Abstract:
:We study the folding thermodynamics and kinetics of the Pin1 WW domain, a three-stranded beta-sheet protein, by using all-atom (except nonpolar hydrogens) discontinuous molecular dynamics simulations at various temperatures with a Gō model. The protein exhibits a two-state folding kinetics near the folding transition temperature. A good agreement between our simulations and the experimental measurements by the Gruebele group has been found, and the simulation sheds new insights into the structure of transition state, which is hard to be straightforwardly captured in experiments. The simulation also reveals that the folding pathways at approximately the transition temperature and at low temperatures are much different, and an intermediate state at a low temperature is predicted. The transition state of this small beta-protein at its folding transition temperature has a well-established hairpin 1 made of beta1 and beta2 strands while its low-temperature kinetic intermediate has a formed hairpin 2 composed of beta2 and beta3 strands. Theoretical results are compared with other simulation results as well as available experimental data. This study confirms that specific side-chain packing in an all-atom Gō model can yield a reasonable prediction of specific folding kinetics for a given protein. Different folding behaviors at different temperatures are interpreted in terms of the interplay of entropy and enthalpy in folding process.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Luo Z,Ding J,Zhou Ydoi
10.1529/biophysj.106.102095subject
Has Abstractpub_date
2007-09-15 00:00:00pages
2152-61issue
6eissn
0006-3495issn
1542-0086pii
S0006-3495(07)71470-4journal_volume
93pub_type
杂志文章abstract::Encapsulation of proteins within lipid inverse bicontinuous cubic phases (Q2) has been widely studied for many applications, such as protein crystallization or drug delivery of proteins for food and pharmaceutical purposes. However, the use of the lipid sponge (L3) phase for encapsulation of proteins has not yet been ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.07.031
更新日期:2019-09-03 00:00:00
abstract::The analysis of peptide and protein partitioning in lipid membranes is of high relevance for the understanding of biomembrane function. We used statistical thermodynamics analysis to demonstrate the effect of peptide mixing behavior on heat capacity profiles of lipid membranes with the aim to predict peptide aggregati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75047-4
更新日期:2003-04-01 00:00:00
abstract::Fluorescent proteins are often used as reporters of transcriptional activity. Here we present a mathematical characterization of a novel fluorescent reporter that was recently engineered to have a short half-life (approximately 12 min). The advantage of this destabilized protein is that it can track the transient tran...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.122200
更新日期:2008-03-15 00:00:00
abstract::In a contracting muscle, myosin cross-bridges extending from thick filaments pull the interdigitating thin (actin-containing) filaments during cyclical ATP-driven interactions toward the center of the sarcomere, the structural unit of striated muscle. Cross-bridge attachments in the sarcomere have been reported to exh...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2020.01.002
更新日期:2020-03-10 00:00:00
abstract::A new method is presented to measure local cytoplasmic deformation and rate of deformation in motile active neutrophils. The deformation is expressed in terms of biomechanical strains and strain rates. For this purpose small phagocytosed latex microspheres were used as intracellular markers. Planar Lagrangian and Eule...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82379-1
更新日期:1990-08-01 00:00:00
abstract::Lateral organization of cholesterol in dioleoyl-phosphatidylcholine (DOPC) lipid bilayers at high cholesterol concentration (>45 mol%) was investigated using steady-state fluorescence anisotropy and fluorescent resonance energy transfer techniques. The recently devised Low Temperature Trap method was used to prepare c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74221-6
更新日期:2004-03-01 00:00:00
abstract::Atherosclerosis is a disease initiated by lipoprotein aggregation and deposition in artery walls. In this study, the de novo low-density lipoprotein aggregation process was examined. Nine major intermediates were identified in two stages of the aggregation process. In the aggregation stage, low-density lipoprotein mol...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75887-0
更新日期:2001-10-01 00:00:00
abstract::Melittin has been reported to form toroidal pores under certain conditions, but the atomic-resolution structure of these pores is unknown. A 9-μs all-atom molecular-dynamics simulation starting from a closely packed transmembrane melittin tetramer in DMPC shows formation of a toroidal pore after 1 μs. The pore remains...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.04.006
更新日期:2015-05-19 00:00:00
abstract::Atrial fibrosis has been implicated in the development and maintenance of atrial arrhythmias, and is characterized by expansion of the extracellular matrix and an increased number of fibroblasts (Fbs). Electrotonic coupling between atrial myocytes and Fbs may contribute to the formation of an arrhythmogenic substrate....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.07.054
更新日期:2009-10-21 00:00:00
abstract::The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been ob...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.05.050
更新日期:2012-07-18 00:00:00
abstract::In the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.11.004
更新日期:2010-02-17 00:00:00
abstract::When cells migrate through constricting pores, they incur DNA damage and develop genomic variation. Experiments show that this damage is not due to DNA breakage from mechanical stress on chromatin in the deformed nucleus. Here we propose a model for a mechanism by which nuclear deformation can lead to DNA damage. We t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.04.037
更新日期:2017-06-06 00:00:00
abstract::The effects of Mg++ on the spatial organization of nuclei from rat hepatocytes are analyzed in the range 0-60 mM, in the presence of suitable concentrations of KCl to reproduce physiological conditions. It is shown that the scatter-signal distribution measured by means of a flow microfluorimeter is greatly affected by...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83938-2
更新日期:1985-04-01 00:00:00
abstract::The calyx of Held is a giant nerve terminal that forms a glutamatergic synapse in the auditory pathway. Due to its large size, it offers a number of advantages for biophysical studies, including voltage-clamp of both pre- and postsynaptic compartments and the loading with indicator dyes and caged compounds. Three aspe...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2016.12.017
