A polyclonal antibody (anticentrin) distinguishes between two types of fibrous flagellar roots in green algae

Summary The two main types of fibrous flagellar roots present in the flagellar apparatus of green algae (system I and system II fibers) are immunologically distinct as indicated by the localization of a Ca²⁺-modulated contractile protein (centrin) exclusively in one type (system II fibers) but not in the other type (system I fibers). A polyclonal antibody generated against the major protein of the striated flagellar roots (system II fibers) of the quadriflagellate green algaTetraselmis striata was used to localize centrin by immunofluorescence and pre- and postembedding immunogold electron microscopy in the flagellar apparatus ofSpermatozopsis similis, S. exsultans, Chlamydomonas reinhardtii, Dunaliella bioculata, Polytomella parva and gametes ofMonostroma grevillei andEnteromorpha sp. Whereas the antibody recognizes centrin in connecting fibers and system II fibers, no labeling occurs in system I fibers in all taxa investigated. This study presents the first evidence that system I fibers lack centrin and indicates that the two main types of fibrous flagellar roots in green algae are biochemically distinct.     

Freeze-Fracture Study of the Bloodstream Form of Trypanosoma brucei gambiense

The ultrastructure of Trypanosoma brucei gambiense was investigated by the freeze-fracture method. Three different regions of the continuous plasma membrane; cell body proper, flagellar pocket, and flagellum were compared in density and distribution of the intramembranous particles (IMP's). The IMP-density was highest in the flagellar pocket membrane and lowest in flagellum. Intra membranous particles of the cell body membrane were distributed uniformly on both the protoplasmic (P) and exoplasmic (E) faces. On the P face of the flagellar membrane, a single row of IMP-clusters was seen along the juncture of the flagllum to the cell body. Since the spacing of the IMP-clusters was almost equal to the spacing of the paired rivet structures observed in thin section, these clusters likely are related to the junction of flagellum and cell body. At the neck of the flagellar pocket, several linear arrays of IMP's were found on the P face of the flagellar membrane, while on the E face rows of depressions were seen. At the flagellar base, the clusters of IMP's were only seen on the P face. On the flagellar pocket membrane, particle-rich depressions and linear particle arrays were also found on the P face, while on the E face such special particle arrangements were not recognized. These particle-rich depressions may correspond to the sites of pinocytosis of the bloodstream forms which have been demonstrated in thin sections.     

Flagellar Development During the Cell Cycle in Chlamydomonas reinhardtii

Flagellar development during the asexual synchronous cell cycle of Chlamydomonas reinhardtii (11.32 aM) was studied by light microscopy. Cell walls of sporangia of different developmental status were dissolved using gamete lysin (g-lysin) enabling direct observation of flagellar development. Flagellar growth in progeny cells exhibits a linear kinetic with a growth rate of 28 nm/min at 30°C leading to a flagellar length of 7–7.5 μm in 4–4.5 h. After this time the flagellar growth rate drops to 2.8 nm/min (as in interphase). Both flagella of a single cell and all flagella within a sporangium grow out at the same time and with the same rate. Cycloheximide (10 μg/ml) completely blocks flagellar development. If cycloheximide is removed flagellar growth resumes at the normal rate with no lag-phase. Flagellar development during the cell cycle in C. reinhardtii differs considerably from the well-studied model system of flagellar regeneration following amputation in the same species.     

THE OCCURRENCE AND STRUCTURE OF FLAGELLAR SCALES IN SOME FRESHWATER CRYPTOPHYTES1

Flagellar scales were found in seven out of eleven fresh-water cryptophytes investigated by shadowing whole cells. All scales examined were 140 to 170 nm in diameter and had a basic seven-sided rosette pattern with delicate interlacing. The results of this study indicate that flagellar scales are common in cryptophytes .     

