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Structural basis for the stabilization of the complement alternative pathway C3 convertase by properdin. Proc Natl Acad Sci U S A 2013; 110:13504-9. [PMID: 23901101 DOI: 10.1073/pnas.1309618110] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Complement is an essential component of innate immunity. Its activation results in the assembly of unstable protease complexes, denominated C3/C5 convertases, leading to inflammation and lysis. Regulatory proteins inactivate C3/C5 convertases on host surfaces to avoid collateral tissue damage. On pathogen surfaces, properdin stabilizes C3/C5 convertases to efficiently fight infection. How properdin performs this function is, however, unclear. Using electron microscopy we show that the N- and C-terminal ends of adjacent monomers in properdin oligomers conform a curly vertex that holds together the AP convertase, interacting with both the C345C and vWA domains of C3b and Bb, respectively. Properdin also promotes a large displacement of the TED (thioester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domains of C3b, which likely impairs C3-convertase inactivation by regulatory proteins. The combined effect of molecular cross-linking and structural reorganization increases stability of the C3 convertase and facilitates recruitment of fluid-phase C3 convertase to the cell surfaces. Our model explains how properdin mediates the assembly of stabilized C3/C5-convertase clusters, which helps to localize complement amplification to pathogen surfaces.
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102
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Protein secondary structure determination by constrained single-particle cryo-electron tomography. Structure 2013; 20:2003-13. [PMID: 23217682 DOI: 10.1016/j.str.2012.10.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 01/24/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series.
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103
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Cho HJ, Hyun JK, Kim JG, Jeong HS, Park HN, You DJ, Jung HS. Measurement of ice thickness on vitreous ice embedded cryo-EM grids: investigation of optimizing condition for visualizing macromolecules. J Anal Sci Technol 2013. [DOI: 10.1186/2093-3371-4-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Cryo-electron microscopy is an excellent method for the structural analysis of biological materials. Advantage of its use over conventional electron microscopy techniques is the preservation of the sample in a near-native, hydrated state. To achieve the analysis with greatly improved structural details, optimization of various parameters involved in sample vitrification is required. Most considerable parameter is the thickness of ice: thick and thin layers are ideally in favor for larger and smaller target objects.
Findings
We measured the thickness of vitreous ice from different types of widely used holey carbon grids using cryo-EM and electron energy loss spectroscopy. It showed that Quantifoil grids are suitable for the structural analysis of large biological macromolecules (>100 nm in size), whereas the use of lacey and C-flat grids are ideal for smaller particles.
Conclusions
This report provides informative details that may help increasing chances of obtaining optimal vitreous ice for various biological objects with different sizes, hence facilitate the successful application of cryo-electron microscopy.
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104
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Correia I, Sung J, Burton R, Jakob CG, Carragher B, Ghayur T, Radziejewski C. The structure of dual-variable-domain immunoglobulin molecules alone and bound to antigen. MAbs 2013; 5:364-72. [PMID: 23572180 DOI: 10.4161/mabs.24258] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A dual-specific, tetravalent immunoglobulin G-like molecule, termed dual variable domain immunoglobulin (DVD-Ig™), is engineered to block two targets. Flexibility modulates Fc receptor and complement binding, but could result in undesirable cross-linking of surface antigens and downstream signaling. Understanding the flexibility of parental mAbs is important for designing and retaining functionality of DVD-Ig™ molecules. The architecture and dynamics of a DVD-Ig™ molecule and its parental mAbs was examined using single particle electron microscopy. Hinge angles measured for the DVD-Ig™ molecule were similar to the inner antigen parental mAb. The outer binding domain of the DVD-Ig™ molecule was highly mobile and three-dimensional (3D) analysis showed binding of inner antigen caused the outer domain to fold out of the plane with a major morphological change. Docking high-resolution X-ray structures into the 3D electron microscopy map supports the extraordinary domain flexibility observed in the DVD-Ig™ molecule allowing antigen binding with minimal steric hindrance.
