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J C Jésior

Publications and source records attributed to J C Jésior.

13 recordsLinked to original sources
PubMed2000

Hydrophilic framework in proteins?

The spatial neighborhood composition of residues was determined in a 511-structure set by taking only side-chain atoms into account to generate a hydrophobicity scale. This scale is symmetrical and has been divided into seven functional groups. Hydrophobic (LIVFMCAWYG) and hydrophilic (PTHSQRNKED) residues obey an equipartition rule: not only are they found in equal proportions, but they play equivalent roles in many of their properties. The nearest neighbors of all residues are always hydrophilic. However, hydrophobic residues are mostly surrounded by other hydrophobic residues located at a peak at 3.9 A, while hydrophilic residues show three peaks at 5.0, 6.5, and 8.0 A, suggesting a hydrophilic structural framework. This leads us to question the importance of hydrophobic cores believed to be at the origin of protein folding.

Amino Acid Sequence↗
PubMed1995

Structure of the ferredoxin from Clostridium acidurici: model at 1.8 A resolution.

Ferredoxins (Fd) are electron-carrier proteins, the active sites of which are organized around clusters made of iron and inorganic sulfur. The Fd from Clostridium acidurici is 55 amino acids long and contains two [4Fe-4S] clusters. Crystals have been obtained in the space group P4(3)2(1)2, a = b = 34.441 (5), c = 74.778 (9) A. The structure was solved by molecular replacement using the Fd from Peptostreptcoccus asaccharolyticus as a search model, these two ferredoxins having 37 residues in common. Refinement using molecular-dynamics techniques was then initiated. Successive rounds of model building and refinement gave a structure that includes 45 water molecules with R = 15%. At this stage, the electron-density map clearly revealed discrepancies in the position of two amino acids in the published primary sequence. Refinement based on these modifications led to R = 14.3% for 3921 reflections up to 1.8 A, resolution. The geometry of the two clusters has been found to be in good agreement with that previously obtained at a lower resolution. Interactions of polypeptide chain with the [4Fe-4S] clusters, the cluster geometry as well as the hydrogen bonds involving S, Sgamma, N and water molecules are reported.

Journal Article↗
PubMed1989

Use of low-angle diamond knives leads to improved ultrastructural preservation of ultrathin sections.

Low-angle diamond knives, one of them with an angle as low as 14.6 degrees, have been tested to measure compression induced during the sectioning of polystyrene latex spheres embedded in epoxy resins. Compression diminishes roughly proportional to the sectioning angle (sum of knife and clearance angles). The beneficial application of low-angle diamond knives in biology and material science is illustrated by sections through a muscle fiber (compression reduced by a factor of 3), sections through a collagen fiber (meridional resolution improved by a factor of 2) and sections through a copper grid bar (reduced curling). These low-angle diamond knives are as resistant as the classical knives having angles of 45 degrees and are routinely used by the author. Low-angle diamond knives with angles down to 35 degrees are now commercially available.

Animals↗
PubMed1988

Gap junction structures. VIII. Membrane cross-sections.

Profiles of negatively stained gap junctions have been measured by grid sectioning. After normal levels of electron irradiation, the membrane thickness shrinks to about half that of unirradiated controls, but no shrinkage occurs in the hexagonal lattice plane. Even under low irradiation conditions, there is significant thinning of the membranes. Edge views, in which rows of connexons are aligned parallel to the beam, were obtained from grid sections, folds in normal negatively stained specimens, and sections of a positively stained specimen. Averaging these micrographs with the translational and mirror symmetry of the projected lattice image displays conserved and variable features in the stain distribution of different specimens. Variations in the relative amount of negative stain in the gap at the surfaces and in the channel are uncorrelated with the irradiation but appear to depend on the local staining conditions and the integrity of the connexons. The dimensions measured from previously unirradiated grid sections, folds, and positively stained sections are in accord with x-ray diffraction measurements. Radiation-induced shrinkage can be accounted for by mass loss principally from the membrane bilayer. Disordering of the surface structure appears to be correlated with the radiation sensitivity of the bilayer; in contrast, the gap structure is well preserved under a variety of conditions.

Animals↗
PubMed1987

Electron-irradiation-induced flattening of negatively stained 2D protein crystals.

The thickness of negatively stained 2D crystalline arrays of the bladder membrane does not vary significantly during air drying and exposure to high vacuum. High-dose electron irradiation reduces the thickness to about 60% of the native value. These results, together with the fact that the same behaviour has been observed on another 2D system (gap junctions), indicate that the flattening induced by an electron beam on 2D crystals may be general. The implications for 3D reconstruction of negatively stained objects are discussed.

