Insulin Receptor: Structure Via 3D EM Reconstruction, Crystallography and NMR Reveals Details of Ligand Binding and Mechanism of Transmembrane Signalling

2000 ◽  
Vol 6 (S2) ◽  
pp. 274-275
Author(s):  
F.P. Ottensmeyer ◽  
R.Z.T. Luo ◽  
D.R. Beniac ◽  
A.B. Fernandes ◽  
C.C. Yip
Keyword(s):  
Low Dose ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
Helical Structure ◽  
Dimensional Structure ◽  
Icosahedral Symmetry ◽  
Great Success ◽  
Single Particles ◽  
Radiation Induced ◽  
3D Em

For over 25 years a major effort in electron microscopy of macromolecules has been the determination of the three dimensional structure from the two-dimensional electron micrographs of such specimens. Great success has been realized when the macromolecule or complex takes the form of an array such as a 2D crystal (1,2), a helical structure (3,4) or one with icosahedral symmetry (5,6). However, for molecules which do not form such arrays, and in the limit only exist as single particles, a number of challenges have had to be addressed. No easy averaging of noisy low dose images is possible due to the lack of lateral and rotational symmetry. Random unknown orientations of the particles have to be determined, a process exacerbated by noise if low dose images are used as input. Alternatively, higher dose images result in radiation-induced structural alterations of the macromolecule.

scholarly journals Tripleurin XIIc: Peptide Folding Dynamics in Aqueous and Hydrophobic Environment Mimic Using Accelerated Molecular Dynamics

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 358 ◽  
Author(s):  
Chetna Tyagi ◽  
Tamás Marik ◽  
András Szekeres ◽  
Csaba Vágvölgyi ◽  
László Kredics ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Principal Component ◽  
Helical Structure ◽  
Fungal Species ◽  
Dimensional Structure ◽  
Peptide Backbone ◽  
Water Solvent ◽  
Leibler Divergence ◽  
Folding Dynamics ◽  
Beta Hairpin

Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-terminal 1,2-amino alcohol along with non-standard amino acid residues. New peptaibols named tripleurins were recently identified from a strain of the filamentous fungal species Trichoderma pleuroti, which is known to cause green mould disease on cultivated oyster mushrooms. To understand the mode of action of these peptaibols, the three-dimensional structure of tripleurin (TPN) XIIc, an 18-mer peptide, was elucidated using an enhanced sampling method, accelerated MD, in water and chloroform solvents. Non-standard residues were parameterized by the Restrained Electrostatic Potential (RESP) charge fitting method. The dihedral distribution indicated towards a right-handed helical formation for TPN XIIc in both solvents. Dihedral angle based principal component analysis revealed a propensity for a slightly bent, helical folded conformation in water solvent, while two distinct conformations were revealed in chloroform: One that folds into highly bent helical structure that resembles a beta-hairpin and another with an almost straight peptide backbone appearing as a rare energy barrier crossing event. The hinge-like movement of the terminals was also observed and is speculated to be functionally relevant. The convergence and efficient sampling is addressed using Cartesian PCA and Kullback-Leibler divergence methods.

scholarly journals Structure of Isolated Nucleocapsids from Venezuelan Equine Encephalitis Virus and Implications for Assembly and Disassembly of Enveloped Virus

2003 ◽  
Vol 77 (1) ◽  
pp. 659-664 ◽  
Author(s):  
Angel Paredes ◽  
Kathy Alwell-Warda ◽  
Scott C. Weaver ◽  
Wah Chiu ◽  
Stanley J. Watowich
Keyword(s):  
Conformational Changes ◽  
Rna Virus ◽  
Three Dimensional ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Dimensional Structure ◽  
Icosahedral Symmetry ◽  
Venezuelan Equine Encephalitis ◽  
Equine Encephalitis Virus ◽  
Enveloped Virus

