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Biomedical subjects

P D Thomas

Publications and source records attributed to P D Thomas.

At least 19 recordsLinked to original sources
PubMed1999

A non-toxic analogue of a coeliac-activating gliadin peptide: a basis for immunomodulation?

BACKGROUND: A-gliadin residues 31-49 (peptide A) binds to HLA-DQ2 and is toxic to coeliac small bowel. Analogues of this peptide, which bind to DQ2 molecules but are non-toxic, may be a potential route to inducing tolerance to gliadin in patients with coeliac disease. METHODS: Toxicity was investigated with small bowel organ culture in six patients with untreated coeliac disease, four with treated coeliac disease and six controls. Analogue peptides comprised alanine substituted variants of peptide A at L31 (peptide D), P36 (E), P38 (F), P39 (G) and P42 (H). RESULTS: Peptides D and E were toxic in biopsies from some patients. Peptides F, G and H were not toxic. CONCLUSIONS: Peptide F, which binds to DQ2 more strongly than peptide A, is not toxic in patients with coeliac disease in-vitro; this could be an initial step towards investigation of the induction of tolerance to gliadin in patients affected by coeliac disease.

Adult↗
PubMed1999

Is gliadin mispresented to the immune system in coeliac disease? A hypothesis.

The primary pathogenic trigger in coeliac disease (CD) is still unknown. We present the hypothesis that in CD the enterocytes could metabolize gliadin through an immunogenic pathway instead of a tolerogenic one. The result of this abnormal presentation of gliadin to the immune system would be the activation of lamina propria T cells, followed by the onset of enteropathy.

Antigen-Presenting Cells↗
PubMed1998

Synthesis and antitumour effect of the melanogenesis-based antimelanoma agent N-propionyl-4-S-cysteaminylphenol.

Chemotherapy of malignant melanoma is still a great challenge, as no effective drugs are available. The development of melanogenesis-based drugs is a promising area of research because melanogenesis is a unique biochemical pathway operating only in melanoma cells (and their normal counterparts) so that the tumour can be targeted. We have been using cysteinylphenol, a sulphur-containing analogue of tyrosine, and derivatives for that purpose. N-Acetyl-4-S-cysteaminylphenol was found to have the best antimelanoma effect in cell culture systems and in mice bearing B16 melanoma tumours. It also caused depigmentation of the skin, suggesting the possibility of use as a hypopigmenting agent. To improve the efficiency of the drug, we thought of replacing the acetyl group in N-acetyl-4-S-cysteaminylphenol with a propionyl group in the hope that increased hydrophobicity would increase the cellular uptake of the drug. N-Propionyl-4-S-cysteaminylphenol was synthesized by condensing 4-hydroxythiophenol with 2-ethyl-2-oxazoline. The drug showed both cytostatic and cytocidal effects in a human melanotic melanoma cell line. The drug was found to be a good depigmenting agent for the black hair follicles of C57 black mice when given s.c. for 14 days. A 10-day treatment with N-propionyl-4-S-cysteaminylphenol at 300 mg/kg body weight reduced the growth rate of B16 melanoma s.c. tumours in mice by 36%. The propionyl derivative was found to increase the life span of mice bearing melanoma more effectively than did the acetyl derivative.

Animals↗
PubMed1998

Fat distribution and changes in the blood brain barrier in a rat model of cerebral arterial fat embolism.

This study was designed to determine the distribution of fat which reaches the brain by the internal carotid artery, and the consequent alterations in the blood brain barrier, in a rat model of cerebral arterial fat embolism. The distribution of the blood flow in this model was determined by the injection of radiolabelled microspheres. Over 44% were trapped in the brain, 43% in the extracerebral tissues of the head and neck, and 7% in the lungs. Over 30% of radiolabelled triolein was present within the brain 30 min after injection, and 4% still remained after 17 days. Approximately 25% of the triolein which went to the brain moved through the cerebral vessels and left within the first 15 min. The majority of the triolein distributed to the ipsilateral cerebral hemisphere, with significantly less to the contralateral cerebral hemisphere, brain stem and cerebellum. The blood brain barrier opened, as measured by uptake of 99mTc, within the first 15 min and remained open for at least 3 days. A significant percentage of fat reaching the brain persists for days, and causes rapid and long-lasting damage to the blood brain barrier.

Animals↗
PubMed1998

Fulminant desquamative interstitial pneumonitis.

A previously well, 48-year-old female presented with a short history of respiratory distress and fever for which no cause could be found. Open lung biopsy was not contributory. She died within nine days of presentation of hypoxia and multi-organ failure. Post mortem examination revealed the pattern of desquamative interstitial pneumonitis.

Female↗
PubMed1996

An iterative method for extracting energy-like quantities from protein structures.

We present a method (ENERGI) for extracting energy-like quantities from a data base of protein structures. In this paper, we use the method to generate pairwise additive amino acid "energy" scores. These scores are obtained by iteration until they correctly discriminate a set of known protein folds from decoy conformations. The method succeeds in lattice model tests and in the gapless threading problem as defined by Maiorov and Crippen [Maiorov, V. N. & Crippen, G. M. (1992) J. Mol. Biol. 227, 876-888]. A more challenging test of threading a larger set of test proteins derived from the representative set of Hobohm and Sander [Hobohm, U. & Sander, C. (1994) Protein Sci. 3, 522-524] is used as a "workbench" for exploring how the ENERGI scores depend on their parameter sets.

Amino Acid Sequence↗
PubMed1996

Statistical potentials extracted from protein structures: how accurate are they?

