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Journal Issue - Volume 14 Issue 9 (September 2005)

Abstract A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi‐residue functions can evolve on...

  • A response to Michael Lynch

  • Michael J. Behe, David W. Snoke
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.051674105 (p 2226-2227)

Abstract Transmissible spongiform encephalopathies (TSEs) are believed to be caused by an unconventional infectious agent, the prion protein. The pathogenic and infectious form of prion protein, PrPSc, is able to aggregate and form amyloid fibrils, very stable and resistant to most disinfecting processes and common proteases. Under specific conditions, PrPSc in bovine spongiform encephalopathy (BSE) brain tissue was found degradable by a...

Abstract The gene encoding the Mycobacterium tuberculosis Rv2536 protein is present in the Mycobacterium tuberculosis complex (as assayed by PCR) and transcribed (as determined by RT‐PCR) in M. tuberculosis H37Rv, M. tuberculosis H37Ra, M. bovis BCG, and M. africanum strains. Rabbits immunized with synthetic polymer peptides from this protein produced antibodies specifically recognizing a 25‐kDa band in mycobacterial sonicate. U937 and A549 cells were used...

Abstract Aggregation of partially folded intermediates populated during protein folding processes has been described for many proteins. Likewise, partially unfolded chains, generated by perturbation of numerous proteins by heat or chemical denaturants, have also been shown to aggregate readily. However, the process of protein aggregation from native‐state conditions is less well understood. Granulocyte‐colony stimulating factor...

Abstract Recombinant human interleukin‐1 receptor antagonist (IL‐1ra) in aqueous solutions unfolds and aggregates when subjected to hydrostatic pressures greater than about 180 MPa. This study examined the mechanism and thermodynamics of pressure‐induced unfolding and aggregation of IL‐1ra. The activation free energy for growth of aggregates (ΔG∓aggregation) was found to be 37 ± 3 kJ/mol, whereas the activation volume (ΔV∓aggregation) was −120...

Abstract The biological activity of the double‐ring chaperonin GroEL is regulated by complex allosteric interactions, which include positive intra‐ring and negative inter‐ring cooperativity. To further characterize inter‐ring communication, the nucleotide‐induced absorbance changes in the vibrational spectrum of the chaperonin GroEL, of two single‐point mutants suppressing one inter‐ring ionic contact (E461K and E434K) and of a...

Abstract N‐methyl‐d‐aspartate (NMDA) receptors are involved in mediating excitatory synaptic transmissions in the brain and have been implicated in numerous neurologic disorders. The proximal amino‐terminal domains (ATDs) of NMDA receptors constitute many modulatory binding sites that may serve as potential drug targets. There are few biochemical and structural data on the ATDs of NMDA receptors, as it is difficult to produce the...

Abstract Flavodoxin II from Azotobacter vinelandii is a “long‐chain” flavodoxin and has one of the lowest E1 midpoint potentials found within the flavodoxin family. To better understand the relationship between structural features and redox potentials, the oxidized form of the C69A mutant of this flavodoxin was crystallized and its three‐dimensional structure determined to a resolution of 2.25 Å by molecular replacement. Its overall fold is...

Abstract The serine penicillin‐recognizing proteins have been extensively studied. They show a wide range of substrate specificities accompanied by multidomain features. Their adaptation capacity has resulted in the emergence of pathogenic bacteria resistant to β‐lactam antibiotics. The most divergent enzymatic activities in this protein family are those of the Ochrobactrum anthropi D‐aminopeptidase and of the Streptomyces R61...

Abstract A family of genetically‐encoded metabolite sensors has been constructed using bacterial periplasmic binding proteins (PBPs) linearly fused to protein fluorophores. The ligand‐induced conformational change in a PBP allosterically regulates the relative distance and orientation of a fluorescence resonance energy transfer (FRET)‐compatible protein pair. Ligand binding is transduced into a macroscopic FRET observable, providing...

Abstract Previous reports detailing mutational effects within the hydrophobic core of human acidic fibroblast growth factor (FGF‐1) have shown that a symmetric primary structure constraint is compatible with a stably folded protein. In the present report, we investigate symmetrically related pairs of buried hydrophobic residues in FGF‐1 (termed “mini‐cores”) that are not part of the central core. The effect upon the stability and...

Abstract Both NMR and IR studies of carbonyl (13C′) isotopomers of designed helices can provide residue‐level details regarding the fractional occurrence and melting behavior of helical ϕ/ψ angles along the sequence of helical peptides, details that cannot be obtained from CD or 1H‐NMR studies. We have studied a classic series of helical models, Ac‐YGG‐(KAXAA)3K‐NH2 (X=A,V), in both aqueous and helix‐favoring media containing fluoroalcohol...

Abstract The P22 tailspike protein folds by forming a folding competent monomer species that forms a dimeric, then a non‐native trimeric (protrimer) species by addition of folding competent monomers. We have found three residues, R549, R563, and D572, which play a critical role in both the stability of the native tailspike protein and assembly and maturation of the protrimer. King and colleagues reported previously that substitution...

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