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Journal Issue - Volume 5 Issue 10 (October 1996)

Abstract The crystal structure of human interleukin‐10 (IL‐10) was refined at 1.6 Å resolution against X‐ray diffraction data collected at 100 K with the use of synchrotron radiation. Although similar to the IL‐10 structure determined previously at room temperature, this low‐temperature IL‐10 structure contains, in addition, four N‐terminal residues, three sulfate anions, and 175 extra water molecules. Whereas the main‐chain...

Abstract DCoH, the dimerization cofactor of hepatocyte nuclear factor 1 (HNF‐1), functions as both a transcriptional coactivator and a pterin dehydratase. To probe the relationship between these two functions, the X‐ray crystal structures of the free enzyme and its complex with the product analogue 7,8‐dihydrobiopterin were refined at 2.3 Å resolution. The ligand binds at four sites per tetrameric enzyme, with little apparent...

Abstract Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the...

Abstract The PotD protein from Escherichia coli is one of the components of the polyamine transport system present in the periplasm. This component specifically binds either spermidine or putrescine. The crystal structure of the E. coli PotD protein complexed with spermidine was solved at 1.8 Å resolution and revealed the detailed substrate‐binding mechanism. The structure provided the detailed conformation of the bound spermidine. Furthermore,...

Abstract A new sequence motif library StrProf was constructed characterizing the groups of related proteins in the PDB three‐dimensional structure database. For a representative member of each protein family, which was identified by cross‐referencing the PDB with the PIR superfamily classification, a group of related sequences was collected by the BLAST search against the nonredundant protein sequence database. For every group, the...

Abstract The metabolism of hyperthermophilic microorganisms can function properly at temperatures close to 100 °C. It follows that they are equipped with both thermostable enzymes and mechanisms that handle labile metabolites. We wanted to understand how stable and active phosphoribosyl anthranilate isomerase (tPRAI) from the hyperthermophile Thermotoga maritima is at its optimum growth temperature of 80 °C, and how its thermolabile substrate,...

Abstract Significantly different m values (1.9–2.7 kcal mol−1 M−1) were observed for point mutations at a single, solvent‐exposed site (T53) in a variant of the B1 domain of streptococcal Protein G using guanidine hydrochloride (GuHCl) as a denaturant. This report focuses on elucidating the energetic and structural implications of these m‐value differences in two Protein G mutants, containing Ala and Thr at position 53. These two proteins ...

Abstract A role for charge‐based interactions in protein stability at the monomer or dimer level is well known. We show here that such interactions can also be important for the higher‐order structures of microtubule assembly. Alkali metal chlorides increase the rate of polymerization of pure tubulin driven by either taxol or dimethyl sulfoxide. The effect is cation selective, exhibiting a sequence Na+ > K+ > Li+ > Cs +,...

Abstract 9‐(Dicyanovinyl) julolidine (DCVJ) is a fluorescent probe, which binds to a unique site on the tubulin dimer and exhibits different properties that are dependent upon its oligomeric state (Kung & Reed, 1989). DCVJ binds to tubulin, the tubulin‐colchicine complex, and the tubulin‐ruthenium red complex equally well, but binds tighter to the ANS‐tubulin complex than to tubulin alone. The energy transfer studies indicate a...

Abstract We describe a new computer algorithm for finding low‐energy conformations of proteins. It is a chain‐growth method that uses a heuristic bias function to help assemble a hydrophobic core. We call it the Core‐directed chain Growth method (CG). We test the CG method on several well‐known literature examples of HP lattice model proteins [in which proteins are modeled as sequences of hydrophobic (H) and polar (P) monomers],...

Abstract The crystal structure of calcium‐calmodulin (CaM) reveals a protein with a typical dumbbell structure. Various spectroscopic studies have suggested that the central linker region of CaM, which is α‐helical in the crystal structure, is flexible in solution. In particular, NMR studies have indicated the presence of a flexible backbone between residues Lys 77 and Asp 80. This flexibility is related directly to the function of...

Abstract A three‐dimensional model of the photosystem II (PSII) reaction center from the cyanobacterium Synechocystis sp. PCC 6803 was generated based on homology with the anoxygenic purple bacterial photosynthetic reaction centers of Rhodobacter sphaeroides and Rhodopseudomonas viridis, for which the X‐ray crystallographic structures are available. The model was constructed with an alignment of D1 and D2 sequences with the L and M subunits of the...

Abstract The urea‐induced equilibrium unfolding of ovine placental lactogen, purified from ovine placenta, was followed by size‐exclusion chromatography, far‐UV CD, and intrinsic tryptophan fluorescence. The data obtained by each of these methods showed a poor fit to a two‐state model involving only a native and an unfolded form. A satisfactory fit required, instead, a model that involved a stable, partially folded form in addition...

Abstract Recognition of self peptides bound to the class I major histocompatibility complex molecule HLA‐B27 is thought to trigger proliferation of autoreactive T cells and result in autoimmune arthritic diseases. Previous work from other laboratories established that a predominant feature of endogenous peptides eluted from purified B27 is an arginine at position 2. We studied the binding of peptides containing both natural and...

Abstract When bovine β‐lactoglobulin (β‐LG) was refolded after extensive denaturation in 4.8 M guanidine hydrochloride (GuHCl), the functional activity of the protein, retinol binding, as measured by the enhancement of this ligand's fluorescence, was completely recovered. In contrast, the room‐temperature tryptophan phosphorescence lifetime of the refolded protein, a local measure of the residue environment, was ∽10 ms, significantly shorter...

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