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At least 253 records · Page 14Linked to original sources
PubMed1996

Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests.

The role of polar and charged side chains in partially buried protein environments has been probed in a variant of Arc repressor (MYL) in which hydrophobic interactions between Met31, Tyr36, and Leu40 replace the wild-type salt-bridge interactions between Arg31, Glu36, and Arg40. In the absence of this salt-bridge triad, three additional side chains were identified by continuum electrostatic calculations as incurring larger desolvation penalties during folding than were recovered in favorable electrostatic interactions in the folded state. These side chains (Asn29, Ser44, and Glu48) were mutated singly and collectively to alanine in the MYL background, and the thermodynamic stabilities of the resulting mutant proteins were found to be increased by 0.1 to 1.3 kcal/mol of dimer. All of the mutants displayed cooperative thermal melts and appeared to have well-packed hydrophobic cores by near-UV circular dichroism spectroscopy, indicating that conformational specificity is maintained. The Arc variant (MYL-NA29/SA44/EA48) in which the entire six-residue polar network is replaced by nonpolar groups is 5.1 kcal/mol of dimer more stable than wild type, indicating that the strategy of replacing buried or partially buried charged and polar side chains with hydrophobic residues can lead to substantial stabilization.

Calorimetry↗
PubMed2005

Computational approach to the rational design of molecularly imprinted polymers for voltammetric sensing of homovanillic acid.

A methodology based on density functional theory calculations for the design of molecularly imprinted polymers (MIPs) is described. The method allows the rational choice of the most suitable monomer and polymerization solvent among a set of chemicals traditionally used in MIP formulations for the molecular imprinting of a given template. It is based on the comparison of the stabilization energies of the prepolymerization adducts between the template and different functional monomers. The effect of the polymerization solvent is included using the polarizable continuum model. A voltammetric sensor for homovanillic acid was constructed using different MIPs as recognition element, confirming that the solvent (toluene) and functional monomer (methacrylic acid) selected according to the theoretical predictions lead to the most efficient molecular recognition sensing phase. With the voltammetric sensor prepared using the MIP designed according to the theoretical predictions, a linear response for concentrations of homovanillic acid between 5 x 10(-8) and 1 x 10(-5) M can be obtained. The limit of detection is 7 x 10(-9) M. The selectivity obtained for homovanillic acid over other structurally related compounds buttresses the validity of this strategy of design.

Computer Simulation↗
PubMed2005

EXAMINE: a computational approach to reconstructing gene regulatory networks.

Reverse-engineering of gene networks using linear models often results in an underdetermined system because of excessive unknown parameters. In addition, the practical utility of linear models has remained unclear. We address these problems by developing an improved method, EXpression Array MINing Engine (EXAMINE), to infer gene regulatory networks from time-series gene expression data sets. EXAMINE takes advantage of sparse graph theory to overcome the excessive-parameter problem with an adaptive-connectivity model and fitting algorithm. EXAMINE also guarantees that the most parsimonious network structure will be found with its incremental adaptive fitting process. Compared to previous linear models, where a fully connected model is used, EXAMINE reduces the number of parameters by O(N), thereby increasing the chance of recovering the underlying regulatory network. The fitting algorithm increments the connectivity during the fitting process until a satisfactory fit is obtained. We performed a systematic study to explore the data mining ability of linear models. A guideline for using linear models is provided: If the system is small (3-20 elements), more than 90% of the regulation pathways can be determined correctly. For a large-scale system, either clustering is needed or it is necessary to integrate information in addition to expression profile. Coupled with the clustering method, we applied EXAMINE to rat central nervous system development (CNS) data with 112 genes. We were able to efficiently generate regulatory networks with statistically significant pathways that have been predicted previously.

Algorithms↗
PubMed1998

New experimental and computational approaches to the analysis of gene expression.

