Abstract:
:Universal features of the peptide aggregation process suggest a common mechanism, with a first-order phase transition in aqueous solutions of the peptides being the driving force. Small system sizes strongly affect the stability of the minor phase in the two-phase region. We show manifestations of this effect in aqueous solutions of fragments of the islet amyloid polypeptide, using computer simulation methods and invoking various approaches in characterizing clustering and aggregate formation. These systems with peptide concentrations deeply inside the immiscibility region show two distinct stable states, which interchange with time: one state contains a peptide aggregate; and the other state has an aggregate that is noticeably dissolved. The first state is relevant for macroscopic systems, whereas the second one is artificial. At a fixed concentration, the occurrence probability of the aggregate state vanishes upon decreasing the system size, thus indicating the necessity to apply a finite size-scaling for meaningful studies of peptide aggregation by simulations. The effect observed may be one of the factors responsible for the difference between intracellular and extracellular aggregation and fibrillization of polypeptides. The finite size of biological cells or their compartments may be playing a decisive role in hampering intracellular aggregation of highly insoluble amyloidogenic proteins, whereas aggregation is unavoidable in the extracellular space at the same peptide concentration.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Singh G,Brovchenko I,Oleinikova A,Winter Rdoi
10.1529/biophysj.108.136226subject
Has Abstractpub_date
2008-10-01 00:00:00pages
3208-21issue
7eissn
0006-3495issn
1542-0086pii
S0006-3495(08)78463-7journal_volume
95pub_type
杂志文章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::4',6-diamidino-2-phenylindole (DAPI), netropsin, and pentamidine are minor groove binders that have terminal -C(NH2)2+ groups. The hydration changes that accompany their binding to the minor groove of the (AATT)2 sequence have been studied using the osmotic stress technique with fluorescence spectroscopy. The affinity...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.097451
更新日期:2007-02-01 00:00:00
abstract::A new model is proposed to account for the apparent conductance changes of the sodium, or early, channel in nerve fiber membranes. In this model it is assumed that the channels are gated at the interior side of the membrane and are resistively limited at the exterior side by sodium selective barriers of high resistanc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(71)86261-6
更新日期:1971-11-01 00:00:00
abstract::Deciphering the mechanisms underlying the high sensitivity of cells to mechanical microenvironments is crucial for understanding many physiological and pathological processes, e.g., stem cell differentiation and cancer cell metastasis. Here, a cytoskeletal tensegrity model is proposed to study the reorientation of pol...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.08.036
更新日期:2016-10-04 00:00:00
abstract::Two different spin labels, N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl)iodoacetamide (IPSL) and (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate (MTSSL), and two different fluorescent labels 5-((((2-iodoacetyl)amino)-ethyl)amino)naphtalene-1-sulfonic acid (IAEDANS) and 6-bromoacetyl-2-dimetylaminon...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76253-4
更新日期:2001-06-01 00:00:00
abstract::The effect of peptides, corresponding to sequences in the skeletal muscle dihydropyridine receptor II-III loop, on Ca(2+) release from sarcoplasmic reticulum (SR) and on ryanodine receptor (RyR) calcium release channels have been compared in preparations from normal and malignant hyperthermia (MH)-susceptible pigs. Pe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76147-4
更新日期:2001-04-01 00:00:00
abstract::We have constructed a theory for diffusion through the pore of a single-ion channel by taking a limit of a random walk around a cycle of states. Similar to Levitt's theory of single-ion diffusion, one obtains boundary conditions for the Nernst-Planck equation that guarantee that the pore is occupied by at most one ion...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79374-8
更新日期:1996-10-01 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::Intracellular passive Ca2+, buffering was measured in voltage-clamped rat ventricular myocytes. Cells were loaded with indo-1 (K+ salt) to an estimated cytosolic concentration of 44 +/- 5 microM (Mean +/- SEM, n = 5), and accessible cell volume was estimated to be 24.5 +/- 3.6 pl. Ca2+ transport by the sarcoplasmic re...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80652-6
更新日期:1994-10-01 00:00:00
abstract::Calmodulin (CaM) expression is upregulated upon HIV-1 infection and interacts with proteins involved in viral processing, including the multifunctional HIV-1 MA protein. We present here the results of studies utilizing small-angle neutron scattering with contrast variation that, when considered in the light of earlier...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.06.042
更新日期:2012-08-08 00:00:00
abstract::Effects of adducts of [PtCl(NH3)3]Cl or chlorodiethylenetriamineplatinum(II) on DNA stability were studied with emphasis on thermodynamic origins of that stability. Oligodeoxyribonucleotide duplexes (15-bp) containing the single, site-specific monofunctional adduct at G-residues of the central sequences TGT/ACA or 5'-...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.051771
更新日期:2005-02-01 00:00:00
abstract::A filopodium is a cytoplasmic projection, exquisitely built and regulated, which extends from the leading edge of the migrating cell, exploring the cell's neighborhood. Commonly, filopodia grow and retract after their initiation, exhibiting rich dynamical behaviors. We model the growth of a filopodium based on a stoch...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.123778
