Biomedical subjects

H Isambert

Publications and source records attributed to H Isambert.

6 recordsLinked to original sources

PubMed2005

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots.

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically 'entangled' helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at http://kinefold.curie.fr/.

Algorithms↗

PubMed2003

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n2) clustering algorithm that computes time averages over a continuously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 105-fold for short, multistable molecules (<or=150 bases). We performed extensive folding statistics on random and natural RNA sequences and found that pseudoknots are distributed unevenly among RNA structures and account for up to 30% of base pairs in G+C-rich RNA sequences (online RNA-folding kinetics server including pseudoknots: http://kinefold.u-strasbg.fr).

Algorithms↗

PubMed2003

Probing complex RNA structures by mechanical force.

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpreted by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.

Computer Simulation↗

PubMed2002

Undulation instability of lipid membranes under an electric field.

The influence of an external electric field on a poorly conductive membrane such as a lipid bilayer is studied theoretically. The unbalanced electric stress created by an ionic current across a non-perfectly flat membrane gives rise to a destabilizing surface energy enhancing undulations. The deformation of a membrane attached to a frame is derived and the electrohydrodynamic instability of a free floating membrane is studied. We find a most unstable mode of undulation, of wavelength in the microm range, connected to the crossover between membrane and solvent dominated dissipations.

Elasticity↗

PubMed2000

Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme.

A quantitative understanding of nucleic acid hybridization is essential to many aspects of biotechnology, such as DNA microarrays, as well as to the structure and folding kinetics of RNA. However, predictions of nucleic acid secondary structures have long been impeded by the presence of helices interior to loops, so-called pseudoknots, which impose complex three-dimensional conformational constraints. In this paper we compute the pseudoknot free energies analytically in terms of known standard parameters, and we show how the results can be included in a kinetic Monte Carlo code to follow the succession of secondary structures during quenched or sequential folding. For the hepatitis delta virus ribozyme, we predict several nonnative stems on the folding path, characterize a kinetically trapped state, interpret several experimentally characterized mutations in terms of the folding path, and suggest how hybridization with other parts of the genome inactivates the newly formed ribozyme.

Base Sequence↗

PubMed1995

Flexibility of actin filaments derived from thermal fluctuations. Effect of bound nucleotide, phalloidin, and muscle regulatory proteins.

Single actin filaments undergoing brownian movement in two dimensions were observed at 20 degrees C in fluorescence optical video microscopy. The persistence length (Lp) was derived from the analysis of either the cosine correlation function or the average transverse fluctuations of a series of recorded shapes of filaments assembled from rhodamine-action. Phalloidin-stabilized filaments had a persistence length of 18 +/- 1 micron, in agreement with recent observations. In the absence of phalloidin, rhodamine-labeled filaments could be observed under a variety of solution conditions once diluted in free unlabeled G-actin at the appropriate critical concentration. Such nonstabilized F-ADP-actin filaments had the same Lp of 9 +/- 0.5 microns, whether they had been assembled from ATP-G-actin or from ADP-G-actin, and independently of the tightly bound divalent metal ion. In the presence of BeF3-, which mimics the gamma-phosphate of ATP, F-ADP-BeF3-actin was appreciably more rigid, with Lp = 13.5 microns. Hence, newly formed F-ADP-Pi-actin filaments are more rigid than "old" F-ADP-actin filaments, a fact which has implications in actin-based motility processes. In the presence of skeletal tropomyosin and troponin, filaments were rigid (Lp = 20 +/- 1 micron) in the off state (-Ca2+), and flexible (Lp = 12 microns) in the on state (+Ca2+), consistent with the steric blocking model. In agreement with x-ray diffraction data, no appreciable difference was recorded between the off and on states using smooth muscle tropomyosin and caldesmon (Lp = 20 +/- 1 micron). In conclusion, this method allows accurate measurement of small (< or = 15%) changes in mechanical properties of actin filaments in correlation with their biological functions.

Actin Cytoskeleton↗