Public and private EST (Expressed Sequence Tag) programs provide access to a large number of ESTs from a number of plant species, including Arabidopsis, corn, soybean, rice, wheat. In addition to the homology of each EST to genes in GenBank, information about homology to all other ESTs in the data base can be obtained. To estimate expression levels of genes represented in the DuPont EST data base we count the number of times each gene has been seen in different cDNA libraries, from different tissues, developmental stages or induction conditions. This quantitation of message levels is quite accurate for highly expressed messages and, unlike conventional Northern blots, allows comparison of expression levels between different genes. Lists of most highly expresses genes in different libraries can be compiled. Also, if EST data is available for cDNA libraries derived from different developmental stages, gene expression profiles across development can be assembled. We present an example of such a profile for soybean seed development. Gene expression data obtained from Electronic Northern analysis can be confirmed and extended beyond the realm of highly expressed genes by using high density DNA arrays. The ESTs identified as interesting can be arrayed on nylon or glass and probed with total labeled cDNA first strand from the tissue of interest. Two-color fluorescent labeling allows accurate mRNA ratio measurements. We are currently using the DNA array technology to study chemical induction of gene expression and the biosynthesis of oil, carbohydrate and protein in developing seeds.

Blotting, Northern↗
PubMed2006

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Prediction of the biological effect of missense substitutions has become important because they are often observed in known or candidate disease susceptibility genes. In this paper, we carried out a 3-step analysis of 1514 missense substitutions in the DNA-binding domain (DBD) of TP53, the most frequently mutated gene in human cancers. First, we calculated two types of conservation scores based on a TP53 multiple sequence alignment (MSA) for each substitution: (i) Grantham Variation (GV), which measures the degree of biochemical variation among amino acids found at a given position in the MSA; (ii) Grantham Deviation (GD), which reflects the 'biochemical distance' of the mutant amino acid from the observed amino acid at a particular position (given by GV). Second, we used a method that combines GV and GD scores, Align-GVGD, to predict the transactivation activity of each missense substitution. We compared our predictions against experimentally measured transactivation activity (yeast assays) to evaluate their accuracy. Finally, the prediction results were compared with those obtained by the program Sorting Intolerant from Tolerant (SIFT) and Dayhoff's classification. Our predictions yielded high prediction accuracy for mutants showing a loss of transactivation ( approximately 88% specificity) with lower prediction accuracy for mutants with transactivation similar to that of the wild-type (67.9 to 71.2% sensitivity). Align-GVGD results were comparable to SIFT (88.3 to 90.6% and 67.4 to 70.3% specificity and sensitivity, respectively) and outperformed Dayhoff's classification (80 and 40.9% specificity and sensitivity, respectively). These results further demonstrate the utility of the Align-GVGD method, which was previously applied to BRCA1. Align-GVGD is available online at http://agvgd.iarc.fr.

Amino Acid Sequence↗
PubMed2006

Role of sequence and conformation on the photochemistry and the photophysics of A-T DNA dimers: an experimental and computational approach.

The role of base sequence and conformation on the photochemistry and photophysics of thymidylyl (3'-5')-2'-deoxyadenosine sodium salt (TpdA) and 2-deoxyadenylyl (3'-5')-thymidine ammonium salt (dApT) was studied. To this end, nanosecond transient absorption at 266 nm, steady-state irradiation at 254 nm, and quantum chemical calculations were used. The transient absorption spectra show the solvated electron broad band in the visible region for each dinucleotide. In addition, low-intensity absorption bands are observed in the UV region, which are attributed to the deprotonated and protonated neutral radicals of adenine and thymine bases. Photoionization (PI) occurs by one- and two-photon pathways; the latter accounting for approximately 70% of the net PI yield. A diffusion-limited rate constant of 2.0 x 10(10) M(-1) s(-1) was obtained for the reaction of the neutral molecule with the photoejected electron in both sequences. The photodestruction yield, measured from the chromophore loss at 260 nm, decreases in the presence of well-known electron scavengers. This suggests the participation of base radical anions as one of the photodegradation pathways, which is higher in TpdA than in dApT. The intermediacy of a radical ion pair (charge separated state) between the adjacent adenine and thymine bases is proposed in the formation of the [2 + 2] cycloadduct intermediate. The [2 + 2] cycloadduct intermediate is known to be the precursor of the thymine-adenine eight-member ring photoproduct (TA*). Conformational constrains in the radical ion pair are suggested to explain the absence of the TA* photoproduct in dApT. This hypothesis is supported by semiempirical calculations performed on all relevant reactive intermediates proposed to participate in the mechanism of formation of TA*. Altogether, the results show that sequence and conformation profoundly influence the photochemistry and the photophysics of these DNA model systems.