ABSTRACT Venezuelan equine encephalitis virus (VEEV) is an important human and equine pathogen in the Americas, with widespread reoccurring epidemics extending from South America to the southern United States. Most troubling, VEEV has been made into a weapon by several countries and is currently restricted by the Centers for Disease Control and Prevention as a potential biological warfare and terrorism agent. To facilitate the development of antiviral compounds, the structure of the nucleocapsid isolated from VEEV has been determined by electron cryomicroscopy and image reconstruction and represents the first three-dimensional structure of a nucleocapsid isolated from a single-stranded enveloped RNA virus. The isolated VEEV nucleocapsid undergoes significant reorganization relative to its structure within VEEV. However, the isolated nucleocapsid clearly exhibits T=4 icosahedral symmetry, and its characteristic nucleocapsid hexons and pentons are preserved. The diameter of the isolated nucleocapsid is ∼11.5% larger than that of the nucleocapsid within VEEV, with radial expansion being greatest near the hexons. Significantly, this is the first direct structural evidence showing that a simple enveloped virus undergoes large conformational changes during maturation, suggesting that the lipid bilayer and the transmembrane proteins of simple enveloped viruses provide the energy necessary to reorganize the nucleocapsid during maturation.

scholarly journals Three-Dimensional Structure of the Neisseria meningitidis Secretin PilQ Determined from Negative-Stain Transmission Electron Microscopy

2003 ◽  
Vol 185 (8) ◽  
pp. 2611-2617 ◽  
Author(s):  
Richard F. Collins ◽  
Robert C. Ford ◽  
Ashraf Kitmitto ◽  
Ranveig O. Olsen ◽  
Tone Tønjum ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Outer Membrane ◽  
Protein Complex ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Type Iv ◽  
Negative Stain ◽  
Dominant Feature

ABSTRACT The PilQ secretin from the pathogenic bacterium Neisseria meningitidis is an integral outer membrane protein complex which plays a crucial role in the biogenesis of type IV pili. We present here the first three-dimensional structure of this type of secretin at 2.5-nm resolution, obtained by single-particle averaging methods applied to the purified protein complex visualized in a negative stain. In projection, the PilQ complex is circular, with a donut-like appearance. When viewed from the side it has a rounded, conical profile. The complex was demonstrated to have 12-fold rotational symmetry, and this property was used to improve the quality of the density map by symmetry averaging. The dominant feature of the structure is a cavity, 10 nm deep, within the center of the molecule. The cavity is funnel-shaped in cross section, measures 6.5 nm in diameter at the top of the complex, and tapers to a closed point, effectively blocking formation of a continuous pore through the PilQ complex. These results suggest that the complex would have to undergo a conformational change in order to accommodate an assembled pilus fiber of diameter 6.5 nm running through the outer membrane.

scholarly journals Crystal structure ofrac-3,9-bis(2,6-difluorophenyl)-2,4,8,10-tetraoxaspiro[5.5]undecane

2015 ◽  
Vol 71 (2) ◽  
pp. o127-o128 ◽  
Author(s):  
Liang Chen ◽  
Zhengyi Li ◽  
Linlin Jin ◽  
Xiaoqiang Sun ◽  
Zhiming Wang
Keyword(s):  
Crystal Structure ◽  
Carbon Atom ◽  
Hydrogen Bonds ◽  
Rotation Axis ◽  
Rotational Symmetry ◽  
Condensation Reaction ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Aromatic Rings ◽  
Compound C

The title compound, C19H16F4O4, was prepared by the condensation reaction of 2,6-difluorobenzaldehyde and pentaerythritol. The whole molecule is generated by twofold rotational symmetry. The two six-membered O-heterocycles adopt chair conformations through a shared spiro-carbon atom that is located on the crystallographic twofold rotation axis. In this conformation, the two aromatic rings are located at the equatorial positions of the O-heterocycles. The conformation of this doubly substituted tetraoxaspiro system is chiral. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming layers parallel to (100). These layers are linked by C—H...F hydrogen bonds into a three-dimensional structure.

scholarly journals Structural studies on the antimicrobial peptide Brevinin 1E by spectroscopic methods

2003 ◽  
Vol 17 (2-3) ◽  
pp. 127-138 ◽  
Author(s):  
Woo-Sung Son ◽  
Ji-Sun Kim ◽  
Hyung-Eun Kim ◽  
Sang-Ho Park ◽  
Bong-Jin Lee
Keyword(s):  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Three Dimensional ◽  
Helical Structure ◽  
Structural Motif ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Random Structure ◽  
Three Dimensional Structure ◽  
Pharmacologically Active

