Search PubMed⌕ Search

Biomedical subjects

M Peyrard

Publications and source records attributed to M Peyrard.

At least 19 recordsLinked to original sources
PubMed2006

Bubbles and denaturation in DNA.

The local opening of DNA is an intriguing phenomenon from a statistical-physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code cannot take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois (PBD) model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular-dynamics studies, were premature. This could either imply that the present PBD model should be improved or that biological activity can only be predicted in a more complex framework that involves interactions with proteins and super helical stresses. In this article, we give a detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as a function of position and bubble size and the so-called l-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.

Computer Simulation↗
PubMed2005

The dynamics of water in nanoporous silica studied by dielectric spectroscopy.

Broad-band dielectric spectroscopy is used to investigate the dynamics of hydration water on the surface of the cylindrical pores of a nanostructured silica material (MCM-41, with pore diameter of 3.2 nm) at various hydrations, in the temperature range 250-150 K. We focus our attention on orientational relaxations that shift from 0.5 MHz at 250 K to less than 1 Hz at 150 K. The measurements distinguish the relaxation of the hydroxyl groups at the surface of silica from the orientational dynamics of hydration water which strongly depends on the degree of hydration. Although it is significantly faster than the dynamics of water in ice, the orientational relaxation of "non-freezing" water has an activation energy comparable to that in ice when the hydration layer is complete and approximately two-molecule thick.

Adsorption↗
PubMed2005

Model for DNA hairpin denaturation.

We investigate the thermal denaturation of DNA hairpins using molecular dynamics simulations of a simple model describing the molecule at a scale of a nucleotide. The model allows us to analyze the different interacting features that determine how an hairpin opens, such as therole of the loop and the properties intrinsic to the stem.

Computer Simulation↗
PubMed2004

Nonintegrable Schrodinger discrete breathers.

In an extensive numerical investigation of nonintegrable translational motion of discrete breathers in nonlinear Schrödinger lattices, we have used a regularized Newton algorithm to continue these solutions from the limit of the integrable Ablowitz-Ladik lattice. These solutions are shown to be a superposition of a localized moving core and an excited extended state (background) to which the localized moving pulse is spatially asymptotic. The background is a linear combination of small amplitude nonlinear resonant plane waves and it plays an essential role in the energy balance governing the translational motion of the localized core. Perturbative collective variable theory predictions are critically analyzed in the light of the numerical results.

Journal Article↗
PubMed2003

Dynamics and melting of a thin confined film.

Molecular dynamics is used to investigate the melting of a thin lubricant film confined between two crystalline surfaces. The dynamics of the film is significantly affected by the substrate, both in the solid and in the molten phases. The solid phase, able to sustain shear stress, shows, however, large diffusional motions of the atoms. The melting temperature depends strongly on the confinement. A phenomenological microscopic theory, based on the Lindemann criterion, is proposed to explain this effect.

Journal Article↗
PubMed2002

Controlling the energy flow in nonlinear lattices: a model for a thermal rectifier.

We address the problem of heat conduction in 1D nonlinear chains; we show that, acting on the parameter which controls the strength of the on-site potential inside a segment of the chain, we induce a transition from conducting to insulating behavior in the whole system. Quite remarkably, the same transition can be observed by increasing the temperatures of the thermal baths at both ends of the chain by the same amount. The control of heat conduction by nonlinearity opens the possibility to propose new devices such as a thermal rectifier.

Journal Article↗
PubMed2001

Glass transition in protein hydration water.

A model of two-dimensional water is studied in order to analyze recent dielectric measurements on protein hydration water. The frustration introduced by the coupling of the water molecules to the protein surface prevents a true crystallization and induces a smooth transition to a glassy state that is detected by its structure factor and the stretched exponential behavior of the cage correlation function that measures the rate of change of the hydrogen bond network around each molecule. The spectrum of the fluctuations in the vicinity of the glass transition exhibits 1/f(alpha) noise in agreement with the dielectric measurements. The results suggest that two-dimensional water, which can be probed by dielectric measurements, could be an interesting system to study the glassy behavior of water.

Journal Article↗
PubMed2001

Friction in a solid lubricant film.

Molecular-dynamics study of a thin (one to five layers) lubricant film between two substrates in moving contact are performed using Langevin equations with an external damping coefficient depending on distance and velocity of atoms relative the substrates, motivated by microscopic configurations. They show that the minimal friction coefficient is obtained for the solid-sliding regime. A detailed analysis of the results, the comparison with other microscopic modeling approaches of friction, and the evaluation of quantities that can be compared to experiments, such as the velocity of the transition from stick slip to smooth sliding, are used to discuss the relevance of the microscopic simulations of friction.

Journal Article↗
PubMed2001

Physical aspects of the weakly hydrated protein surface.