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Affiliation(s)
- Ivan Correia
- Protein Analytics; AbbVie Bioresearch Center; Worcester, MA USA
| | - Joyce Sung
- NanoImaging Services, Inc.; La Jolla, CA USA
| | - Randall Burton
- Protein Analytics; AbbVie Bioresearch Center; Worcester, MA USA
| | - Clarissa G Jakob
- Department of Structural Biology; AbbVie Laboratories; Abbott Park, IL USA
| | | | - Tariq Ghayur
- Biologics; AbbVie Bioresearch Center; Worcester, MA USA
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105
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Fitzpatrick AWP, Debelouchina GT, Bayro MJ, Clare DK, Caporini MA, Bajaj VS, Jaroniec CP, Wang L, Ladizhansky V, Müller SA, MacPhee CE, Waudby CA, Mott HR, De Simone A, Knowles TPJ, Saibil HR, Vendruscolo M, Orlova EV, Griffin RG, Dobson CM. Atomic structure and hierarchical assembly of a cross-β amyloid fibril. Proc Natl Acad Sci U S A 2013; 110:5468-73. [PMID: 23513222 PMCID: PMC3619355 DOI: 10.1073/pnas.1219476110] [Citation(s) in RCA: 412] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale--including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy--we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils.
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Affiliation(s)
- Anthony W. P. Fitzpatrick
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Galia T. Debelouchina
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Marvin J. Bayro
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daniel K. Clare
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Marc A. Caporini
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Vikram S. Bajaj
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Christopher P. Jaroniec
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Luchun Wang
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Vladimir Ladizhansky
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Cait E. MacPhee
- School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - Christopher A. Waudby
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Helen R. Mott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom; and
| | - Alfonso De Simone
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Helen R. Saibil
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Elena V. Orlova
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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106
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Slingsby C, Wistow GJ, Clark AR. Evolution of crystallins for a role in the vertebrate eye lens. Protein Sci 2013; 22:367-80. [PMID: 23389822 PMCID: PMC3610043 DOI: 10.1002/pro.2229] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/16/2013] [Accepted: 01/17/2013] [Indexed: 12/18/2022]
Abstract
The camera eye lens of vertebrates is a classic example of the re-engineering of existing protein components to fashion a new device. The bulk of the lens is formed from proteins belonging to two superfamilies, the α-crystallins and the βγ-crystallins. Tracing their ancestry may throw light on the origin of the optics of the lens. The α-crystallins belong to the ubiquitous small heat shock proteins family that plays a protective role in cellular homeostasis. They form enormous polydisperse oligomers that challenge modern biophysical methods to uncover the molecular basis of their assembly structure and chaperone-like protein binding function. It is argued that a molecular phenotype of a dynamic assembly suits a chaperone function as well as a structural role in the eye lens where the constraint of preventing protein condensation is paramount. The main cellular partners of α-crystallins, the β- and γ-crystallins, have largely been lost from the animal kingdom but the superfamily is hugely expanded in the vertebrate eye lens. Their structures show how a simple Greek key motif can evolve rapidly to form a complex array of monomers and oligomers. Apart from remaining transparent, a major role of the partnership of α-crystallins with β- and γ-crystallins in the lens is to form a refractive index gradient. Here, we show some of the structural and genetic features of these two protein superfamilies that enable the rapid creation of different assembly states, to match the rapidly changing optical needs among the various vertebrates.
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Affiliation(s)
- Christine Slingsby
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom.
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107
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Abstract
In this issue of Structure, Roberts et al. discuss how cryo-electron microscopy single particle reconstructions of the microtubule-based motor dynein reveal dramatic nucleotide-dependent conformational changes. They provide insight into dynein force generation and hint at shared mechanisms with other AAA+ unfoldases.
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Affiliation(s)
- Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK.