Skin extracts of frogs are a rich source of pharmacologically active peptides such as caeruleins, tachykinins, bradykinins, thyrotropin-releasing hormone, bombesin-like and opioid peptides. A large variety of antimicrobial peptides has been isolated fromRanaspecies. These peptides, grouped in several families on the basis of differing length and distinct activity, were found to have one structural motif in common: an intramolecular disulfide bridge located at the C-terminal end, forming a seven-member ring, which was designated ‘Rana box’. Brevinin 1E is a 24-residue antimicrobial peptide isolated from the skin of a frog,Rana brevipoda. This peptide shows a broad range of antimicrobial activity against prokaryotic cells but shows very much hemolytic activity against human red blood cells. The solution structure of Brevinin 1E was studied by using CD (circular dichroism) and NMR (nuclear magnetic resonance) spectroscopy. CD investigation revealed that Brevinin 1E adopts random structure in aqueous solution but adopts mainlyα-helical structure in TFE/water (6 : 4, v/v) solution. The three-dimensional structure of Brevinin 1E was determined in 60% TFE/water solution using homonuclear NMR spectroscopy. This peptide showed mainly anα-helical structure with amphipathic property. Its three-dimensional structure is similar to those of other peptides such as magainin, nigrocin and ranalexin. Therefore, Brevinin 1E can be classified into the family of antimicrobial peptides containing a single linearα-helix that interact with target microbial membrane, leading to cell death through disruption of membrane integrity.

Three-Dimensional Structure of Helical and Zigzagged Nanowires Using Electron Tomography

2008 ◽  
Vol 1144 ◽  
Author(s):  
Han Sung Kim ◽  
Yoon Myung ◽  
Chang Hyun Kim ◽  
Seung Yong Bae ◽  
Jae-Pyoung Ahn ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
High Resolution ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Helical Structure ◽  
Axial Direction ◽  
Dimensional Structure ◽  
Gan Nanowires ◽  
Transmission Electron

ABSTRACTElectron tomography and high-resolution transmission electron microscopy were used to characterize the unique three-dimensional structures of helical or zigzagged GaN, ZnGa2O4 and Zn2SnO4 nanowires. The helical GaN nanowires adopt a helical structure that consists of six equivalent <0-111> growth directions with the axial [0001] direction. The ZnGa2O4 nanosprings have four equivalent <011> growth directions with the [001] axial direction. The zigzagged Zn2SnO4 nanowires consisted of linked rhombohedrons structure having the side edges matched to the <011> direction, and the [111] axial direction.

scholarly journals The BAR Domain Proteins: Molding Membranes in Fission, Fusion, and Phagy

2006 ◽  
Vol 70 (1) ◽  
pp. 37-120 ◽  
Author(s):  
Gang Ren ◽  
Parimala Vajjhala ◽  
Janet S. Lee ◽  
Barbara Winsor ◽  
Alan L. Munn
Keyword(s):  
Transcriptional Repression ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Helical Structure ◽  
Secretory Vesicle ◽  
Membrane Curvature ◽  
Dimensional Structure ◽  
Valuable Insight ◽  
Bar Domain ◽  
Bar Domain Proteins

SUMMARY The Bin1/amphiphysin/Rvs167 (BAR) domain proteins are a ubiquitous protein family. Genes encoding members of this family have not yet been found in the genomes of prokaryotes, but within eukaryotes, BAR domain proteins are found universally from unicellular eukaryotes such as yeast through to plants, insects, and vertebrates. BAR domain proteins share an N-terminal BAR domain with a high propensity to adopt α-helical structure and engage in coiled-coil interactions with other proteins. BAR domain proteins are implicated in processes as fundamental and diverse as fission of synaptic vesicles, cell polarity, endocytosis, regulation of the actin cytoskeleton, transcriptional repression, cell-cell fusion, signal transduction, apoptosis, secretory vesicle fusion, excitation-contraction coupling, learning and memory, tissue differentiation, ion flux across membranes, and tumor suppression. What has been lacking is a molecular understanding of the role of the BAR domain protein in each process. The three-dimensional structure of the BAR domain has now been determined and valuable insight has been gained in understanding the interactions of BAR domains with membranes. The cellular roles of BAR domain proteins, characterized over the past decade in cells as distinct as yeasts, neurons, and myocytes, can now be understood in terms of a fundamental molecular function of all BAR domain proteins: to sense membrane curvature, to bind GTPases, and to mold a diversity of cellular membranes.