更新日期:2017-01-24 00:00:00
abstract::Results are presented of nonphotochemical-hole-burning experiments on the mitochondrial specific dye rhodamine 800 incubated with two human ovarian surface epithelial cell lines: OSE(tsT)-14 normal cells and OV167 carcinoma cells. This dye is selective for the plasma and inner membranes of the mitochondria, as shown b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74945-5
更新日期:2003-02-01 00:00:00
abstract::Recently, it has become clear that the influenza virus fusion protein, hemagglutinin (HA), produces membrane destabilization and fusion by a multistep process, which involves the aggregation of the HAs to form a fusion site. While the details of this process are under debate, it is important to recognize that proposin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81622-3
更新日期:1992-08-01 00:00:00
abstract::Molecular dynamics simulations are presented for a Thermus aquaticus (Taq) DNA polymerase I complex (consisting of the protein, the primer-template DNA strands, and the incoming nucleotide) subjected to external forces. The results obtained with a force applied to the DNA template strand provide insights into the effe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.103.039313
更新日期:2004-09-01 00:00:00
abstract::Gigaohm recordings have been made from glutamate receptor channels in excised, outside-out patches of collagenase-treated locust muscle membrane. The channels in the excised patches exhibit the kinetic state switching first seen in megaohm recordings from intact muscle fibers. Analysis of channel dwell time distributi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82367-5
更新日期:1990-07-01 00:00:00
abstract::Molecular recognition between biotinylated bovine serum albumin and polyclonal, biotin-directed IG antibodies has been measured directly under various buffer conditions using an atomic force microscope (AFM). It was found that even highly structured molecules such as IgG antibodies preserve their specific affinity to ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79814-4
更新日期:1996-05-01 00:00:00
abstract::Purple membranes were adsorbed on freestanding lipid bilayers, termed nano-black lipid membranes (nano-BLMs), suspending the pores of porous alumina substrates with average pore diameters of 280 nm. Nano-BLMs were obtained by first coating the upper surface of the highly ordered porous alumina substrates with a thin g...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.059550
更新日期:2005-08-01 00:00:00
abstract::Information processing and decision-making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years, however, both experimentalists and theorists have begun to appreciate that cellular decision-making can also be performed at the level of a s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.07.040
更新日期:2012-09-05 00:00:00
abstract::Computational methods that predict three-dimensional structures from amino acid sequences have become increasingly accurate and have provided insights into structure-function relationships for proteins in the absence of structural data. However, the accuracy of computational structural models requires experimental app...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74251-4
更新日期:2004-03-01 00:00:00
abstract::The four-alpha-helix bundle mimics the transmembrane domain of the Cys-loop receptor family believed to be the protein target for general anesthetics. Using high resolution NMR, we solved the structure (Protein Data Bank ID: 2I7U) of a prototypical dimeric four-alpha-helix bundle, (Aalpha(2)-L1M/L38M)(2,) with designe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.117838
更新日期:2008-06-01 00:00:00
abstract::De novo formation of cell pairs was used to examine the gating properties of single gap junction channels. Two separate cells of an insect cell line (clone C6/36, derived from the mosquito Aedes albopictus) were pushed against each other to provoke formation of gap junction channels. A dual voltage-clamp method was us...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80521-1
更新日期:1994-08-01 00:00:00
abstract::The temporal dynamics of the concentrations of several proteins are tightly regulated, particularly for critical nodes in biological networks such as transcription factors. An important mechanism to control transcription factor levels is through autoregulatory feedback loops where the protein can bind its own promoter...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.005
更新日期:2011-09-21 00:00:00
abstract::The processes of cell growth and budding of the yeast cells Saccharomyces cerevisiae, which were gently immobilized on 3% agar and submerged in culture medium, were successfully imaged with an atomic force microscope for 6-7 h. Similar experiments on chemically fixed cells did not detect any appreciable change in thei...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80147-5
更新日期:1995-12-01 00:00:00
abstract::The freshwater polyp Hydra can regenerate from tissue fragments or random cell aggregates. We show that the axis-defining step ("symmetry breaking") of regeneration requires mechanical inflation-collapse oscillations of the initial cell ball. We present experimental evidence that axis definition is retarded if these o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.09.062
更新日期:2009-02-18 00:00:00
abstract::The E5 oncoprotein is the major transforming protein of bovine papillomavirus type 1. This 44-residue transmembrane protein can interact with the platelet-derived growth factor receptor β, leading to ligand-independent activation and cell transformation. For productive interaction, E5 needs to dimerize via a C-termina...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.06.073
更新日期:2010-09-22 00:00:00
abstract::The geometry of domains in phospholipid bilayers of binary (1:1) mixtures of synthetic lecithins with a difference in chain length of four methylene groups has been studied by two independent, direct and complementary methods. Grazing incidence diffraction of neutrons provided gel domain sizes of less than 10 nm in bo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77952-4
更新日期:1998-05-01 00:00:00
abstract::The structure of the unusually long (∼100 amino-acid residues) N-terminal domain of the light-harvesting protein CP29 of plants is not defined in the crystal structure of this membrane protein. We studied the N-terminus using two electron paramagnetic resonance (EPR) approaches: the rotational diffusion of spin labels...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.11.4506
更新日期:2014-03-18 00:00:00