The fine structure of Leishmania enriettii in the guinea pig

A study of the fine structure of Leishmania enriettii in the guinea-pig has been presented. There was close similarity to other members of the same genus and the finding of 2–3 axonemes (rhizoplasts) reported previously by other workers in non-dividing protozoa of the same species has not been confirmed. The functions of the main organelles and the morphological differences observed in comparison with those of other species have been reviewed.     

Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus

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Automated identification of binding sites for phosphorylated ligands in protein structures

Phosphorylation is a crucial step in many cellular processes, ranging from metabolic reactions involved in energy transformation to signaling cascades. In many instances, protein domains specifically recognize the phosphogroup. Knowledge of the binding site provides insights into the interaction, and it can also be exploited for therapeutic purposes. Previous studies have shown that proteins interacting with phosphogroups are highly heterogeneous, and no single property can be used to reliably identify the binding site. Here we present an energy‐based computational procedure that exploits the protein three‐dimensional structure to identify binding sites involved in the recognition of phosphogroups. The procedure is validated on three datasets containing more than 200 proteins binding to ATP, phosphopeptides, and phosphosugars. A comparison against other three generic binding site identification approaches shows higher accuracy values for our method, with a correct identification rate in the 80–90% range for the top three predicted sites. Addition of conservation information further improves the performance. The method presented here can be used as a first step in functional annotation or to guide mutagenesis experiments and further studies such as molecular docking. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

Identification of protein functional surfaces by the concept of a split pocket

The function of a protein is often fulfilled via molecular interactions on its surfaces, so identifying the functional surface(s) of a protein is helpful for understanding its function. Here, we introduce the concept of a split pocket, which is a pocket that is split by a cognate ligand. We use a geometric approach that is site‐specific. Specifically, we first compute a set of all pockets in the protein with its ligand(s) and a set of all pockets with the ligand(s) removed and then compare the two sets of pockets to identify the split pocket(s) of the protein. To reduce the search space and expedite the process of surface partitioning, we design probe radii according to the physicochemical textures of molecules. Our method achieves a success rate of 96% on a benchmark test set. We conduct a large‐scale computation to identify ～19,000 split pockets from 11,328 structures (1.16 million potential pockets); for each pocket, we obtain residue composition, solvent‐accessible area, and molecular volume. With this database of split pockets, our method can be used to predict the functional surfaces of unbound structures. Indeed, the functional surface of an unbound protein may often be found from its similarity to remotely related bound forms that belong to distinct folds. Finally, we apply our method to identify glucose‐binding proteins, including unbound structures. Our study demonstrates the power of geometric and evolutionary matching for studying protein functional evolution and provides a framework for classifying protein functions by local spatial patterns of functional surfaces. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl‐tRNA synthetase enzymes

Orthogonal aminoacyl‐tRNA synthetase/tRNA pairs from archaea have been evolved to facilitate site specific in vivo incorporation of unnatural amino acids into proteins in Escherichia coli. Using this approach, unnatural amino acids have been successfully incorporated with high translational efficiency and fidelity. In this study, CHARMM‐based molecular docking and free energy calculations were used to evaluate rational design of specific protein–ligand interactions for aminoacyl‐tRNA synthetases. A series of novel unnatural amino acid ligands were docked into the p‐benzoyl‐L ‐phenylalanine tRNA synthetase, which revealed that the binding pocket of the enzyme does not provide sufficient space for significantly larger ligands. Specific binding site residues were mutated to alanine to create additional space to accommodate larger target ligands, and then mutations were introduced to improve binding free energy. This approach was used to redesign binding sites for several different target ligands, which were then tested against the standard 20 amino acids to verify target specificity. Only the synthetase designed to bind Man‐α‐O‐Tyr was predicted to be sufficiently selective for the target ligand and also thermodynamically stable. Our study suggests that extensive redesign of the tRNA synthatase binding pocket for large bulky ligands may be quite thermodynamically unfavorable. Proteins 2010. © 2010 Wiley‐Liss, Inc.