failures as a function of sample and data characteristics, we define practical concerns, considerations, and concepts for optimally applying HT-SAXS techniques to biological samples.
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1324
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Castelletto V, Gouveia RJ, Connon CJ, Hamley IW, Seitsonen J, Ruokolainen J, Longo E, Siligardi G. Influence of elastase on alanine-rich peptide hydrogels. Biomater Sci 2014; 2:867-874. [DOI: 10.1039/c4bm00001c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The self-assembly of the alanine-rich amphiphilic peptides Lys(Ala)6Lys (KA6K) and Lys(Ala)6Glu (KA6E) with homotelechelic or heterotelechelic charged termini respectively has been investigated in aqueous solution. The latter forms enzyme-degradable hydrogels.
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Affiliation(s)
- V. Castelletto
- School of Chemistry
- Food Biosciences and Pharmacy
- University of Reading
- Reading RG6 6AD, UK
| | - R. J. Gouveia
- School of Chemistry
- Food Biosciences and Pharmacy
- University of Reading
- Reading RG6 6AD, UK
| | - C. J. Connon
- School of Chemistry
- Food Biosciences and Pharmacy
- University of Reading
- Reading RG6 6AD, UK
| | - I. W. Hamley
- School of Chemistry
- Food Biosciences and Pharmacy
- University of Reading
- Reading RG6 6AD, UK
| | - J. Seitsonen
- Department of Applied Physics
- Aalto University School of Science
- FI-00076 Aalto, Finland
| | - J. Ruokolainen
- Department of Applied Physics
- Aalto University School of Science
- FI-00076 Aalto, Finland
| | - E. Longo
- Diamond Light Source Ltd
- Harwell Science and Innovation campus
- Didcot, UK
| | - G. Siligardi
- Diamond Light Source Ltd
- Harwell Science and Innovation campus
- Didcot, UK
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1325
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Shtykova EV, Baratova LA, Fedorova NV, Radyukhin VA, Ksenofontov AL, Volkov VV, Shishkov AV, Dolgov AA, Shilova LA, Batishchev OV, Jeffries CM, Svergun DI. Structural analysis of influenza A virus matrix protein M1 and its self-assemblies at low pH. PLoS One 2013; 8:e82431. [PMID: 24358182 PMCID: PMC3865061 DOI: 10.1371/journal.pone.0082431] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 10/24/2013] [Indexed: 11/19/2022] Open
Abstract
Influenza A virus matrix protein M1 is one of the most important and abundant proteins in the virus particles broadly involved in essential processes of the viral life cycle. The absence of high-resolution data on the full-length M1 makes the structural investigation of the intact protein particularly important. We employed synchrotron small-angle X-ray scattering (SAXS), analytical ultracentrifugation and atomic force microscopy (AFM) to study the structure of M1 at acidic pH. The low-resolution structural models built from the SAXS data reveal a structurally anisotropic M1 molecule consisting of a compact NM-fragment and an extended and partially flexible C-terminal domain. The M1 monomers co-exist in solution with a small fraction of large clusters that have a layered architecture similar to that observed in the authentic influenza virions. AFM analysis on a lipid-like negatively charged surface reveals that M1 forms ordered stripes correlating well with the clusters observed by SAXS. The free NM-domain is monomeric in acidic solution with the overall structure similar to that observed in previously determined crystal structures. The NM-domain does not spontaneously self assemble supporting the key role of the C-terminus of M1 in the formation of supramolecular structures. Our results suggest that the flexibility of the C-terminus is an essential feature, which may be responsible for the multi-functionality of the entire protein. In particular, this flexibility could allow M1 to structurally organise the viral membrane to maintain the integrity and the shape of the intact influenza virus.
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Affiliation(s)
- Eleonora V. Shtykova
- Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
| | - Lyudmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Victor A. Radyukhin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | | | - Vladimir V. Volkov
- Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
| | | | - Alexey A. Dolgov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Liudmila A. Shilova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Oleg V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
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1326
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Cherry AL, Finta C, Karlström M, Jin Q, Schwend T, Astorga-Wells J, Zubarev RA, Del Campo M, Criswell AR, de Sanctis D, Jovine L, Toftgård R. Structural basis of SUFU-GLI interaction in human Hedgehog signalling regulation. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2563-79. [PMID: 24311597 PMCID: PMC3852661 DOI: 10.1107/s0907444913028473] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/16/2013] [Indexed: 12/13/2022]
Abstract
Hedgehog signalling plays a fundamental role in the control of metazoan development, cell proliferation and differentiation, as highlighted by the fact that its deregulation is associated with the development of many human tumours. SUFU is an essential intracellular negative regulator of mammalian Hedgehog signalling and acts by binding and modulating the activity of GLI transcription factors. Despite its central importance, little is known about SUFU regulation and the nature of SUFU-GLI interaction. Here, the crystal and small-angle X-ray scattering structures of full-length human SUFU and its complex with the key SYGHL motif conserved in all GLIs are reported. It is demonstrated that GLI binding is associated with major conformational changes in SUFU, including an intrinsically disordered loop that is also crucial for pathway activation. These findings reveal the structure of the SUFU-GLI interface and suggest a mechanism for an essential regulatory step in Hedgehog signalling, offering possibilities for the development of novel pathway modulators and therapeutics.