"Statistical potentials" are energies widely used in computer algorithms to fold, dock, or recognize protein structures. They are derived from: (1) observed pairing frequencies of the 20 amino acids in databases of known protein structures, and (2) approximations and assumptions about the physical process that these quantities measure. Using exact lattice models, we construct a rigorous test of those assumptions and approximations. We find that statistical potentials often correctly rank-order the relative strengths of interresidue interactions, but they do not reflect the true underlying energies because of systematic errors arising from the neglect of excluded volume in proteins. We find that complex residue-residue distance dependences observed in statistical potentials, even those among charged groups, can be largely explained as an indirect consequence of the burial of non-polar groups. Our results suggest that current statistical potentials may have limited value in protein folding algorithms and wherever they are used to provide energy-like quantities.

Algorithms↗
PubMed1995

A test of lattice protein folding algorithms.

We report a blind test of lattice-model-based search strategies for finding global minima of model protein chains. One of us (E.I.S.) selected 10 compact conformations of 48-mer chains on the three-dimensional cubic lattice and used their inverse folding algorithm to design HP (H, hydrophobic; P, polar) sequences that should fold to those "target" structures. The sequences, but not the structures, were sent to the UCSF group (K.Y., K.M.F., P.D.T., H.S.C., and K.A.D.), who used two methods to attempt to find the globally optimal conformations: "hydrophobic zippers" and a constraint-based hydrophobic core construction (CHCC) method. The CHCC method found global minima in all cases, and the hydrophobic zippers method found global minima in some cases, in minutes to hours on workstations. In 9 out of 10 sequences, the CHCC method found lower energy conformations than the 48-mers were designed to fold to. Thus the search strategies succeed for the HP model but the design strategy does not. For every sequence the global energy minimum was found to have multiple degeneracy with 10(3) to 10(6) conformations. We discuss the implications of these results for (i) searching conformational spaces of simple models of proteins and (ii) how these simple models relate to proteins.

Algorithms↗
PubMed1995

Principles of protein folding--a perspective from simple exact models.

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse.

Amino Acid Sequence↗
PubMed1995

A simple protein folding algorithm using a binary code and secondary structure constraints.

We describe an algorithm to predict tertiary structures of small proteins. In contrast to most current folding algorithms, it uses very few energy parameters. Given the secondary structural elements in the sequence--alpha-helices and beta-strands--the algorithm searches the remaining conformational space of a simplified real-space representation of chains to find a minimum energy of an exceedingly simple potential function. The potential is based only on a single type of favorable interaction between hydrophobic residues, an unfavorable excluded volume term of spatial overlaps and, for sheet proteins, an interstrand hydrogen bond interaction. Where appropriate, the known disulfide bonds are constrained by a square-law potential. Conformations are searched by a genetic algorithm. The model predicts reasonably well the known tertiary folds of seven out of the 10 small proteins we consider. We draw two conclusions. First, for the proteins we tested, this exceedingly simple potential function is no worse than others having hundreds of energy parameters in finding the right general tertiary structures. Second, despite its simplicity, the potential function is not the weak link in this algorithm. Differences between our predicted structures and the correct targets can be ascribed to shortcomings in our search strategy. This potential function may be useful for testing other conformational search strategies.

Algorithms↗
PubMed1995

Divalent cations control cell-substrate adhesion and laminin expression in normal and malignant human melanocytes in early and late stages of cellular differentiation.

Integrins are a class of adhesion molecules that depends on divalent cations for proper function. This study examined whether human normal melanocytes and malignant (metastatic) melanocytes with early and late stages of cellular differentiation (G361 and SK-MEL-23, respectively) would differ in integrin-mediated adhesion to fibronectin, laminin, as well as collagens type I and type IV, and whether divalent cations could influence the strength of adhesion ability. Integrin subunit expression was determined by flow cytometry using integrin subunit-specific antibodies as probes. Integrin-specific adhesion was determined using soluble glycine-arginine-glycine-asparagine-serine peptide and integrin subunit-specific antibodies as functional blocking agents. This study shows that both normal and malignant melanocytes adhere to extracellular matrices in a divalent cation-dependent manner, and adhesion strength varies with the cation species. Integrins can be rapidly activated by small alterations in cation concentration, manganese being the most potent. There were marked differences in substrate adhesion between normal melanocytes and metastatic malignant melanoma cells, but these differences were not related to the stage of cellular differentiation. All the three cell types, however, expressed the same integrin subunits at approximately the same levels. This suggests that substrate adhesion of melanocytes and melanoma cells might involve some integrin-independent mechanisms as well. Manganese, in particular, appears to cause adhesion by activating both integrin-dependent and -independent mechanisms.

Amino Acid Sequence↗
PubMed1995

Dual role of melanins and melanin precursors as photoprotective and phototoxic agents: inhibition of ultraviolet radiation-induced lipid peroxidation.

Ultraviolet radiation (UVR) is one of the risk factors for skin cancer and the main inducer of melanin pigmentation, the major protective mechanism of mammalian skin against radiation damage. The melanin pigments, eumelanin and pheomelanin, are likely to be important in protection against UVR, but their precursors are generally considered as phototoxic. The available data suggest DNA damage as the mechanism of phototoxicity. However, the effect of melanin precursors on membrane damage through lipid peroxidation, another important and probably more relevant (from the point-of-view of the melanosomal confinement of these molecules) mechanism of phototoxicity, not known. As a model system for UVR-melanin-membrane interactions, we irradiated liposomes in the presence of eumelanin, pheomelanin and two of their major precursors, 5,6-dihydroxyindole (DHI) and 5-S-cysteinyldopa (SCD). The presence of the two melanin precursors substantially reduced the formation of lipid peroxidation products resulting from UVR exposure. The antioxidant activity of the melanin precursors was diminished under strong prooxidant conditions (presence of Fe3+). These results suggest that melanin precursors may have an important role in the protection of skin against the harmful effects of UVR including photocarcinogenesis.

Animals↗