Abstract:
:Theoretical models predict that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how the denatured state is represented), the level of stabilization predicted can be very different. In this study, we represented the native and denatured states atomistically, with conformations sampled from explicit-solvent molecular dynamics simulations at room temperature and high temperature, respectively. We then designed an efficient algorithm to calculate the allowed fraction, f, when the protein molecule is placed inside a box of crowders. That a fraction of placements of the protein molecule is disallowed because of volume exclusion by the crowders leads to an increase in chemical potential, given by Deltamu = -k(B)T lnf. The difference in Deltamu between the native and denatured states predicts the effect of crowding on the folding free energy. Even when the crowders occupied 35% of the solution volume, the stabilization reached only 1.5 kcal/mol for cytochrome b562. The modest stabilization predicted is consistent with experimental studies. Interestingly, a mixture of different sized crowders was found to exert a greater effect than the sum of the individual species of crowders. The stabilization of crowding on the binding stability of barnase and barstar, based on atomistic modeling of the proteins, was similarly modest. These findings have profound implications for macromolecular crowding inside cells.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Qin S,Zhou HXdoi
10.1016/j.bpj.2009.03.066subject
Has Abstractpub_date
2009-07-08 00:00:00pages
12-9issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(09)00901-1journal_volume
97pub_type
杂志文章abstract::Membrane domains known as rafts are rich in cholesterol and sphingolipids, and are thought to be thicker than the surrounding membrane. If so, monolayers should elastically deform so as to avoid exposure of hydrophobic surfaces to water at the raft boundary. We calculated the energy of splay and tilt deformations nece...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.048223
更新日期:2005-02-01 00:00:00
abstract::A simple technique for forming "black" lipid bilayer membranes containing negligible amounts of alkyl solvent is described. The membranes are formed by the method of Mueller et al (Circulation. 1962. 26:1167.) from glyceryl monooleate (GMO) dispersed in squalene. The squalene forms an annulus to satisfy the boundary c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85453-8
更新日期:1978-09-01 00:00:00
abstract::Collagenase H (ColH) from Clostridium histolyticum is a multimodular protein composed of a collagenase module (activator and peptidase domains), two polycystic kidney disease-like domains, and a collagen-binding domain. The interdomain conformation and its changes are very important for understanding the functions of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.02.022
更新日期:2013-04-02 00:00:00
abstract::Equilibrium binding ligands usually increase protein thermal stability by an amount proportional to the concentration and affinity of the ligand. High-throughput screening for the discovery of drug-like compounds uses an assay based on thermal stabilization. The mathematical description of this stabilization is well d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.134973
更新日期:2008-10-01 00:00:00
abstract::Structural changes in frog skeletal muscle were studied using x-ray diffraction with a time resolution of 0.53-1.02 ms after a single electrical stimulus at 8 degrees C. Tension began to drop at 6 ms (latency relaxation), reached a minimum at 8 ms, and then twitch tension developed. The intensity of the meridional ref...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74925-X
更新日期:2003-02-01 00:00:00
abstract::hbAP0 is a model membrane protein designed to possess an anesthetic-binding cavity in its hydrophilic domain and a cation channel in its hydrophobic domain. Grazing incidence x-ray diffraction shows that hbAP0 forms four-helix bundles that are vectorially oriented within Langmuir monolayers at the air-water interface....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.072348
更新日期:2006-05-01 00:00:00
abstract::The effects of the Ca(2+)-induced Ca2+ release blocker procaine on individual sarcoplasmic reticulum Ca2+ release channels have been examined in planar lipid bilayers. Procaine did not reduce the single channel conductance nor appreciably shorten the mean open times of the channel; rather, it increased the longest clo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81465-6
更新日期:1993-04-01 00:00:00
abstract::The primary processes of the photochemical cycle of light-adapted bacteriorhodopsin (BR) were studied by various experimental techniques with a time resolution of 5 x 10(-13) s. The following results were obtained. (a) After optical excitation the first excited singlet state S(1) of bacteriorhodopsin is observed via i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83692-X
更新日期:1986-03-01 00:00:00
abstract::Octyl-beta-thioglucopyranoside (octyl thioglucoside, OTG) is a nonionic surfactant used for the purification, reconstitution, and crystallization of membrane proteins. The thermodynamic properties of the OTG-membrane partition equilibrium are not known and have been investigated here with high-sensitivity titration ca...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78285-7
更新日期:1997-11-01 00:00:00
abstract::Early afterdepolarizations (EADs) are voltage oscillations that occur during the repolarizing phase of the cardiac action potential and cause cardiac arrhythmias in a variety of clinical settings. EADs occur in the setting of reduced repolarization reserve and increased inward-over-outward currents, which intuitively ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.05.011
更新日期:2012-06-20 00:00:00
abstract::The membrane disruption mechanism of pandinin 1 (pin1), an antimicrobial peptide isolated from the venom of the African scorpion, was studied using 31P, 13C, 1H solid-state and multidimensional solution-state NMR spectroscopy. A high-resolution NMR solution structure of pin1 showed that the two distinct alpha-helical ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.070292
更新日期:2005-12-01 00:00:00
abstract::To understand the thermodynamic exclusion of Na(+) relative to K(+) from the S(2) site of the selectivity filter, the distribution P(X)(epsilon) (X = K(+) or Na(+)) of the binding energy (epsilon) of the ion with the channel is analyzed using the potential distribution theorem. By expressing the excess chemical potent...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.12.3917
更新日期:2009-03-18 00:00:00
abstract::The mechanosensitive channel of large conductance (MscL) belongs to a family of transmembrane channel proteins in bacteria and functions as a safety valve that relieves the turgor pressure produced by osmotic downshock. MscL gating can be triggered solely by stretching of the membrane. This work reports an effort to u...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.109850