Animals↗
PubMed1987

Yeast tRNA(Asp)-aspartyl-tRNA synthetase complex: low resolution crystal structure.

Yeast aspartyl-tRNA synthetase, a dimer of molecular weight 125,000, and two molecules of its cognate tRNA (Mr = 24160) cocrystallize in the cubic space group I432 (a = 354 A). The crystal structure was solved to low resolution using neutron and X-ray diffraction data. Neutron single crystal diffraction data were collected in five solvents differing by their D2O content in order to use the contrast variation method to distinguish between the protein and tRNA. The synthetase was first located at 40 A resolution using the 65% D2O neutron data (tRNA matched) tRNA molecules were found at 20 A resolution using both neutron and X-ray data. The resulting model was refined against 10 A resolution X-ray data, using density modification and least-squares refinement of the tRNA positions. The crystal structure solved without a priori phase knowledge, was confirmed later by isomorphous replacement. The molecular model of the complex is in good agreement with results obtained in solution by probing the protected part of the tRNA by chemical reagents.

Amino Acyl-tRNA Synthetases↗
PubMed1985

Three-dimensional molecular shape determination from a limited number of projections.

A real space method allowing the reconstruction of negatively stained crystalline objects from a limited number of projections is presented. The method is based on the assumption that only two density levels are required to describe an ideally negatively stained object (that of the volume occupied by the object and that of the volume occupied by the stain). The method is illustrated by the reconstruction of the asymmetric unit of catalase microcrystals using only the three principal projections. It is shown that other projections can then be predicted to a good approximation.

Animals↗
PubMed1985

How to avoid compression: a model study of latex sphere grid sections.

The parameters which might play a role in the compression of plastic-embedded objects are studied. The compression is measured on spherical polystyrene latex particles, used as markers in the grid sectioning technique. By changing independently the hardness of the latex particles through a controlled electron irradiation and the hardness of the embedding medium, it is shown that compression is a local event depending only on the mechanical properties of the sectioned object and not on the properties of its surrounding materials. It is demonstrated on one hand that the intrinsic resin compression diminishes as resin hardness increases, and on the other hand that the latex compression can be completely eliminated after a preliminary irradiation by electrons (the electron-induced vulcanization is equivalent to a hardening). It is thus concluded that compression could be greatly reduced or eliminated if objects were sufficiently hardened during their preparation. Several preparation procedures for biological specimens are suggested. For comparison latex has also been irradiated 31/2 days near a 25 000-Ci 60Co gamma source and near the core of an 8-MW nuclear reactor. Neither of these irradiations was sufficient to produce a hardening equivalent to that of the electron irraidation.

Electrons↗
PubMed1984

[Micrometric in situ marking apparatus for an object on a microscope grid. Application of observation of serial sections].

A device for the precise localization (better than 0.5 micron) of an object on a grid has been developed and connected to the translation system of an electron microscope. Applied to biological thin sections, this device enables to easily find and to observe a selected microcrystal projection obtained by the grid sectioning technique. Moreover, low dose observations on ribbons of ultrathin sections can be made because the information is repeated in the successive sections of the ribbon: With the device the position of the selected object is determined at high dose in one section and low dose measurement is made on the following section.

Microscopy, Electron↗
PubMed1982

The grid sectioning technique: a study of catalase platelets.

The grid sectioning technique has been used to obtain the two missing principal axis projections of orthorhombic catalase platelets and to measure directly the unit cell c-value. The negatively stained platelets have a unit cell c-dimension of half that proposed by Unwin (1975) from powder X-ray diffraction. The precision of the grid sectioning technique in positioning sections along a specimen axis shows that the growth fault lines usually observed on negatively stained catalase platelets are rows of missing molecules filled with stain. From these sections conclusions are drawn concerning the action of negative stain on a specimen, the microtomy process, and the specimen/supporting film interaction. Finally the value of microtomy for detailed structural analysis of biological objects is emphasized.

Catalase↗
PubMed1982

A new approach for the visualization of molecular arrangement in biological micro-crystals.

Biological molecules often form micro-crystals that are in a size range that is unsuited for study either by X-ray crystallography or by electron microscopy. The method described here allows the use of most of these crystals. It consists of cutting sections through the crystal deposited on a grid after a preliminary observation in the electron microscope to determine its precise location. It allows visualization of the crystal molecular packing in any plane normal to the grid plane at the resolution usually obtained by negative staining. If the crystal is thin enough, two orthogonal views of the same crystal can be obtained. The orientation and the position of the sections along the crystal axis are precisely determined using latex particles as reference points. Crystals as small as 1 micrometer in length can be studied.

Biopolymers↗