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Affiliation(s)
- Amy L Cherry
- Department of Biosciences and Nutrition and Center for Biosciences, Karolinska Institutet, Novum, Hälsovägen 7, SE-141 83 Huddinge, Sweden
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1327
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Ruszkowski M, Szpotkowski K, Sikorski M, Jaskolski M. The landscape of cytokinin binding by a plant nodulin. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2365-80. [PMID: 24311578 PMCID: PMC3852650 DOI: 10.1107/s0907444913021975] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022]
Abstract
Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant hormones called cytokinins are involved in the nodulation process. In the model legume Medicago truncatula, nodulin 13 (MtN13), which belongs to the pathogenesis-related proteins of class 10 (PR-10), is expressed in the outer cortex of the nodules. In general, PR-10 proteins are small and monomeric and have a characteristic fold with an internal hydrophobic cavity formed between a seven-stranded antiparallel β-sheet and a C-terminal α-helix. Previously, some PR-10 proteins not related to nodulation were found to bind cytokinins such as trans-zeatin. Here, four crystal structures of the MtN13 protein are reported in complexes with several cytokinins, namely trans-zeatin, N6-isopentenyladenine, kinetin and N6-benzyladenine. All four phytohormones are bound in the hydrophobic cavity in the same manner and have excellent definition in the electron-density maps. The binding of the cytokinins appears to be strong and specific and is reinforced by several hydrogen bonds. Although the binding stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule bound in each subunit. The ligand-binding site in each cavity is formed with the participation of a loop element from the other subunit, which plugs the only entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in solution, as confirmed by small-angle X-ray scattering (SAXS).
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Affiliation(s)
- M. Ruszkowski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - K. Szpotkowski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - M. Sikorski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - M. Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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1328
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Brookes E, Pérez J, Cardinali B, Profumo A, Vachette P, Rocco M. Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler ( US-SOMO) enhanced SAS module. J Appl Crystallogr 2013; 46:1823-1833. [PMID: 24282333 PMCID: PMC3831300 DOI: 10.1107/s0021889813027751] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/09/2013] [Indexed: 12/04/2022] Open
Abstract
Fibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of the UltraScan Solution Modeler (US-SOMO; http://somo.uthscsa.edu/), an open-source suite of utilities with advanced graphical user interfaces whose initial goal was the hydrodynamic modeling of biomacromolecules, were implemented and applied to this problem. They include the correction of baseline drift due to the accumulation of material on the SAXS capillary walls, and the Gaussian decomposition of non-baseline-resolved HPLC-SAXS elution peaks. It was thus possible to resolve at least two species co-eluting under the fibrinogen main monomer peak, probably resulting from in-column degradation, and two others under an oligomers peak. The overall and cross-sectional radii of gyration, molecular mass and mass/length ratio of all species were determined using the manual or semi-automated procedures available within the US-SOMO SAS module. Differences between monomeric species and linear and sideways oligomers were thus identified and rationalized. This new US-SOMO version additionally contains several computational and graphical tools, implementing functionalities such as the mapping of residues contributing to particular regions of P(r), and an advanced module for the comparison of primary I(q) versus q data with model curves computed from atomic level structures or bead models. It should be of great help in multi-resolution studies involving hydrodynamics, solution scattering and crystallographic/NMR data.
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Affiliation(s)
- Emre Brookes
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA
| | - Javier Pérez
- Beamline SWING, Synchrotron SOLEIL, L’Orme des Merisiers, BP48, Saint-Aubin, Gif sur Yvette, France
| | - Barbara Cardinali
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aldo Profumo
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Patrice Vachette
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS UMR 8619, UPS 11, Orsay, France
- Université Paris-Sud 11, Bâtiment 430, Orsay, France
| | - Mattia Rocco
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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1329
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Murakami MT, Rodrigues NC, Gava LM, Honorato RV, Canduri F, Barbosa LR, Oliva G, Borges JC. Structural studies of the Trypanosoma cruzi Old Yellow Enzyme: Insights into enzyme dynamics and specificity. Biophys Chem 2013; 184:44-53. [DOI: 10.1016/j.bpc.2013.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 12/15/2022]
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1330
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Szambowska A, Tessmer I, Kursula P, Usskilat C, Prus P, Pospiech H, Grosse F. DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding. Nucleic Acids Res 2013; 42:2308-19. [PMID: 24293646 PMCID: PMC3936751 DOI: 10.1093/nar/gkt1217] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound long (113-mer or 80-mer) single-stranded DNA fragments with a higher affinity than shorter ones (34-mer). hCdc45 displayed a preference for 3′ protruding strands and bound tightly to single-strand/double-strand DNA junctions, such as those presented by Y-shaped DNA, bubbles and displacement loops, all of which appear transiently during the initiation of DNA replication. Collectively, our findings suggest that hCdc45 not only binds to but also slides on DNA with a 3′–5′ polarity and, thereby acts as a molecular ‘wedge’ to initiate DNA strand displacement.