We review the physical properties of water on the surface of weakly hydrated proteins and present some theoretical models used to understand them. The first part concerns mainly structural properties and introduces a model for two-dimensional clusters of water molecules. The second part is devoted to dynamical properties of the hydrated protein surface. Dielectric measurements which provide an evidence for proton conductivity due to the percolation of the network of surface water molecules and for the glass dynamics of migrating protons when temperature is lowered are reviewed. These results can be associated with the concept of frustration and analyzed with two models, an Ising model to describe the proton jumps and the model of two-dimensional surface water which exhibits a glassy dynamiques of the water molecules. Biological implications of these properties of hydration water are briefly discussed.

Animals↗
PubMed2000

Order of the phase transition in models of DNA thermal denaturation.

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with nu( perpendicular) = -beta = 1,nu(||) = gamma/2 = 2 (characteristic of short-range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents nu( perpendicular) = -beta = 1/2,nu(||) = gamma/2 = 1.

DNA↗
PubMed2000

Collective proton transport with weak proton-proton coupling

A mechanism based on the peculiar dynamical properties of the hydrogen bond is suggested to describe fast proton transfers in hydrogen-bonded chains with realistic (weak) intersite proton-proton interactions. For this purpose, a two-sublattice model is suggested and studied analytically that admits an exact soliton solution. The solitons, which are topological objects (kinks and antikinks) on the one hand, but dynamical entities (like Boussinesq solitons) on the other hand, are shown to have a sufficiently large width to allow free propagation along the chain.

Journal Article↗
PubMed1999

The human LARGE gene from 22q12.3-q13.1 is a new, distinct member of the glycosyltransferase gene family.

Meningioma, a tumor of the meninges covering the central nervous system, shows frequent loss of material from human chromosome 22. Homozygous and heterozygous deletions in meningiomas defined a candidate region of >1 Mbp in 22q12.3-q13.1 and directed us to gene cloning in this segment. We characterized a new member of the N-acetylglucosaminyltransferase gene family, the LARGE gene. It occupies >664 kilobases and is one of the largest human genes. The predicted 756-aa N-acetylglucosaminyltransferase encoded by LARGE displays features that are absent in other glycosyltransferases. The human like-acetylglucosaminyltransferase polypeptide is much longer and contains putative coiled-coil domains. We characterized the mouse LARGE ortholog, which encodes a protein 97.75% identical with the human counterpart. Both genes reveal ubiquitous expression as assessed by Northern blot analysis and in situ histochemistry. Chromosomal mapping of the mouse gene reveals that mouse chromosome 8C1 corresponds to human 22q12.3-q13.1. Abnormal glycosylation of proteins and glycosphingolipids has been shown as a mechanism behind an increased potential of tumor formation and/or progression. Human tumors overexpress ganglioside GD3 (NeuAcalpha2,8NeuAcalpha2, 3Galbeta1,4Glc-Cer), which in meningiomas correlates with deletions on chromosome 22. It is the first time that a glycosyltransferase gene is involved in tumor-specific genomic rearrangements. An abnormal function of the human like-acetylglucosaminyltransferase protein may be linked to the development/progression of meningioma by altering the composition of gangliosides and/or by effect(s) on other glycosylated molecules in tumor cells.

Amino Acid Sequence↗
PubMed1999

Duplications on human chromosome 22 reveal a novel Ret Finger Protein-like gene family with sense and endogenous antisense transcripts.

Analysis of 600 kb of sequence encompassing the beta-prime adaptin (BAM22) gene on human chromosome 22 revealed intrachromosomal duplications within 22q12-13 resulting in three active RFPL genes, two RFPL pseudogenes, and two pseudogenes of BAM22. The genomic sequence of BAM22vartheta1 shows a remarkable similarity to that of BAM22. The cDNA sequence comparison of RFPL1, RFPL2, and RFPL3 showed 95%-96% identity between the genes, which were most similar to the Ret Finger Protein gene from human chromosome 6. The sense RFPL transcripts encode proteins with the tripartite structure, composed of RING finger, coiled-coil, and B30-2 domains, which are characteristic of the RING-B30 family. Each of these domains are thought to mediate protein-protein interactions by promoting homo- or heterodimerization. The MID1 gene on Xp22 is also a member of the RING-B30 family and is mutated in Opitz syndrome (OS). The autosomal dominant form of OS shows linkage to 22q11-q12. We detected a polymorphic protein-truncating allele of RFPL1 in 8% of the population, which was not associated with the OS phenotype. We identified 6-kb and 1.2-kb noncoding antisense mRNAs of RFPL1S and RFPL3S antisense genes, respectively. The RFPL1S and RFPL3S genes cover substantial portions of their sense counterparts, which suggests that the function of RFPL1S and RFPL3S is a post-transcriptional regulation of the sense RFPL genes. We illustrate the role of intrachromosomal duplications in the generation of RFPL genes, which were created by a series of duplications and share an ancestor with the RING-B30 domain containing genes from the major histocompatibility complex region on human chromosome 6.