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108
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Kaeser A, Fischer I, Abbel R, Besenius P, Dasgupta D, Gillisen MAJ, Portale G, Stevens AL, Herz LM, Schenning APHJ. Side chains control dynamics and self-sorting in fluorescent organic nanoparticles. ACS NANO 2013; 7:408-416. [PMID: 23256849 DOI: 10.1021/nn305477u] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To develop fluorescent organic nanoparticles with tailored properties for imaging and sensing, full control over the size, fluorescence, stability, dynamics, and supramolecular organization of these particles is crucial. We have designed, synthesized, and fully characterized 12 nonionic fluorene co-oligomers that formed self-assembled fluorescent nanoparticles in water. In these series of molecules, the ratio of hydrophilic ethylene glycol and hydrophobic alkyl side chains was systematically altered to investigate its role on the above-mentioned properties. The nanoparticles consisting of π-conjugated oligomers containing polar ethylene glycol side chains were less stable and larger in size, while nanoparticles self-assembled from oligomers containing nonpolar pendant chains were more stable, smaller, and generally had a higher fluorescence quantum yield. Furthermore, the dynamics of the molecules between the nanoparticles was enhanced if the number of hydrophilic side chains increased. Energy transfer studies between naphthalene and benzothiadiazole fluorene co-oligomers with the same side chains showed no exchange of molecules between the particles for the apolar molecules. For the more polar systems, the exchange of molecules between nanoparticles took place at room temperature or after annealing. Self-assembled nanoparticles consisting of π-conjugated oligomers having different side chains caused self-sorting, resulting either in the formation of domains within particles or the formation of separate nanoparticles. Our results show that we can control the stability, fluorescence, dynamics, and self-sorting properties of the nanoparticles by simply changing the nature of the side chains of the π-conjugated oligomers. These findings are not only important for the field of self-assembled nanoparticles but also for the construction of well-defined multicomponent supramolecular materials in general.
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Affiliation(s)
- Adrien Kaeser
- Laboratory of Functional Organic Materials and Devices, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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109
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Karimi Nejadasl F, Karuppasamy M, Newman ER, McGeehan JE, Ravelli RBG. Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:58-66. [PMID: 23254656 PMCID: PMC3526921 DOI: 10.1107/s0909049512044408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/25/2012] [Indexed: 06/01/2023]
Abstract
The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.
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Affiliation(s)
- Fatemeh Karimi Nejadasl
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Manikandan Karuppasamy
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Emily R. Newman
- Biophysics Laboratories, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - John E. McGeehan
- Biophysics Laboratories, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Raimond B. G. Ravelli
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
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110
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Milne JLS, Borgnia MJ, Bartesaghi A, Tran EEH, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S. Cryo-electron microscopy--a primer for the non-microscopist. FEBS J 2012. [PMID: 23181775 DOI: 10.1111/febs.12078] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cryo-electron microscopy (cryo-EM) is increasingly becoming a mainstream technology for studying the architecture of cells, viruses and protein assemblies at molecular resolution. Recent developments in microscope design and imaging hardware, paired with enhanced image processing and automation capabilities, are poised to further advance the effectiveness of cryo-EM methods. These developments promise to increase the speed and extent of automation, and to improve the resolutions that may be achieved, making this technology useful to determine a wide variety of biological structures. Additionally, established modalities for structure determination, such as X-ray crystallography and nuclear magnetic resonance spectroscopy, are being routinely integrated with cryo-EM density maps to achieve atomic-resolution models of complex, dynamic molecular assemblies. In this review, which is directed towards readers who are not experts in cryo-EM methodology, we provide an overview of emerging themes in the application of this technology to investigate diverse questions in biology and medicine. We discuss the ways in which these methods are being used to study structures of macromolecular assemblies that range in size from whole cells to small proteins. Finally, we include a description of how the structural information obtained by cryo-EM is deposited and archived in a publicly accessible database.
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Affiliation(s)
- Jacqueline L S Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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111
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112
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Longenecker JG, Mamin HJ, Senko AW, Chen L, Rettner CT, Rugar D, Marohn JA. High-gradient nanomagnets on cantilevers for sensitive detection of nuclear magnetic resonance. ACS NANO 2012; 6:9637-45. [PMID: 23033869 PMCID: PMC3535834 DOI: 10.1021/nn3030628] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Detection of magnetic resonance as a force between a magnetic tip and nuclear spins has previously been shown to enable sub-10 nm resolution 1H imaging. Maximizing the spin force in such a magnetic resonance force microscopy (MRFM) experiment demands a high field gradient. In order to study a wide range of samples, it is equally desirable to locate the magnetic tip on the force sensor. Here we report the development of attonewton-sensitivity cantilevers with high-gradient cobalt nanomagnet tips. The damage layer thickness and saturation magnetization of the magnetic material were characterized by X-ray photoelectron spectroscopy and superconducting quantum interference device magnetometry. The coercive field and saturation magnetization of an individual tip were quantified in situ using frequency-shift cantilever magnetometry. Measurements of cantilever dissipation versus magnetic field and tip–sample separation were conducted. MRFM signals from protons in a polystyrene film were studied versus rf irradiation frequency and tip–sample separation, and from this data the tip field and tip-field gradient were evaluated. Magnetic tip performance was assessed by numerically modeling the frequency dependence of the magnetic resonance signal. We observed a tip-field gradient ∂B(z)(tip)/∂z estimated to be between 4.4 and 5.4 MT m(–1), which is comparable to the gradient used in recent 4 nm resolution 1H imaging experiments and larger by nearly an order of magnitude than the gradient achieved in prior magnet-on-cantilever MRFM experiments.
