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Journal Issue - Volume 14 Issue 2 (February 2005)

Abstract The Critical Assessment of PRedicted Interactions (CAPRI) experiment was designed in 2000 to test protein docking algorithms in blind predictions of the structure of protein–protein complexes. In four years, 17 complexes offered by crystallographers as targets prior to publication, have been subjected to structure prediction by docking their two components. Models of these complexes were submitted by predictor groups and...

Abstract We previously reported the construction of a family of reagentless fluorescent biosensor proteins by the structure‐based design of conjugation sites for a single, environmentally sensitive small molecule dye, thus providing a mechanism for the transduction of ligand‐induced conformational changes into a macroscopic fluorescence observable. Here we investigate the microscopic mechanisms that may be responsible for the...

Abstract Endo‐β‐1,4‐xylanases of the family 11 glycosyl‐hydrolases are catalytically active over a wide range of pH. Xyl1 from Streptomyces sp. S38 belongs to this family, and its optimum pH for enzymatic activity is 6. Xyn11 from Bacillus agaradhaerens and XylJ from Bacillus sp. 41M‐1 share 85% sequence identity and have been described as highly alkalophilic enzymes. In an attempt to better understand the alkalophilic adaptation of xylanases, the...

Abstract Furin proteolytically cleaves a wide variety of proprotein substrates mainly within the trans‐Golgi network (TGN) but also at the cell membrane and in endosomal compartments where pH is more acidic. Incorporation of furin recognition sequences within the reactive site loop (RSL) of α1‐antitrypsin (AT) leads to the production of furin inhibitors. In an attempt to design more stable, potent, and specific serpin‐based inhibitors, we...

Abstract Many protein–protein docking algorithms generate numerous possible complex structures with only a few of them resembling the native structure. The major challenge is choosing the near‐native structures from the generated set. Recently it has been observed that the density of conserved residue positions is higher at the interface regions of interacting protein surfaces, except for antibody–antigen complexes, where a very low...

Abstract The stability toward thermal and urea denaturation was measured for HAMLET (human α‐lactalbumin made lethal to tumor cells) and α‐lactalbumin, using circular dichroism and fluorescence spectroscopy as well as differential scanning calorimetry. Under all conditions examined, HAMLET appears to have the same or lower stability than α‐lactalbumin. The largest difference is seen for thermal denaturation of the calcium free (apo) forms,...

Abstract The structure of a chaperonin caging a substrate protein is not quite clear. We made engineered group II chaperonins fused with a guest protein and analyzed their structural and functional features. Thermococcus sp. KS‐1 chaperonin α‐subunit (TCP) which forms an eightfold symmetric double‐ring structure was used. Expression plasmids were constructed which carried two or four TCP genes ligated head to tail in phase and a target protein...

Abstract The β‐turn is the most common type of nonrepetitive structure in globular proteins, comprising ∼25% of all residues; however, a detailed understanding of effects of specific residues upon β‐turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF‐1) is a member of the β‐trefoil superfold and contains a total of five β‐hairpin structures (antiparallel β‐sheets connected by a reverse turn)....

Abstract Using a recently developed program (SCOPmap) designed to automatically assign new protein structures to existing evolutionary‐based classification schemes, we identify a evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA‐man), dihydroxyacetone kinase (Dak), and DegV. Several lines of evidence support unification of these three folds into a single superfamily: statistically...

Abstract The effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly β‐sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal...

Abstract Gag protein oligomerization, an essential step during virus assembly, results in budding of spherical virus particles. This process is critically dependent on the spacer p2, located between the capsid and the nucleocapsid proteins. P2 contributes also, in association with NCp7, to specific recognition of the HIV‐1 packaging signal resulting in viral genome encapsidation. There is no structural information about the 20 last...

Abstract Superoxide dismutases (SODs) are a family of metalloenzymes that catalyze the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Iron superoxide dismutases (FeSODs) are only expressed in some prokaryotes and plants. A new and highly active FeSOD with an unusual subcellular localization has recently been isolated from the plant Vigna unguiculata (cowpea). This protein functions as a homodimer and, in...

Abstract This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A2 (PLA2) and also to a PLA2 with Asp 49. The fatty acid identified as n‐tridecanoic acid is observed at the substrate recognition site of PLA2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA2 was determined using the cDNA method. Three‐dimensional structure has been solved by the...

Abstract Protein subunits of several RNA viruses are known to undergo post‐assembly, autocatalytic cleavage that is required for infectivity. Nudaurelia capensis ω virus (Nω V) is one of the simplest viruses to undergo an autocatalytic cleavage, making it an excellent model to understand both assembly and the mechanism of autoproteolysis. Heterologous expression of the coat protein gene of Nω V in a baculovirus system results in the...

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