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PubMed2004

Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.

We show that residues at the interfaces of protein-protein complexes have higher side-chain energy than other surface residues. Eight different sets of protein complexes were analyzed. For each protein pair, the complex structure was used to identify the interface residues in the unbound monomer structures. Side-chain energy was calculated for each surface residue in the unbound monomer using our previously developed scoring function.1 The mean energy was calculated for the interface residues and the other surface residues. In 15 of the 16 monomers, the mean energy of the interface residues was higher than that of other surface residues. By decomposing the scoring function, we found that the energy term of the buried surface area of non-hydrogen-bonded hydrophilic atoms is the most important factor contributing to the high energy of the interface regions. In spite of lacking hydrophilic residues, the interface regions were found to be rich in buried non-hydrogen-bonded hydrophilic atoms. Although the calculation results could be affected by the inaccuracy of the scoring function, patch analysis of side-chain energy on the surface of an isolated protein may be helpful in identifying the possible protein-protein interface. A patch was defined as 20 residues surrounding the central residue on the protein surface, and patch energy was calculated as the mean value of the side-chain energy of all residues in the patch. In 12 of the studied monomers, the patch with the highest energy overlaps with the observed interface. The results are more remarkable when only three residues with the highest energy in a patch are averaged to derive the patch energy. All three highest-energy residues of the top energy patch belong to interfacial residues in four of the eight small protomers. We also found that the residue with the highest energy score on the surface of a small protomer is very possibly the key interaction residue.

Amino Acids↗

PubMed1990

Two different RNA polymerase II initiation complexes can assemble on the rat brain creatine kinase promoter.

The rat brain creatine kinase (CKB) gene has a structurally complex promoter. Although it contains a consensus RNA polymerase II TATA box, this is located at -60 relative to the main transcription start site, an unprecedented distance for mammalian TATA boxes. Steady-state messenger RNA for CKB is extremely abundant in brain, yet barely detectable in liver. Using a nuclear run-on analysis, we show that this difference is due, at least in part, to a difference in the rate at which CKB is transcribed in these tissues. We also demonstrate a tissue-specific hypersensitive site in the promoter region of the CKB gene. In vitro transcription experiments using nuclear extract isolated from liver, brain, and HeLa cells show a marked difference in the way these extracts recognize the CKB promoter. Two different preinitiation complexes can assemble on the CKB promoter, one which initiated at the same downstream start-site used in normal adult rat brain and one which initiated 35 base pairs further upstream. Extracts from brain form exclusively the downstream initiating complex. However, liver extracts favor formation of the upstream initiating complex, but formation of this complex can be blocked if brain or HeLa extract is added first. We demonstrate that the upstream consensus TATA box can function as a TATA box to mediate upstream initiation, but is not required for downstream initiation. We have shown previously that brain and HeLa cell nuclear extracts contain an abundant factor, TARP, which binds to the upstream consensus TATA box and have proposed that this factor is distinct from the classical TATA box binding factor TFIID. We propose that binding of TARP to the upstream consensus TATA box may block formation of the upstream initiating complex.

Animals↗

PubMed2004

Structural investigation of amylose complexes with small ligands: helical conformation, crystalline structure and thermostability.

Crystalline amylose complexes were prepared with decanal, 1-butanol, menthone and alpha-naphtol. Their crystalline structure and the related helical conformation, determined by wide angle X-ray diffraction (WAXD) and 13C CPMAS solid state NMR, were assigned to V6I, V6II, V6III and V8 types, respectively. It was possible to propose some hypotheses on the possible nature of interactions and especially intra-/inter-helical inclusion. Some shifts in the NMR C1 carbon signals were attributed to the presence of ligand in specific sites inside the structure for a same type of V6 helical conformation. Moreover, the crystallinity and polymorphic changes induced by desorption/rehydration were studied. A general increase of the carbon resonances sharpness upon rehydration has been observed, but also a V6II-V6I transition when decreasing the water content. Differential scanning calorimetry (DSC) experiments were also performed to approach the thermostability of the four types of complex and also the way they form again after melting/cooling sequences.

Amylose↗

PubMed2003

The nuclear pore complex: nucleocytoplasmic transport and beyond.

Over the past two years, it has become evident that there is an unexpected link between nuclear pore complex structure and dynamics, nucleocytoplasmic transport and chromosome segregation. In addition, a tomographic three-dimensional reconstruction of native nuclear pore complexes preserved in thick amorphous ice has unveiled a number of new structural features of this supramolecular machine. These data, together with some of the elementary physical principles that underlie nucleocytoplasmic transport, will be discussed in this review.

