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Journal Issue - Volume 2 Issue 6 (June 1993)

Abstract The molten globule model for the beginning of the folding process, which originated with Kuwajima's studies of α‐lactalbumin (Kuwajima, K., 1989, Proteins Struct. Funct. Genet. 6, 87–103, and references therein), states that, for those proteins that exhibit equilibrium molten globule intermediates, the molten globule is a major kinetic intermediate near the start of the folding pathway. Pulsed hydrogen‐deuterium exchange measurements...

  • Catching a common fold

  • Tom L. Blundell, Mark S. Johnson
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560020602 (p 877-883)

Abstract Protein structures come in families. Are families “closely knit” or “loosely knit” entities? We describe a measure of relatedness among polymer conformations. Based on weighted distance maps, this measure differs from existing measures mainly in two respects: (1) it is computationally fast, and (2) it can compare any two proteins, regardless of their relative chain lengths or degree of similarity. It does not require...

Abstract The peptide (Gly‐l‐Tyr‐l‐Asp‐l‐Lys‐l‐Tyr)6, referred to as F4–6, was synthesized as a model for a schistosome eggshell protein in which the Gly‐Tyr‐Asp‐Lys‐Tyr consensus sequence is repeated over 40 times. Analysis by CD, Fourier transform infrared spectroscopy, potentiometric and spectrophotometric titrations, NMR, and molecular modeling suggests that F4–6 forms some type of left‐handed structure. A likely possibility ...

Abstract The crystal structure for an antibody‐antigen system, that of the anti‐hen egg lysozyme monoclonal antibody HyHEL‐5 complexed to lysozyme, is used as the starting point for computer simulations of diffusional encounters between the two proteins. The investigation consists of two parts: first, the linearized Poisson‐Boltzmann equation is solved to determine the long‐range electrostatic forces between antibody and antigen,...

Abstract In the R form of ATCase complexed with the bisubstrate analogue, N‐(phosphonacetyl)‐l‐aspartate, large temperature factors are reported for the allosteric domains of the regulatory chains. We studied the conformational flexibility of the holoenzyme with molecular dynamics simulations and rigid body (TLS) analysis. The results of the molecular dynamics simulations suggest that, although local atomic fluctuations account for the...

Abstract The usefulness of representing an ensemble of NMR‐derived protein structures by a single structure has been investigated. Two stereochemical properties have been used to assess how a single structure relates to the ensemble from which it was derived, namely the distribution of ϕΨ torsion angles and the distribution of χ1 torsion angles. The results show that the minimized average structure derived from the ensemble (a total of 11...

Abstract The effects of several DNA molecules on the free energy of subunit association of Arc repressor were measured. The association studies under equilibrium conditions were performed by the dissociating perturbation of hydrostatic pressure. The magnitude of stabilization of the subunit interaction was determined by the specificity of the protein‐DNA interaction. Operator DNA stabilized the free energy of association by about...

Abstract Studies of Cys2‐His2 zinc finger domains have revealed that the structures of individual finger domains in solution determined by NMR spectroscopy are strikingly similar to the structure of fingers bound to DNA determined by X‐ray diffraction. Therefore, detailed structural analyses of single finger domains that contain amino acid substitutions known to affect DNA binding in the whole protein can yield information...

Abstract Eukaryotic cytochrome c possesses an ATP‐binding site of substantial specificity and high affinity that is conserved between highly divergent species and which includes the invariant residue arginine91. Such evolutionary conservatism strongly suggests a physiological role for ATP binding that demands further investigation. We report the preparation of adducts of the protein and the affinity labels 8‐azido adenosine 5′‐triphosphate,...

Abstract The transmembrane PTPase HPTPβ differs from its related family members in having a single rather than a tandemly duplicated cytosolic catalytic domain. We have expressed the 354‐amino acid, 41‐kDa human PTPβ catalytic fragment in Escherichia coli, purified it, and assessed catalytic specificity with a series of pY peptides. HPTPβ shows distinctions from the related LAR PTPase and T cell CD45 PTPase domains: it recognizes phosphotyrosyl peptides of...

Abstract The effect of decreased protein flexibility on the stability and calcium binding properties of calbindin D9k has been addressed in studies of a disulfide bridged calbindin D9k mutant, denoted (L39C + P43M + I73C), with substitutions Leu 39 → Cys, Ile 73 → Cys, and Pro 43 → Met. Backbone 1H NMR assignments show that the disulfide bond, which forms spontaneously under air oxidation, is well accommodated. The disulfide is inserted on the opposite end...

Abstract Treatment of the catalytic (C) trimer of Escherichia coli aspartate transcarbamoylase (ATCase) with α‐chymotrypsin by a procedure similar to that used by Chan and Enns (1978, Can. J. Biochem. 56, 654‐658) has been shown to yield an intact, active, proteolytically cleaved trimer containing polypeptide fragments of 26, 000 and 8, 000 MW. Vmax of the proteolytically cleaved trimer (CPC) is 75% that of the wild‐type C trimer, whereas Km for aspartate...

Abstract Despite the complexity of Escherichia coli aspartate transcarbamoylase (ATCase), composed of 12 polypeptide chains organized as two catalytic (C) trimers and three regulatory (R) dimers, it is possible to form active stable enzyme in vivo even with fragmented catalytic (c) chains. Based on the observation that chymotryptic digestion of the C trimers yields an active protein that can be dissociated into fragmented chains and...

Abstract Using a functional lactose permease mutant devoid of Cys residues (C‐less permease), each amino‐acid residue in putative transmembrane helices IX and X and the short intervening loop was systematically replaced with Cys (from Asn‐290 to Lys‐335). Thirty‐four of 46 mutants accumulate lactose to high levels (70‐100% or more of C‐less), and an additional 7 mutants exhibit lower but highly significant lactose accumulation. As...

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