更新日期:2008-05-15 00:00:00
abstract::The activity of the voltage-gated Na+ channel is subjected to modulation through covalent modifications. It has been previously shown that brain Na+ currents are reduced following the activation of the protein kinase A (PKA) pathway, but the effect of the phosphorylation on the gating mechanism of the channel has not ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)76882-7
更新日期:1999-07-01 00:00:00
abstract::The development of scanning probe techniques has made it possible to examine protein-protein interactions at the level of individual molecular pairs. A calibrated optical tweezers, along with immunoglobulin G (IgG)-coated polystyrene microspheres, has been used to detect individual surface-linked Staphylococcus protei...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76263-7
更新日期:2001-06-01 00:00:00
abstract::Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.06.046
更新日期:2011-08-17 00:00:00
abstract::Despite the recognition that actin filaments are important for numerous cellular processes, and decades of investigation, the dynamics of in vitro actin filaments are still not completely understood. Here, we follow the time evolution of the length distribution of labeled actin reporter filaments in an unlabeled F-act...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.07.009
更新日期:2011-08-17 00:00:00
abstract::Myelin basic protein (MBP) is predominantly found in the membranes of the myelin sheath of the central nervous system and is involved in important protein-protein and protein-lipid interactions in vivo and in vitro. Furthermore, divalent transition metal ions, especially Zn(2+) and Cu(2+), seem to directly affect the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.08.022
更新日期:2010-11-03 00:00:00
abstract::Cell-reorganized fibronectin layers on polymer films providing a gradation of the binding strength between protein and substrate were analyzed by combined fluorescence and scanning force microscopy. The nanoscale fibronectin patterns exhibited paired parallel fibrils with characteristic spacings of 156, 233, 304, and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.048074
更新日期:2005-01-01 00:00:00
abstract::The heterologous expression and purification of membrane proteins represent major limitations for their functional and structural analysis. Here we describe a new method of incorporation of transmembrane proteins in planar lipid bilayer starting from 1 pmol of solubilized proteins. The principle relies on the direct i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.087791
更新日期:2006-11-01 00:00:00
abstract::The dependences of the steady-state critical concentration and average filament length of actin solutions, on the filament branching and capping rates, are calculated using a rate methodology based on the total number of actin filaments. The methodology generalizes calculations of the "treadmilling" actin concentratio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.061598
更新日期:2005-07-01 00:00:00
abstract::Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.11.011
更新日期:2010-03-03 00:00:00
abstract::Small angle x-ray and neutron scattering are techniques that give solution structures for large macromolecules. The creation of physically realistic atomistic models from known high-resolution structures to determine joint x-ray and neutron scattering best-fit structures offers a, to our knowledge, new method that sig...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.10.024
更新日期:2019-12-03 00:00:00
abstract::Aromatic monocarboxylic acids are known to significantly potentiate the mechanical response of skeletal muscle fibers. In this study we investigated the effects of enantiomers of 2-(4-chlorophenoxy)propionic acid, chemically one of the simplest aromatic monocarboxylic acids with chiral properties, on mechanical thresh...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82515-7
更新日期:1990-01-01 00:00:00
abstract::The bacterial flagellar motor (BFM) is a molecular machine that rotates the helical filaments and propels the bacteria swimming toward favorable conditions. In our previous works, we built a stochastic conformational spread model to explain the dynamic and cooperative behavior of BFM switching. Here, we extended this ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.02.023
更新日期:2016-03-29 00:00:00
abstract::The elastic properties of cylindrical segments of sarcolemma were studied in single striated fibers of the frog semitendinosus muscle. All measurements were made on membranes of retraction zones, cell segments from which the sarcoplasm had retracted. Quantitative morphological studies indicated that three deforming fo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(70)86312-3
更新日期:1970-05-01 00:00:00
abstract::Cationic lipid-DNA (CL-DNA) complexes are abundantly used in nonviral gene therapy clinical applications. Surface functionality is the next step in developing these complexes as competent, target-specific gene carriers. Poly(ethylene glycol) (PEG) is the natural choice to serve as a protective coat or act as a tether ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74190-9
更新日期:2004-02-01 00:00:00
abstract::The presence of tryptophan residues as intrinsic fluorophores in most proteins makes them an obvious choice for fluorescence spectroscopic analyses of such proteins. Membrane proteins have been reported to have a significantly higher tryptophan content than soluble proteins. The role of tryptophan residues in the stru...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78116-5
更新日期:1997-08-01 00:00:00
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::Noncanonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, in which they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.09.002
更新日期:2020-10-20 00:00:00
abstract::The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these proc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(63)86831-9
更新日期:1963-11-01 00:00:00