Active Transport, Cell Nucleus↗

PubMed2002

[Differentiation potential of human stem cells--approaches to tissue engineering and to cell transplantation].

The prospect of future clinical applications of human stem cells is one of the major arguments for the use of embryonic stem cells. Scientists are currently developing methods to culture and isolate different somatic cell types. The enormous capacity for proliferation of embryonic and certain adult stem cells combined with suitable protocols to differentiate these cells may allow the production of sufficient amounts even of those cell types which cannot be expanded in the terminal differentiated state. The ability to generate large quantities of certain somatic cells in vitro has led to the first cell transplantation-based therapeutic concepts and clinical studies. Even today comparatively simply structured in vitro-engineered tissues are applied clinically. However, to grow larger and more complex structures, a variety of problems including their vascularisation and the development of suitable matrices have to be resolved. In the long term, tissue engineering offers an as yet incalculable potential for future medical applications and may finally allow the development and clinical transplantation of complex tissues or even whole organs.

Cell Culture Techniques↗

PubMed2000

Polynuclear chromium(III) carboxylates. 1. Synthesis, structure, and magnetic properties of an octanuclear complex with a ring structure.

A novel cyclic octanuclear chromium(III) complex with hydroxo and acetato bridging ligands was isolated and its structure determined by X-ray crystallography. The complex [Cr8(OH)12(OAc)12] (1) (OAc- = CH3CO2-), as found in crystals of 1.34H2O, is obtained by refluxing an aqueous solution of the trinuclear "basic" chromium acetate. 1.34H2O crystallizes in the tetragonal space group I42d with the following unit cell dimensions: a = 16.592(2) A, c = 31.557(4) A, V = 8687(1) A3, and Z = 2. A total of 2000 unique data with I > 3 sigma (I) were used to solve and refine the structure to R(Fo) = 0.066 and Rw(Fo) = 0.085. The structure consists of eight Cr(III) ions that form a ring structure and are bridged by hydroxo and acetato ligands. Each of the two neighboring metal atoms in 1 is bridged either by two OH- ligands and one OAc- ligand, with a Cr...Cr distance of 2.949(2) A, or by two OAc- ligands and one OH- ligand, with a Cr...Cr distance of 3.383(2) A in an alternating fashion. The complex resides on a crystallographic 4 center, and the overall symmetry of 1 is S4. The magnetic susceptibility of 1.34H2O was measured in the temperature range of 5-240 K. Our theoretical modeling of the susceptibility data indicates alternating antiferromagnetic exchange interactions between adjacent spin 3/2 Cr3+ ions around the ring, of magnitude J/kB = 13.7 and 8.9 K, respectively.

Journal Article↗

PubMedDate not supplied

[Circular dichroism of DNA complexes with dyes. III. Effect of latent optical activity and the structure of the complexes].

Circular dichroism anisotropy was studied both theoretically and experimentally for the complexes of DNA and dsRNA with dyes (proflavine, 2,7-di-t-butyl proflavine, "Hoechst-33258") and antibiotics (distamycin A, netropsin and olivomycin). Theoretical analysis showed that general features of CD anisotropy, revealed in the previous studies (CD components--delta epsilon parallel to and delta epsilon perpendicular--are ten times or more bigger than the CD-effect without orientation, and delta epsilon parallel to approximately 2 delta epsilon perpendicular) are due to the existence of a specific effect named "latent" optical activity (LOA). This effect can be observed in many cases of non-chiral symmetrical chromophores if they are oriented. The effect is due to the excitation of an electrical dipole transition and a perpendicular magnetic dipole transition (or quadrupole transition) of a molecule. The amplitude and the sign of the LOA-effect depends on the orientation of the chromophores with respect to the light beam; with a random orientation the mutual compensation of LOA-effects of different chromophores happens and no LOA-effect appears. The analitycal expressions relating the value of LOA-effect of the system with electronical characteristics of the chromophores and the geometrical parametra of their arrangement was obtained. The experimental data obtained for the oriented complexes of DNA and dsRNA with proflavine made it possible to determine an angle between the chromophore and the plane perpendicular to the DNA axis--gamma. For the calf thymus DNA gamma = = + 1.8 +/- 0.4 degrees, for the phage T2 DNA gamma = + 2.2 +/- 0.4 degrees, and for phage f2 dsRNA gamma=--3.5 +/- +/- 0.5 degrees. These results, obtained at relatively low concentrations of the bound proflavine (r approximately 0.01), are in accordance with the intercalating mode of the dye binding. A study of CD anisotropy of DNA complexes with other ligands showed that many different chromophores possess LOA-effect. This phenomenon can be used to obtain both spectroscopic and structural information about the systems similar to those reported here.

