A structural proteomics filter: prediction of the quaternary structural type of hetero-oligomeric proteins on the basis of their sequences

2007 ◽  
Vol 40 (6) ◽  
pp. 986-989 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Structural Biology ◽  
Three Dimensional ◽  
Structural Type ◽  
Computational Method ◽  
Structural Proteomics ◽  
Dimensional Structure ◽  
Protein Chain ◽  
Oligomeric Proteins ◽  
Single Protein ◽  
A Chain

A protein chain can correspond to a monomeric protein or it can form, together with other chains, oligomeric assemblies, which can be either homo-oligomers or hetero-oligomers. In the latter case, the three-dimensional structure of the single protein chain is unlikely to be determined, since it will probably be difficult to express and crystallize. A computational method is presented here that allows one to predict if a chain participates in hetero-oligomeric assemblies, on the basis of its amino acid composition, with accuracy close to 80%. Such a technique should improve the success rate of structural biology projects.

scholarly journals Insights into the molecular basis of sperm–egg recognition in mammals

Reproduction ◽  
2004 ◽  
Vol 127 (4) ◽  
pp. 417-422 ◽  
Author(s):  
Tanya Hoodbhoy ◽  
Jurrien Dean
Keyword(s):  
Zona Pellucida ◽  
Three Dimensional ◽  
Explanatory Models ◽  
Dimensional Structure ◽  
Side Chain ◽  
Egg Recognition ◽  
Three Dimensional Structure ◽  
Sperm Binding ◽  
Single Protein

The zona pellucida surrounding the egg and pre-implantation embryo is required for in vivo fertility and early development. Explanatory models of sperm–egg recognition need to take into account the ability of sperm to bind to ovulated eggs, but not to two-cell embryos. For the last two decades, investigators have sought to identify an individual protein or carbohydrate side chain as the ‘sperm receptor’. However, recent genetic data in mice are more consistent with the three-dimensional structure of the zona pellucida, rather than a single protein (or carbohydrate), determining sperm binding. The mouse and human zonae pellucidae contain three glycoproteins (ZP1, ZP2, ZP3) and, following fertilization, ZP2 is proteolytically cleaved. The replacement of endogenous mouse proteins with human ZP2, ZP3 or both does not alter taxon specificity of sperm binding or prevent fertility. Surprisingly, human ZP2 is not cleaved following fertilization and intact ZP2 correlates with persistent sperm binding to two-cell embryos. Taken together, these data support a model in which the cleavage status of ZP2 modulates the three-dimensional structure of the zona pellucida and determines whether sperm bind (uncleaved) or do not (cleaved).

scholarly journals Poly[(μ3-5-hydroxyisophthalato)[μ2-1,1′-(1,4-phenylene)bis(1H-imidazole)]copper]

IUCrData ◽  
2016 ◽  
Vol 1 (11) ◽  
Author(s):  
Hong-Hong Tao ◽  
Yu-Han Chen ◽  
Ya-Sai Liu ◽  
Zhuo-Ga Deji
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Supramolecular Network ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Bridging Ligands ◽  
Trigonal Bipyramidal ◽  
A Chain ◽  
Organic Linker ◽  
Distorted Trigonal Bipyramidal

The title compound, [Cu(C8H4O5)(C12H10N4)]n, was obtained by the reaction of copper(II) nitrate hydrate, with the OH-BDC organic linker and bib molecules [OH-BDC = 5-hydroxyisophthalic acid and bib = 1,4-bis(imidazol-1-yl)benzene]. The asymmetric unit comprises one CuIIcation, one OH-BDC−2dianion and a bib ligand. The CuIIion is coordinated by three carboxylate O atoms and two bib-N atoms, all from bridging ligands, to form a slightly distorted trigonal–bipyramidal geometry. The CuIIions are bridged by OH-BDC−2ligands, forming a chain along the [100] direction; the chains are connected by bib molecules to form a two-dimensional net. In topological terms, considering the CuIIatoms as nodes and the OH-BDC−2ligands as linkers, the two-dimensional structure can be simplified as a typical 2-nodal 3,5 L2 plane network. The crystal structure features O—H...O hydrogen bonds between OH-BDC−2anions, resulting in a three-dimensional supramolecular network.

scholarly journals Three-dimensional Structure of Abrin-a A-chain Having Ribosome Inactivating Activity.

