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B Robson

Publications and source records attributed to B Robson.

69 records · Page 4Linked to original sources
PubMed1976

The mechanism of folding of globular proteins. Suitability of a penicillinase from Staphylococcus Aureus as a model for refolding studies.

1. A homogeneous preparation of penicillinase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) was isolated and purified from cultures of Staphylococcus aureus by a simple two-stage procedure. 2. The native protein contains 20-30% helix as determined by optical-rotatory-dispersion and circular-dichroism measurements. Some 54(+/-5)% of the 13 tyrosine residues are exposed to solvent molecules of diameter 0.44 and 0.94 nm. 3. Conditions that allow full recovery of enzymic activity and native conformation from the fully unfolded state in 4M-guanidinium chloride were defined. 4. Refolding of the protein was shown to be inhibited by intermolecular interaction, by small changes in ionization and by low concentrations (0.025 M) of phenol.

Guanidines↗
PubMed1976

The mechanism of folding of globular proteins. Equilibria and kinetics of conformational transitions of penicillinase from Staphylococcus aureus involving a state of intermediate conformation.

1. The thermodynamically reversible unfolding and refolding of penicillinase between the native and fully unfolded states were followed by using guanidinium chloride as denaturant. 2. The equilibria, studied by optical rotation, u.v. absorption, viscosity and enzyme activity, show the presence of a state of intermediate conformation, termed state H, which is stable at 20 degrees C in 0.8 M-guanidinium chloride. 3. The physical properties of this state show that it is slightly expanded with an intrinsic viscosity of 8 ml-g-1, that the 13 tyrosine residues, which are distributed through the primary sequence, are maximally exposed to the solvent and that the helix content is the same as that of the native state. 4. The kinetics of the transition between the native state, state H and the fully unfolded state were followed by u.v. absorption and by optical rotation. They are interpreted as showing that state H lies on the folding pathway between the native and fully unfolded states. 5. The transition between the native state and state H exhibits monophasic unfolding kinetics and biphasic refolding kinetics. This indicates that there must be at least two intermediate states in this process, at least one of which lies on the folding pathway which may also involve cul-de-sac paths. 6. The results are discussed in terms of a mechanism involving rapid stabilization of nucleation regions in a moderately compact but internally solvated structure, with 'native format' [Anfinsen (1973) Science 181, 233-230] secondary structure stabilized by tertiary interaction. The final and rate-limiting step in refolding involves shuffling of these structural elements into the native state. 7. This model is discussed in relation to folding in vivo.

Guanidines↗
PubMed1974

Analysis of code relating sequences to conformation in globular prtoeins. Theory and application of expected information.

1. An information theory analysis of the folding of a globular protein is proposed. 2. The folding is seen as a transfer of information between two messages, the primary sequence and the biologically active conformation. 3. It is shown how the information transferred was estimated by inspection of proteins of known primary sequence and conformation. 4. In this estimation, concerted use of subjective (Bayesian) probabilities leads to a more robust approach which can be employed whether the number of proteins of known sequence and conformation is large or small. 5. Further, it is demonstrated that the problem then becomes a very simple algebraic formulation for information estimates. 6. Finally, it is shown how this process of information theory analysis can be reversed to predict the conformation of a protein by using its primary sequence and the above information estimates obtained from other proteins. 7. The present paper provides the theoretical basis for the derivation and application of a stereochemical alphabet (Robson & Pain, 1974a,c), and for an investigation of the effects of residues on the conformations of their neighbours (Robson & Pain, 1974b).

Amino Acid Sequence↗
PubMed1974

Analysis of the code relating sequence to conformation in globular proteins. Development of a stereochemical alphabet on the basis of intra-residue information.

1. The relation of primary sequence to all residue backbone conformations was explored to test out starting conformations for protein folding. 2. Information theory was used to obtain measures of information which quantitate the role of each residue in determining its own conformation; i.e. intra-residue information. 3. The information measures are plotted as a function of varphi, psi peptide-backbone angles and varphi, psi contour maps obtained for each of the 20 amino acids. These show characteristic differences between residues. 4. To find practical ways of relating sequence to varphi, psi angles, several types of stereochemical alphabet were investigated. The value of these was tested by using them to predict the varphi, psi angles of nine different proteins. 5. A difference plot was constructed to show regions of the sequence that require little or no information extra to the intra-residue information in order to predict a correct conformation. These regions are suggested to be candidates for nucleating sites in the protein.

Amino Acid Sequence↗
PubMed1974

Analysis of the code relating sequence to conformation in globular proteins. An informational analysis of the role of the residue in determining the conformation of its neighbours in the primary sequence.

