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Journal Issue - Volume 6 Issue 10 (October 1997)

Abstract The AAA protein family, a recently recognized group of Walker‐type ATPases, has been subjected to an extensive sequence analysis. Multiple sequence alignments revealed the existence of a region of sequence similarity, the so‐called AAA cassette. The borders of this cassette were localized and within it, three boxes of a high degree of conservation were identified. Two of these boxes could be assigned to substantial parts of...

Abstract The Ca2+‐binding epidermal growth factor (cbEGF)‐like module is a structural component of numerous diverse proteins and occurs almost exclusively within repeated motifs. Notch‐1, a fundamental receptor for cell fate decisions, contains 36 extracellular EGF modules in tandem, of which 21 are potentially Ca2+‐binding. We report the Ca2+‐binding properties of EGF11‐12 and EGF10‐13 from human Notch‐1 (hNEGF11‐12 and hNEGF10‐13), modules...

Abstract A simple model of sphere packing has been investigated as an ideal model for long‐range interactions for the packing of non‐bonded residues in protein structures. By superposing all residues, the geometry of packing around a central residue is investigated. It is found that all residues conform almost perfectly to this lattice model for sphere packing when a radius of 6.5 Å is used to define non‐bonded (virtual) interacting...

Abstract The conformation of NAD bound to diphtheria toxin (DT), an ADP‐ribosylating enzyme, has been compared to the conformations of NAD(P) bound to 23 distinct NAD(P)‐binding oxidoreductase enzymes, whose structures are available in the Brookhaven Protein Data Bank. For the oxidoreductase enzymes, NAD(P) functions as a cofactor in electron transfer, whereas for DT, NAD is a labile substrate in which the N‐glycosidic bond between...

Abstract Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N‐terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP‐site and deoxythymidine‐5′‐monophosphate (dTMP), deoxythymidine (dT), or idoxuridine‐5′‐phosphate (5‐iodo‐dUMP) at the substrate‐site were refined to 2.75 Å, 2.8 Å, and 3.0 Å resolution, respectively. TK catalyzes the phosphorylation of dT resulting in...

Abstract The histidine‐containing protein (HPr) of bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) serves a central role in a series of phosphotransfer reactions used for the translocation of sugars across cell membranes. These studies report the high‐definition solution structures of both the unphosphorylated and histidine phosphorylated (P‐His) forms of HPr from Bacillus subtilis. Consistent with previous NMR...

Abstract Clusterin is a ubiquitous, heterodimeric glycoprotein with multiple possible functions that are likely influenced by glycosylation. Identification of oligosaccharide attachment sites and structural characterization of oligosaccharides in human serum clusterin has been performed by mass spectrometry and Edman degradation. Matrix‐assisted laser desorption ionization mass spectrometry revealed two molecular weight species of...

Abstract Temperature‐induced denaturation transitions of different structural forms of apomyoglobin were studied monitoring intrinsic tryptophan fluorescence. It was found that the tryptophans are effectively screened from solvent both in native and acid forms throughout most of the temperature range tested. Thus, the tryptophans' surroundings do not show a considerable change in structure where major protein conformational...

Abstract The energetics of cavity formation in proteins is evaluated with two different approaches and results are analyzed and compared to experimental data. In the first approach, free energy of cavity formation is extracted by RMS fitting from the distribution of numbers of cavities, N, with different volumes, Vcav' in 80 high‐resolution protein structures. It is assumed that the distribution of number of cavities according to their volume ...

Abstract Triosephosphate isomerase (TIM), from the hyperthemophilic bacterium Thermotoga maritima, has been shown to be covalently linked to phosphoglycerate kinase (PGK) forming a bifunctional fusion protein with TIM as the C‐terminal portion of the subunits of the tetrameric protein (Schurig et al., EMBO J 14:442‐451, 1995). To study the effect of the anomalous state of association on the structure, stability, and function of Thermotoga TIM,...

Abstract Models of ligand binding are often based on four assumptions: (1) steric fit: that binding is determined mainly by shape complementarity; (2) native binding: that ligands mainly bind to native states; (3) locality: that ligands perturb protein structures mainly at the binding site; and (4) continuity: that small changes in ligand or protein structure lead to small changes in binding affinity. Using a generalization of the...

Abstract Glutathione S‐transferase (GST) from Schistosoma japonicum, which is widely used for the production of fusion proteins in the cytoplasm of Escherichia coli, was employed as a functional fusion module that effects dimer formation of a recombinant protein and confers enzymatic reporter activity at the same time. For this purpose GST was linked via a flexible spacer to the C‐terminus of the thiol‐protease inhibitor cystatin, whose binding...

Abstract Thioredoxin reductase (TrxR) from Escherichia coli consists of two globular domains connected by a two‐stranded β sheet: an FAD domain and a pyridine nucleotide binding domain. The latter domain contains the redox‐active disulfide composed of Cys 135 and Cys 138. TrxR is proposed to undergo a conformational change whereby the two domains rotate 66° relative to each other (Waksman G, Krishna TSR, Williams CH Jr, Kuriyan J, 1994, ...

Abstract The temperature induced unfolding of barstar wild‐type of bacillus amyloliquefaciens (90 residues) has been characterized by differential scanning microcalorimetry. The process has been found to be reversible in the pH range from 6.4 to 8.3 in the absence of oxygen. It has been clearly shown by a ratio of δHvH/δHcal near 1 that denaturation follows a two‐state mechanism. For comparison, the C82A mutant was also studied. This mutant...

Abstract Hydrogen/deuterium exchange behavior of human recombinant [C22A] FK506 binding protein (C22A FKBP) has been determined by protein fragmentation, combined with electrospray Fourier transform ion cyclotron resonance mass spectrometry (MS). After a specified period of H/D exchange in solution, C22A FKBP was digested by pepsin under slow exchange conditions (pH 2.4, 0°C), and then subjected to on‐line HPLC/MS for deuterium...

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