Acridines↗

PubMed2006

Habitat structure is associated with the expression of carotenoid-based coloration in nestling blue tits Parus caeruleus.

We investigated how the expression of carotenoid-based plumage coloration (lightness and chroma) in nestling blue tits Parus caeruleus is associated with forest structure in oak forests of central Spain. We found evidence of a reduced expression of carotenoid-based coloration in nestlings growing up in successionally young and structurally simple forest territories. Our results suggest that breast feather coloration can be used as an indicator of nestling quality because nestlings with more intense yellow plumage coloration had larger body size and stronger immune responses to the injection of phytohemagglutinin (PHA). Given the association of forest structural complexity with carotenoid-based plumage coloration, our findings suggest that variation in habitat structure may have a significant impact on forest birds in their first stages of life which has implications for forest management practices.

Animals↗

PubMed1986

Protein crosslinking reagents containing a selenoethylene linker are cleaved by mild oxidation.

A homobifunctional cleavable crosslinking reagent containing a selenoethylene group in the linker, and related reagents, have been synthesized and tested in a model system involving formation of a complex between albumin and cytochrome c. Functionally, complex formation was suggested by albumin inhibition of the ascorbate reduction of cytochrome c. Structurally, complex formation was demonstrated by crosslinking and subsequent separation of crosslinked complex from non-crosslinked proteins by SDS-polyacrylamide gel electrophoresis. The crosslinks were found to be cleavable by mild oxidation with low concentrations of periodate or with N-chlorobenzenesulfonamide immobilized on polystyrene beads (Iodo-Beads).

Albumins↗

PubMed1980

Histology of normal aortas in birds with emphasis on intimal thickening.

Published studies of normal aortic structure have been infrequent in birds despite a high prevalence of spontaneous atherosclerosis relative to mammals, and a feeling that this prevalence of atherosclerosis might be related to the pecularities of aortic structure in birds. We describe aortic structure in 26 birds, including 22 species and 12 families. All aortas had a complex structure similar to hat of the White Carneau pigeon which has been carefully studied. Diffuse intimal thickening (DIT) was found in the elastic zones in 22 of the 26 aortas. This lesion has not been previously described as such, and consisted of multiple longitudinally oriented elastic laminae apparently synthesized by interlamellar connective tissue cells, the latter being peculiar to the avian aorta. Focal intimal thickenings were very common in the non-elastic zones of the aortas, and were composed of smooth muscle cells and elastic laminae similar to the DIT of mammals. Their location suggested that blood flow patterns might be an important influence in their development. The fact that atherosclerotic lesions usually occurred in the non-elastic zones of the avian aorta suggested that some property of the elastic zone or the interlamellar connective tissue cells might inhibit the development of atherosclerosis.

Animals↗

PubMed1991

Structure of the human interferon alpha receptor.

The structure of the IFN alpha receptor has been studied by methods such as affinity crosslinking and gel chromatography over the last 8 years. The recent development of monoclonal antibodies against the receptor, and the cloning of an IFN alpha receptor cDNA has provided new important tools to understand the IFN alpha receptor structure. Thus, it has become obvious that the IFN alpha receptor has a more complex structure than first anticipated, probably involving more than one subunit. This review analyzes the present knowledge about the structure of the IFN alpha receptor, as well as many unresolved issues concerning this topic.

Animals↗

PubMed2000

Role of rap in the biogenesis of lipoprotein receptors.

The LDL receptor gene family is composed of several endocytic receptors that share structural homology and function in cellular uptake of various ligands including lipoprotein particles. The complex structure of these lipoprotein receptors is highlighted by the presence of clusters of cysteine-rich ligand-binding repeats. An important feature that is shared by all these receptors is the inhibition of ligand interaction by a 39-kDa receptor-associated protein (RAP). Recent studies have shown that under physiological conditions RAP serves as a molecular chaperone to assist the folding of lipoprotein receptors and their safe passage through the secretory pathway. Several non-exclusive models have been proposed regarding the molecular mechanisms of RAP function as an antagonist for ligand interaction with the receptors and as a molecular chaperone within the early secretory pathway. Elucidation of these mechanisms may provide insights into how biogenesis of lipoprotein receptors can be regulated via the expression of RAP under physiological and pathological conditions.

Carrier Proteins↗

PubMed2005

Classification of wheat varieties based on structural features of arabinoxylans as revealed by endoxylanase treatment of flour and grain.

