Abstract:
:Biological spread cells exist in a perpetually fluctuating state and therefore cannot be described in terms of a unique deterministic system. For modeling approaches to provide novel insight and uncover new mechanisms that drive cell behavior, a framework is required that progresses from traditional deterministic methods (whereby simulation of an experiment predicts a single outcome). In this study, we implement a new, to our knowledge, modeling approach for the analysis of cell spreading on ligand-coated substrates, extending the framework for nonequilibrium thermodynamics of cells developed by Shishvan et al. to include active focal adhesion assembly. We demonstrate that the model correctly predicts the coupled influence of surface collagen density and substrate stiffness on cell spreading, as reported experimentally by Engler et al. Low surface collagen densities are shown to result in a high probability that cells will be restricted to low spread areas. Furthermore, elastic free energy induced by substrate deformation lowers the probability of observing a highly spread cell, and, consequentially, lower cell tractions affect the assembly of focal adhesions. Experimentally measurable observables such as cell spread area and aspect ratio can be directly postprocessed from the computed homeostatic ensemble of (several million) spread states. This allows for the prediction of mean and SDs of such experimental observables. This class of cell mechanics modeling presents a significant advance on conventional deterministic approaches.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
McEvoy E,Shishvan SS,Deshpande VS,McGarry JPdoi
10.1016/j.bpj.2018.11.007subject
Has Abstractpub_date
2018-12-18 00:00:00pages
2451-2460issue
12eissn
0006-3495issn
1542-0086pii
S0006-3495(18)31228-1journal_volume
115pub_type
杂志文章abstract::Receptor activity modifying proteins (RAMPs) are a family of single-pass transmembrane proteins that dimerize with G-protein-coupled receptors. They may alter the ligand recognition properties of the receptors (particularly for the calcitonin receptor-like receptor, CLR). Very little structural information is availabl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.084582
更新日期:2006-07-15 00:00:00
abstract::Some low molecular weight biomolecules, i.e., NAD(P)H, are unstable at high temperatures. The use of these biomolecules by thermophilic microorganisms has been scarcely analyzed. Herein, NADH stability has been studied at different temperatures and viscosities. NADH decay increased at increasing temperatures. At incre...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.07.024
更新日期:2016-08-23 00:00:00
abstract::N-BAR domains are protein modules that bind to and induce curvature in membranes via a charged concave surface and N-terminal amphipathic helices. Recently, molecular dynamics simulations have demonstrated that the N-BAR domain can induce a strong local curvature that matches the curvature of the BAR domain surface fa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.121160
更新日期:2008-08-01 00:00:00
abstract::We have considered whether lecithin surface films below the gel-liquid crystal transition temperature, Tc, are in unique physical states. In general, below Tc, equilibrium films do not exist when surface pressures, pi, exceed about 0.1 dyn/cm. Since surface pressure-surface area isotherms of lecithin films below Tc al...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(77)85615-4
更新日期:1977-06-01 00:00:00
abstract::Fluorescence recovery after photobleaching (FRAP) has been used previously to investigate the kinetics of binding to biological surfaces. The present study adapts and further develops this technique for the quantification of mass transport and reaction parameters in bulk media. The technique's ability to obtain the bu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82089-6
更新日期:1991-09-01 00:00:00
abstract::We introduce dual-color time-integrated fluorescence cumulant analysis (TIFCA) to analyze fluorescence fluctuation spectroscopy data. Dual-color TIFCA utilizes the bivariate cumulants of the integrated fluorescent intensity from two detection channels to extract the brightness in each channel, the occupation number, a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.086181
更新日期:2006-10-01 00:00:00
abstract::The barbiturate pentobarbital binds to gamma-aminobutyric acid type A (GABA(A)) receptors, and this interaction plays an important role in the anesthetic action of this drug. Depending on its concentration, pentobarbital can potentiate (approximately 10-100 microM), activate (approximately 100-800 microM), or block (a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.09.037
更新日期:2009-01-01 00:00:00
abstract::Using the molecular dynamics simulation technique, we studied the changes occurring in a dipalmitoylphosphatidylcholine (DPPC):cholesterol (CH) membrane at 50 mol% sterol when cholesterol is replaced with cholesterol sulfate (CS). Our simulations were performed at constant pressure and temperature on a nanosecond time...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76719-1
更新日期:2000-04-01 00:00:00
abstract::The adsorption of hydrophobic ions such as tetraphenylborate to thin lipid membranes is known to saturate at approximately 0.1 ion/(nm)2. This saturation can be quantitatively explained by electrostatic repulsion between the ions if they are treated as discrete, mobile particles that adsorb within the lipid at least p...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84489-5
更新日期:1982-07-01 00:00:00
abstract::The effect of ionic strength on the macroscopic and microscopic redox potentials and the heme environment of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F have been investigated by NMR and electrochemical methods. The redox potentials of this tetraheme protein are found to be ionic strength-dependent. Especiall...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)74067-6
更新日期:1998-09-01 00:00:00
abstract::To assay cell cycle progression in synchronized culture of yeast we have applied dielectric spectroscopy to its real-time monitoring. The dielectric monitoring is based on the electromagnetic induction method, regarded as a nonelectrode method, which has resolved the problems encountered in measurements with metal ele...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77487-4
更新日期:1999-06-01 00:00:00
abstract::In addition to being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. Though much is known about the biochemistry of this code, little is understood regarding the different fiber structures through whi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.09.055
更新日期:2009-02-01 00:00:00
abstract::A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use of a set of linear thermodynamic constraints in addition to th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.093138
更新日期:2007-03-01 00:00:00
