Effect of the electronic and physicochemical parameters on the carcinogenesis activity of some sulfa drugs using QSAR analysis based on genetic-MLR and genetic-PLS.

A quantitative structure activity relationship study has been applied to a data set of 18 sulfa drugs with carcinogenesis activity. Semi-empirical quantum chemical calculation (AM1 method) was used to find the optimum 3D geometry of the studied molecules. Two types of molecular descriptors including chemical and electronic was used to derive a quantitative relation between the carcinogenesis activity and structural properties. Two multi-parametric equations with good statistical qualities were obtained using genetic algorithms multiple linear regression (GA-MLR) methods. In addition, genetic algorithm-partial least squares (GA-PLS) regression was used to model the structure-activity relationships, more accurately. The results confirmed the superiority of the results obtained by GA-PLS relative to GA-MLR. The significant effect of the HOMO energy on the carcinogenic activity was explained in the context of the shape of this orbital.

Rational design of thermally stable proteins: relevance to bionanotechnology.

Design of thermally stable proteins is spurred by their applications in bionanotechnology. There are three major issues governing this: first, the upper limit on the temperature at which proteins remain physiologically active and are available for technological applications (answers may emerge from the discovery of new, natural hyperthermophilic enzymes that are active above 125 degrees C or from the selection of mutants of hyperthermophilic enzymes that are more stable); second, the use of hyperthermophilic enzymes as molecular templates to design highly stable enzymes that have high activity at low temperatures; third, the link between rigidity and flexibility to thermostability and activity, respectively. We review progress in these areas.

Ultrastructure of dental enamel afflicted with hypoplasia: an atomic force microscopic study.

The ultrastructure of the human tooth enamel from a patient diagnosed with hypoplasia (HYP) was investigated using atomic force microscopy (AFM) and compared with the surface of normal human tooth enamel. Hypoplasia is a hereditary defect of dental enamel in which the enamel is deficient in either quality or quantity. AFM results presented for the HYP tooth enamel clearly demonstrate that the apatite crystal morphology in hypoplasia tooth enamel is perturbed in the diseased state which could result from a defective synthesis of the extracellular matrix proteins, e.g., amelogenin, by the ameloblasts. HYP enamel consisting of loosely packed, very small grains does not present a tendency for association, as in the case of the normal healthy tooth. Indeed, the enamel surface affected by HYP is porous and is made of much smaller grains. In some samples, the HYP part of enamel surface appeared in the form of a point-defect, which we believe may be associated with the early stages of the HYP deformation.

An atomic force microscopic study of the ultrastructure of dental enamel afflicted with amelogenesis imperfecta.

The ultrastructure of human tooth enamel from a patient diagnosed to have amelogenesis imperfecta (AI) was investigated using atomic force microscopy (AFM) and compared with normal human tooth enamel. AI is a hereditary defect of dental enamel in which the enamel is deficient in either quality or quantity. Tissue-specific proteins, especially amelogenins, have been postulated to play a central role in amelogenesis. The secondary structure of amelogenin has been assigned an important role in directing the architecture of hydroxyapatite (HA) enamel crystallites and an alteration of the secondary structure of amelogenin is expected to result in an altered architecture of the mineral phase in human enamel. Previous studies have shown that the human amelogenin gene encodes for a mutant protein in which a conserved Pro is mutated to a Thr residue (Pro-->Thr); such a mutation should be expected to cause a disoriented pattern of the mineral phase in enamel. AFM results presented for the AI tooth enamel clearly demonstrate that the apatite crystal morphology in AI tooth enamel is perturbed in the diseased state; this might result from a defective synthesis of the extracellular matrix proteins, e.g. amelogenin, by the ameloblasts.

Human pancreatic thread protein, an exocrine thread protein with possible implications to Alzheimer's disease: secondary structure in solution at acid pH.

The secondary structure of human pancreatic thread protein (HPTP) in solution at acid pH was derived using Fourier transform infrared (FT-IR) and laser Raman spectroscopic studies. The experimentally derived secondary structure of HPTP was compared with the secondary structure obtained by the Chou-Fasman algorithm. Pancreatic thread protein is a major exocrine secretory protein that in vitro forms filamentous bundles reminiscent of the paired helical filaments of Alzheimer's disease (AD). PTP immunoreactivity in brains afflicted with AD has been demonstrated previously and high levels of its mRNA in the developing human brain have also been reported in the literature. The above studies suggest that AD is associated with enhanced expression of PTP-related transcripts with interneuronal accumulation of PTP-like proteins. The experimentally derived secondary structure of HPTP consists of a significant proportion of beta-sheets and beta-turns and lesser amounts of alpha-helical structures. The beta-sheet component presumably plays an important role in the pH-dependent globule-fibril transformation of HPTP leading to antiparallel beta-sheet structure in the aggregated state. The secondary structure of HPTP and its globule-fibril transformation lend credence to the belief that AD may be viewed as a conformational disease.

