Abstract:
:The vibrational energy relaxation of a selected vibrational mode in cytochrome c--a C-D stretch in the terminal methyl group of Met80--has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. As demonstrated in the pioneering work of Romesberg and co-workers, isotopic labeling of the C-H (to C-D) stretch in alkyl side chains shifts the stretching frequency to the transparent region of the protein's density of states, making it an effective and versatile probe of protein structure and dynamics. Molecular dynamics trajectories of solvated cytochrome c were run at 300 K, and vibrational population relaxation times were estimated using the classical Landau-Teller-Zwanzig model and a number of semiclassical theories of resonant and two-phonon vibrational relaxation processes. The C-D stretch vibrational population relaxation time is estimated to be T(1) = 14-40 ps; the relatively close agreement between various semiclassical estimates of T(1) lends support to the applicability of those expressions. Normal mode calculations were used to identify the dominant coupling between the protein and C-D oscillator. All bath modes strongly coupled to the C-D stretch are in close proximity. Angle bending modes in the terminal methyl group of Met80 appear to be the most likely acceptor modes defining the mechanism of population relaxation of the C-D vibration.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Bu L,Straub JEdoi
10.1016/S0006-3495(03)74575-5subject
Has Abstractpub_date
2003-09-01 00:00:00pages
1429-39issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(03)74575-5journal_volume
85pub_type
杂志文章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 availability of very high magnetic fields of up to 170,000 gauss made it worthwhile to pursue the search for a critical change in the rate of four enzyme substrate reactions. The four enzymes were ribonuclease, polyphenol oxidase, peroxidase, and aldolase. The experiments showed that, to within +/-3%, no detectabl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(67)86583-4
更新日期:1967-03-01 00:00:00
abstract::The ionophore properties of magainin I, an antimicrobial and amphipathic peptide from the skin of Xenopus, were investigated in planar lipid bilayers. Circular dichroism studies, performed comparatively with alamethicin, in small or large unilamellar phospholipidic vesicles, point to a smaller proportion of alpha-heli...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82746-8
更新日期:1989-11-01 00:00:00
abstract::Keratin intermediate filaments form dynamic intracellular networks, which span the entire cytoplasm and provide mechanical strength to the cell. The mechanical resilience of the keratin intermediate filament network itself is determined by filament bundling. The bundling process can be reproduced in artificial conditi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.05.024
更新日期:2020-07-07 00:00:00
abstract::We demonstrate the first, to our knowledge, integration of stimulated emission depletion (STED) with selective plane illumination microscopy (SPIM). Using this method, we were able to obtain up to 60% improvements in axial resolution with lateral resolution enhancements in control samples and zebrafish embryos. The in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.12.3748
更新日期:2011-04-20 00:00:00
abstract::A number of membrane proteins act via binding at the water/lipid bilayer interface. An important example of such proteins is provided by the gating-modifier toxins that act on voltage-gated potassium (Kv) channels. They are thought to partition to the headgroup region of lipid bilayers, and so provide a good system fo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.130971
更新日期:2008-10-01 00:00:00
abstract::We analyze a model based on receptor modification for the cAMP signaling system that controls aggregation of the slime mold Dictyostelium discoideum after starvation. The model takes into account both the desensitization of the cAMP receptor by reversible phosphorylation and the activation of adenylate cyclase that fo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83275-7
更新日期:1987-11-01 00:00:00
abstract::To probe the complexity of the cell membrane organization and dynamics, it is important to obtain simple physical observables from experiments on live cells. Here we show that fluorescence correlation spectroscopy (FCS) measurements at different spatial scales enable distinguishing between different submicron confinem...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.067959
更新日期:2005-12-01 00:00:00
abstract::Fatty acid binding proteins play an important role in the transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the gap is lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.12.005
更新日期:2020-01-21 00:00:00
abstract::We have obtained new insights into the behavior of a class of excitable systems when a stimulus, or parameter, is slowly tuned through a threshold value. Such systems do not accommodate no matter how slowly a stimulus ramp is applied, and the stimulus value at onset of repetitive activity shows a curious, nonmonotonic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)82988-6
更新日期:1988-09-01 00:00:00
abstract::The goal of this paper is to examine the origins and relative importance of primary and secondary sources of electric and magnetic fields for excitable tissue. It is shown that for axonal and cardiac tissue a comparison of the relative field strength from both primary and secondary sources shows only the latter to be ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84521-9
更新日期:1982-09-01 00:00:00