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Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute for Age Research -Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany, Laboratory of Molecular Biology IBB PAS, Affiliated with University of Gdansk, Wita Stwosza 59 Gdansk, Poland, Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, Josef Schneider Strasse 2, 7080 Wurzburg, Germany, Department of Biochemistry, Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland, Department of Chemistry, University of Hamburg/DESY, Notkestrasse 85, 22607 Hamburg, Germany, Biocenter Oulu, P.O. Box 3000, University of Oulu, Oulu 90014, Finland and Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
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1331
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Alaidarous M, Ve T, Casey LW, Valkov E, Ericsson DJ, Ullah MO, Schembri MA, Mansell A, Sweet MJ, Kobe B. Mechanism of bacterial interference with TLR4 signaling by Brucella Toll/interleukin-1 receptor domain-containing protein TcpB. J Biol Chem 2013; 289:654-68. [PMID: 24265315 DOI: 10.1074/jbc.m113.523274] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Upon activation of Toll-like receptors (TLRs), cytoplasmic Toll/interleukin-1 receptor (TIR) domains of the receptors undergo homo- or heterodimerization. This in turn leads to the recruitment of adaptor proteins, activation of transcription factors, and the secretion of pro-inflammatory cytokines. Recent studies have described the TIR domain-containing protein from Brucella melitensis, TcpB (BtpA/Btp1), to be involved in virulence and suppression of host innate immune responses. TcpB interferes with TLR4 and TLR2 signaling pathways by a mechanism that remains controversial. In this study, we show using co-immunoprecipitation analyses that TcpB interacts with MAL, MyD88, and TLR4 but interferes only with the MAL-TLR4 interaction. We present the crystal structure of the TcpB TIR domain, which reveals significant structural differences in the loop regions compared with other TIR domain structures. We demonstrate that TcpB forms a dimer in solution, and the crystal structure reveals the dimerization interface, which we validate by mutagenesis and biophysical studies. Our study advances the understanding of the molecular mechanisms of host immunosuppression by bacterial pathogens.
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1332
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Amenitsch H, Benetti F, Ramos A, Legname G, Requena JR. SAXS structural study of PrP(Sc) reveals ~11 nm diameter of basic double intertwined fibers. Prion 2013; 7:496-500. [PMID: 24247356 DOI: 10.4161/pri.27190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A sample of purified Syrian hamster PrP27-30 prion fibers was analyzed by synchrotron small-angle X-ray scattering (SAXS). The SAXS pattern obtained was fitted to a model based on infinitely long cylinders with a log-normal intensity distribution, a hard-sphere structure factor and a general Porod term for larger aggregates. The diameter calculated for the cylinders determined from the fit was 11.0 ± 0.2 nm. This measurement offers an estimation of the diameter of PrP(Sc) fibers in suspension, i.e., free of errors derived from estimations based on 2D projections in transmission electron microscopy images, subjected to further possible distortions from the negative stain. This diameter, which corresponds to a maximum diameter of approximately 5.5 nm for each of the two intertwined protofilaments making up the fibers, rules out the possibility that PrP(Sc) conforms to a stack of in-register, single-rung flat PrP(Sc) monomers; rather, PrP(Sc) subunits must necessarily coil, most likely several times, into themselves.
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Affiliation(s)
- Heinz Amenitsch
- Institute of Inorganic Chemistry; Graz University of Technology; Graz, Austria
| | - Federico Benetti
- Laboratory of Prion Biology; Department of Neuroscience; Scuola Internazionale Superiore di Studi Avanzati (SISSA); Trieste, Italy
| | - Adriana Ramos
- CIMUS Biomedical Research Institute & Department of Medicine; University of Santiago de Compostela-IDIS; Santiago de Compostela, Spain
| | - Giuseppe Legname
- Laboratory of Prion Biology; Department of Neuroscience; Scuola Internazionale Superiore di Studi Avanzati (SISSA); Trieste, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medicine; University of Santiago de Compostela-IDIS; Santiago de Compostela, Spain
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1333
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Andresen K, Jimenez-Useche I, Howell SC, Yuan C, Qiu X. Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal. PLoS One 2013; 8:e78587. [PMID: 24265699 PMCID: PMC3827064 DOI: 10.1371/journal.pone.0078587] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.
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Affiliation(s)
- Kurt Andresen
- Department of Physics, Gettysburg College, Gettysburg, Pennsylvania, United States of America
- * E-mail:
| | - Isabel Jimenez-Useche
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Steven C. Howell
- Department of Physics, George Washington University, Washington, District of Columbia, United States of America
| | - Chongli Yuan
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Xiangyun Qiu
- Department of Physics, George Washington University, Washington, District of Columbia, United States of America
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1334
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Wang W, Hou H, Du Q, Zhang W, Liu G, Shtykova EV, Xu J, Liu P, Dong Y. Solution small angle X-ray scattering (SAXS) studies of RecQ from Deinococcus radiodurans and its complexes with junction DNA substrates. J Biol Chem 2013; 288:32414-32423. [PMID: 24068706 PMCID: PMC3820876 DOI: 10.1074/jbc.m113.502112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/14/2013] [Indexed: 11/06/2022] Open
Abstract
RecQ helicases, essential enzymes for maintaining genome integrity, possess the capability to participate in a wide variety of DNA metabolisms. They can initiate the homologous recombination repair pathway by unwinding damaged dsDNA and suppress hyper-recombination by promoting Holliday junction (HJ) migration. To learn how DrRecQ participates in the homologous recombination repair pathway, solution structures of Deinococcus radiodurans RecQ (DrRecQ) and its complexes with DNA substrates were investigated by small angle x-ray scattering. We found that the catalytic core and the most N-terminal HRDC (helicase and RNase D C-terminal) domain (HRDC1) undergo a conformational change to a compact state upon binding to a junction DNA. Furthermore, models of DrRecQ in complexes with two kinds of junction DNA (fork junction and HJ) were built based on the small angle x-ray scattering data, and together with the EMSA results, possible binding sites were proposed. It is demonstrated that two DrRecQ molecules bind to the opposite arms of HJ. This architecture is similar to the RuvAB complex and is hypothesized to be highly conserved in the other HJ migration proteins. This work provides us new clues to understand the roles DrRecQ plays in the RecFOR pathway.