1995 ◽  
Vol 71 (3) ◽  
pp. 104-107
Author(s):  
Tetsuya KOHNO ◽  
Toshiya SENDA ◽  
Hideki NARUMI ◽  
Shigenobu KIMURA ◽  
Yukio MITSUI
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
A Chain

scholarly journals Characterisation of a Novel A-Superfamily Conotoxin

Biomedicines ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. 128
Author(s):  
David T. Wilson ◽  
Paramjit S. Bansal ◽  
David A. Carter ◽  
Irina Vetter ◽  
Annette Nicke ◽  
...  
Keyword(s):  
Nicotinic Acetylcholine Receptor ◽  
Disulfide Bonds ◽  
Three Dimensional ◽  
Structural Type ◽  
Dimensional Structure ◽  
Na Channels ◽  
Nicotinic Acetylcholine ◽  
Therapeutic Leads ◽  
Helical Region

Conopeptides belonging to the A-superfamily from the venomous molluscs, Conus, are typically α-conotoxins. The α-conotoxins are of interest as therapeutic leads and pharmacological tools due to their selectivity and potency at nicotinic acetylcholine receptor (nAChR) subtypes. Structurally, the α-conotoxins have a consensus fold containing two conserved disulfide bonds that define the two-loop framework and brace a helical region. Here we report on a novel α-conotoxin Pl168, identified from the transcriptome of Conus planorbis, which has an unusual 4/8 loop framework. Unexpectedly, NMR determination of its three-dimensional structure reveals a new structural type of A-superfamily conotoxins with a different disulfide-stabilized fold, despite containing the conserved cysteine framework and disulfide connectivity of classical α-conotoxins. The peptide did not demonstrate activity on a range of nAChRs, or Ca2+ and Na+ channels suggesting that it might represent a new pharmacological class of conotoxins.

scholarly journals Pr5Si3N9

2009 ◽  
Vol 65 (6) ◽  
pp. i43-i43 ◽  
Author(s):  
Saskia Lupart ◽  
Wolfgang Schnick
Keyword(s):  
Crystal Structure ◽  
Rare Earth ◽  
Radio Frequency ◽  
Single Crystals ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Mirror Plane ◽  
Three Dimensional Structure ◽  
A Chain ◽  
Branched Chains

Single crystals of Pr5Si3N9, pentapraseodymium trisilicon nonanitride, were obtained by the reaction of elemental praseodymium with silicon diimide in a radio-frequency furnace at 1873 K. The crystal structure consists of a chain-like Si—N substructure of corner-sharing SiN4tetrahedra. An additionalQ1-type [SiN4] unit is attached to every second tetrahedron directed alternately in opposite directions. The resulting branched chains interlock with each other, building up a three-dimensional structure. The central atoms of theQ1-type [SiN4] unit and of its attached tetrahedron are situated on a mirror plane, as are two of the four crystallographically unique Pr3+ions. The latter are coordinated by six to ten N atoms, with Pr—N distances similar to those of other rare earth nitridosilicates.

scholarly journals Raman optical activity: A new light on proteins, carbohydrates and glycoproteins

2006 ◽  
Vol 28 (3) ◽  
pp. 27-31 ◽  
Author(s):  
Laurence D. Barron
Keyword(s):  
Structural Biology ◽  
Optical Activity ◽  
Large Range ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
The Novel ◽  
X Ray ◽  
X Ray Crystallography ◽  
Raman Optical Activity

The core techniques of structural biology, namely X-ray crystallography and multidimensional NMR, are often not applicable to many important samples due to fundamental experimental problems, such as the lack of suitable crystals in the X-ray case or excessive size or flexibility for NMR. Carbohydrates and glycoproteins are especially challenging in this respect. The novel technique of vibrational ROA (Raman optical activity), which combines the advantages of vibrational spectroscopy with the extra sensitivity to three-dimensional structure of chiroptical methods such as CD (circular dichroism), has much promise for studying a large range of biomolecules, from the smallest to the largest, in aqueous solution. Among other things, it is capable of providing structural information about both the polypeptide and the carbohydrate structure of intact glycoproteins and should become an indispensable spectroscopy tool for glycobiology.