abstract::DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge neutralization by cellular anionic lipids. As a model system to test this possibility, fluorescence resonance energy transfer between DNA and lipid covalently labeled with Cy3 and BODIPY, respectively, was used to mo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.042895
更新日期:2004-08-01 00:00:00
abstract::Bacterial swimming speed is sometimes known to increase with viscosity. This phenomenon is peculiar to bacterial motion. Berg and Turner (Nature. 278:349-351, 1979) indicated that the phenomenon was caused by a loose, quasi-rigid network formed by polymer molecules that were added to increase viscosity. We mathematica...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75204-1
更新日期:2002-08-01 00:00:00
abstract::Protein solution rheology data in the biophysics literature have incompletely identified factors that govern hydrodynamics. Whereas spontaneous protein adsorption at the air/water (A/W) interface increases the apparent viscosity of surfactant-free globular protein solutions, it is demonstrated here that irreversible c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.01.007
更新日期:2013-02-19 00:00:00
abstract::The nanomechanical response of supported lipid bilayers has been studied by force spectroscopy with atomic force microscopy. We have experimentally proved that the amount of ions present in the measuring system has a strong effect on the force needed to puncture a 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer wi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.064030
更新日期:2005-09-01 00:00:00
abstract::A method for generating angular forces around sigma-bonded transition metal ions is generalized to treat pi-bonded configurations. The theoretical approach is based on an analysis of ligand-field and small-cluster Hamiltonians based on the moments of the electron state distribution. The functional forms that are obtai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75675-5
更新日期:2001-07-01 00:00:00
abstract::A method for determination of the orientation of adsorbed structure-stable proteins using Total Internal Reflection Fluorescence is outlined. The theory has been elaborated for orientation studies on adsorbed free base cytochrome c, of which the prophyrin can be used as an intrinsic fluorescent label. The ratio of flu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82616-3
更新日期:1990-05-01 00:00:00
abstract::The human brain may be regarded as an irreversible system which is constrained by a fixed inflow of free energy in the form of chemical nourishment from within the body and information from the environment. The evolution of the internal spontaneous process may be described as a path on the saddle surface of entropy pr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(65)86763-7
更新日期:1965-11-01 00:00:00
abstract::Deuterium magnetic resonance is applied to the study of the liquid crystalline and gel phases, and of the phase transition, of a multilamellar dispersion of chain perdeuterated (d62)-dipalmitoyl phosphatidylcholine/H2O. Analysis of the deuterium spectra in terms of the moments of the spectra allows one to make quantit...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(79)85222-4
更新日期:1979-09-01 00:00:00
abstract::The polymorphic phase behavior of bovine heart cardiolipin (CL) in the presence of different divalent cations and the kinetics of CL vesicle fusion induced by these cations have been investigated. (31)P-NMR measurements of equilibrium cation-CL complexes showed the lamellar-to-hexagonal (L(alpha)-H(II)) transition tem...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77041-4
更新日期:1999-10-01 00:00:00
abstract::The observation of biological processes at the molecular scale in real time requires high spatial and temporal resolution. Magnetic tweezers are straightforward to implement, free of radiation or photodamage, and provide ample multiplexing capability, but their spatiotemporal resolution has lagged behind that of other...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.10.018
更新日期:2015-11-17 00:00:00
abstract::Femtosecond time-resolved transient absorption spectroscopy was employed to characterize for the first time the primary photoisomerization dynamics of a bacterial phytochrome system in the two thermally stable states of the photocycle. The 85-kDa phytochrome Cph1 from the cyanobacterium Synechocystis PCC 6803 expresse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75460-X
更新日期:2002-02-01 00:00:00
abstract::The triplet state absorption and phosphorescence of Zn and Pd derivatives of myoglobin were compared. Both metal derivatives exhibit long triplet state lifetimes at room temperature, but whereas the Pd derivative showed exponential decay and an isosbestic point in the transient absorption spectra, the decay of the Zn ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82363-8
更新日期:1990-07-01 00:00:00
abstract::Myofilament extensibility is a key structural parameter for interpreting myosin cross-bridge kinetics in striated muscle. Previous studies reported much higher thick-filament extensibility at low tension than the better-known and commonly used values at high tension, but in interpreting mechanical studies of muscle, a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.08.038
更新日期:2018-10-16 00:00:00
abstract::Cell adhesion to extracellular matrix is mediated by receptor-ligand interactions. When a cell first contacts a surface, it spreads, exerting traction forces against the surface and forming new bonds as its contact area expands. Here, we examined the changes in shape, actin polymerization, focal adhesion formation, an...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.054320
更新日期:2005-07-01 00:00:00
abstract::Many toxins and antimicrobial peptides permeabilize membrane vesicles by forming multimeric pores. Determination of the size of such pores is an important first step for understanding their structure and the mechanism of their self-assembly. We report a simple method for sizing pores in vesicles based on the different...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78822-2
更新日期:1997-04-01 00:00:00
abstract::Epithelial injury induces rapid recruitment of antimicrobial leukocytes to the wound site. In zebrafish larvae, activation of the epithelial NADPH oxidase Duox at the wound margin is required early during this response. Before injury, leukocytes are near the vascular region, that is, ∼100-300 μm away from the injury s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.03.021
更新日期:2017-05-09 00:00:00
abstract::Single molecule force spectroscopy methods, such as optical and magnetic tweezers and atomic force microscopy, have opened up the possibility to study biological processes regulated by force, dynamics of structural conformations of proteins and nucleic acids, and load-dependent kinetics of molecular interactions. Amon...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2013.08.007
更新日期:2013-09-17 00:00:00