A current assessment of photosystem II structure

1996 ◽  
Vol 16 (2) ◽  
pp. 159-187 ◽  
Author(s):  
William V. Nicholson ◽  
Robert C. Ford ◽  
Andreas Holzenburg
Keyword(s):  
Photosystem Ii ◽  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
X Ray Diffraction ◽  
Membrane Protein Complex ◽  
Fast Absorption ◽  
Current Assessment ◽  
Electron Microscopical ◽  
A Current

This review covers the recent progress in the elucidation of the structure of photosystem II (PSII). Because much of the structural information for this membrane protein complex has been revealed by electron microscopy (EM), the review will also consider the specific technical and interpretation problems that arise with EM where they are of particular relevance to the structural data. Most recent reviews of photosystem II structure have concentrated on molecular studies of the PSII genes and on the likely roles of the subunits that they encode or they were mainly concerned with the biophysical data and fast absorption spectroscopy largely relating to electron transfer in various purified PSII preparations. In this review, we will focus on the approaches to the three-dimensional architecture of the complex and the lipid bilayer in which it is located (the thylakoid membrane) with special emphasis placed upon electron microscopical studies of PSII-containing thylakoid membranes. There are a few reports of 3D crystals of PSII and of associated X-ray diffraction measurements and although little structural information has so far been obtained from such studies (because of the lack of 3D crystals of sufficient quality), the prospects for such studies are also assessed.

scholarly journals Protein Structure Determination in Living Cells

2019 ◽  
Vol 20 (10) ◽  
pp. 2442 ◽  
Author(s):  
Teppei Ikeya ◽  
Peter Güntert ◽  
Yutaka Ito
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Information ◽  
Nuclear Overhauser Effect ◽  
Protein Structures ◽  
Three Dimensional ◽  
Structural Data ◽  
Sample Tube ◽  
In Cells

To date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect’ structural information from peak patterns and chemical shift changes but not ‘direct’ data explicitly including interatomic distances and angles. To fully understand the functions and physical properties of proteins inside cells, it is indispensable to obtain explicit structural data or determine three-dimensional (3D) structures of proteins in cells. Whilst the short lifetime of cells in a sample tube, low sample concentrations, and massive background signals make it difficult to observe NMR signals from proteins inside cells, several methodological advances help to overcome the problems. Paramagnetic effects have an outstanding potential for in-cell structural analysis. The combination of a limited amount of experimental in-cell data with software for ab initio protein structure prediction opens an avenue to visualise 3D protein structures inside cells. Conventional nuclear Overhauser effect spectroscopy (NOESY)-based structure determination is advantageous to elucidate the conformations of side-chain atoms of proteins as well as global structures. In this article, we review current progress for the structure analysis of proteins in living systems and discuss the feasibility of its future works.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

Structural Analysis of Proteins on Lipid Substrates

2000 ◽  
Vol 6 (S2) ◽  
pp. 1182-1183
Author(s):  
Elizabeth M. Wilson-Kubalek
Keyword(s):  
Structural Information ◽  
Rapid Determination ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Complexes ◽  
Structural Data ◽  
X Ray Crystallography ◽  
Helical Protein ◽  
3D Structure Determination

Electron microscopy (EM) has become an increasingly powerful method for the determination of three-dimensional (3D) structures of proteins and macromolecular complexes. EM offers advantages over X-ray crystallography and NMR for obtaining structural information about proteins in physiological conditions, as components of large assemblies, that cannot be obtained in large quantity, or that fail to yield 3D crystals. EM has been used to obtain structural data from images of isolated molecules and molecular complexes, two-dimensional (2D) protein crystals, and helical protein arrays. Helically arranged proteins allow the most rapid determination of 3D maps because they contain a complete range of equally spaced molecular views, therefore no tilting of the sample with respect to the electron beam is required. However, so far 3D structure determination of helical assemblies has been limited to proteins that naturally adopt this organization and to proteins that fortuitously crystallize as helices.

scholarly journals Electrospinning synthesis of 3D porous NiO nanorods as anode material for lithium-ion batteries

2016 ◽  
Vol 34 (2) ◽  
pp. 227-232 ◽  
Author(s):  
Xiang Wei Kong ◽  
Rong Liang Zhang ◽  
Sheng Kui Zhong ◽  
Ling Wu
Keyword(s):  
Anode Material ◽  
Specific Capacity ◽  
3D Structure ◽  
Three Dimensional ◽  
Lithium Ion ◽  
Metallic Nickel ◽  
X Ray Diffraction ◽  
X Ray ◽  
Electrospinning Method ◽  
A Current