abstract::Missense mutations in the membrane-binding actin-based motor protein, myosin-1a (Myo1a), have recently been linked to sensorineural deafness in humans. One of these mutations, E385D, impacts a residue in the switch II region of the motor domain that is present in virtually all members of the myosin superfamily. We sou...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.107.122689
更新日期:2008-01-15 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::Multiple nanosecond duration molecular dynamics simulations were performed on the transmembrane region of the Torpedo nicotinic acetylcholine receptor embedded within a bilayer mimetic octane slab. The M2 helices and M2-M3 loop regions were free to move, whereas the outer (M1, M3, M4) helix bundle was backbone restrai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.052878
更新日期:2005-05-01 00:00:00
abstract::Primary embryonic chick cells have been evaluated on the basis of their capacity to repair photochemical lesions produced in the deoxyribonucleic acid (DNA) by ultraviolet (UV) radiation. The fate of one prominent class of UV photoproducts, cyclobutane pyrimidine dimers, was monitored by an in vitro enzymatic assay. U...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(74)85926-6
更新日期:1974-06-01 00:00:00
abstract::We report detection and quantification of ultraviolet (UV) damage in DNA at a single molecule level by atomic force microscopy (AFM). By combining the supercoiled plasmid relaxation assay with AFM imaging, we find that high doses of medium wave ultraviolet (UVB) and short wave ultraviolet (UVC) light not only produce ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.108209
更新日期:2007-09-01 00:00:00
abstract::A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000-000) has been used for computing the end-to-end distance distribut...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)74002-0
更新日期:1998-02-01 00:00:00
abstract::Variation in the amplitude of miniature postsynaptic currents (mPSCs) generated by individual quanta of neurotransmitter is a major contributor to the variance of evoked synaptic responses. Here we explore the possible origins of this variability by developing a mathematical description of mPSC generation and consider...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79325-6
更新日期:1996-09-01 00:00:00
abstract::We describe two enhancements of the planar bilayer recording method which enable low-noise recordings of single-channel currents activated by voltage steps in planar bilayers formed on apertures in partitions separating two open chambers. First, we have refined a simple and effective procedure for making small bilayer...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82376-6
更新日期:1990-08-01 00:00:00
abstract::The cytoskeletal activity of motile or adherent cells is frequently seen to induce detectable displacements of sufficiently compliant substrata. The physics of this phenomenon is discussed in terms of the classical theory of small-strain, plane-stress elasticity. The main results of such analysis is a transform expres...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79767-9
更新日期:1996-04-01 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
abstract::We have used admittance analysis together with the black lipid membrane technique to analyze electrogenic reactions within the Na(+) branch of the reaction cycle of the Na(+)/K(+)-ATPase. ATP release by flash photolysis of caged ATP induced changes in the admittance of the compound membrane system that are associated ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76496-4
更新日期:2000-11-01 00:00:00
abstract::This paper describes a new technique that can be used to study chloroplast volume regulation in vivo. Nuclear magnetic resonance spectroscopy was used to measure relative amounts of chloroplast water in Acer platanoides leaves as they dried in air, and also in leaf disks exposed to aqueous polyethylene glycol, sucrose...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81930-6
更新日期:1992-05-01 00:00:00
abstract::Membranes made of dimyristoylphosphatidylcholine and cholesterol, one of the simplest paradigms for the study of liquid ordered-disordered phase separation, were investigated using a pulse-EPR spin-labeling method in which bimolecular collision of molecular oxygen with the nitroxide spin label is measured. This method...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.097568
更新日期:2007-03-01 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::CLC anion channels are homodimeric proteins. Each subunit is comprised of 18 α-helices designated "A-R" and an intracellular carboxy-terminus containing two cystathionine-β-synthase (CBS1 and CBS2) domains. Conformational coupling between membrane and intracellular domains via poorly understood mechanisms is required ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.09.037
更新日期:2016-11-01 00:00:00
abstract::Bipolar tetraether lipids (BTLs) are abundant in crenarchaeota, which thrive in both thermophilic and nonthermophilic environments, with wide-ranging growth temperatures (4-108°C). BTL liposomes can serve as membrane models to explore the role of BTLs in the thermal stability of the plasma membrane of crenarchaeota. I...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.09.061
更新日期:2010-11-17 00:00:00
abstract::Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the re...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.02.018
更新日期:2020-05-05 00:00:00
abstract::Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.058677
更新日期:2005-08-01 00:00:00
abstract::Coat protein (COP) I and COP II complexes are involved in the transport of proteins between the endoplasmic reticulum and the Golgi apparatus in eukaryotic cells. The formation of COP I/II complexes at membrane surfaces is an early step in vesicle formation and is mastered by p24, a type I transmembrane protein. Oligo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.09.021
更新日期:2019-11-05 00:00:00