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  • 1
    Electronic Resource
    Electronic Resource
    The use of colloidal metal particles in protein blotting (1987)
    Weinheim : Wiley-Blackwell
    Electrophoresis 8 (1987), S. 403-409 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Two procedures are described for staining the overall protein pattern on transfer membranes. Both methods involve the use of colloidal metal particles. AuroDye staining is based on the interaction of anionic colloidal gold particles with cationic proteins at low pH. The method is highly sensitive, but limited to nitrocellulose and polyvinylidene difluoride membranes. FerriDye comprises an incubation in a cationic iron (hydrous) oxide sol and subsequent intensification with potassium hexacyanoferrate in acidic medium. FerriDye is of intermediate sensitivity, but there are no limitations concerning membranes. It can be used on nitrocellulose-, nylon-and polyvinylidene difluoride-based membranes. An immunodetection procedure is described which uses colloidal gold-labelled secondary antibodies to visualize antigen-antibody interactions. This signal can be significantly enhanced by silver. The procedure explained uses a new light-insensitive and user-friendly silver enhancement system.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150080907
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  • 2
    Electronic Resource
    Electronic Resource
    Activation of retinal rod cyclic GMP-phosphodiesterase by transducin: Characterization of the complex formed by phosphodiesterase inhibitor and transducin α-subunit (1986)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 1 (1986), S. 188-193 
    Details
    ISSN: 0887-3585
    Keywords: G-protein ; phototransduction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The GTP-binding subunit of transducin (Tα) activates the cGMP phosphodiesterase (PDE) of bovine retinal rods by relieving the constraint imposed by the inhibitory subunit PDEγ. We have isolated and characterized the complex Tα.GTPγS-PDEγ formed when Tα is activated by the nonhydrolyzable analog GTPγS. Sedimentation and light-scattering techniques demonstrate that, in contrast to free Tγ.GTPγS, which is soluble, the Tα.GTPγS-PDEγ complex, as well as Tα.GTP-PDEγ, is membrane bound at cytosolic ionic strength. It is eluted from the membrane at low ionic strength as a monomeric and 1:1 stoichiometric complex. The relative affinities of PDEγ for PDEαβ and for Tα.GTP are discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340010210
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  • 3
    Electronic Resource
    Electronic Resource
    Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida (1992)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 12 (1992), S. 105-110 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; protein sequences ; protein design de novo ; protein engineering ; computer algorithms ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded β-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Fingerclasp, a dimer of interdigitating β-β-α units, the simplest variant of the “handshake” structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather - a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340120203
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  • 4
    Electronic Resource
    Electronic Resource
    Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 262-273 
    Details
    ISSN: 0887-3585
    Keywords: hierarchical assignment ; cereal grain ; mistletoe ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high-resolution crystal structure. In addition, a two-step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin.The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945 Å resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107-113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S. W., Glöckner, J. Biochemistry 20:33-37, 1981) as modified (Manavalan, P., Johnson, W. C., Jr. Anal. Biochem. 167:76-85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane-active toxins homologous to crambin (α1- and β-purothionin, phoratoxin A and B, an viscotoxin A3 and B).The new program SEQ (pronounced “seek”) was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location.Both CD-arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of Purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040405
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  • 5
    Electronic Resource
    Electronic Resource
    Substrate specificities in class A β-lactamases: Preference for penams vs. cephams. The role of residues 237 (1989)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 275-283 
    Details
    ISSN: 0887-3585
    Keywords: mutagenesis ; structure-function relationships ; enzymatic catalysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Site saturation mutagenesis has been carried out at Ala-237 in RTEM-1 β-lactamase to assess the role of this site in modulating differences in specificity of β-lactamases for penams vs. cephams as substrates. (An Ala-237 Thr mutation had previously been shown to increase activity on cephems by about 30-80%.1,2) Screening of all 19 possibles mutants on penams and cephems revealed the even more active Ala-237 Asn mutant. Detailed kinnetic analysis showns that this mutant has about four times the activity toward cephalothin and cephalosporin C as the wild-type enzyme. Both mutations reduce the activity toward penams to about 10% that of RETM-1 β-lactamase and lower by about 5°C the tempreature at which the enzyme denatures. Functional properties of the other mutants have also been surveyed. The most intresting aspect of these results is that two quite disparate amino acids, theronine and asparagine, when intorduced for Ala-237, cause such similar changes in enzyme specificity while more similar residues do not alter the catalytic properties of the enzyme to such a significant degree.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340060310
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  • 6
    Electronic Resource
    Electronic Resource
    Crystallization of the bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domain of the human trifunctional enzymeThis is NRCC publication No. 39937. (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 479-480 
    Details
    ISSN: 0887-3585