AbstractThree-dimensional NiO nanorods were synthesized as anode material by electrospinning method. X-ray diffraction results revealed that the product sintered at 400 °C had impure metallic nickel phase which, however, became pure NiO phase as the sintering temperature rose. Nevertheless, the nanorods sintered at 400, 500 and 600 °C had similar diameters (∼200 nm).The NiO nanorod material sintered at 500 °C was chip-shaped with a diameter of 200 nm and it exhibited a porous 3D structure. The nanorod sintered at 500 °C had the optimal electrochemical performance. Its discharge specific capacity was 1127 mAh·g−1 initially and remained as high as 400 mAh·g−1 at a current density of 55 mA·g−1 after 50 cycles.

scholarly journals Brattforsite, Mn19(AsO3)12Cl2, a new arsenite mineral related to magnussonite, from Brattforsgruvan, Nordmark, Värmland, Sweden

2021 ◽  
Author(s):  
Dan Holtstam ◽  
Cristian Biagioni ◽  
Ulf Hålenius
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Type Specimen ◽  
Structural Topology ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Calculated Density ◽  
X Ray ◽  
Cell Parameters ◽  
Density Values

AbstractBrattforsite is an approved mineral (IMA2019-127), with ideal formula Mn19(AsO3)12Cl2. Associated minerals in the type specimen from the Brattfors mine, Nordmark (Värmland, Sweden) include jacobsite, alleghanyite, phlogopite, calcite and dolomite. Brattforsite, forming subhedral, mostly equant crystals up to 0.5 mm across, is orange to reddish-brown with a white streak, and translucent with a resinous to vitreous lustre. The fracture is uneven to subconchoidal, and no cleavage is observed. It is very weakly pleochroic in yellow, optically biaxial (–) with 2V = 44(5)° and has calculated mean refractive index of 1.981. Measured and calculated density values are 4.49(1) and 4.54(1) g·cm− 3, respectively. Chemical analyses yields (in wt%): MgO 0.62, CaO 1.26, MnO 48.66, FeO 0.13, As2O3 46.72, Cl 2.61, H2Ocalc 0.07, O ≡ Cl –0.59, sum 99.49, corresponding to the empirical formula (Mn17.67Ca0.58Mg0.40Fe0.05)∑18.70As12.17O35.90Cl1.90(OH)0.20, based on 38 (O + Cl + OH) atoms per formula unit. The five strongest Bragg peaks in the powder X-ray diffraction pattern are [d (Å), I (%), (hkl)]: 2.843,100, ($$ \overline{4} $$ 4 - 44); 2.828, 99, (444); 1.731, 32, (880); 2.448, 28, (800); 1.739, 25, (088). Brattforsite is monoclinic and pseudotetragonal, space group I2/a, with unit-cell parameters a = 19.5806(7), b = 19.5763(7), c = 19.7595(7) Å, β = 90.393(3)°, V = 7573.9(5) Å3 and Z = 8. The crystal structure was solved and refined to an R1 index of 3.4 % for 7445 reflections [Fo > 4σ(Fo)]. Brattforsite has the same overall structural topology as magnussonite (i.e., the species can be considered as homeotypic), but with 12 independent tetrahedrally coordinated As sites and 21 Mn sites with varying (4–8) coordination. The Mn-centered polyhedra, bonded through edge- and face-sharing, give rise to a three-dimensional framework. The (AsO3)3− groups are bonded to this framework through corner- and edge-sharing. Spectroscopic measurements (optical absorption, Raman, FTIR) carried out support the interpretation of the compositional and structural data.

scholarly journals AlphaFold-Predicted Structures of KCTD Proteins Unravel Previously Undetected Relationships among the Members of the Family

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1862
Author(s):  
Luciana Esposito ◽  
Nicole Balasco ◽  
Giovanni Smaldone ◽  
Rita Berisio ◽  
Alessia Ruggiero ◽  
...  
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
Protein Family ◽  
General Sequence ◽  
Btb Domain ◽  
The Family ◽  
Three Dimensional Models ◽  
Definition Of ◽  
Sequence Similarities