Tyrosyl interactions in the folding and unfolding of bovine pancreatic ribonuclease A: a study of tyrosine-to-phenylalanine mutants.

Three tyrosine-to-phenylalanine mutants of ribonuclease A (Y25F, Y92F, and Y97F) are investigated for their enzymatic activities, molecular stabilities, and unfolding/refolding kinetics. These mutants exhibit 80, 90, and 80%, respectively, of the catalytic activity of the wild-type enzyme. Thermal, Gdn.HCl, and pH transition measurements indicate that Y25F and Y97F are less stable than the wild-type protein, whereas the bulk of the thermodynamic and kinetic evidence indicates that Y92F is as stable as the wild-type protein. Differences in molar extinction coefficients indicate that tyrosines 25, 92, and 97 contribute 38, 13, and 39%, respectively, to the absorption difference between the folded and unfolded states, in general agreement with previous studies but possibly indicating the contribution of a fourth tyrosine residue to account for the remaining 10%. Stopped-flow single- and double-jump kinetic experiments were carried out on the wild-type and three mutant proteins. At least one tyrosine residue besides tyrosine 92 contributes to the slow fluorescence-unfolding phase; the likely candidate for this residue is tyrosine 115 which monitors the cis-trans isomerization of the X-Pro114 peptide bond. Tyrosines 25 and 97 are involved in interactions that retard conformational unfolding and accelerate conformational refolding as well as the cis-trans proline isomerization of the slow-refolding phases, presumably by stabilizing the major beta-hairpin structure of RNase A. These interactions may contribute to the strong pH dependence of the folding and unfolding of ribonuclease A. In contrast, tyrosine 92 does not affect the folding and unfolding rates significantly. An improved "box" model of proline isomerization under unfolding conditions was derived from exhaustive fitting of all possible box models. The kinetic data support the identification of Pro93 as the proline whose isomerization distinguishes the slow-refolding species (USII and USI) from the other, faster-refolding species (Uvf, Uf, and Um), implying that Pro93 isomerizes in the slow-refolding reactions USI --> N and IN --> N. Similarly, Pro114 seems to distinguish between the very fast-refolding species Uvf and the fast-refolding species Uf. Lastly, Pro117 seems to distinguish the major slow-refolding species USII from the minor slow-refolding species USI and the medium-refolding species Um from the fast- and very fast-refolding species.

Modeling study on the cleavage step of the self-splicing reaction in group I introns.

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

The multiple-minima problem in small peptides revisited. The Threshold Accepting approach.

A recently reported optimization method, known as Threshold Accepting, was tested for the purpose of locating the structure of several peptide molecules with the lowest conformational energy. A comparison with previous results obtained with the Simulated Annealing technique was made. Our study indicate Threshold Accepting as a better technique in locating such structures.

Global minimum energy conformations of thyrotropin releasing hormone analogs by simulated annealing. II.

Lowest conformational energy structures of seventeen thyrotropin releasing hormone analogs have been studied by simulated annealing. A surprising conformational similarity was observed for the peptide backbone. The possible role of each substituent in its biological activity is inferred. A composite hydrogen-bonding environment is proposed for the TRH with respect to receptor binding.

Applications of simulated annealing to the multiple-minima problem in small peptides.

A Simulated Annealing method has been implemented to overcome the multiple minima problem inherent in finding the global minimum of small peptides with 2, 3, 5, 10 and 24 dihedral angles. The algorithm works much better if one introduces the anticorrelations observed in Molecular Dynamics.

Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196.

A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

Molecular modelling of protein-nucleic acid interactions.

Computer modeling techniques to study the interaction of proteins with nucleic acids are presented. The methods utilize information from genetic and chemical modification experiments and macromolecular structural constraints. These techniques, in addition to computer model building procedures and theoretical energy calculations, are illustrated for the study of the lac and cro repressor-operator systems. Our predicted interactions between lac and its operator agree with those recently reported for lac based upon sequence alignment with the cro repressor. Several molecular models of the putative helical segment of cro interacting with its OR3 operator are presented. These models are reflective of intermediate conformations experienced by the repressor in recognition of the operator sequence. The results of our studies are further discussed in terms of the design of short peptides interacting with nucleic acid sequences and the evolutionary requirements in establishing these repressor interactions.