Adenine↗
PubMed2000

Asymmetry and magnetism in bis(oximato)-bridged heterobimetallic compounds: a computational approach.

A density functional study of exchange coupling was carried out for a series of heterobinuclear oximato-bridged transition metal complexes. Model calculations were used to examine the influence of the electronic configuration of the metal atoms on the coupling constants. This analysis was complemented by a study of the variation of the coupling constant with the most usual structural distortions within this family of compounds. The influence of the nature of the terminal ligands as well as that of the symmetry on the bridge were also investigated.

Journal Article↗
PubMed2004

Computational approaches to activity in rhodium-catalysed hydroformylation.

In this theoretical study on rhodium-catalysed hydroformylation we examine an unmodified hydridorhodium(I) carbonyl system a together with three variants modified by the model phosphane ligands PF3 (system b), PH3 (system c) and PMe3 (system d), which show increasing basicity on the Tolman chi parameter scale. The olefinic substrate for all systems is ethene. Based on the dissociative hydroformylation mechanism, static and dynamic quantum-mechanical approaches are made for preequilibria and the whole catalytic cycle. Agreement with experimental results was achieved with regard to the predominance of phosphane monocoordination in systems b-d, different sensitivity of unmodified and modified systems towards hydrogen pressure and the early location of the rate-determining step. Neither the catalytic cycle as a whole nor olefin insertion as an important selectivity-determining step gives a clear picture of activity differences among a-d. However, the crucial first catalytic step, association of ethene to the active species [HRhL3] (L=CO, PR3), may play the key role in the experimentally observed higher activity of a and systems with less basic phosphane ligands modelled by b.

Journal Article↗
PubMed2005

Iodine monochloride-amine complexes: an experimental and computational approach to new chiral electrophiles.

Lactonizations are important steps in many synthetic sequences. Substrate-controlled reactions that use chiral auxiliaries or chiral alkenes have already been studied in depth. This study focuses on stereoselective reagent-controlled iodolactonizations, by application of a new method that uses complexes of iodine monochloride and various donor molecules. (R)-1,2,3,4-Tetrahydro-1-naphthylamine and other amines with similar structures were found to be efficient in the iodocyclization of 4-aryl-4-pentenoic acids. Calculations were performed on complexes of (R)-1,2,3,4-tetrahydro-1-naphthylamine with XCl (X = I, H) to identify possible reactive species in these iodocyclizations. Calculations were carried out at various levels of theory, including B3 LYP/6-31+G (d,p) by using a modified SDD basis set for iodine.

Journal Article↗
PubMed1994

A computational approach to the relationship between radiation induced double strand breaks and translocations.

A theoretical framework is presented which provides a quantitative analysis of radiation induced translocations between the ab1 oncogene on CH9q34 and a breakpoint cluster region, bcr, on CH 22q11. Such translocations are associated frequently with chronic myelogenous leukemia. The theory is based on the assumption that incorrect or unfaithful rejoining of initial double strand breaks produced concurrently within the 200 kbp intron region upstream of the second abl exon, and the 16.5 kbp region between bcr exon 2 and exon 6 interact with each other, resulting in a fusion gene. for an x-ray dose of 100 Gy, there is good agreement between the theoretical estimate and the one available experimental result. The theory has been extended to provide dose response curves for these types of translocations. These curves are quadratic at low doses and become linear at high doses.

Animals↗
PubMed1993

Non-discrete biomolecular computing: an approach to computational complexity.

