Abstract:
:We describe simulations of absorption difference spectra in strongly coupled photosynthetic antennas. In the presence of large resonance couplings, distinctive features arise from excited-state absorption transitions between one- and two-exciton levels. We first outline the theory for the heterodimer and for the general N-pigment system, and we demonstrate the transition between the strong and weak coupling regimes. The theory is applied to Fenna-Matthews-Olson (FMO) bacteriochlorophyll a protein trimers from the green photosynthetic bacterium Prosthecochloris aestuarii and then compared with experimental low-temperature absorption difference spectra of FMO trimers from the green bacterium Chlorobium tepidum.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Buck DR,Savikhin S,Struve WSdoi
10.1016/S0006-3495(97)78644-2subject
Has Abstractpub_date
1997-01-01 00:00:00pages
24-36issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(97)78644-2journal_volume
72pub_type
杂志文章abstract::Recent NMR structural characterization studies showed that a seven-residue segment (FKKGERL) from the src SH3 domain adopts the nativelike diverging type II beta-turn in aqueous solution in support of the prediction based on the I-sites library of sequence structural motifs. We study the conformational variability and...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74966-2
更新日期:2003-03-01 00:00:00
abstract::The phase transitions of dipalmitoylphosphatidylethanolamine (DPPE) in excess water have been examined by low-angle time-resolved x-ray diffraction and calorimetry at low scan rates. The lamellar subgel/lamellar liquid-crystalline (L(c) --> L(alpha)), lamellar gel/lamellar liquid-crystalline (L(beta) --> L(alpha)), an...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81873-8
更新日期:1992-03-01 00:00:00
abstract::The pathway to membrane fusion in synthetic and biological systems is thought to pass through hemifusion, in which the outer leaflets are fused while the inner leaflets engage in a hemifusion diaphragm (HD). Fusion has been proposed to be completed by lysis of the expanded HD that matures from a localized stalklike in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.06.041
更新日期:2012-08-22 00:00:00
abstract::We have studied the photoinduced volume changes, energetics, and kinetics in the early steps of the bacteriorhodopsin (BR) photocycle with pulsed, time-resolved photoacoustics. Our data show that there are two volume changes. The fast volume change ( < or = 200 ns) is an expansion (2.5 +/- 0.3 A3/molecule) and is obse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79235-4
更新日期:1996-07-01 00:00:00
abstract::Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived fr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.109868
更新日期:2008-02-01 00:00:00
abstract::An experimental procedure is described which consists of cutting the canal duct, inserting a micropipette and administering known volumetric displacements to the cupula. The cupula is made visible by dying the endolymph. Known displacements are administered to the cupula, and the time constant of the return to its equ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(76)85720-7
更新日期:1976-06-01 00:00:00
abstract::Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, and relative position of the SNP on duplex hybridization and SNP resolution were determined. Our theoretical model of...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.107.105320
更新日期:2007-05-15 00:00:00
abstract::The kinetics of oxygen geminate binding with the taxonomic substates of MbO2 are reported. The maximum entropy method was used to analyze the rebinding kinetics of MbCO and MbO2 monitored in the Soret. The resulting rate distributions were found to consist of a small number of overlapping bands. A global parametric fi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75561-6
更新日期:2002-04-01 00:00:00
abstract::Here we present a model for maltodextrin translocation through maltoporin channels. In a first step, our theoretical analysis does consider the case of a single binding site for a given substrate in a structurally unaffected channel with a possibly different entrance barrier on either side. It is shown how by means of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)70025-3
更新日期:2003-05-01 00:00:00
abstract::Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly foc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.07.042
更新日期:2018-10-16 00:00:00
abstract::The molecular code of specific DNA recognition by proteins as a paradigm in molecular biology remains an unsolved puzzle primarily because of the subtle interplay between direct protein-DNA interaction and the indirect contribution from water and ions. Transformation of the nonspecific, low affinity complex to a speci...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.063263
更新日期:2005-08-01 00:00:00
abstract::Many different cell types are able to migrate by formation of a thin actin-based cytoskeletal extension. Recently, it became evident that this extension consists of two distinct substructures, designated lamellipodium and lamellum, which differ significantly in their kinetic and kinematic properties as well as their b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.134817
更新日期:2008-12-15 00:00:00
abstract::The cytoplasmic surface of the BR (initial) state of bacteriorhodopsin is characterized by a cluster of three carboxylates that function as a proton-collecting antenna. Systematic replacement of most of the surface carboxylates indicated that the cluster is made of D104, E161, and E234 (Checover, S., Y. Marantz, E. Na...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75179-5
更新日期:2002-07-01 00:00:00
abstract::Ataxin-1 is a human protein responsible for spinocerebellar ataxia type 1, a hereditary disease associated with protein aggregation and misfolding. Essential for ataxin-1 aggregation is the anomalous expansion of a polyglutamine tract near the protein N-terminus, but the sequence-wise distant AXH domain modulates and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.01.048