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Affiliation(s)
- Wenjia Wang
- From the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Haifeng Hou
- From the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Du
- the Department of Plant Sciences, College of Agriculture and Nature Resources, University of Connecticut, Storrs, Connecticut 06269
| | - Wen Zhang
- the Department of Physiology, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Guangfeng Liu
- From the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Eleonora V Shtykova
- the Institute of Crystallography, Russian Academy of Sciences, Moscow 117333, Russia
| | - Jianhua Xu
- From the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Liu
- From the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China,.
| | - Yuhui Dong
- From the Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China,.
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1335
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The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc. Biochim Biophys Acta Gen Subj 2013; 1840:535-44. [PMID: 24128931 DOI: 10.1016/j.bbagen.2013.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/17/2013] [Accepted: 10/07/2013] [Indexed: 11/22/2022]
Abstract
BACKGROUND In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the metal-binding protein ZinT was suggested to operate as an accessory component of ZnuABC in periplasmic zinc recruitment. Since ZinT is known to form a ZinT-ZnuA complex in the presence of Zn(II) it was proposed to transfer Zn(II) to ZnuA. The present work was undertaken to test this claim. METHODS ZinT and its structural relationship with ZnuA have been characterized by multiple biophysical techniques (X-ray crystallography, SAXS, analytical ultracentrifugation, fluorescence spectroscopy). RESULTS The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with Zn(II) yield a KD value of 22±2nM for ZinT, while those with ZnuA point to one high affinity (KD<20nM) and one low affinity Zn(II) binding site (KD in the micromolar range). Sedimentation velocity experiments established that Zn(II)-bound ZinT interacts with ZnuA, whereas apo-ZinT does not. The model of the ZinT-ZnuA complex derived from small angle X-ray scattering experiments points to a disposition that favors metal transfer as the metal binding cavities of the two proteins face each other. CONCLUSIONS ZinT acts as a Zn(II)-buffering protein that delivers Zn(II) to ZnuA. GENERAL SIGNIFICANCE Knowledge of the ZinT-ZnuA relationship is crucial for understanding bacterial Zn(II) uptake.
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1336
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Petoukhov MV, Billas IML, Takacs M, Graewert MA, Moras D, Svergun DI. Reconstruction of quaternary structure from X-ray scattering by equilibrium mixtures of biological macromolecules. Biochemistry 2013; 52:6844-55. [PMID: 24000896 DOI: 10.1021/bi400731u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recent renaissance in small-angle X-ray scattering (SAXS) made this technique a major tool for the low-resolution structural characterization of biological macromolecules in solution. The major limitation of existing methods for reconstructing 3D models from SAXS is imposed by the requirement of solute monodispersity. We present a novel approach that couples low-resolution 3D SAXS reconstruction with composition analysis of mixtures. The approach is applicable to polydisperse and difficult to purify systems, including weakly associated oligomers and transient complexes. Ab initio shape analysis is possible for symmetric homo-oligomers, whereas rigid body modeling is applied also to dissociating complexes when atomic structures of the individual subunits are available. In both approaches, the sample is considered as an equilibrium mixture of intact complexes/oligomers with their dissociation products or free subunits. The algorithms provide the 3D low-resolution model (for ab initio modeling, also the shape of the monomer) and the volume fractions of the bound and free state(s). The simultaneous fitting of multiple scattering data sets collected under different conditions allows one to restrain the modeling further. The possibilities of the approach are illustrated in simulated and experimental SAXS data from protein oligomers and multisubunit complexes including nucleoproteins. Using this approach, new structural insights are provided in the association behavior and conformations of estrogen-related receptors ERRα and ERRγ. The possibility of 3D modeling from the scattering by mixtures significantly widens the range of applicability of SAXS and opens novel avenues in the analysis of oligomeric mixtures and assembly/dissociation processes.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation , Notkestrasse 85, Hamburg 22607, Germany
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1337
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Møller M, Nielsen SS, Ramachandran S, Li Y, Tria G, Streicher W, Petoukhov MV, Cerione RA, Gillilan RE, Vestergaard B. Small angle X-ray scattering studies of mitochondrial glutaminase C reveal extended flexible regions, and link oligomeric state with enzyme activity. PLoS One 2013; 8:e74783. [PMID: 24098668 PMCID: PMC3787022 DOI: 10.1371/journal.pone.0074783] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 08/07/2013] [Indexed: 11/18/2022] Open
Abstract
Glutaminase C is a key metabolic enzyme, which is unregulated in many cancer systems and believed to play a central role in the Warburg effect, whereby cancer cells undergo changes to an altered metabolic profile. A long-standing hypothesis links enzymatic activity to the protein oligomeric state, hence the study of the solution behavior in general and the oligomer state in particular of glutaminase C is important for the understanding of the mechanism of protein activation and inhibition. In this report, this is extensively investigated in correlation to enzyme concentration or phosphate level, using a high-throughput microfluidic-mixing chip for the SAXS data collection, and we confirm that the oligomeric state correlates with activity. The in-depth solution behavior analysis further reveals the structural behavior of flexible regions of the protein in the dimeric, tetrameric and octameric state and investigates the C-terminal influence on the enzyme solution behavior. Our data enable SAXS-based rigid body modeling of the full-length tetramer states, thereby presenting the first ever experimentally derived structural model of mitochondrial glutaminase C including the N- and C-termini of the enzyme.
