Showing papers in "Biophysical Journal in 2005"

TL;DR: It is found that optical deformability is sensitive enough to monitor the subtle changes during the progression of mouse fibroblasts and human breast epithelial cells from normal to cancerous and even metastatic state, and suggests using optical deformable as an inherent cell marker for basic cell biological investigation and diagnosis of disease.

TL;DR: New methods to automatically build models of macromolecular complexes from high-resolution structures or homology models of their subunits or domains against x-ray or neutron small-angle scattering data are presented and allow one to construct interconnected models without steric clashes.

TL;DR: Fundamental principles governing SHG phase matching with the tightly focusing optics used in microscopy are discussed, which are crucial to the design and development of forthcoming diagnostic and research tools.

TL;DR: Observations indicate that protein diffusion in the cell cytoplasm and nucleus should be anomalous as well, with consequences for measurements of solute diffusion coefficients in cells and for the modeling of cellular processes relying on diffusion.

TL;DR: Through large-scale molecular dynamics simulations, the permeability of the alpha-hemolysin/lipid bilayer complex for water and ions is studied and the side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance.

TL;DR: The ensemble folding of two 21-residue alpha-helical peptides has been studied using all-atom simulations under several variants of the AMBER potential in explicit solvent and extensive sampling results in complete convergence to ensemble equilibrium.

TL;DR: A high sensitivity of migration in synthetic networks to both MMP modulators is demonstrated: inhibition led to an almost complete suppression of Migration in PEG hydrogels, whereas MMP upregulation increased the fraction of migrating cells significantly.

TL;DR: In this article, the electron density profiles of the fully hydrated fluid phases of DMPC and dilauroylphosphatidylcholine (DLPC) were obtained at 30 degrees C.

TL;DR: This work precisely quantified the effect of localization errors in the determination of the mean-squared displacement, and showed that the static contribution can be confidently corrected in dynamics studies by using static experiments performed at a similar noise-to-signal ratio.

TL;DR: The new method of pulsed interleaved excitation (PIE), which can be used to extend the capabilities of multiple-color fluorescence imaging, fluorescence cross-correlation spectroscopy (FCCS), and single-pair fluorescence resonance energy transfer (spFRET) measurements, is demonstrated.

TL;DR: Novel extensions to ICS are developed that probe spatial correlations in previously inaccessible temporal windows and are used to determine for the first time spatially resolved diffusions of paxillin-EGFP stably expressed in CHOK1 cells.

TL;DR: The results indicate a specific calcium-mediated interaction between dioleoylphosphatidylserine molecules and mica, and it is shown that the use of PLL-g-PEG modified tips considerably improves the AFM imaging of surface-bound vesicles and bilayer patches and the effects of theAFM tip on the apparent size and shape of these soft structures.

TL;DR: This study is believed to capture the essence of several dynamical phenomena observed experimentally and provides a framework for further developments and for new applications.

TL;DR: The sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) is used to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRET-induced signal, and for differences in the detection efficiency and quantum yield of the probes.

TL;DR: It is shown that fluorescence correlation spectroscopy (FCS) measurements at different spatial scales enable distinguishing between different submicron confinement models, and the so-called FCS diffusion law is introduced.

TL;DR: Using space-time image correlation spectroscopy (STICS), the STICS method permits us to generate complete transport maps of proteins within subregions of the basal membrane even if the protein concentration is too high to perform single particle tracking measurements.

TL;DR: A dynamical model for the coupling of a population of circadian oscillators in the SCN is presented and experimentally testable predictions are that phases of individual cells are governed by their intrinsic periods and efficient synchronization is achieved when the average neurotransmitter concentration would dampen individual oscillators.

TL;DR: A liquefied network structure evolution algorithm is devised and implemented that relaxes shear stress everywhere in the network and generates cytoskeleton structures that mimic experimental observations.

TL;DR: The theory suggests that F-actin barbed ends have to be focused and protected from capping once every hundred seconds per micron of the leading edge to initiate the observed number of filopodia, and the model generates testable predictions about how filopidial length, rate of growth, and interfilopodial distance should depend on the number of bundled filaments, membrane resistance, lamellipodial protrusion rate, and G-actIn diffusion coefficient.

TL;DR: To distinguish growth at barbed and pointed ends, image drift correction and maximum intensity projections were used to reveal points where single N-ethylmaleimide inactivated myosins attach filaments to the glass coverslip and association rates at high actin concentrations and dissociation rates near and below the critical actin concentration were estimated.

TL;DR: The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins, and could be crucial for the folding and stability of the unique three-dimensional structure of proteins.

TL;DR: This study is the first to monitor the dynamic changes in the cell shape, spreading rate, and forces exerted during the early stages (first several hours) of endothelial cell adhesion.

TL;DR: It is found that the forces exerted by the cells are proportional to the spring constant of the pillars meaning that, on average, the cells deform the pillars by the same amount whatever their rigidity.

TL;DR: A new mathematical model for avascular tumor growth and development that spans three distinct scales is presented and predicts the microenvironmental conditions required for tumor cell survival and accurately predicts spheroid growth curves under different external nutrient supply conditions.

TL;DR: Results show that a tightly bound water layer adjacent to the OEG-SAMs is mainly responsible for the large repulsive hydration force.

TL;DR: It is thought that the living cell must definitely be thought of as a material with a large and continuous distribution of relaxation time constants which cannot be described by models with a finite number of springs and dash-pots.

TL;DR: Statistical-thermodynamic models for the excluded volume interaction between an unfolded polypeptide chain and a hard sphere or hard rod cosolute are presented, permitting estimation of the free energy of transfer of a polypeptic chain with fixed radius of gyration from a dilute (ideal) solution to a solution containing volume fraction of either cosolute.

TL;DR: From atomic force microscopy, it is found that most of the fibrils from hen egg white lysozyme have a thickness of approximately 4 nm and have a coiled structure with a periodicity of approximately 30 nm and show characteristic defects after every four or five turns.

TL;DR: The model reveals conditions that could prevent rafts from forming, and a mechanism that can cause rafts to remain small, and defines the parameters that control raft merger.

TL;DR: A novel pathway for generation of prefibrillar aggregates of TTR is explored, which provides important insight into TTR misfolding and suggests that unbound ThT dramatically increases its fluorescence quantum yield when bound to amyloid fibrils; however, the mechanism behind this property is unknown.