Arabinoxylans (AX) are cell wall polysaccharides of complex structure involved in many aspects of wheat flour end uses. The study of the variations of AX structure can lead to the identification of genes involved in their biosynthesis, and thus in the control of the various aspects of grain quality related to their presence. A method is proposed to identify AX variations directly in whole grain by enzymatic degradation. An endoxylanase from Trichoderma viride was used to extract AX from a collection of 20 wheat cultivars (Triticum aestivum L.). Enzymatic degradation products were analyzed by HPAEC and multivariate analysis techniques (principal component analysis, canonical correlation analysis, and cluster analysis) were applied to analyze chromatographic data. The method evidenced variations in the proportion of mono- and disubstitution of the xylan backbone by arabinose side chains, allowing classification of the different varieties according to the structural features of AX. A similar classification was obtained starting from flour or whole grain, indicating that the method was specific of AX from endosperm tissues. In conclusion, the method combining endoxylanase treatment of wheat grain and the analysis of degradation products, e.g., enzymatic fingerprinting, can be applied to collections of wheat cultivars, and possibly other cereals in order to establish quantitative trait loci related to the biosynthesis of AX.

Cell Wall↗

PubMed2006

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.

The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C(4) photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.

Animals↗

PubMed2002

Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition.

Base Pairing↗

PubMed2004

ViTO: tool for refinement of protein sequence-structure alignments.

UNLABELLED: ViTO is a graphical application, including an editor, of multiple sequence alignment and a three-dimensional (3D) structure viewer. It is possible to manipulate alignments containing hundreds of sequences and to display a dozen structures. ViTO can handle so-called 'multiparts' alignments to allow the visualization of complex structures (multi-chain proteins and/or small molecules and DNA) and the editing of the corresponding alignment. The 3D viewer and the alignment editor are connected together allowing rapid refinement of sequence-structure alignment by taking advantage of the immediate visualization of resulting insertions/deletions and strict conservations in their structural context. More generally, it allows the mapping of informations about the sequence conservation extracted from the alignment onto the 3D structures in a dynamic way. ViTO is also connected to two comparative modelling programs, SCWRL and MODELLER. These features make ViTO a powerful tool to characterize protein families and to optimize the alignments for comparative modelling. AVAILABILITY: http://bioserv.cbs.cnrs.fr/VITO/DOC/. SUPPLEMENTARY INFORMATION: http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html.

Amino Acid Sequence↗

PubMedDate not supplied

The stentless porcine valve.

Recognition of the long-term results of homografts has brought about a renewed interest in stentless valves. This has been matched by the introduction of several glutaraldehyde preserved porcine stentless prostheses. The early experience indicates that these valves are technically somewhat simpler to insert than homografts and are associated with satisfactory early and immediate-term results. In particular, they appear to offer an earlier and more complete resolution of left ventricular hypertrophy. Correct insertion of a stentless porcine valve needs meticulous attention to detail and awareness of the precise anatomical features of the aortic root, which is a complex structure. Although the myocardial ischemic and cardiopulmonary bypass times are longer for the more complex insertion of this prosthesis, our studies indicate that this has no serious disadvantage to the patient and is more than matched by an improved hemodynamic performance associated with more stable left ventricular function. The theoretical advantages of a stentless valve substitute in the aortic position seem clear. Further detailed prospective studies are needed to report on the long-term performance of this valve.

Animals↗

PubMed1998

Ret finger protein is a normal component of PML nuclear bodies and interacts directly with PML.

The ret finger protein (rfp) is a member of the B-box zinc finger gene family many of which may function in growth regulation and in the appropriate context become oncogenic. Members of this family are nuclear proteins that possess a characteristic tripartite motif consisting of the RING and B-box zinc binding domains and a coiled-coil domain. The promyelocytic leukemia gene (PML), another B-box family member, produces a protein product that is detected within punctate nuclear structures called PML nuclear bodies (NBs) or PML oncogenic domains (PODs). These NBs are complex structures that consist of a number of different proteins many of which have yet to be identified. In the disease acute promyelocytic leukemia (APL) a fusion protein, PML-RARA, is produced through the t(15:17) translocation. In APL the morphology of the NBs is altered. We report that rfp co-localizes with PML in a subset of the PML NBs and that it interacts directly with PML. This interaction is mediated through the rfp B-box and the distal two coils. In contrast, homomultimerization of rfp preferentially involves the B-box and the proximal coil. The association of rfp with the PML NBs is altered by mutations that affect rfp/PML interaction and in NB4 cells that are derived from APL patients. When treated with retinoic acid, rfp reassociates with the NBs in a pattern similar to non APL cells. Additionally, we found that rfp colocalizes with PML-RARA protein produced in APL patients. These results suggest that rfp, along with the other known/unknown components of PML NBs, have an important role in regulating cellular growth and differentiation.

Amino Acid Sequence↗