scholarly journals Structural and Functional Analyses of PolyProline-II helices in Globular Proteins

2016 ◽  
Author(s):  
Prasun Kumar ◽  
Manju Bansal
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Aromatic Amino Acids ◽  
Dimensional Structure ◽  
Protein Chain ◽  
Left Handed ◽  
Polyproline Ii ◽  
Backbone Torsion Angle ◽  
Functional Analyses ◽  
Flanking Regions

PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which the constituent residues have the backbone torsion angle (φ,ψ) values of (-75°, 145°) and take up extended left handed conformation, lacking any intra-helical hydrogen bonds. They are found to occur very frequently in protein structures with their number exceeding that of π-helices, though it is considerably less than that of α-helices and β-strands. A relatively new procedure, ASSP, for the identification of regular secondary structures using Cα trace identifies 3597 PPII helices in 3582 protein chains, solved at resolution ≤ 2.5Å. Taking advantage of this significantly expanded database of PPII-helices, we have analyzed the functional and structural roles of PPII helices as well as determined the amino acid propensity within and around them. Though Pro residues are highly preferred, it is not a mandatory condition for the formation of PPII-helices, since ~40% PPII-helices were found to contain no Proline residues. Aromatic amino acids are avoided within this helix, while Gly, Asn and Asp residues are preferred in the proximal flanking regions. These helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0ű0.1Å respectively. A majority (~72%) of PPII-helices were found to occur in conjunction with α-helices and β-strands, and serve as linkers as well. The analysis of various intra-helical non-bonded interactions revealed frequent presence of C-H...O H-bonds. PPII-helices participate in maintaining the three-dimensional structure of proteins and are important constituents of binding motifs involved in various biological functions.

scholarly journals Crystal structure of a host–guest complex of the tris-urea receptor, 3-(4-nitrophenyl)-1,1-bis{2-[3-(4-nitrophenyl)ureido]ethyl}urea, that encapsulates hydrogen-bonded chains of dihydrogen phosphate anions with separate tetra-n-butylammonium counter-ions

2019 ◽  
Vol 75 (3) ◽  
pp. 319-323
Author(s):  
Ruyu Wang ◽  
Xi Shu ◽  
Yu Fan ◽  
Shoujian Li ◽  
Yongdong Jin ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Dihydrogen Phosphate ◽  
Phosphate Anion ◽  
Compound C ◽  
Counter Ions ◽  
A Chain ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

The title compound, C25H25N9O9·C16H36N+·H2PO4 − (I) or (C25H25N9O9)·(n-Bu4N+)·(H2PO4 −) (systematic name: 3-(4-nitrophenyl)-1,1-bis{2-[3-(4-nitrophenyl)ureido]ethyl}urea tetrabutylammonium dihydrogen phosphate), comprises a tris-urea receptor (R), a dihydrogen phosphate anion and a tetra-n-butylammonium cation. It crystallizes with two independent formula units in the asymmetric unit. The conformations of the two tris-urea receptors are stabilized by N—H...O and C—H...O intramolecular hydrogen bonds. Each dihydrogen phosphate anion has two O—H...O intermolecular hydrogen-bonding interactions with the other dihydrogen phosphate anion. Inversion-related di-anion units are linked by further O—H...O hydrogen bonds, forming a chain propagating along the a-axis direction. Each dihydrogen phosphate anion makes a total of four N—H...O(H2PO4 −) hydrogen bonds with two ureido subunits from two different tris-urea receptors, hence each tris-urea receptor provides the two ureido subunits for the encapsulation of the H2PO4 − hydrogen-bonded chain. There are numerous intermolecular C—H...O hydrogen bonds present involving both receptor molecules and the tetra-n-butylammonium cations, so forming a supramolecular three-dimensional structure. One of the butyl groups and one of the nitro groups are disordered over two positions of equal occupancy.

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