更新日期:2008-05-01 00:00:00
abstract::In the intestinal epithelium, proliferated epithelial cells ascend the crypts and villi and shed at the villus tips into the gut lumen. In this study, we theoretically investigate the roles of the villi on cell turnover. We present a stochastic model that focuses on the duration over which cells migrate the shortest p...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2021.01.003
更新日期:2021-01-13 00:00:00
abstract::We have investigated classical nuclear localization sequence (NLS) mediated protein trafficking by measuring biomolecular dynamics within living cells using two-photon fluorescence correlation spectroscopy. By directly observing the behavior of specific molecules in their native cellular environment, it is possible to...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.01.050
更新日期:2009-05-06 00:00:00
abstract::Cell-mediated contraction plays a critical role in many physiological and pathological processes, notably organized contraction during wound healing. Implantation of an appropriately formulated (i.e., mean pore size, chemical composition, degradation rate) three-dimensional scaffold into an in vivo wound site effectiv...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.095471
更新日期:2007-10-15 00:00:00
abstract::The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94-233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfoldin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.07.024
更新日期:2011-09-07 00:00:00
abstract::Photoreverse reactions of octopus rhodopsin (Rh) from acid-metarhodopsin (Acid-Meta), which is the final product of the photoreaction of Rh, to Rh were studied by the time-resolved transient absorption and transient grating methods. The time course of the absorption signal showed a rapid change within 500 ns followed ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.101741
更新日期:2007-05-15 00:00:00
abstract::We study the folding mechanism of a triple beta-strand WW domain from the Formin binding protein 28 (FBP28) at atomic resolution with explicit water model using replica exchange molecular dynamics computer simulations. Extended sampling over a wide range of temperatures to obtain the free energy, enthalpy, and entropy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.076406
更新日期:2006-06-01 00:00:00
abstract::The spontaneous folding of two Neisseria outer membrane proteins, opacity-associated (Opa)(60) and Opa(50) into lipid vesicles was investigated by systematically varying bulk and membrane properties. Centrifugal fractionation coupled with sodium dodecyl sulfate polyacrylamide gel electrophoresis mobility assays enable...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.03.025
更新日期:2011-05-04 00:00:00
abstract::Conditions for which a ligand reversibly bound to a cell surface dissociates and then rebinds to the surface have been theoretically examined. The coupled differential equations that describe reaction at the interface between sites on a plane and three-dimensional solution have been described previously (Thompson, N. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77836-1
更新日期:1998-03-01 00:00:00
abstract::This paper describes the relation between the quantum yield of photosynthesis in the red alga Porphyridium cruentum, and the spectral composition of light, changed by filtering white light through aqueous phycobilin solutions of increasing optical density. At sufficiently high densities of the filter solution, no meas...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(60)86876-2
更新日期:1960-09-01 00:00:00
abstract::The adhesion of giant unilamellar phospholipid vesicles to planar substrates coated with extracellular matrix mimetic cushions of hyaluronan is studied using quantitative reflection interference contrast microscopy. The absolute height of the vesicle membrane at the vicinity of the substrate is measured by considering...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.105544
更新日期:2007-11-01 00:00:00
abstract::Escherichia coli B phr(-), which is not photoreactivable under certain conditions, has been shown to exhibit photoreactivation of killing in the logarithmic growth phase at 3341 A. Dependence of the reaction upon (a) wavelength, (b) dose, and (c) dose rate of the reactivating radiation, as well as upon (d) temperature...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(65)86703-0
更新日期:1965-01-01 00:00:00
abstract::In the plant blue-light sensor phototropin, illumination of the chromophoric LOV domains causes activation of the serine/threonine kinase domain. Flavin mononucleotide (FMN) is a chromophore molecule in the two LOV domains (LOV1 and LOV2), but only LOV2 is responsible for kinase activation. Previous studies reported a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.12.3924
更新日期:2009-04-08 00:00:00
abstract::The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation, and switching mechanism of the motor. In a previous article, we explained the ge...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.01.023
更新日期:2009-04-22 00:00:00
abstract::A detailed treatment is provided of the various free-energy terms that contribute to the transfer of a polyalanine alpha-helix from the aqueous phase into lipid bilayers. In agreement with previous work, the hydrophobic effect is found to provide the major driving force for helix insertion. However, an opposing effect...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79744-8
更新日期:1996-04-01 00:00:00
abstract::To determine why elements of central pattern generators phase lock in a particular pattern under some conditions but not others, we tested a theoretical pattern prediction method. The method is based on the tabulated open loop pulsatile interactions of bursting neurons on a cycle-by-cycle basis and was tested in close...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.046193
更新日期:2004-10-01 00:00:00
abstract::It has been accepted that the force produced by a skeletal muscle myofibril depends on its cross-sectional area but not on the number of active sarcomeres because they are arranged in series. However, a previous study performed by our group showed that blocking actomyosin interactions within an activated myofibril and...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.03.007
更新日期:2020-04-21 00:00:00
abstract::Intensities of x-ray scattering from a series of fragmented rabbit muscle sarcoplasmic reticulum (SR) samples have been measured over the range x = 0.05 to s = 0.25. By varying the relative concentrations of lipid and protein (chiefly the Mg++-dependent, Ca++- stimulated ATPase) in the membranes of this series, and by...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84835-7
更新日期:1981-04-01 00:00:00