更新日期:2013-03-19 00:00:00
abstract::The nucleus has a smooth, regular appearance in normal cells, and its shape is greatly altered in human pathologies. Yet, how the cell establishes nuclear shape is not well understood. We imaged the dynamics of nuclear shaping in NIH3T3 fibroblasts. Nuclei translated toward the substratum and began flattening during t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.07.006
更新日期:2015-08-18 00:00:00
abstract::We present a hybrid computational methodology to predict multiple energetically accessible conformations for G protein-coupled receptors (GPCRs) that might play a role in binding to ligands and different signaling partners. To our knowledge, this method, termed ActiveGEnSeMBLE, enables the first quantitative energy pr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.04.028
更新日期:2016-06-21 00:00:00
abstract::We investigated self-adhesion between highly negatively charged aggrecan macromolecules extracted from bovine cartilage extracellular matrix by performing atomic force microscopy (AFM) imaging and single-molecule force spectroscopy (SMFS) in saline solutions. By controlling the density of aggrecan molecules on both th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.09.002
更新日期:2010-11-17 00:00:00
abstract::Molecular chaperones are large proteins or protein complexes from which many proteins require assistance in order to fold. One unique property of molecular chaperones is the cavity they provide in which proteins fold. The interior surface residues which make up the cavities of molecular chaperone complexes from differ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.10.040
更新日期:2012-12-19 00:00:00
abstract::Microstructured surfaces provide a unique framework to probe cell migration and cytoskeletal dynamics in a standardized manner. Here, we report on the steady-state occupancy probability of cells in asymmetric two-state microstructures that consist of two fibronectin-coated adhesion sites connected by a thin guidance c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.11.3389
更新日期:2020-02-04 00:00:00
abstract::During inflammation, flowing leukocytes tether to and roll on vascular surfaces through the association and dissociation of selectin/ligand bonds. The interactions of P- and L- selectins with their respective ligands exhibit catch-slip bonds, such that increasing force initially prolongs and then shortens bond lifetim...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.05.040
更新日期:2010-08-09 00:00:00
abstract::The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.08.042
更新日期:2012-10-03 00:00:00
abstract::To study why pancreatic beta-cells prefer to burst as a multi-cellular complex, we have formulated a stochastic model for bursting clusters of excitable cells. Our model incorporated a delayed rectifier K+ channel, a fast voltage-gated Ca2+ channel, and a slow Cai-blockable Ca2+ channel. The fraction of ATP-sensitive ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)82976-X
更新日期:1988-09-01 00:00:00
abstract::Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompat...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2016.03.015
更新日期:2016-04-26 00:00:00
abstract::In ubiquitination, cullin-RING E3 ubiquitin ligases (CRLs) assist in ubiquitin transfer from ubiquitin-conjugating enzyme E2 to the substrate. Neddylation, which involves NEDD8 transfer from E2 to E3-cullin, stimulates ubiquitination by inducing conformational change in CRLs. However, deneddylation, which removes NEDD...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.05.021
更新日期:2010-08-04 00:00:00
abstract::The possibility that the chlorophyll (chl) ring distortions observed in the crystal structures of chl-protein complexes are involved in the transition energy modulation, giving rise to the spectral forms, is investigated. The out-of-plane chl-macrocycle distortions are described using an orthonormal set of deformation...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.104554
更新日期:2007-09-15 00:00:00
abstract::Fusion of a vesicle with its target membrane is preceded by tethering or docking. However, the physical mechanism of vesicle-tethering is unknown. To study this mechanism, we used eosinophil secretory granules, which undergo stimulated homotypic fusion events inside the cell during degranulation. Using a dual optical ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.132670
更新日期:2008-11-15 00:00:00
abstract::Förster resonance energy transfer (FRET)-based biosensors for the quantitative analysis of intracellular signaling, including sensors for monitoring cyclic adenosine monophosphate (cAMP), are of increasing interest. The measurement of the donor/acceptor emission ratio in tandem biosensors excited at the donor excitati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.125666
更新日期:2008-12-01 00:00:00
abstract::The glutamate-activated current in photoreceptors has been attributed both to a sodium/glutamate transporter and to a glutamate-activated chloride channel. We have further studied the glutamate-activated current in single, isolated photoreceptors from the tiger salamander using noise analysis on whole-cell patch-clamp...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79613-3
更新日期:1996-02-01 00:00:00
abstract::Choice of network topology for gene regulation has been a question of interest for a long time. How do simple and more complex topologies arise? In this work, we analyze the topology of the marRAB operon in Escherichia coli, which is associated with control of expression of genes associated with conferring resistance ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.08.017
更新日期:2015-10-06 00:00:00
abstract::Two-photon excitation (TPE) spectra of Fura-2, -4F, -6F, -FF, and Furaptra were characterized using a tunable (750-850 nM) ultra-short pulse laser. Two-photon fluorescence of these dyes was studied in free solution and in the cytosol of isolated rabbit ventricular cardiomyocytes. The TPE spectra of the Ca(2+)-free and...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74241-1
更新日期:2004-03-01 00:00:00