1. The effect exerted by a residue on the conformation of neighbouring residues was analysed by using data from nine globular proteins of known sequence and conformation. 2. An information measure was used which estimated the role of a residue in influencing neighbouring conformations and also its tendency to influence the lengths of runs of residues in that conformation. This measure was estimated for each residue in all conformations defined by domains on the varphi, psi diagram. 3. Plots of the information measure yielded an intercept, which was a measure of intra-residue information for a residue. The slope was a measure of the statistical co-operativity or tendency of the residue to influence the occurrence of its neighbours in runs of a particular conformation. Both parameters are a function of the residue type. Statistical co-operativity is found in the alpha(1)-helical (H(1)) and beta-pleated-sheet (P(2)) conformations and, to a lesser extent, in their distorted variants H(2) and P(1). 4. The directional nature of these influences for H(1) and P(2) conformations is illustrated by plots of the information measure against the distance m from the residue, for m=-10 to +10. 5. The results for statistical co-operativity are discussed in relation to theories of helix-coil and pleated-sheet-coil transitions. The value of the information-theory-derived parameters in obtaining s parameters for the Zimm & Bragg (1959) equations is illustrated. 6. Directional effects are discussed with particular relation to mechanisms of the termination of helices and the involvement of the alpha(II) conformation and also to discontinuities in pleated-sheet conformations.

Amino Acid Sequence↗
PubMed1974

Analysis of the code relating sequence to conformation in globular proteins. The distribution of residue pairs in turns and kinks in the backbone chain.

1. The residue pair is considered as the fundamental unit which differentiates alpha-helix, beta-pleated sheet and the various turns and kink structures of the protein backbone. 2. The HPLG alphabet (Robson & Pain, 1974) is used to group pairs of residues, giving 16 possible conformational pairs, all of which are found with differing frequencies in the nine proteins examined. 3. The frequencies of occurrence of the 16 different types of turn or kink are analysed in relation to the constituent amino acids. Those containing the L or G conformation are of low frequency and are grouped for purposes of this analysis. 4. The distribution of amino acids within all the conformational pairs is non-random, with distinct preferences shown by certain residues. 5. All pairs containing an L or G conformation require the presence of a glycine or a proton-donor side chain. 6. The results are discussed in terms of the determination of these ;random' structures by local interactions.

Amino Acid Sequence↗
PubMed1968

Biochemical effects of the hypoglycaemic compound pent--4-enoic acid and related non-hypoglycaemic fatty acids.

1. The effects of the hypoglycaemic compound, pent-4-enoic acid, and of four structurally related non-hypoglycaemic compounds (pentanoic acid, pent-2-enoic acid, cyclopropanecarboxylic acid and cyclobutanecarboxylic acid), on the oxidation of saturated fatty acids by rat liver mitochondria were determined. 2. The formation of (14)CO(2) from [1-(14)C]palmitate was strongly inhibited by 0.01mm-pent-4-enoic acid. 3. The inhibition of oxygen uptake was less than that of (14)CO(2) formation, presumably because fumarate was used as a sparker. 4. The oxidation of [1-(14)C]-butyrate, -octanoate or -laurate was not strongly inhibited by 0.01mm-pent-4-enoic acid. 5. The other four non-hypoglycaemic compounds did not inhibit the oxidation of any saturated fatty acid when tested at 0.01mm concentration, though they all inhibited strongly at 10mm. 6. The oxidation of [1-(14)C]-myristate and -stearate, but not of [1-(14)C]decanoate, was strongly inhibited by 0.01mm-pent-4-enoic acid. 7. The oxidation of [1-(14)C]palmitate was about 50% carnitine-dependent under the experimental conditions used. 8. The percentage inhibition of [1-(14)C]palmitate oxidation by pent-4-enoic acid was the same whether carnitine was present or not. 9. Acetoacetate formation from saturated fatty acids was inhibited by 0.1mm-cyclopropanecarboxylic acid to a greater extent than their oxidation. 10. The other compounds tested inhibited acetoacetate formation from saturated fatty acids proportionately to the inhibition of oxidation. 11. Possible mechanisms for the inhibition of long-chain fatty acid oxidation by pent-4-enoic acid are discussed. 12. There was a correlation between the ability to inhibit long-chain fatty acid oxidation and hypoglycaemic activity in this series of compounds.

Acetoacetates↗
PubMedDate not supplied

Prediction of HIV vaccine.

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Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

FHIT RNA and protein expression in oral squamous cell carcinomas.

BACKGROUND: To investigate the possible role of FHIT, a possible tumour suppressor gene, in oral carcinogenesis, we examined 17 oral squamous cell carcinomas (OSCCs) for genetic alterations. MATERIALS AND METHODS: Fresh tissue was obtained during surgery, snap-frozen in liquid nitrogen and stored at -70 degrees C. Nested PCR amplification to examine the integrity of FHIT mRNA was performed on the reverse transcribed complementary DNA obtained from the frozen normal and tumour tissue. Immunohistochemistry was done on formal in-fixed paraffin-embedded tissue protein from the same cases using a polyclonal antiserum against the full length Fhit. RESULTS: Twelve out 17 (71%) OSCCs showed reduced or absent Fhit protein and half of the cases with reduced Fhit protein exhibited aberrant RT-PCR products. CONCLUSION: Immunohistochemical detection of Fhit protein expression in OSCCs is the more sensitive method to determine the status of Fhit in these tumours, in agreement with previous studies of other tumour types.

Acid Anhydride Hydrolases↗