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Journal Issue - Volume 7 Issue 4 (April 1998)

Abstract Proteolytic enzymes are synthesized as inactive precursors, or “zymogens,” to prevent unwanted protein degradation, and to enable spatial and temporal regulation of proteolytic activity. Upon sorting or appropriate compartmentalization, zymogen conversion to the active enzyme typically involves limited proteolysis and removal of an “activation segment.” The sizes of activation segments range from dipeptide units to...

Abstract The crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6322 to a resolution of 2.2 Å. This protease is bound with a 14‐mer peptide representing the central region of the NS4A protein. There are two molecules of the NS31_180‐NS4A21′‐34′ complex per asymmetric unit. Each displays a familiar chymotrypsin‐like fold that includes two β‐barrel domains and four short α‐helices....

Abstract A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N‐ and C‐termini. Isothermal titration calorimetric studies show that the association constant has been...

Abstract Nine nonnative conformations of ubiquitin, generated during two different thermal denaturation trajectories, were simulated under nearly native conditions (62 °C). The simulations included all protein and solvent atoms explicitly, and simulation times ranged from 1‐2.4 ns. The starting structures had α‐carbon root‐mean‐square deviations (RMSDs) from the crystal structure of 4‐12 Å and radii of gyration as high as 1.3 times...

Abstract Human tissue kallikrein, a trypsin‐like serine protease involved in blood pressure regulation and inflammation processes, was expressed in a deglycosylated form at high levels in Pichia pastoris, purified, and crystallized. The crystal structure at 2.0 Å resolution is described and compared with that of porcine kallikrein and of other trypsin‐like proteases. The active and S1 sites (nomenclature of Schechter I, Berger A, 1967, Biochem...

Abstract Leukemia inhibitory factor (LIF), a member of the gpl30 family of helical cytokines, is involved in the hemopoietic and neural systems. The LIF signal transducing complex contains two receptor molecules, the LIF receptor (LIFR) and gp130. The extracellular region of the LIFR is unique in that it includes three membrane‐proximal fibronectin type III domains and two cytokine binding domains (CBDs) separated by an...

Abstract Analysis of the heterogeneity of packing in proteins showed that different groups of the protein preferentially contribute to low‐ or high‐density regions. Statistical distribution reveals the two preferable values for packing density in the form of two peaks. One peak occurs in the range of densities 0.55‐0.65, the other occurs in the range 0.75‐0.8. The high‐density peak is originated primarily by high packing inside the...

Abstract Two related mammalian proteins, bactericidal/permeability‐increasing protein (BPI) and lipopolysaccharide‐binding protein (LBP), share high‐affinity binding to lipopolysaccharide (LPS), a glycolipid found in the outer membrane of Gram‐negative bacteria. The recently determined crystal structure of human BPI permits a structure/function analysis, presented here, of the conserved regions of these two proteins sequences. In...

Abstract A glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that contribute to the binding, the structures of GPb in the native T state conformation and in complex with glucopyranose spirohydantoin have been determined at 100 K to 2.0 Å and 1.8...

Abstract Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin‐like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H‐bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this...

Abstract Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK, is modified to allow it to rapidly fit multiple conformations of ligands. Conformations of a given molecule are pre‐calculated in the same frame...

Abstract The discontinuous interleukin‐10(IL‐10)/interleukin‐10 receptor (IL‐10R) combining site was mapped using sets of overlapping peptides derived from both binding partners bound to continuous cellulose membranes. Low affinity binding of single regions of the discontinuous contact sites on IL‐10 and IL‐10R could be identified due to (1) high peptide density on the membrane support, (2) incubation with high protein...

Abstract Cytochrome b562 is a four‐helix‐bundle protein containing a non‐covalently bound b‐type heme prosthetic group. In the absence of heme, cytochrome b562 remains highly structured under native conditions. Here we report thermodynamic data for the thermal denaturation of the holo‐ and apoproteins as determined by differential scanning calorimetry. Thermal denaturation of holocytochrome b562 is a highly reversible process, and unexpectedly does not...

Abstract The refolding of Clostridium symbiosum glutamate dehydrogenase (GDH) involves the formation of an inactive structured monomeric intermediate prior to its concentration‐dependent association. The structured monomer obtained after removal of guanidinium chloride was stable and competent for reconstitution into active hexamers. Site‐directed mutagenesis of C. symbiosum gdh gene was performed to replace the residues Arg‐61 and Phe‐187...

Abstract The singular value decomposition (SVD) analysis was applied to a large set of far‐ultraviolet circular dichroism (far‐UV CD) spectra (100‐400 spectra) of horse heart cytochrome c (cyt c). The spectra were collected at pH 1.7‐5.0 in (NH4)2SO4, sorbitol and 2,2,2‐trifluoroethanol (TFE) solutions. The present purpose is to develop a rigorous matrix method applied to far‐UV CD spectra to resolve in details conformational properties of...

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