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Biomedical subjects

C Micheletti

Publications and source records attributed to C Micheletti.

17 recordsLinked to original sources
PubMed2001

Conformations of proteins in equilibrium.

We introduce a simple theoretical approach for an equilibrium study of proteins with known native-state structures. We test our approach with results on well-studied globular proteins, chymotrypsin inhibitor (2ci2), barnase, and the alpha spectrin SH3 domain, and present evidence for a hierarchical onset of order on lowering the temperature with significant organization at the local level even at high temperatures. A further application to the folding process of HIV-1 protease shows that the model can be reliably used to identify key folding sites that are responsible for the development of drug resistance.

Animals↗
PubMed2001

Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways.

Drug resistance to HIV-1 protease involves the accumulation of multiple mutations in the protein. We investigate the role of these mutations by using molecular dynamics simulations that exploit the influence of the native-state topology in the folding process. Our calculations show that sites contributing to phenotypic resistance of FDA-approved drugs are among the most sensitive positions for the stability of partially folded states and should play a relevant role in the folding process. Furthermore, associations between amino acid sites mutating under drug treatment are shown to be statistically correlated. The striking correlation between clinical data and our calculations suggest a novel approach to the design of drugs tailored to bind regions crucial not only for protein function, but for folding as well.

Amino Acid Sequence↗
PubMed2001

Learning effective amino acid interactions through iterative stochastic techniques.

The prediction of the three-dimensional structures of the native states of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential task for solving this problem within coarse-grained models is the deduction of effective interaction potentials between the amino acids. Over the years, several techniques have been developed to extract potentials that are able to discriminate satisfactorily between the native and nonnative folds of a preassigned protein sequence. In general, when these potentials are used in actual dynamical folding simulations, they lead to a drift of the native structure outside the quasinative basin. In this article, we present and validate an approach to overcome this difficulty. By exploiting several numerical and analytical tools, we set up a rigorous iterative scheme to extract potentials satisfying a prerequisite of any viable potential: the stabilization of proteins within their native basin (less than 3-4 A RMSD). The scheme is flexible and is demonstrated to be applicable to a variety of parameterizations of the energy function, and it provides in each case the optimal potentials.

Amino Acids↗
PubMed2001

A self-consistent knowledge-based approach to protein design.

A simple and very efficient protein design strategy is proposed by developing some recently introduced theoretical tools which have been successfully applied to exactly solvable protein models. The design approach is implemented by using three amino acid classes and it is based on the minimization of an appropriate energy function. For a given native state the results of the design procedure are compared, through a statistical analysis, with the properties of an ensemble of sequences folding in the same conformation. If the success rate is computed on those sites designed with high confidence, it can be as high as 80%. The method is also able to identify key sites for the folding process: results for 2ci2 and barnase are in very good agreement with experimental results.

Amino Acid Sequence↗
PubMed2001

Menkes disease: case report of an uncommon presentation with white matter lesions.

Menkes disease is a rare X-linked disorder related to a defect in the copper metabolism. According to the current literature, the most frequent neuroimaging findings are cortical atrophy, chronic subdural effusion or hygroma, and vascular abnormalities. White matter lesions may be present before other features of the disease and may evolve into atrophy. We hereby report a case of Menkes disease with typical history and progression, and an early phase imaging study with important white matter abnormalities, which could have lead to diagnostic difficulties.

Brain↗
PubMed2000

Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies.

A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out optimally automated subdivisions of protein fragments into classes of similarity. The goal is to provide the minimal set of protein oligomers (termed "oligons" for brevity) that is able to represent any other fragment. At variance with previous studies in which recurrent local motifs were classified, our concern is to provide simplified protein representations that have been optimised for use in automated folding and/or design attempts. In such contexts, it is paramount to limit the number of degrees of freedom per amino acid without incurring loss of accuracy of structural representations. The suggested method finds, by construction, the optimal compromise between these needs. Several possible oligon lengths are considered. It is shown that meaningful classifications cannot be done for lengths greater than six or smaller than four. Different contexts are considered for which oligons of length five or six are recommendable. With only a few dozen oligons of such length, virtually any protein can be reproduced within typical experimental uncertainties. Structural data for the oligons are made publicly available.

Algorithms↗
PubMed2000

Optimal shapes of compact strings.

Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest packing fraction; only recently has it been proved that the answer for infinite systems is a face-centred-cubic lattice. This simply stated problem has had a profound impact in many areas, ranging from the crystallization and melting of atomic systems, to optimal packing of objects and the sub-division of space. Here we study an analogous problem--that of determining the optimal shapes of closely packed compact strings. This problem is a mathematical idealization of situations commonly encountered in biology, chemistry and physics, involving the optimal structure of folded polymeric chains. We find that, in cases where boundary effects are not dominant, helices with a particular pitch-radius ratio are selected. Interestingly, the same geometry is observed in helices in naturally occurring proteins.

Collagen↗
PubMed2000

Role of secondary motifs in fast folding polymers: a dynamical variational principle.

A fascinating and open question challenging biochemistry, physics, and even geometry is the presence of highly regular motifs such as alpha helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.

Kinetics↗
PubMed1998

Design of proteins with hydrophobic and polar amino acids.

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of 20 single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75%, independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse-graining of the 20 kinds of amino acids into just two effective types.

Algorithms↗
PubMed1994

Towards new formulations for polyacrylamide matrices: N-acryloylaminoethoxyethanol, a novel monomer combining high hydrophilicity with extreme hydrolytic stability.

Matrices for electrokinetic separations, based on a unique class of mono- and disubstituted (on the amido nitrogen) acrylamides such as e.g., N-acryloylaminoethoxyethanol (AAEE) and acrylamido-N,N-diethoxyethanol, offer the following advantages: (i) strong resistance to alkaline hydrolysis (most zone separations occurring at basic pH values), (ii) high hydrophilicity and (iii) greater porosity, due to the higher molecular weight of the monomers. When compared with conventional poly(acrylamide), a poly(AAEE) matrix, when subjected to mild alkaline hydrolysis (0.1 N NaOH, 70 degrees C) appears to be 500 times more stable. Such stability is also confirmed under strong alkaline hydrolysis (1 N NaOH, 100 degrees C) as well as under mild and strong acidic hydrolysis. Mildly hydrolyzed poly(AAEE) matrices still perform extremely well in both conventional isoelectric focusing and immobilized pH gradients, techniques which are quite sensitive to traces of acrylate in the polymer coil. Conversely, mildly hydrolyzed poly(acrylamide) matrices, when used in isoelectric focusing, generate pH gradients between pH 4 and 5, having an inflection point (pH 4.6) equivalent to the pK value of acrylic acid. This novel class of monomers shows great promise for future applications in all electrokinetic methodologies.

Acrylamides↗
PubMed1992

Crafting strategy: a constituency plan for the future.

1. The difference in planning and crafting strategy is the level of involvement in the process. It is the crafting of strategy that requires the involvement of state and local constituencies. 2. Creating vision enables constituencies to clarify and realize what they really want, independently of what presently seems possible at the state or local level. 3. By developing an ideal reality or vision first, a bridge can be built between the current and desired organization without loss of purpose. The purpose of the organization is defined by AAOHN's Mission Statement. 4. The bridge is built by using a decision making process similar to the nursing process.

Humans↗
PubMed1986

Respiration rate, heart rate, and body temperature values in cynomolgus monkeys (Macaca fascicularis) during barbiturate anesthesia.

Respiration rate, heart rate, and body temperature values were obtained from 14 cynomolgus monkeys (Macaca fascicularis) during neurosurgery under barbiturate anesthesia. Vital sign values markedly declined below baseline during the early stages of surgery, steadily increased as surgery progressed and neared completion, and finally returned to baseline by the end of the postsurgical recovery period. There was considerable variability among the 14 monkeys, but the ranking of each monkey relative to the others remained constant across the period of observation. The findings suggested that the cynomolgus monkey may be more sensitive to barbiturates than the rhesus monkey, and cynomolgus monkeys may exhibit considerable individual differences in their sensitivity to barbiturates.

Anesthesia, General↗
PubMed1979

[Enzymatic induction during isoniazid therapy (author's transl)].

Enzyme induction by isoniazid was studied by urinary D-glucaric acid estimation in slow and fast acetylators. Isoniazid administration increases significantively the D-glucaric acid elimination in the two classes of patients. In fast acetylators, the glucaricaciduria increases regularly up to 1.8 fold the physiological level in 30 days. In slow acetylators, after a progressive elevation during 20 days, the glucaricaciduria reaches quickly a 3 fold increase after 30 days. When a classic inducer such as phenobarbital is administrated in association with isoniazid, induction is stimulated in the two groups of patients. The estimation of plasmatic free isoniazid seems to indicate that the acetylation rate of isoniazid is not on the dependance of the induction process when the drug is administrated alone. In contrast, this rate increases when the association isoniazid-phenobarbital is administrated to slow acetylators. Possible consequences on the hepatic toxicity of isoniazid are discussed.

Acetylation↗