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113
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Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proc Natl Acad Sci U S A 2012; 109:18821-6. [PMID: 23112201 DOI: 10.1073/pnas.1216549109] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction into a 3D density map. This process is limited by the number and quality of the particle images, the accuracy of the initial model, and the compositional and conformational heterogeneity. Here, we describe a structure determination method that avoids the reconstruction procedure. The atomic structures of the individual complex components are assembled by optimizing a match against 2D EM class-average images, an excluded volume criterion, geometric complementarity, and optional restraints from proteomics and chemical cross-linking experiments. The optimization relies on a simulated annealing Monte Carlo search and a divide-and-conquer message-passing algorithm. Using simulated and experimentally determined EM class averages for 12 and 4 protein assemblies, respectively, we show that a few class averages can indeed result in accurate models for complexes of as many as five subunits. Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined.
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114
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Ruigrok VJB, Levisson M, Hekelaar J, Smidt H, Dijkstra BW, van der Oost J. Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches. Int J Mol Sci 2012; 13:10537-10552. [PMID: 22949878 PMCID: PMC3431876 DOI: 10.3390/ijms130810537] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 12/11/2022] Open
Abstract
Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.
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Affiliation(s)
- Vincent J. B. Ruigrok
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Mark Levisson
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Johan Hekelaar
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands; E-Mails: (J.H.); (B.W.D.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
| | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands; E-Mails: (J.H.); (B.W.D.)
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands; E-Mails: (M.L.); (H.S.)
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115
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Pandurangan AP, Topf M. RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps. Bioinformatics 2012; 28:2391-3. [PMID: 22796953 DOI: 10.1093/bioinformatics/bts446] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. RESULTS Here we present the RIBFIND server, a tool for identifying RBs in protein structures. The server identifies RBs in proteins by calculating spatial proximity between their secondary structural elements. AVAILABILITY The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk. CONTACT a.pandurangan@mail.cryst.bbk.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Arun Prasad Pandurangan
- Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK.
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116
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Andersson BV, Skoglund C, Uvdal K, Solin N. Preparation of amyloid-like fibrils containing magnetic iron oxide nanoparticles: effect of protein aggregation on proton relaxivity. Biochem Biophys Res Commun 2012; 419:682-6. [PMID: 22382020 DOI: 10.1016/j.bbrc.2012.02.077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 02/11/2012] [Indexed: 11/30/2022]
Abstract
A method to prepare amyloid-like fibrils functionalized with magnetic nanoparticles has been developed. The amyloid-like fibrils are prepared in a two step procedure, where insulin and magnetic nanoparticles are mixed simply by grinding in the solid state, resulting in a water soluble hybrid material. When the hybrid material is heated in aqueous acid, the insulin/nanoparticle hybrid material self assembles to form amyloid-like fibrils incorporating the magnetic nanoparticles. This results in magnetically labeled amyloid-like fibrils which has been characterized by Transmission Electron Microscopy (TEM) and electron tomography. The influence of the aggregation process on proton relaxivity is investigated. The prepared materials have potential uses in a range of bio-imaging applications.
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Affiliation(s)
- B Viktor Andersson
- Biomolecular and Organic Electronics, Department of Physics, Chemistry, and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
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117
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Tao F(F. Synthesis, catalysis, surface chemistry and structure of bimetallic nanocatalysts. Chem Soc Rev 2012; 41:7977-9. [DOI: 10.1039/c2cs90093a] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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