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Affiliation(s)
- Magda Møller
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Søren S. Nielsen
- Department of Structural Biophysics, University of Copenhagen, Copenhagen, Denmark
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, New York, United States of America
| | - Sekar Ramachandran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Yuxing Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Hamburg, Germany
- Center for Bioinformatics, University of Hamburg, Hamburg, Germany
| | - Werner Streicher
- Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Maxim V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Hamburg, Germany
| | - Richard A. Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Medicine, Cornell University, Ithaca, New York, United States of America
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, New York, United States of America
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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1338
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Pauw BR. Everything SAXS: small-angle scattering pattern collection and correction. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:383201. [PMID: 23988669 DOI: 10.1088/0953-8984/25/38/383201] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
For obtaining reliable nanostructural details of large amounts of sample--and if it is applicable--small-angle scattering (SAS) is a prime technique to use. It promises to obtain bulk-scale, statistically sound information on the morphological details of the nanostructure, and has thus led to many a researcher investing their time in it over the last eight decades of development. Due to pressure from scientists requesting more details on increasingly complex nanostructures, as well as the ever improving instrumentation leaving less margin for ambiguity, small-angle scattering methodologies have been evolving at a high pace over the past few decades. As the quality of any results can only be as good as the data that go into these methodologies, the improvements in data collection and all imaginable data correction steps are reviewed here. This work is intended to provide a comprehensive overview of all data corrections, to aid the small-angle scatterer to decide which are relevant for their measurement and how these corrections are performed. Clear mathematical descriptions of the corrections are provided where feasible. Furthermore, as no quality data exist without a decent estimate of their precision, the error estimation and propagation through all these steps are provided alongside the corrections. With these data corrections, the collected small-angle scattering pattern can be made of the highest standard, allowing for authoritative nanostructural characterization through its analysis. A brief background of small-angle scattering, the instrumentation developments over the years, and pitfalls that may be encountered upon data interpretation are provided as well.
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Affiliation(s)
- Brian Richard Pauw
- International Center for Young Scientists, National Institute for Materials Science, 1-2-1 Sengen, 305-0047, Tsukuba, Japan.
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1339
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Sander B, Tria G, Shkumatov AV, Kim EY, Grossmann JG, Tessmer I, Svergun DI, Schindelin H. Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2050-60. [DOI: 10.1107/s0907444913018714] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/05/2013] [Indexed: 11/10/2022]
Abstract
Gephyrin is a trimeric protein involved in the final steps of molybdenum-cofactor (Moco) biosynthesis and in the clustering of inhibitory glycine and GABAAreceptors at postsynaptic specializations. Each protomer consists of stably folded domains (referred to as the G and E domains) located at either terminus and connected by a proteolytically sensitive linker of ∼150 residues. Both terminal domains can oligomerize in their isolated forms; however, in the context of the full-length protein only the G-domain trimer is permanently present, whereas E-domain dimerization is prevented. Atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS) reveal a high degree of flexibility in the structure of gephyrin. The results imply an equilibrium between compact and extended conformational states in solution, with a preference for compact states. CD spectroscopy suggests that a partial compaction is achieved by interactions of the linker with the G and E domains. Taken together, the data provide a rationale for the role of the linker in the overall structure and the conformational dynamics of gephyrin.
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1340
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Cerofolini L, Fields GB, Fragai M, Geraldes CFGC, Luchinat C, Parigi G, Ravera E, Svergun DI, Teixeira JMC. Examination of matrix metalloproteinase-1 in solution: a preference for the pre-collagenolysis state. J Biol Chem 2013; 288:30659-30671. [PMID: 24025334 DOI: 10.1074/jbc.m113.477240] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to critically rely on flexibility between the catalytic (CAT) and hemopexin-like (HPX) domains. A rigorous assessment of the most readily accessed conformations in solution is required to explain the onset of substrate recognition and collagenolysis. The present study utilized paramagnetic NMR spectroscopy and small angle x-ray scattering (SAXS) to calculate the maximum occurrence (MO) of MMP-1 conformations. The MMP-1 conformations with large MO values (up to 47%) are restricted into a relatively small conformational region. All conformations with high MO values differ largely from the closed MMP-1 structures obtained by x-ray crystallography. The MO of the latter is ~20%, which represents the upper limit for the presence of this conformation in the ensemble sampled by the protein in solution. In all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. Thus, overall analysis of the highest MO conformations indicated that MMP-1 in solution was poised to interact with collagen and then could readily proceed along the steps of collagenolysis.