scholarly journals In Silico Conformational Analysis of the Short-Sequence Hypomurocin A Peptides

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Zoltán Násztor ◽  
János Horváth ◽  
Balázs Leitgeb
Keyword(s):  
Conformational Analysis ◽  
Theoretical Study ◽  
Three Dimensional ◽  
Helical Structure ◽  
Dimensional Structure ◽  
Side Chain ◽  
Short Sequence ◽  
Structural Stabilization ◽  
Chain Conformations

In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the α-helical structure. Beside the backbone conformations, the side-chain conformations were investigated, and the preferred rotamer states of the side-chains of amino acids were determined. Furthermore, the occurrence of i←i+3 and i←i+4 intramolecular H-bonds was studied, which could play a role in the structural stabilization of β-turns and helical conformations. On the whole, our theoretical study supplied a comprehensive characterization of the three-dimensional structure of short-sequence hypomurocin A peptides.

scholarly journals High Resolution Structure of the Mature Capsid of Ralstonia Solanacearum Bacteriophage ϕRSA1 by Cryo-Electron Microscopy

2021 ◽  
Vol 22 (20) ◽  
pp. 11053
Author(s):  
Grégory Effantin ◽  
Akiko Fujiwara ◽  
Takeru Kawasaki ◽  
Takashi Yamada ◽  
Guy Schoehn
Keyword(s):  
Electron Microscopy ◽  
Ralstonia Solanacearum ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Icosahedral Symmetry ◽  
E Coli ◽  
Covalent Crosslinking ◽  
Cryo Electron Microscopy ◽  
Capsid Shell ◽  
High Resolution Structure

The ϕRSA1 bacteriophage has been isolated from Ralstonia solanacearum, a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature capsid to 3.9 Å resolution by cryo-electron microscopy. The capsid shell, that contains the 39 kbp of dsDNA genome, has an icosahedral symmetry characterized by an unusual triangulation number of T = 7, dextro. The ϕRSA1 capsid is composed solely of the polymerization of the major capsid protein, gp8, which exhibits the typical “Johnson” fold first characterized in E. coli bacteriophage HK97. As opposed to the latter, the ϕRSA1 mature capsid is not stabilized by covalent crosslinking between its subunits, nor by the addition of a decoration protein. We further describe the molecular interactions occurring between the subunits of the ϕRSA1 capsid and their relationships with the other known bacteriophages.

scholarly journals Three-dimensional reconstruction of a simple Z-band in fish muscle.

1991 ◽  
Vol 113 (5) ◽  
pp. 1043-1055 ◽  
Author(s):  
P K Luther
Keyword(s):  
Actin Filament ◽  
Actin Filaments ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Central Plane ◽  
Three Dimensional Structure ◽  
Proximal Site ◽  
Distal Site

The three-dimensional structure of the Z-band in fish white muscle has been investigated by electron microscopy. This Z-band is described as simple, since in longitudinal sections it has the appearance of a single zigzag pattern connecting the ends of actin filaments of opposite polarity from adjacent sarcomeres. The reconstruction shows two pairs of links, the Z-links, between one actin filament and the facing four actin filaments in the adjacent sarcomere. The members of each pair have nearly diametrically opposed origins. In relation to one actin filament, one pair of links appears to bind along the final 10 nm of the actin filament (proximal site) and the other pair binds along a region extending from 5 to 20 nm from the filament end (distal site). Between one pair and the other, there is a rotation of approximately 80 degrees round the filament axis. A Z-link with a proximal site at the end of one actin filament attaches at a distal site on the oppositely oriented actin filaments of the facing sarcomere and vice versa. The length of each Z-link is consistent with the length of an alpha-actinin molecule. An additional set of links located 10-15 nm from the center of the Z-band occurs between actin filaments of the same polarity. These polar links connect the actin filaments along the same direction on each side of the Z-band. The three-dimensional structure appears to have twofold screw symmetry about the central plane of the Z-band. Only approximate twofold rotational symmetry is observed in directions parallel to the actin filaments. Previous models of the Z-band in which four identical and rotationally symmetrical links emanate from the end of one actin filament and span across to the ends of four actin filaments in the adjacent sarcomere are therefore incorrect.

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