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Journal Issue - Volume 13 Issue 6 (June 2004)

Abstract The ankyrin repeat is one of the most frequently observed amino acid motifs in protein databases. This protein–protein interaction module is involved in a diverse set of cellular functions, and consequently, defects in ankyrin repeat proteins have been found in a number of human diseases. Recent biophysical, crystallographic, and NMR studies have been used to measure the stability and define the various topological features...

Abstract Nanoseconds long molecular dynamics (MD) trajectories of differently active complexes of human cyclin‐dependent kinase 2 (inactive CDK2/ATP, semiactive CDK2/Cyclin A/ATP, fully active pT160‐CDK2/Cyclin A/ATP, inhibited pT14‐; pY15‐; and pT14,pY15,pT160‐CDK2/Cyclin A/ATP) were compared. The MD simulations results of CDK2 inhibition by phosphorylation at T14 and/or Y15 sites provide insight into the structural aspects of CDK2...

Abstract The structure of Mth677, a hypothetical protein from Methanobacterium thermoautotrophicum (Mth), has been determined by using heteronuclear nuclear magnetic resonance (NMR) methods on a double‐labeled 15N‐13C sample. Mth677 adopts a novel α+β fold, consisting of two α‐helices (one N terminal and one C terminal) packed on the same side of a central β‐hairpin. This structure is likely shared by its three orthologs, detected in three other...

Abstract Two hydrophobic sequences, 24 and 30 residues long, identify the membrane‐spanning segments of chemoreceptor Trg from Escherichia coli. As in other related chemoreceptors, these helical sequences are longer than the minimum necessary for an α‐helix to span the hydrocarbon region of a biological membrane. Thus, the specific positioning of the segments relative to the hydrophobic part of the membrane cannot be deduced from sequence...

Abstract Antibodies of type IgG may be divided into two classes, called λor κ, depending on the type of light chain. We have identified a conserved pocket between the two domains CH1 and CL of human IgG κ‐Fab, which is not present in the λ type. This pocket was used as a target docking site with the purpose of exploring the possibilities of designing affinity ligands that could function as such even after immobilization to gel. The...

Abstract 7‐Azatryptophan (AW), a noncoded isostere of tryptophan (W), possesses interesting spectral properties. In particular, the presence of a nitrogen atom at position 7 in the indolyl nucleus of AW results in a red shift of the absorption maximum and fluorescence emission by 10 and 46 nm, respectively, compared to W. In the present work, we report the chemical synthesis and the conformational and functional characterization of...

Abstract The α‐hemolysin is an archetypal pore‐forming protein that is secreted from Staphylococcus aureus as a water‐soluble monomer. When the monomer binds to the membrane of a susceptible cell, the membrane‐bound molecules assemble into the lytic heptamer. Although a bilayer or a bilayer‐like environment are essential to toxin assembly, there is no high resolution information on toxin–phospholipid complexes. We have determined the structures...

Abstract The type 1 HIV presents a conical capsid formed by ∼1500 units of the capsid protein, CA. Homodimer‐ization of CA via its C‐terminal domain, CA‐C, constitutes a key step in virion assembly. CA‐C dimerization is largely mediated by reciprocal interactions between residues of its second α‐helix. Here, we show that an N‐terminal‐acetylated and C‐terminal–amidated peptide, CAC1, comprising the sequence of the CA‐C dimerization...

Abstract Antifreeze proteins (AFPs) are synthesized by various organisms to enable their cells to survive subzero environment. These proteins bind to small ice crystals and inhibit their growth, which if left uncontrolled would be fatal to cells. The crystal structures of a number of AFPs have been determined; however, crystallographic analysis of AFP–ice complex is nearly impossible. Molecular modeling studies of AFPs' interaction...

Abstract Several temperature‐sensitive folding (tsf) mutants of the tailspike protein from bacteriophage P22 have been found to fold with lower efficiency than the wild‐type sequence, even at lowered temperatures. Previous refolding studies initiated from the unfolded monomer have indicated that the tsf mutations decrease the rate of structured monomer formation. We demonstrate that pressure treatment of the tailspike aggregates ...

Abstract Pseudomonas aeruginosa alcohol dehydrogenase (PaADH; ADH, EC 1.1.1.1) catalyzes the reversible oxidation of primary and secondary alcohols to the corresponding aldehydes and ketones, using NAD as coenzyme. We crystallized the ternary complex of PaADH with its coenzyme and a substrate molecule and determined its structure at a resolution of 2.3 Å, using the molecular replacement method. The PaADH tetramer comprises four...

Abstract Ski8p is a 44‐kD protein that primarily functions in the regulation of exosome‐mediated, 3′→ 5′ degradation of damaged mRNA. It does so by forming a complex with two partner proteins, Ski2p and Ski3p, which complete a complex that is capable of recruiting and activating the exosome/Ski7p complex that functions in RNA degradation. Ski8p also functions in meiotic recombination in complex with Spo11 in yeast. It is one of the...

Abstract The halide specificity of vanadium‐dependent bromoperoxidase (BPO) from the marine algae, Corallina pilulifera, has been changed by a single amino acid substitution. The residue R397 has been substituted by the other 19 amino acids. The mutant enzymes R397W and R397F showed significant chloroperoxidase (CPO) activity as well as BPO activity. These mutant enzymes were purified and their properties were investigated. The maximal...

Abstract The conformational features of native and mutant forms of sperm‐whale apomyoglobin (apoMb) at neutral pH were probed by limited proteolysis experiments utilizing up to eight proteases of different substrate specificities. It was shown that all proteases selectively cleave apoMb at the level of chain segment 82–94 (HEAELKPLAQSHA), encompassing helix F in the X‐ray structure of the holo form of the native protein; for...

Abstract Heterodimers of rat glutathione S‐transferase A1–1 were formed using one wild‐type subunit and one subunit with a mutation at the interface to evaluate whether the subunits are interactive or independent. Within the subunit interface, we are considering two regions of interactions: one region consists of a “hydrophobic ball and socket” with Phe 52 from one subunit as the ball and Phe 136 from the second subunit as one of...

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