Biomedical subjects

Simon G J Mochrie

Publications and source records attributed to Simon G J Mochrie.

8 recordsLinked to original sources

PubMed2025

Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.

The "holy grail" of chromatin research would be to follow the chromatin configuration in individual live cells over time. One way to achieve this goal would be to track the positions of multiple loci arranged along the chromatin polymer with fluorescent labels. Using distinguishable labels would define each locus uniquely in a microscopic image but would restrict the number of loci that could be observed simultaneously due to experimental limits to the number of distinguishable labels. Using the same label for all loci circumvents this limitation but requires a (currently lacking) framework for how to establish each observed locus identity, i.e., to which genomic position it corresponds. Here, we analyze theoretically, using simulations of Rouse model polymers, how single-particle tracking of multiple identically labeled loci enables the determination of loci identity. We show that the probability of correctly assigning observed loci to genomic positions converges exponentially to unity as the number of observed loci configurations increases. The convergence rate depends only weakly on the number of labeled loci, so that even large numbers of loci can be identified with high fidelity by tracking them across about eight independent chromatin configurations. In the case of two distinct labels that alternate along the chromatin polymer, we find that the probability of the correct assignment converges faster than for same-labeled loci, requiring observation of fewer independent chromatin configurations to establish loci identities. Finally, for a modified Rouse model polymer, which realizes a population of dynamic loops, we find that the success probability also converges to unity exponentially as the number of observed loci configurations increases, albeit slightly more slowly than for a classical Rouse model polymer. Altogether, these results establish particle tracking of multiple identically or alternately labeled loci over time as a feasible way to infer temporal dynamics of the coarse-grained configuration of the chromatin polymer in individual living cells.

Chromatin↗

PubMed2006

Surface and interfacial dynamics of polymeric bilayer films.

The theory for surface dynamics of the thermally excited fluctuations on a homogenous single-layer film of arbitrary depth is generalized to describe surface and interfacial dynamics of polymeric liquid bilayer films in terms of susceptibilities, power spectra, and characteristic relaxation time constants. The effects on surface dynamics originating from viscosity inhomogeneities close to the surface and interfacial regions are investigated by the bilayer theory and compared with the surface dynamics of homogeneous single-layer films under nonslip and slip boundary conditions. Our bilayer theory can also be extended to study interfacial dynamics of more generalized multilayer systems. The effects of viscoelasticity and van der Waals interactions on surface and interfacial dynamics are also briefly discussed.

Journal Article↗

PubMed2006

Relationship between structural and stress relaxation in a block-copolymer melt.

The relationship between structural relaxation on molecular length scales and macroscopic stress relaxation was explored in a disordered block-copolymer melt. Experiments show that the structural relaxation time, measured by x-ray photon correlation spectroscopy is larger than the terminal stress relaxation time, measured by rheology, by factors as large as 100. We demonstrate that the structural relaxation data are dominated by the diffusion of intact micelles while the stress relaxation data are dominated by contributions due to disordered concentration fluctuations.

Journal Article↗

PubMed2005

A new folding paradigm for repeat proteins.

The folding/unfolding transitions of a series of designed consensus tetratricopeptide repeat proteins are quantitatively described by the classical one-dimensional Ising model, which thus represents a new folding paradigm for repeat proteins. Moreover, for the first time for any protein, a theoretical model predicts the folding/unfolding transition midpoint and the width of the transition.

Amino Acid Motifs↗

PubMed2005

A recurring theme in protein engineering: the design, stability and folding of repeat proteins.

Repeat proteins are ubiquitous and are involved in a myriad of essential processes. They are typically non-globular structures that act as diverse scaffolds for the mediation of protein-protein interactions. These excitingly different structures, which arise from tandem arrays of a repeated structural motif, have generated significant interest with respect to protein engineering and design. Recent advances have been made in the design and characterisation of repeat proteins. The highlights include re-engineering of binding specificity, quantitative models of repeat protein stability and kinetic studies of repeat protein folding.

Humans↗

PubMed2003

The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme.

Large RNAs can collapse into compact conformations well before the stable formation of the tertiary contacts that define their final folds. This study identifies likely physical mechanisms driving these early compaction events in RNA folding. We have employed time-resolved small-angle X-ray scattering to monitor the fastest global shape changes of the Tetrahymena ribozyme under different ionic conditions and with RNA mutations that remove long-range tertiary contacts. A partial collapse in each of the folding time-courses occurs within tens of milliseconds with either monovalent or divalent cations. Combined with comparison to predictions from structural models, this observation suggests a relaxation of the RNA to a more compact but denatured conformational ensemble in response to enhanced electrostatic screening at higher ionic concentrations. Further, the results provide evidence against counterion-correlation-mediated attraction between RNA double helices, a recently proposed model for early collapse. A previous study revealed a second 100 ms phase of collapse to a globular state. Surprisingly, we find that progression to this second early folding intermediate requires RNA sequence motifs that eventually mediate native long-range tertiary interactions, even though these regions of the RNA were observed to be solvent-accessible in previous footprinting studies under similar conditions. These results help delineate an analogy between the early conformational changes in RNA folding and the "burst phase" changes and molten globule formation in protein folding.

Animals↗

PubMed2003

Measuring the nematic order of suspensions of colloidal fd virus by x-ray diffraction and optical birefringence.

The orientational distribution function of the nematic phase of suspensions of the semiflexible rodlike virus fd is measured by x-ray diffraction as a function of concentration and ionic strength. X-ray diffraction from a single-domain nematic phase of fd is influenced by interparticle correlations at low angle, while only intraparticle scatter contributes at high angle. Consequently, the angular distribution of the scattered intensity arises from only the single-particle orientational distribution function at high angle but it also includes spatial and orientational correlations at low angle. Experimental measurements of the orientational distribution function from both the interparticle (structure factor) and intraparticle (form factor) scattering were made to test whether the correlations present in interparticle scatter influence the measurement of the single-particle orientational distribution function. It was found that the two types of scatter yield consistent values for the nematic order parameter. It was also found that x-ray diffraction is insensitive to the orientational distribution function's precise form, and the measured angular intensity distribution is described equally well by both Onsager's trial function and a Gaussian. At high ionic strength, the order parameter S of the nematic phase coexisting with the isotropic phase approaches theoretical predictions for long semiflexible rods S=0.55, but deviations from theory increase with decreasing ionic strength. The concentration dependence of the nematic order parameter also better agrees with theoretical predictions at high ionic strength indicating that electrostatic interactions have a measurable effect on the nematic order parameter. The x-ray order parameters are shown to be proportional to the measured birefringence, and the saturation birefringence of fd is determined enabling a simple, inexpensive way to measure the order parameter. Additionally, the spatial ordering of nematic fd was probed. Measurements of the nematic structure factor revealed a single large peak in contrast to nematics of rigid rods.

Journal Article↗

PubMed2002

Rapid compaction during RNA folding.

We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

Animals↗