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Journal Issue - Volume 3 Issue 12 (December 1994)

  • A year of progress

  • Hans Neurath
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560031201 (p 2165-2165)

Abstract The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2‐state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, δGu(H2O), range from...

Abstract High‐sensitivity differential scanning calorimetry and CD spectroscopy have been used to probe the structural stability and measure the folding/unfolding thermodynamics of a Pro117 → Gly variant of staphylococcal nuclease. It is shown that at neutral pH the thermal denaturation of this protein is well accounted for by a 2‐state mechanism and that the thermally denatured state is a fully hydrated unfolded polypeptide. At pH ...

Abstract Strong sequence similarity has been reported among WrbA (the Trp repressor‐binding protein of Escherichia coli); Ycp4, a protein of unknown function from the budding yeast Saccharomyces cerevisiae; P25, the pap1‐dependent protein of the fission yeast Schizosaccharomyces pombe; and the translation product of a partial cDNA sequence from rice seedling root (Oryza sativa, locus Ricr02421a; here referred to as RicR). Further homology search with the profile...

Abstract An analysis of internal packing defects or “cavities” (both empty and water‐containing) within protein structures has been undertaken and includes 3 cavity classes: within domains, between domains, and between protein subunits. We confirm several basic features common to all cavity types but also find a number of new characteristics, including those that distinguish the classes. The total cavity volume remains only a small...

Abstract Three thousand eight hundred ninety‐nine β‐turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive β‐turn positional potentials for turn types I' and II' for the first time and to provide updated potentials for formation of the more common types I, II, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms...

Abstract In the N‐terminal domain of λ repressor, the Asp 14 side chain forms an intrahelical, hydrogen bond/salt bridge with the Arg 17 side chain and a tertiary hydrogen bond with the Ser 77 side chain. By measuring the stabilities to urea denaturation of the wild‐type N‐terminal domain and variants containing single, double, and triple alanine substitutions at positions 14, 17, and 77, the side‐chain interaction energies, the...

Abstract Bovine pancreatic trypsin inhibitor (BPTI) is stabilized by 3 disulfide bonds, between cysteines 30‐51, 5‐55, and 14‐38. To better understand the influence of disulfide bonds on local protein structure and dynamics, we have measured amide proton exchange rates in 2 folded variants of BPTI, [5‐55]A]a and [30‐51; 14‐38]V5A55, which share no common disulfide bonds. These proteins resemble disulfide‐bonded intermediates that accumulate in...

Abstract The 3‐dimensional crystal structure of glutathione S‐transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV‐1) (Muster T et al., 1993, J Virol 67:6642–6647) was determined at 2.5 Å resolution. The structure of the 3‐3 isozyme rat GST of the μ gene class (Ji X, Zhang P, Armstrong RN, Gilliland GL, 1992, Biochemistry...

Abstract The flavin prosthetic group (FAD) of p‐hydroxybenzoate hydroxylase from Pseudomonas fluorescens was replaced by a stereochemical analog, which is spontaneously formed from natural FAD in alcohol oxidases from methylotrophic yeasts. Reconstitution of p‐hydroxybenzoate hydroxylase from apoprotein and modified FAD is a rapid process complete within seconds. Crystals of the enzyme–substrate complex of modified FAD‐containing...

Abstract The X‐ray crystal structure of prethrombin2 (pre2), the immediate inactive precursor of α‐thrombin, has been determined at 2.0 Å resolution complexed with hirugen. The structure has been refined to a final R‐value of 0.169 using 14,211 observed reflections in the resolution range 8.0–2.0 Å. A total of 202 water molecules have also been located in the structure. Comparison with the hirugen–thrombin complex showed that, apart from the...

Abstract The transition of the colicin E1 channel polypeptide from a water‐soluble to membrane‐bound state occurs in vitro at acid pH values that are associated with an unfolded channel structure whose properties qualitatively resemble those of a “molten globule,” or “compact unfolded,” intermediate state. The role of such a state for activity was tested by comparing the pH dependence of channel‐induced solute efflux and the...

Abstract Interleukin‐6 (IL‐6) is a multifunctional cytokine that plays an important role in host defense. It has been predicted that IL‐6 may fold as a 4 α‐helix bundle structure with up‐up‐down‐down topology. Despite a high degree of sequence similarity (42%) the human and mouse IL‐6 polypeptides display distinct species‐specific activities. Although human IL‐6 (hIL‐6) is active in both human and mouse cell assays, mouse IL‐6...

Abstract By using a lactose permease mutant containing a single Cys residue in place of Val 331 (helix X), conformational changes induced by ligand binding were studied. With right‐side‐out membrane vesicles containing Val 331 → Cys permease, lactose transport is inactivated by either N‐ethylmaleimide (NEM) or 7‐diethylamino‐3‐(4′‐maleimidylphenyl)‐4‐methylcoumarin (CPM). Remarkably, β,d‐galactopyranosyl 1‐thio‐β,d‐galactopyranoside ...

Abstract Deletion of putative transmembrane helix III from the lactose permease of Escherichia coli results in complete loss of transport activity. Similarly, replacement of this region en bloc with 23 contiguous Ala, Leu, or Phe residues abolishes active lactose transport. The observations suggest that helix III may contain functionally important residues; therefore, this region was subjected to Cys‐scanning mutagenesis. Using a functional...

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