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Affiliation(s)
| | - Gregg B Fields
- the Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987,.
| | - Marco Fragai
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Carlos F G C Geraldes
- the Center for Neuroscience and Cell Biology and; the Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, P.O. Box 3046, 3001-401 Coimbra, Portugal, and
| | - Claudio Luchinat
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy,.
| | - Giacomo Parigi
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Dmitri I Svergun
- the EMBL, c/o DESY, Notkestrasse 85, Geb. 25 A, 22603 Hamburg, Germany
| | - João M C Teixeira
- From the CERM and; the Center for Neuroscience and Cell Biology and; the Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, P.O. Box 3046, 3001-401 Coimbra, Portugal, and
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1341
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Koch C, Tria G, Fielding AJ, Brodhun F, Valerius O, Feussner K, Braus GH, Svergun DI, Bennati M, Feussner I. A structural model of PpoA derived from SAXS-analysis—Implications for substrate conversion. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1449-57. [DOI: 10.1016/j.bbalip.2013.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/29/2013] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
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1342
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Jain R, Petri M, Kirschbaum S, Feindt H, Steltenkamp S, Sonnenkalb S, Becker S, Griesinger C, Menzel A, Burg TP, Techert S. X-ray scattering experiments with high-flux X-ray source coupled rapid mixing microchannel device and their potential for high-flux neutron scattering investigations. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:109. [PMID: 24092048 DOI: 10.1140/epje/i2013-13109-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 12/13/2012] [Accepted: 07/26/2013] [Indexed: 06/02/2023]
Abstract
Small-angle X-ray scattering provides global, shape-sensitive structural information about macromolecules in solution. Its extension to time dimension in the form of time-resolved SAXS investigations and combination with other time-resolved biophysical methods contributes immensely to the study of protein dynamics. TR-SAXS can also provide unique information about the global structures of transient intermediates during protein dynamics. An experimental set-up with low protein consumption is essential for an extensive use of TR-SAXS experiments on protein dynamics. In this direction, a newly developed 20-microchannel microfluidic continuous-flow mixer was combined with SAXS. With this set-up, we demonstrate ubiquitin unfolding dynamics after rapid mixing with the chaotropic agent Guanidinium-HCl within milliseconds using only ∼ 40 nanoliters of the protein sample per scattering image. It is suggested that, in the future, this new TR-SAXS platform will help to increase the use of time-resolved small-angle X-ray scattering, wide-angle X-ray scattering and neutron scattering experiments for studying protein dynamics in the early millisecond regime. The potential research field for this set-up includes protein folding, protein misfolding, aggregation in amyloidogenic diseases, function of intrinsically disordered proteins and various protein-ligand interactions.
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Affiliation(s)
- R Jain
- Structural Dynamics of (Bio)chemical Systems, MPI-BPC, Am Fassberg 11, 37077, Goettingen, Germany
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1343
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Pham CLL, Kirby N, Wood K, Ryan T, Roberts B, Sokolova A, Barnham KJ, Masters CL, Knott RB, Cappai R, Curtain CC, Rekas A. Guanidine hydrochloride denaturation of dopamine-induced α-synuclein oligomers: A small-angle X-ray scattering study. Proteins 2013; 82:10-21. [DOI: 10.1002/prot.24332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 05/10/2013] [Accepted: 05/19/2013] [Indexed: 01/18/2023]
Affiliation(s)
- Chi L. L. Pham
- Department of Pathology and Bio21 Molecular Science and Technology Institute; The University of Melbourne; Victoria 3010 Australia
| | - Nigel Kirby
- SAXS/WAXS Beamline, The Australian Synchrotron; Clayton Victoria 3168 Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation (ANSTO); Kirrawee New South Wales 2232 Australia
| | - Timothy Ryan
- The University of Melbourne, Florey Institute of Neuroscience and Mental Health; Victoria 3010 Australia
| | - Blaine Roberts
- The University of Melbourne, Florey Institute of Neuroscience and Mental Health; Victoria 3010 Australia
| | - Anna Sokolova
- Australian Nuclear Science and Technology Organisation (ANSTO); Kirrawee New South Wales 2232 Australia
| | - Kevin J. Barnham
- The University of Melbourne, Florey Institute of Neuroscience and Mental Health; Victoria 3010 Australia
| | - Colin L. Masters
- The University of Melbourne, Florey Institute of Neuroscience and Mental Health; Victoria 3010 Australia
| | - Robert B. Knott
- Australian Nuclear Science and Technology Organisation (ANSTO); Kirrawee New South Wales 2232 Australia
| | - Roberto Cappai
- Department of Pathology and Bio21 Molecular Science and Technology Institute; The University of Melbourne; Victoria 3010 Australia
| | - Cyril C. Curtain
- Department of Pathology and Bio21 Molecular Science and Technology Institute; The University of Melbourne; Victoria 3010 Australia
- The University of Melbourne, Florey Institute of Neuroscience and Mental Health; Victoria 3010 Australia
| | - Agata Rekas
- Australian Nuclear Science and Technology Organisation (ANSTO); Kirrawee New South Wales 2232 Australia
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1344
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Yan R, Konarev PV, Iannuzzi C, Adinolfi S, Roche B, Kelly G, Simon L, Martin SR, Py B, Barras F, Svergun DI, Pastore A. Ferredoxin competes with bacterial frataxin in binding to the desulfurase IscS. J Biol Chem 2013; 288:24777-87. [PMID: 23839945 PMCID: PMC3750173 DOI: 10.1074/jbc.m113.480327] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/03/2013] [Indexed: 11/06/2022] Open
Abstract
The bacterial iron-sulfur cluster (isc) operon is an essential machine that is highly conserved from bacteria to primates and responsible for iron-sulfur cluster biogenesis. Among its components are the genes for the desulfurase IscS that provides sulfur for cluster formation, and a specialized ferredoxin (Fdx) whose role is still unknown. Preliminary evidence suggests that IscS and Fdx interact but nothing is known about the binding site and the role of the interaction. Here, we have characterized the interaction using a combination of biophysical tools and mutagenesis. By modeling the Fdx·IscS complex based on experimental restraints we show that Fdx competes for the binding site of CyaY, the bacterial ortholog of frataxin and sits in a cavity close to the enzyme active site. By in vivo mutagenesis in bacteria we prove the importance of the surface of interaction for cluster formation. Our data provide the first structural insights into the role of Fdx in cluster assembly.