Adaptor Protein Complex 1↗
PubMed1998

Cloning, expression pattern, and chromosomal assignment to 16q23 of the human gamma-adaptin gene (ADTG).

Adaptins are important components of clathrin-coated vesicles transporting ligand-receptor complexes from the plasma membrane or from the trans-Golgi network to lysosomes. Adaptins, together with medium and small subunits, form a heterotetrameric complex called an adaptor, whose role is to promote the formation of clathrin-coated pits and vesicles. We present the cloning and sequencing of the human gamma-adaptin cDNA (HGMW-approved symbol ADTG) consisting of 3723 bp with an open reading frame capable of encoding a protein of 825 amino acids, 98.9% identical to the mouse protein. Northern blot analysis of the mouse and human gamma-adaptin genes revealed a ubiquitous and abundant expression, except in human adult lung. Using a monochromosomal somatic cell hybrid panel and fluorescence in situ hybridization, we mapped this gene to human chromosome 16q23, which is syntenic with mouse chromosome 8, band D. In addition, we localized genes for two other components of the AP-1 adaptor, i.e., the medium (AP47) and small (AP19) subunits, to chromosomes 19 and 7, respectively. Expression analysis of these genes in human tissues revealed ubiquitously expressed transcripts of approximately 2.5 and 1.5 kb, respectively.

Adaptor Protein Complex gamma Subunits↗
PubMed1997

A high ratio of insulin-like growth factor II/insulin-like growth factor binding protein 2 messenger RNA as a marker for anaplasia in meningiomas.

Insulin-like growth factors (IGFs) I and II have been implicated as autocrine or paracrine growth promoters. These growth factors bind to specific receptors, and the response is modulated by interaction with IGF-binding proteins (IGFBPs). We observed a strong correlation between anaplastic/atypical histopathology and a high IGF-II/IGFBP-2 mRNA ratio in a set of 68 sporadic meningiomas. A strong correlation was also found between clinical outcome and IGF-II/IGFBP-2 ratio, whereas previously used histochemical markers were less correlated to outcome. We suggest that a high IGF-II/IGFBP-2 mRNA ratio may be a sign of biologically aggressive behavior in meningiomas that can influence treatment strategies. We propose that low IGFBP-2 levels in combination with increased levels of IGF-II would result in more free IGF-II and consequently greater stimulation of proliferation.

Adult↗
PubMed1997

Characterization of the mouse beta-prime adaptin gene; cDNA sequence, genomic structure, and chromosomal localization.

Adaptins are important subunits of heterotetrameric complexes called adaptors, which participate in the clathrin-coated, vesicle-mediated endocytosis and intracellular receptor transport. The gene family of adaptins is divided into three classes, alpha, beta, and gamma, with further subdivision into beta- and beta-prime components. Two beta-prime adaptins, the rat AP105a and the human BAM22, have previously been characterized. The BAM22 gene is located on human Chromosome (Chr) 22q12 and can be considered a candidate meningioma tumor suppressor gene. We report here the characterization of the mouse ortholog of the BAM22 gene, and we suggest the name adtb1 for the mouse gene. Like the BAM22 gene, the adtb1 transcript is highly and ubiquitously expressed. We provide 3885-bp cDNA sequence, which entirely covers the open reading frame of the adtb1, capable of encoding a protein of 943 amino acids. The adtb1 protein is highly conserved (>96% identity) when compared with AP105a and BAM22 proteins. We also report the genomic organization of adtb1, which is similar to the BAM22 gene. The adtb1 gene has been assigned to mouse Chr 11, band 11A2, which confirms the synteny between human Chr 22q12 and mouse Chr 11.

Adaptor Protein Complex 1↗
PubMed1996

Structure of the promoter and genomic organization of the human beta'-adaptin gene (BAM22) from chromosome 22q12.

Adaptins are major structural components of heterotetrameric protein complexes called adaptors, which are essential in intracellular receptor transport via clathrin-coated vesicles. beta-adaptins constitute one of three known classes (alpha, beta, gamma) of adaptins, including beta and beta' subtypes. We previously cloned the human beta'-adaptin gene (BAM22) (GDB symbol, ADTB1) from chromosome 22q12 and proposed its involvement in the development of meningiomas. Here we describe the genomic organization of this gene, which consists of 22 exons spanning over approximately 100 kb. We also report results from point mutation screening of 7 randomly chosen exons analyzed in 110 sporadic meningiomas. As part of the genomic characterization of the BAM22 locus, we sequenced 40 kb covering exons 1-4 and 12 kb upstream from the start of gene transcription. Analysis of the sequence suggests that the BAM22 gene has a CG-rich promoter.

Adaptor Protein Complex 1↗