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J L Popot

Publications and source records attributed to J L Popot.

At least 37 records · Page 2Linked to original sources
PubMed1994

Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study.

We have applied a search strategy for determining the optimal packing of protein secondary structure elements to the rotational positioning of the seven transmembrane helices of bacteriorhodopsin. The search is based on the assumption that the relative orientations of the helices within the bundle are conditioned principally by inter-helix side-chain interactions and that the extra-helical parts of the protein have only a minor influence on the bundle conformation. Our approach performs conformational energy optimization using a predetermined set of side-chain rotamers and appropriate methods for sampling the conformational space of peptide fragments with fixed backbone geometries. The final solution obtained for bacteriorhodopsin places each of the seven helices to a precision of a few degrees in rotation around the helical axis and to a few tenths of an ångström in translation along the helical axis with respect to the best experimental structure obtained by electron diffraction, except for helix D, where our results support the suggestion that this helix should be displaced along its axis toward its N terminus. The perspectives of such an approach for the determination of the structures of other transmembrane helical bundles are discussed.

Bacteriorhodopsins↗
PubMed1993

Identification of two 4-kDa miniproteins in the cytochrome b6f complex from Chlamydomonas reinhardtii.

Two low molecular weight subunits (ca. 4 kDa) have been identified in highly purified preparations of cytochrome b6f from the green unicellular alga Chlamydomonas reinhardtii. The N-terminus of the first one is blocked. It is synthesized in the chloroplast. It cross reacts with an antiserum raised against a synthetic peptide with the C-terminal sequence of the predicted product of the chloroplast gene petG. The homologue of this protein had been previously identified by other authors in the b6f complex from maize. The N-terminal sequence of the second subunit does not correspond to any known protein. This polypeptide, provisionally named petX, is synthesized in the cytosol. An antiserum has been raised against the corresponding synthetic peptide. Immunoblotting experiments show that neither petG nor petX are present in thylakoid membranes from a b6f-less strain of C. reinhardtii.

Animals↗
PubMed1992

Identification of mitochondrial proteins in membrane preparations from Chlamydomonas reinhardtii.

Preparations enriched in Chlamydomonas reinhardtii thylakoids have proven useful in the study of photosynthesis. Many of their polypeptides however remain unidentified. We report here on three of those, h1 (34 kDa), h2 (11 kDa), and P3 (63 kDa). h1, h2, and P3 are present in all tested mutants of C. reinhardtii lacking either one or several of the photosynthetic chain complexes or depleted in thylakoid membranes. h2 is an ascorbate-reducible, soluble c550-type cytochrome encoded in the nucleus. It cross-reacts immunologically with mitochondrial cytochromes c from various sources and contains a hexapeptide encoded in C. reinhardtii cytochrome c cDNA. P3, a nuclear-encoded peripheral protein, cross-reacts with various ATP synthase beta subunits. Its N-terminal sequence is encoded in C. reinhardtii mitochondrial beta subunit cDNA. h1 behaves as an integral hemoprotein; it is absent in a mitochondrial mutant that carries a deletion in apocytochrome b gene. We conclude that C. reinhardtii mitochondrial membranes copurify with thylakoid membranes. h1 is part of the cytochrome bc1 complex, h2 is cytochrome c, and P3 is the beta subunit of mitochondrial ATP synthase.

Amino Acid Sequence↗
PubMed1991

Pelizaeus-Merzbacher disease: a valine to phenylalanine point mutation in a putative extracellular loop of myelin proteolipid.

In the central nervous system, myelin proteolipid protein isoforms (PLP and DM20) play an essential structural role in myelination. It has been shown in several species that myelination is impaired by molecular defects resulting from single base mutations in the PLP gene. We have used DNA amplification by polymerase chain reaction to study the PLP gene coding regions from 17 patients in 15 unrelated families with similar Pelizaeus-Merzbacher phenotype. In one case amplification of peripheral nerve PLP/DM20 cDNAs revealed that a silent T----C transition was unrelated to the disease. In one family a nonsilent mutation was identified that leads to a phenylalanine substitution for valine-218 in PLP/DM20 proteins. We investigated the inheritance of the mutant allele in 19 subjects of this four-generation family and found a strict cosegregation of the Phe218 substitution with transmission and expression of the disease. The effect of the Val218----Phe mutation is discussed in the frame of a recently suggested topological model of PLP/DM20, according to which Val218 is part of an extracellular loop that connects the last two of four membrane-spanning alpha-helices.

Animals↗
PubMed1991

Major Myelin proteolipid: the 4-alpha-helix topology.

Several conflicting models have been proposed for the membrane arrangement of the major myelin proteolipid (PLP). We have compared features of the sequence of PLP with those of other eukaryotic integral membrane proteins, with the view of identifying the most likely transmembrane topology. A new, simple model is suggested, which features four hydrophobic alpha-helices spanning the whole thickness of the lipid bilayer. Its orientation may be such that both the N- and C-termini face the cytosol. None of the biochemical, biophysical or immunological experiments hitherto reported provides incontrovertible evidence against the model. The effect or absence thereof of various PLP mutations is discussed in the frame of the proposed 4-helix topology.

