Abstract:
:Ionotropic glutamate receptors are essential for fast synaptic nerve transmission. Recent x-ray structures for the ligand-binding (S1S2) region of the GluR2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-sensitive receptor have suggested how differences in protein/ligand interactions may determine whether a ligand will behave as a full agonist. We have used multiple molecular dynamics simulations of 2-5 ns duration to explore the structural dynamics of GluR2 S1S2 in the presence and absence of glutamate and in a complex with kainate. Our studies indicate that not only is the degree of domain closure dependent upon interactions with the ligand, but also that protein/ligand interactions influence the motion of the S2 domain with respect to S1. Differences in domain mobility between the three states (apo-S1S2, glutamate-bound, and kainate-bound) are surprisingly clear-cut. We discuss how these changes in dynamics may provide an explanation relating the mechanism of transmission of the agonist-binding event to channel opening. We also show here how the glutamate may adopt an alternative mode of binding not seen in the x-ray structure, which involves a key threonine (T480) side chain flipping into a new conformation. This new conformation results in an altered pattern of hydrogen bonding at the agonist-binding site.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Arinaminpathy Y,Sansom MS,Biggin PCdoi
10.1016/S0006-3495(02)75430-1subject
Has Abstractpub_date
2002-02-01 00:00:00pages
676-83issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(02)75430-1journal_volume
82pub_type
杂志文章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::A mathematical model is formulated for the development of a population of cells in which the individual members may grow and divide or die. A given cell is characterized by its age and volume, and these parameters are assumed to determine the rate of volume growth and the probability per unit time of division or death...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(67)86592-5
更新日期:1967-07-01 00:00:00
abstract::The sarcoplasmic reticulum channel (ryanodine receptor) from cardiac myocytes was reconstituted into planar lipid bilayers consisting of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) in varying ratios. The channel activity parameters, i.e., open probability an...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74532-9
更新日期:2003-08-01 00:00:00
abstract::The properties of phosphatidylcholines (PCs) having a perdeuterated stearic acid, 18:0d35, in the sn-1 position and the fatty acid 18:0, 18:1 omega 9, 18:2 omega 6, 18:3 omega 3, 20:4 omega 6, 20:5 omega 3, or 22:6 omega 3 at the sn-2 position were investigated in a matrix of dioleoylphosphatidylethanolamine (DOPE) by...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79223-8
更新日期:1996-07-01 00:00:00
abstract::In permeabilized single fibers of fast (psoas) and slow (soleus) muscle from the rabbit, the effect of pH on isometric myofibrillar ATPase activity and force was studied at 15 degrees C, in the pH range 6.4-7.9. ATPase activity was measured photometrically by enzymatic coupling of the regeneration of ATP to the oxidat...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80727-1
更新日期:1994-12-01 00:00:00
abstract::Recent studies have demonstrated that caffeine can act as an antimutagen and inhibit the cytoxic and/or cytostatic effects of some DNA intercalating agents. It has been suggested that this inhibitory effect may be due to complexation of the DNA intercalator with caffeine. In this study we employ optical absorption, fl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79587-5
更新日期:1996-01-01 00:00:00
abstract::Morphine spin labeled on the phenolic hydroxy group has been prepared using commercially available reagents and characterized by thin layer chromatography, mass spectroscopy, and electron spin resonance spectroscopy. It has been shown that morphine modified in this way retains some opiate activity, does not pass throu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(75)85889-9
更新日期:1975-11-01 00:00:00
abstract::The resonance Raman spectrum of the second intermediate in the bacteriorhodopsin cycle, bL550, is obtained by a simple flow technique. The Schiff base linkage in this intermediate appears to be protonated, contrary to previous suggestion. The fingerprint region of the spectrum of bL550 does not closely match those of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(79)85269-8
更新日期:1979-06-01 00:00:00
abstract::Cholesterol is abundant in plasma membranes and exhibits a variety of interactions throughout the membrane. Chemical potential accounts for thermodynamic consequences of molecular interactions, and quantifies the effective concentration (i.e., activity) of any substance participating in a process. We have developed, t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.12.042
更新日期:2018-02-27 00:00:00
abstract::Proteins are denatured in aqueous urea solution. The nature of the molecular driving forces has received substantial attention in the past, whereas the question how urea acts at different phases of unfolding is not yet well understood at the atomic level. In particular, it is unclear whether urea actively attacks fold...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.01.051
更新日期:2009-05-06 00:00:00
abstract::In this article, we explore the information content of molecular force-field calculations. We make use of exhaustive lattice models of molecular conformations and reduced alphabet sequences to determine the relative resolving power of pairwise interaction-based force fields. We find that sequence-specific interactions...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.059618
更新日期:2005-11-01 00:00:00
abstract::Effects of alkali cations on the nuclear magnetic resonance intensity of 23Na were studied in rat liver homogenate. The loss in the resonance intensity of 23Na in the homogenate was able to be divided into two components, one of which is abolished by the addition of Cs+ ("Cs-sensitive component"), the other being inse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(76)85779-7
更新日期:1976-12-01 00:00:00