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Affiliation(s)
- Robert Yan
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Petr V. Konarev
- the European Molecular Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg D-22603, Germany, and
| | - Clara Iannuzzi
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Salvatore Adinolfi
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | | | - Geoff Kelly
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Léa Simon
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Stephen R. Martin
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
| | - Béatrice Py
- the Aix-Marseille Université and
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, UMR 7283, CNRS, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Frédéric Barras
- the Aix-Marseille Université and
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, UMR 7283, CNRS, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Dmitri I. Svergun
- the European Molecular Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg D-22603, Germany, and
| | - Annalisa Pastore
- From the MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom
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1345
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Structure-informed design of an enzymatically inactive vaccine component for group A Streptococcus. mBio 2013; 4:mBio.00509-13. [PMID: 23919999 PMCID: PMC3735194 DOI: 10.1128/mbio.00509-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Streptococcus pyogenes (group A Streptococcus [GAS]) causes ~700 million human infections/year, resulting in >500,000 deaths. There is no commercial GAS vaccine available. The GAS surface protein arginine deiminase (ADI) protects mice against a lethal challenge. ADI is an enzyme that converts arginine to citrulline and ammonia. Administration of a GAS vaccine preparation containing wild-type ADI, a protein with inherent enzymatic activity, may present a safety risk. In an approach intended to maximize the vaccine safety of GAS ADI, X-ray crystallography and structural immunogenic epitope mapping were used to inform vaccine design. This study aimed to knock out ADI enzyme activity without disrupting the three-dimensional structure or the recognition of immunogenic epitopes. We determined the crystal structure of ADI at 2.5 Å resolution and used it to select a number of amino acid residues for mutagenesis to alanine (D166, E220, H275, D277, and C401). Each mutant protein displayed abrogated activity, and three of the mutant proteins (those with the D166A, H275A, and D277A mutations) possessed a secondary structure and oligomerization state equivalent to those of the wild type, produced high-titer antisera, and avoided disruption of B-cell epitopes of ADI. In addition, antisera raised against the D166A and D277A mutant proteins bound to the GAS cell surface. The inactivated D166A and D277A mutant ADIs are ideal for inclusion in a GAS vaccine preparation. There is no human ortholog of ADI, and we confirm that despite limited structural similarity in the active-site region to human peptidyl ADI 4 (PAD4), ADI does not functionally mimic PAD4 and antiserum raised against GAS ADI does not recognize human PAD4. We present an example of structural biology informing human vaccine design. We previously showed that the administration of the enzyme arginine deiminase (ADI) to mice protected the mice against infection with multiple GAS serotypes. In this study, we determined the structure of GAS ADI and used this information to improve the vaccine safety of GAS ADI. Catalytically inactive mutant forms of ADI retained structure, recognition by antisera, and immunogenic epitopes, rendering them ideal for inclusion in GAS vaccine preparations. This example of structural biology informing vaccine design may underpin the formulation of a safe and efficacious GAS vaccine.
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1346
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Dian C, Bernaudat F, Langer K, Oliva MF, Fornerod M, Schoehn G, Müller CW, Petosa C. Structure of a truncation mutant of the nuclear export factor CRM1 provides insights into the auto-inhibitory role of its C-terminal helix. Structure 2013; 21:1338-49. [PMID: 23850454 DOI: 10.1016/j.str.2013.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 11/23/2022]
Abstract
Chromosome region maintenance 1/exportin1/Xpo1 (CRM1) associates with the GTPase Ran to mediate the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 consists of helical hairpin HEAT repeats and a C-terminal helical extension (C-extension) that inhibits the binding of NES-bearing cargos. We report the crystal structure and small-angle X-ray scattering analysis of a human CRM1 mutant with enhanced NES-binding activity due to deletion of the C-extension. We show that loss of the C-extension leads to a repositioning of CRM1's C-terminal repeats and to a more extended overall conformation. Normal mode analysis predicts reduced rigidity for the deletion mutant, consistent with an observed decrease in thermal stability. Point mutations that destabilize the C-extension shift CRM1 to the more extended conformation, reduce thermal stability, and enhance NES-binding activity. These findings suggest that an important mechanism by which the C-extension regulates CRM1's cargo-binding affinity is by modulating the conformation and flexibility of its HEAT repeats.