Amino Acid Sequence↗
PubMed1990

Membrane protein folding and oligomerization: the two-stage model.

We discuss the view that the folding of many, perhaps most, integral membrane proteins can be considered as a two-stage process. In stage I, hydrophobic alpha-helices are established across the lipid bilayer. In stage II, they interact to form functional transmembrane structures. This model is suggested by the nature of transmembrane segments in known structures, refolding experiments, the assembly of integral membrane protein from fragments, and the existence of very small integral membrane protein subunits. It may extend to proteins with a variety of functions, including the formation of transmembrane aqueous channels. The model is discussed in the context of the forces involved in membrane protein folding and the interpretation of sequence data.

Bacteriorhodopsins↗
PubMed1990

The "microassembly" of integral membrane proteins: applications & implications.

We summarize some evidence in favor of the view that the transmembrane region of many, perhaps most integral membrane proteins is made up of an aggregate of hydrophobic alpha-helices, each of which behaves as an autonomous folding domain. Folding of these proteins is seen as a two-stage process during which individual transmembrane helices first form in response to local interactions between the polypeptide and the aqueous and lipid phases, and then pack without extensive rearrangement to yield the three-dimensional structure. This two-stage model is supported by examination of those few structures that are known to a sufficient resolution, by experiments in which functional integral membrane proteins are "microassembled" from separately folded fragments, and by the existence in the inner membranes of organelles of a large number of very small integral subunits, often barely longer than a single transmembrane alpha-helix. We describe application of microassembly to establishing the path of the polypeptide in the tertiary structure of bacteriorhodopsin by neutron diffraction and we briefly discuss its possible role in the biosynthesis of organelle inner membrane complexes and its implications for model building from sequence data.

Amino Acid Sequence↗
PubMed1989

Tertiary structure of bacteriorhodopsin. Positions and orientations of helices A and B in the structural map determined by neutron diffraction.

Positions and rotations of two helices in the tertiary structure of bacteriorhodopsin have been studied by neutron diffraction using reconstituted, hybrid purple membrane samples. Purple membrane was biosynthetically 2H-labeled at non-exchangeable hydrogen positions of leucine and tryptophan residues. Two chymotryptic fragments were purified, encompassing either the first two or the last five of the seven putative transmembrane segments identified in the amino acid sequence of bacteriorhodopsin. The 2H-labeled fragments, diluted to variable extents with the identical, unlabeled fragment, were mixed with their unlabeled counterpart; bacteriorhodopsin was then renatured and reconstituted. The crystalline purple membrane samples thus obtained contained hybrid bacteriorhodopsin molecules in which certain transmembrane segments had been selectively 2H-labeled to various degrees. Neutron diffraction powder patterns were recorded and analyzed both by calculating difference Fourier maps and by model building. The two analyses yielded consistent results. The first and second transmembrane segments in the sequence correspond to helices 1 and 7 of the three-dimensional structure, respectively. Rotational orientations of these two helices were identified using best fits to the observed diffraction intensities. The data also put restrictions on the position of the third transmembrane segment. These observations are discussed in the context of folding models for bacteriorhodopsin, the environment of the retinal Schiff base, and site-directed mutagenesis experiments.

Amino Acid Sequence↗
PubMed1987

Refolding of bacteriorhodopsin in lipid bilayers. A thermodynamically controlled two-stage process.

Possible steps in the folding of bacteriorhodopsin are revealed by studying the refolding and interaction of two fragments of the molecule reconstituted in lipid vesicles. (1) Two denatured bacteriorhodopsin fragments have been purified starting from chymotryptically cleaved bacteriorhodopsin. Cleaved bacteriorhodopsin has been renatured from a mixture of the fragments in Halobacterium lipids/retinal/dodecyl sulfate solution following removal of dodecyl sulfate by precipitation with potassium. The renatured molecules have the same absorption spectrum and extinction coefficient as native cleaved bacteriorhodopsin. They are integrated into small lipid vesicles as a mixture of monomers and aggregates. Extended lattices form during the partial dehydration process used to orient samples for X-ray and neutron crystallography. (2) Correct refolding of cleaved bacterioopsin occurs upon renaturation in the absence of retinal. Regeneration of the chromophore and reformation of the purple membrane lattice are observed following subsequent addition of all-trans retinal. (3) The two chymotryptic fragments have been reinserted separately into lipid vesicles and refolded in the absence of retinal. Circular dichroism spectra of the polypeptide backbone transitions indicate that they have regained a highly alpha-helical structure. The kinetics of chromophore regeneration following reassociation have been studied by absorption spectroscopy. Upon vesicle fusion, the refolded fragments first reassociate, then bind retinal and finally regenerate cleaved bacteriorhodopsin. The complex formed in the absence of retinal is kinetically indistinguishable from cleaved bacterioopsin. The refolded fragments in lipid vesicles are stable for months, both as separate entities and after reassociation. These observations provide further evidence that the native folded structure of bacteriorhodopsin lies at a free energy minimum. They are interpreted in terms of a two-stage folding mechanism for membrane proteins in which stable transmembrane helices are first formed. They subsequently pack without major rearrangement to produce the tertiary structure.