    Keywords: crystallization ; folate ; multifunctional ; twinning ; dehydrogenase ; cyclohydrolase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Methylenetetrahydrofolate([H4] folate) dehydrogenase (D) and methenyl[H4] folate cyclohydrolase (C) coexist as a bifunctional enzyme (DC) or as the amino-terminal domain of a trifunctional enzyme (DCS) where the third activity is 10-formyl[H4]lfolate synthetase (S). Two crystal forms of the DC domain of the human cytosolic DCS enzyme have been grown from polyethyleneglycol solution. The monoclinic P21 crystals diffract to 2.8 Å with a = 72.5 Å, b = 68.5 Å, c = 125.2 Å, and β = 91.8° but were found to be twinned. The orthorhombic P212121 crystals diffract to 2.5 Å with a = 67.7 Å, b = 135.9 Å, c = 61.6 Å, and contain two molecules per asymmetric unit. Proteins 26:479-480 © 1996 Wiley-Liss, Inc.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Refined solution structure of the anti-mammal and anti-insect LqqIII scorpion toxin: Comparison with other scorpion toxins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 360-374 
    Details
    ISSN: 0887-3585
    Keywords: scorpion ; toxin ; NMR ; structure ; hydrophobic potentials ; electrostatic potentials ; CSαβ motif ; sodium channel ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution structure of the anti-mammal and anti-insect LqqIII toxin from the scorpion Leiurus quinquestriatus quinquestriatuswas refined and compared with other long-chain scorpion toxins. This structure, determined by 1H-NMR and molecular modeling, involves an α-helix (18-29) linked to a three-stranded β-sheet (2-6, 33-39, and 43-51) by two disulfide bridges. The average RMSD between the 15 best structures and the mean structure is 0.71 Å for Cα atoms. Comparison between LqqIII, the potent anti-mammal AaHII, and the weakly active variant-3 toxins revealed that the LqqIII three-dimensional structure is closer to that of AaHII than to the variant-3 structure. Moreover, striking analogies were observed between the electrostatic and hydrophobic potentials of LqqIII and AaHII. Several residues are well conserved in long-chain scorpion toxin sequences and seem to be important in protein structure stability and function. Some of them are involved in the CSαβ (Cysteine Stabilized α-helix β-sheet) motif. A comparison between the sequences of the RII rat brain and the Drosophila extracellular loops forming scorpion toxin binding-sites of Na+ channels displays differences in the subsites interacting with anti-mammal or anti-insect toxins. This suggests that hydrophobic as well as electrostatic interactions are essential for the binding and specificity of long-chain scorpion toxins. Proteins 28:360-374, 1997 © 1997 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features (1992)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 12 (1992), S. 299-313 
    Details
    ISSN: 0887-3585
    Keywords: α/β-barrels ; protein structure ; loops ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A systematic survey of seven parallel α/β barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the αβ loops in these proteins - 20 out of a total of 49 - belong to either one of two loop types previously described by Thornton and co-workers. Six loops are of the αβ1 type, with one residue between the α-helix and β-strand, and 13 are of the αβ3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed αβ connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the β-strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In αβ1 connections, the chain enters the β-strand via a residue adopting an extended conformation, while in αβ3 it does so via a residue in a near α-helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the β-sheet surface and of main chain H-bonds in the loop and the β-strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the α-helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified αβ1 and αβ3 loops within the α/β-barrel motifs. They often occur adjacent to each other; αβ3 loops invariably involve even numbered β-strands, while αβ1 loops involve preferentially odd β-strands; all the analyzed proteins contain at least one αβ3 loop in the first half of the eightfold α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel motifs are discussed.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340120402
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  • 9
    Electronic Resource
    Electronic Resource
    Homologous modeling of the lysosomal protective protein/carboxypeptidase L: Structural and functional implications of mutations identified in galactosialidosis patients (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 81-93 
    Details
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180110
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  • 10
    Electronic Resource
    Electronic Resource
    Polar and nonpolar atomic environments in the protein core: Implications for folding and binding (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 264-278 
    Details
    ISSN: 0887-3585
    Keywords: hydrophobic interactions ; protein stability ; hydrophobicity scale ; protein mutant stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic interactions are believed to play an important role in protein folding and stability. Semi-empirical attempts to estimate these interactions are usually based on a model of solvation, whose contribution to the stability of proteins is assumed to be proportional to the surface area buried upon folding. Here we propose an extension of this idea by defining an environment free energy that characterizes the environment of each atom of the protein, including solvent, polar or nonpolar atoms of the same protein or of another molecule that interacts with the protein. In our model, the difference of this environment free energy between the folded state and the unfolded (extended) state of a protein is shown to be proportional to the area buried by nonpolar atoms upon folding. General properties of this environment free energy are derived from statistical studies on a database of 82 well-refined protein structures. This free energy is shown to be able to discriminate misfolded from correct structural models, to provide an estimate of the stabilization due to oligomerization, and to predict the stability of mutants in which hydrophobic residues have been substituted by site-directed mutagenesis, provided that no large structural modifications occur. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200307
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