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Affiliation(s)
- Cyril Dian
- Université de Grenoble Alpes, Institut de Biologie Structurale, 38027 Grenoble, France
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1347
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Modern X-ray scattering studies of complex biological systems. Curr Opin Biotechnol 2013; 24:716-23. [DOI: 10.1016/j.copbio.2013.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/16/2022]
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1348
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Taltynov O, Demeulemeester J, Christ F, De Houwer S, Tsirkone VG, Gerard M, Weeks SD, Strelkov SV, Debyser Z. Interaction of transportin-SR2 with Ras-related nuclear protein (Ran) GTPase. J Biol Chem 2013; 288:25603-25613. [PMID: 23878195 DOI: 10.1074/jbc.m113.484345] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) and other lentiviruses are capable of infecting non-dividing cells and, therefore, need to be imported into the nucleus before integration into the host cell chromatin. Transportin-SR2 (TRN-SR2, Transportin-3, TNPO3) is a cellular karyopherin implicated in nuclear import of HIV-1. A model in which TRN-SR2 imports the viral preintegration complex into the nucleus is supported by direct interaction between TRN-SR2 and HIV-1 integrase (IN). Residues in the C-terminal domain of HIV-1 IN that mediate binding to TRN-SR2 were recently delineated. As for most nuclear import cargoes, the driving force behind HIV-1 preintegration complex import is likely a gradient of the GDP- and GTP-bound forms of Ran, a small GTPase. In this study we offer biochemical and structural characterization of the interaction between TRN-SR2 and Ran. By size exclusion chromatography we demonstrate stable complex formation of TRN-SR2 and RanGTP in solution. Consistent with the behavior of normal nuclear import cargoes, HIV-1 IN is released from the complex with TRN-SR2 by RanGTP. Although in concentrated solutions TRN-SR2 by itself was predominantly present as a dimer, the TRN-SR2-RanGTP complex was significantly more compact. Further analysis supported a model wherein one monomer of TRN-SR2 is bound to one monomer of RanGTP. Finally, we present a homology model of the TRN-SR2-RanGTP complex that is in excellent agreement with the experimental small angle x-ray scattering data.
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Affiliation(s)
- Oliver Taltynov
- From the Laboratory for Molecular Virology and Gene Therapy and
| | | | - Frauke Christ
- From the Laboratory for Molecular Virology and Gene Therapy and
| | | | - Vicky G Tsirkone
- Laboratory for Biocrystallography, KU Leuven, B-3000 Leuven, Belgium
| | - Melanie Gerard
- From the Laboratory for Molecular Virology and Gene Therapy and
| | - Stephen D Weeks
- Laboratory for Biocrystallography, KU Leuven, B-3000 Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, KU Leuven, B-3000 Leuven, Belgium
| | - Zeger Debyser
- From the Laboratory for Molecular Virology and Gene Therapy and.
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1349
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Keown JR, Griffin MDW, Mertens HDT, Pearce FG. Small oligomers of ribulose-bisphosphate carboxylase/oxygenase (Rubisco) activase are required for biological activity. J Biol Chem 2013; 288:20607-15. [PMID: 23720775 PMCID: PMC3711324 DOI: 10.1074/jbc.m113.466383] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/27/2013] [Indexed: 12/24/2022] Open
Abstract
Ribulose-bisphosphate carboxylase/oxygenase (Rubisco) activase uses the energy from ATP hydrolysis to remove tight binding inhibitors from Rubisco, thus playing a key role in regulating photosynthesis in plants. Although several structures have recently added much needed structural information for different Rubisco activase enzymes, the arrangement of these subunits in solution remains unclear. In this study, we use a variety of techniques to show that Rubisco activase forms a wide range of structures in solution, ranging from monomers to much higher order species, and that the distribution of these species is highly dependent on protein concentration. The data support a model in which Rubisco activase forms an open spiraling structure rather than a closed hexameric structure. At protein concentrations of 1 μM, corresponding to the maximal activity of the enzyme, Rubisco activase has an oligomeric state of 2-4 subunits. We propose a model in which Rubisco activase requires at least 1 neighboring subunit for hydrolysis of ATP.
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Affiliation(s)
- Jeremy R. Keown
- From the Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Michael D. W. Griffin
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville Victoria 3010, Australia, and
| | - Haydyn D. T. Mertens
- the Australian Synchrotron, 800 Blackburn Road, Clayton Victoria 3168, Australia
| | - F. Grant Pearce
- From the Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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1350
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Graewert MA, Svergun DI. Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). Curr Opin Struct Biol 2013; 23:748-54. [PMID: 23835228 DOI: 10.1016/j.sbi.2013.06.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
The advances made in small and wide angle X-ray scattering over the past decades have had a large impact on structural biology. Many new insights into challenging biological probes including large and transient complexes, flexible macromolecules as well as other exciting objects of various sizes were gained with this low resolution technique. Here, we review the recent developments in the experimental setups and in software for data collection and analysis, specifically for hybrid approaches. These progresses have allowed scientists to address a number of intriguing questions which could not be answered with other structural methods alone.
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Affiliation(s)
- Melissa A Graewert
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestraße 85, Hamburg 22603, Germany
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