abstract::We study the lateral headgroup interactions among phosphatidylcholine (PC) molecules and among phosphatidylethanolamine (PE) molecules in monolayers and extend our previous models. In this paper, we present an extensive set of pressure-area isotherms and surface potential experiments on monolayers of phospholipids ran...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81964-1
更新日期:1992-06-01 00:00:00
abstract::The effects of temperature (3 degrees-26 degrees C) on the nonlinear components of the displacement current were measured in internally perfused, voltage clamped squid axons. Steps of potential were applied from a holding potential of -70mV (outside ground) to values from -130 to +70mV and either the current or its in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85464-2
更新日期:1978-09-01 00:00:00
abstract::Propagation speed of an impulse is influenced by previous activity. A pulse following its predecessor too closely may travel more slowly than a solitary pulse. In contrast, for some range of interspike intervals, a pulse may travel faster than normal because of a possible superexcitable phase of its predecessor's wake...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84847-3
更新日期:1981-05-01 00:00:00
abstract::Giant vesicles formed of 1,2-dipalmitoylphosphatidylcholine (DPPC) and sterols (cholesterol or ergosterol) in water and water/ethanol solutions have been used to examine the effect of sterol composition and ethanol concentration on the area compressibility modulus (K(a)), overall mechanical behavior, vesicle morpholog...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.057943
更新日期:2005-10-01 00:00:00
abstract::We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.11.4012
更新日期:2012-01-04 00:00:00
abstract::By using an analogy between the magnetization of a paramagnetic material in an external magnetic field and the electric polarization of the lateral wall of outer hair cells in response to the transmembrane potential, we show that, based on experimental data on the charge transfer across the membrane, it is impossible ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.059782
更新日期:2005-05-01 00:00:00
abstract::Using homonuclear (1)H NOESY spectra, with chemical shifts, (3)JH(N)H(α) scalar couplings, residual dipolar couplings, and (1)H-(15)N NOEs, we have optimized and validated the conformational ensembles of the amyloid-β 1-40 (Aβ40) and amyloid-β 1-42 (Aβ42) peptides generated by molecular dynamics simulations. We find t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.04.056
更新日期:2013-06-18 00:00:00
abstract::We argue that membrane viscosity, η(m), plays a prominent role in the thermal fluctuation dynamics of micron-scale lipid domains. A theoretical expression is presented for the timescales of domain shape relaxation, which reduces to the well-known η(m) = 0 result of Stone and McConnell in the limit of large domain size...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2010.07.007
更新日期:2010-09-22 00:00:00
abstract::We study dsDNA-RecA interactions by exerting forces in the pN range on single DNA molecules while the interstrand topological state is controlled owing to a magnetic tweezers setup. We show that unwinding a duplex DNA molecule induces RecA polymerization even at moderate force. Once initial polymerization has nucleate...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.043059
更新日期:2004-10-01 00:00:00
abstract::Intracellular Ca2+ was determined with the fura-2 technique during electrically induced contractions in the rabbit rectococcygeus smooth muscle at 22 degreesC. The muscles were electrically activated to give short, reproducible contractions. Intracellular [Ca2+] increased during activation; the increase in [Ca2+] prec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77630-1
更新日期:1998-10-01 00:00:00
abstract::The α-helical (AH) domain of the hepatitis C virus nonstructural protein NS5A, anchored at the cytoplasmic leaflet of the endoplasmic reticulum, plays a role in viral replication. However, the peptides derived from this domain also exhibit remarkably broad-spectrum virocidal activity, raising questions about their mod...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.11.032
更新日期:2016-01-05 00:00:00
abstract::We present a single virion method to determine absolute distributions of copy number in the protein composition of viruses and apply it to herpes simplex virus type 1. Using two-color coincidence fluorescence spectroscopy, we determine the virion-to-virion variability in copy numbers of fluorescently labeled tegument ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.106351
更新日期:2007-08-15 00:00:00
abstract::A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79942-8
更新日期:1995-08-01 00:00:00
abstract::Deuterium nuclear magnetic resonance was used to monitor lipid acyl-chain orientational order in suspensions of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG) containing Ca(2+) and the lung surfactant proteins SP-A and SP-B separately and together. To distinguish between protein-lipid...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.102681
更新日期:2007-07-01 00:00:00
abstract::Although significant progress has been made toward understanding morphogen-mediated patterning in development, control of the size and shape of tissues via local and global signaling is poorly understood. In particular, little is known about how cell-cell interactions are involved in the control of tissue size. The Hi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.07.002
更新日期:2018-08-21 00:00:00
abstract::A model for the action of vinblastine (VLB) on cells multiplying exponentially in vivo with a generation time, T(G), has been derived. It is based on the assumption that cells attempting to pass through mitosis in the presence of VLB lose their proliferative capacity and that this lethal effect occurs only when the ce...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(66)86646-8
更新日期:1966-03-01 00:00:00
abstract::Carbonic anhydrase (CA) is a thoroughly studied enzyme. Its primary role is the rapid interconversion of carbon dioxide and bicarbonate in the cells, where carbon dioxide is produced, and in the lungs, where it is released from the blood. At the same time, it regulates pH homeostasis. The inhibitory function of sulfon...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2020.08.020
更新日期:2020-10-06 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