One of the most striking features of KCTD proteins is their involvement in apparently unrelated yet fundamental physio-pathological processes. Unfortunately, comprehensive structure–function relationships for this protein family have been hampered by the scarcity of the structural data available. This scenario is rapidly changing due to the release of the protein three-dimensional models predicted by AlphaFold (AF). Here, we exploited the structural information contained in the AF database to gain insights into the relationships among the members of the KCTD family with the aim of facilitating the definition of the structural and molecular basis of key roles that these proteins play in many biological processes. The most important finding that emerged from this investigation is the discovery that, in addition to the BTB domain, the vast majority of these proteins also share a structurally similar domain in the C-terminal region despite the absence of general sequence similarities detectable in this region. Using this domain as reference, we generated a novel and comprehensive structure-based pseudo-phylogenetic tree that unraveled previously undetected similarities among the protein family. In particular, we generated a new clustering of the KCTD proteins that will represent a solid ground for interpreting their many functions.

scholarly journals Crystallization and Preliminary X-ray Diffraction of a Halophilic Archaeal Malate Synthase

2009 ◽  
Vol 8 (2 and 3) ◽  
Author(s):  
Geoffrey Thomas ◽  
Kenneth Lamlenn ◽  
Bruce Howard
Keyword(s):  
Structural Information ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Halophilic Archaea ◽  
Crystal Form ◽  
Dead Sea ◽  
Malate Synthase ◽  
Metabolic Enzyme ◽  
X Ray Diffraction ◽  
X Ray

Malate synthases found in cells of the halophilic Archaea constitute a third isoform of this important metabolic enzyme, in addition to the well characterized A and G isoforms. They share little sequence similarity with these other two isoforms. Database searches using basic local alignments reveal relationships between isoforms A and G, but do not indicate a significant sequence relationship between members of this third isoform and those of isoform G, and only a distant relationship with members of isoform A. This third isoform, which we propose to call isoform H (Halophilic archaeal), is also significantly smaller in size: ~100 residues shorter than isoform A, and ~300 residues shorter than isoform G. Representatives of both isoform A and G have been structurally characterized, but no three-dimensional structural information exists for isoform H. Here we report the crystallization and preliminary X-ray diffraction from a crystal form of an H-isoform member, the malate synthase from the halophilic archaeon Haloferax volcanii, originally isolated from the mud of the Dead Sea. This crystal form diffracts well, and is amenable to single crystal X-ray analysis.

Tissue Engineered and Native Ovine Pulmonary Valves: A High Resolution Three-Dimensional Structural Characterization

2009 ◽  
Author(s):  
Chad E. Eckert ◽  
Brandon T. Mikulis ◽  
Dane Gerneke ◽  
Ian LeGrice ◽  
Danielle Gottlieb ◽  
...  
Keyword(s):  
High Resolution ◽  
Heart Valves ◽  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
Native Valve ◽  
Tissue Engineered Heart Valves

Tissue engineered heart valves (TEHV) have received much attention as a potential pediatric valve replacement therapy, offering a variety of prospective long-term functional improvements over current options. Early in vivo and in vitro efforts have produced TEHV showing increasingly equivalent mechanical and structural properties compared to native valves [1]. Despite these advances, a significant gap in the literature exists regarding detailed 3D structural information of TEHV prior to implantation (in vitro) and after implantation (explants) as well as that of the native valve. The present work was performed to provide high resolution 3D structural data of implanted TEHV, the native pulmonary valve (PV), and pre-implant scaffold to develop an accurate understanding of developing tissue.

Hard X-ray diffraction scanning tomography with sub-micrometre spatial resolution: application to an annealed γ-U0.85Mo0.15particle

2011 ◽  
Vol 44 (5) ◽  
pp. 1111-1119 ◽  
Author(s):  
Hervé Palancher ◽  
Rémi Tucoulou ◽  
Pierre Bleuet ◽  
Anne Bonnin ◽  
Eléonore Welcomme ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Structural Information ◽  
Three Dimensional ◽  
Real Space ◽  
Protective Role ◽  
Diffraction Tomography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Thermally Activated

It is demonstrated that scanning X-ray diffraction tomography of heterogeneous and polycrystalline samples can provide real-space semi-quantitative three-dimensional structural information at a submicrometre spatial resolution. The capabilities of this technique are illustrated by the study of a slice of a spherical particle consisting of a UMo core (about 37 µm in diameter) surrounded by a UMoAl shell (5 µm thick). The technique allows precise characterization of the embedded UMo/UMoAl interface where the phases α-U (in the core), UAl2and U6Mo4Al43(in the shell) are found. Moreover, an unexpected phase (UC) is detected at a trace level. It is shown that the thickness of the UMoAl shell is locally anticorrelated with the amount of UC, suggesting that this phase plays a protective role in inhibiting thermally activated Al diffusion in UMo.

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