Bacteriorhodopsins↗
PubMed1987

Transmembrane topography of the nicotinic acetylcholine receptor delta subunit.

Current folding models for the nicotinic acetylcholine receptor (AChR) predict either four or five transmembrane segments per subunit. The N-terminus of each subunit is almost certainly extracellular. We have tested folding models by determining biochemically the cellular location of an intermolecular disulfide bridge thought to lie at the delta subunit C-terminus. Dimers of AChR linked through the delta-delta bridge were prepared from Torpedo marmorata and T.californica electric organ. The disulfide's accessibility to hydrophilic reductants was tested in a reconstituted vesicle system. In right-side-out vesicles (greater than 95% ACh binding sites outwards), the bridge was equally accessible whether or not vesicles had been disrupted by freeze--thawing or by detergents. Control experiments based on the rate of reduction of entrapped diphtheria toxin and measurements of radioactive reductant efflux demonstrated that the vesicles provide an adequate permeability barrier. In reconstituted vesicles containing AChR dimers in scrambled orientations, right-side-out dimers were reduced to monomers three times more rapidly than inside-out dimers, consistent with the measured rate of reductant permeation. These observations indicate that in reconstituted vesicles the delta-delta disulfide bridge lies in the same aqueous space as the ACh binding sites. They are most easily reconciled with folding models that propose an even number of transmembrane crossing per subunit.

Animals↗
PubMed1986

Reformation of crystalline purple membrane from purified bacteriorhodopsin fragments.

Reconstituted crystalline purple membrane has been prepared starting from denatured bacteriorhodopsin (BR) fragments, native lipids and retinal. The two chymotryptic fragments are thought to contain respectively five and two transmembrane alpha-helices in native BR. The new reconstitution procedure, a modification of that of Huang et al. (1986, J. Biol. Chem., 256, 3802), relies on dodecylsulfate precipitation by potassium ions and yields samples with a high protein-to-lipid ratio (approximately 1:1 w/w). X-ray and neutron diffraction measurements show that in the reconstituted samples BR molecules are arranged in a P3 two-dimensional lattice with the same unit cell dimensions as the native purple membrane lattice. Analysis of reflection intensities indicates that the reconstituted molecules have regained the structure of native BR to 7 A resolution.

Bacteriorhodopsins↗
PubMed1986

Localization of two chymotryptic fragments in the structure of renatured bacteriorhodopsin by neutron diffraction.

The structure of crystalline purple membrane reconstituted from purified bacteriorhodopsin (BR) chymotryptic fragments has been studied by neutron diffraction. In one of the samples studied, the fragment C-2, encompassing the first two predicted transmembrane segments, was prepared from deuterated purple membrane. The diffraction changes when the natural C-2 fragment is substituted by a deuterated one are analysed in terms of a seven-helix model for BR. The assignment of the labelled fragment to one end of the molecule placed new constraints on folding models for the protein.

Bacteriorhodopsins↗
PubMed1984

Image analysis of the heavy form of the acetylcholine receptor from Torpedo marmorata.

The structure of the heavy (H) form of the acetylcholine receptor, which comprises two covalently linked 250,000 Mr oligomers, has been investigated by numerical analysis of electron microscope images. Na-cholate solubilized Torpedo marmorata H-form receptor was reintegrated into artificial lipid vesicles and negatively stained with uranyl acetate prior to imaging in a conventional transmission microscope. The reconstituted preparations exhibited the standard polypeptide composition of the purified receptor (alpha 2 beta gamma delta) and the same transmembrane arrangement as in the native subsynaptic membrane. Covalent disulfide linkage between the two oligomers took place exclusively through the delta chains. In agreement with previous work (Cartaud et al., 1980) the H-form appeared as "doublets" of two coplanar 9 nm rosettes at a center-to-center distance of 9.2 +/- 1.1 nm. The relative angular orientation of the two rosettes in a doublet was examined by correlation analysis in the real space. It exhibited a marked variability, few of the doublets featuring any kind of symmetry, suggesting that the two oligomers of a doublets are connected via an extended and flexible chain or loop. The area of contact between the two rosettes of a doublet therefore does not necessarily represent a reliable clue as to the location of the delta chain within the structure. Averaged images obtained after reorientation and summation of up to 132 rosettes revealed the three major peaks and the two grooves already observed in previous studies. Two additional smaller peaks were identified. Tentative assignment of structural details to individual subunits was deduced from an examination of alpha-bungarotoxin-labeled doublets. The alpha subunits, which carry part or all of the acetylcholine binding sites, are probably located in nonadjacent positions in the vicinity of the newly found peaks. This assignment is consistent with the image analysis of receptor-toxin complexes recently reported by Zingsheim et al. (1982b).

Animals↗