General principles of information processing at the molecular level inherent in simple biological and biomolecular entities can be used to elaborate essentially new non-discrete information-processing devices. These principles are: giant parallelism of information processing; processing mechanisms based on complicated non-linear dynamics; high efficiency of information transformations; considerable behavioral complexity of computational (pseudoelementary) primitives; and the possibility of variation and evolution of the molecular components of information-processing devices, including the possibility of evolutionary learning. Problems of high computational complexity are currently of great practical importance. Non-discrete biomolecular information-processing devices seem to be able to solve effectively some classes of problems of high computational complexity.

Biomedical Engineering↗
PubMed1992

Computational approaches to hippocampal function.

The results of theoretical work have led researchers to suggest that the hippocampal formation may maximize its memory storage capacity by recoding events into patterns that are as dissimilar to one another, and which use as few neurons per event, as possible.

Animals↗
PubMed2005

Comparison of positively charged DNG with DNA duplexes: a computational approach.

Molecular dynamics is used to investigate the structural properties of the cationic DNA analogue deoxynucleic guanidine (DNG), in which a guanidinium group replaces the phosphate moiety of DNA. This study examines the DNG duplex dodecamers d(Ag)(12).d(Tg)(12) and d(Gg)(12).d(Cg)(12), as well as their DNA counterparts. Watson-Crick base-pairing is maintained in the solvated DNG duplex models during the 5ns simulations. The idealized DNG dodecamers assume many parameters characteristic of the corresponding native DNA, assuming B-DNA conformations. Several helical parameters are rather unique to DNG, including buckle, slide, inclination, propeller, and X-displacement. Fewer transitions in backbone torsions occur in the DNG duplexes compared to those of the DNA, which may result from the greater rigidity of the sp(2) hybridized guanidinium group verses the flexible sp(3) phosphate group. The DNG helices have exceptionally shallow major grooves and very deep minor grooves. The major and minor groove widths of DNG are narrower than those of the respective DNA counterparts.

DNA↗
PubMed1997

A computational approach to modeling nucleic acid hairpin structures.

Hairpin is a structural motif frequently observed in both RNA and DNA molecules. This motif is involved specifically in various biological functions (e.g., gene expression and regulation). To understand how these hairpin motifs perform their functions, it is important to study their structures. Compared to protein structural motifs, structures of nucleic acid hairpins are less known. Based on a set of reduced coordinates for describing nucleic acid structures and a sampling algorithm that equilibrates structures using Metropolis Monte Carlo simulation, we developed a method to model nucleic acid hairpin structures. This method was used to predict the structure of a DNA hairpin with a single-guanosine loop. The lowest energy structure from the ensemble of 200 sampled structures has a RMSD of < 1.5 A, from the structure determined using NMR. Additional constraints for the loop bases were introduced for modeling an RNA hairpin with two nucleotides in the loop. The modeled structure of this RNA hairpin has extensive base stacking and an extra hydrogen bond (between the CYT in the loop and a phosphate oxygen), as observed in the NMR structure.

Algorithms↗
PubMed2000

Experimental and computational approach for the evaluation of the biomechanical effects of dental bridge misfit.

Dental bridges supported by osseointegrated implants are commonly used to treat the partially or completely edentulous jaw. The bridges are manufactured in metal alloy using a sequence of technological steps which well match the requirement to get custom overstructures but does not guarantee geometrical and dimensional tolerances. Dentists often experience that a perfect fit of the bridge with the abutments is almost impossible to achieve. When a misfitting bridge is forced on the abutments, deformations may occur inducing a permanent preload at the fixture-bone interface and the greater the misfit the greater is the preload and the risk of implant failure. This work gives an evaluation of the biomechanical effects induced by a misfitting bridge when forced on two supporting dental implants. The strains induced in the bridge have been measured using two purposely designed and fabricated experimental devices allowing different types of misfit. FEM 3D models of the bridge and of the bridge anchored to the bone by implants have been developed. The former has been validated by simulating the same loading conditions as in the experimental tests and comparing the bridge strains. Both models have been used for the evaluation of the stress induced in the bridge and at the fixture-bone interface by bridge length errors. The results show that the method may help to estimate the stress distribution in the bridge and bone as a consequence of different dental bridge misfits.

Biomechanical Phenomena↗