Abstract:
:A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing distinct structural motifs, alpha-helical polyalanine and the beta-hairpin V(5)PGV(5). These studies represent the first known application of this approach to peptide systems. Good agreement between the MS-CG and atomistic models is achieved for several structural properties including radial distribution functions, root mean-square deviation, and radius of gyration. The new MS-CG models are able to preserve the native states of these peptides within approximately 1 A backbone root mean-square deviation during CG simulations. The MS-CG approach, as with most coarse-grained models, has the potential to increase the length and timescales accessible to molecular simulations. However, it is also able to maintain a clear connection to the underlying atomistic-scale interactions.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Zhou J,Thorpe IF,Izvekov S,Voth GAdoi
10.1529/biophysj.106.094425subject
Has Abstractpub_date
2007-06-15 00:00:00pages
4289-303issue
12eissn
0006-3495issn
1542-0086pii
S0006-3495(07)71230-4journal_volume
92pub_type
杂志文章abstract::Analysis of trajectories of dynamical biological objects, such as breeding ants or cell organelles, is essential to reveal the interactions they develop with their environments. Many previous works used a global characterization based on parameters calculated for entire trajectories. In cases where transient behavior ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.080622
更新日期:2006-11-01 00:00:00
abstract::Each gating mechanism controlling permeability in a membrane may be influenced by only a few charge binding sites on the membrane surface, so that fluctuations in the occupancy of these sites are important. Tow extreme cases arise. (a) The time scale of these fluctuations is much shorter than the gating time constant....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85426-5
更新日期:1978-12-01 00:00:00
abstract::We elucidate the physics of protein dynamical transition via 10-100-ns molecular dynamics simulations at temperatures spanning 160-300 K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a crossover from nonstationary to stationary processes that underlie the dynamics of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.07.036
更新日期:2009-10-07 00:00:00
abstract::Stearoylsphingomyelin (SSM) bilayers containing 0, 22, and 50 mol % cholesterol (Chol) and a pentadecanoyl-stearoylphosphatidylcholine (15SPC) bilayer containing 22 mol % Chol were molecular dynamics simulated at two temperatures (37 degrees C and 60 degrees C). 15SPC is the best PC equivalent of SSM. The Chol effect ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.080887
更新日期:2006-11-15 00:00:00
abstract::The size of a cell is central to many functions, including cellular communication and exchange of materials with the environment. This modeling and experimental study focused on understanding how the size of a cell determines its ability to uptake nanometer-scale extracellular materials from the environment. Several m...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.11.3134
更新日期:2019-01-22 00:00:00
abstract::Cardiac transverse (T)-tubules provide a specialized structure for synchronization and stabilization of sarcoplasmic reticulum Ca(2+) release in healthy cardiomyocytes. The application of laser scanning confocal microscopy and the use of fluorescent lipophilic membrane dyes have boosted the discoveries that T-tubule r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.05.013
更新日期:2014-06-17 00:00:00
abstract::The quantitation of human granulocyte movement using a stochastic differential equation is described. The method has the potential to distinguish both positive and negative chemotaxis. Analysis and information concerning cell movements can be obtained for any point in time and distance for the duration of the experime...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(76)85685-8
更新日期:1976-03-01 00:00:00
abstract::It is known that the action of general anesthetics is proportional to their partition coefficient in lipid membranes (Meyer-Overton rule). This solubility is, however, directly related to the depression of the temperature of the melting transition found close to body temperature in biomembranes. We propose a thermodyn...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.099754
更新日期:2007-05-01 00:00:00
abstract::Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vector...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.04.018
更新日期:2018-06-05 00:00:00
abstract::In a cell-populated collagen gel, intrinsic fiber structure visible in differential interference contrast images can provide markers for an in situ strain gauge to quantify cell-gel mechanics, while optical sections of fluorescent protein distribution capture cytoskeletal kinematics. Mechanics quantification can be de...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(03)75077-2
更新日期:2003-04-01 00:00:00
abstract::The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are el...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.105.078154
更新日期:2006-02-15 00:00:00
abstract::Detection of specific nucleic acid sequences is invaluable in biological studies such as genetic disease diagnostics and genome profiling. Here, we developed a highly sensitive and specific detection method that combines an advanced oligonucleotide ligation assay with multicolor single-molecule fluorescence. We demons...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.08.013
更新日期:2018-09-18 00:00:00
abstract::Most of the important types of interactions that occur in cells can be characterized as binding-diffusion type processes, and can be quantified by kinetic rate constants such as diffusion coefficients (D) and binding rate constants (k(on) and k(off)). Confocal FRAP is a potentially important tool for the quantitative ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.09.013
更新日期:2010-11-03 00:00:00
abstract::Cationic antimicrobial cationic peptides (CAMP) have been found in recent years to play a decisive role in hosts' defense against microbial infection. They have also been investigated as a new therapeutic tool, necessary in particular due to the increasing resistance of microbiological populations to antibiotics. The ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.095711
更新日期:2007-04-15 00:00:00
abstract::We present a quantitative analysis of conformational changes of the nucleotide-binding subunits, MalK(2), of the maltose ATP-binding cassette importer MalFGK(2) during the transport cycle. Distance changes occurring between selected residues were monitored in the full transporter by site-directed spin-labeling electro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.132456
更新日期:2008-09-15 00:00:00
abstract::The general theory (Levitt, D. G. 1990. Biophys. J. 59:271-277) is applied to a model channel that resembles the acetylcholine receptor channel (ACH). The model incorporates the known features of the ACH geometry and fixed charge locations. The channel has a wide mouth facing the outer solution, tapering to a narrow r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82221-4
更新日期:1991-02-01 00:00:00
abstract::We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm for choosing a probe set with high specificity for targeted genes under equilibrium conditions. The algorithm as well as ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74837-1
更新日期:2003-01-01 00:00:00
abstract::An equation is derived, which connects two functions P(r) and g(x), the first being related to the scattering intensity by a simple transformation, the second to the elctron density distribution of a spherically symmetric structure. This relation seems to be a suitable starting point for an analysis of shell structure...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(74)85910-2
更新日期:1974-03-01 00:00:00
abstract::Experimental studies have recently demonstrated that fluorescence emission can be quenched by laser light pulses from modern high repetition rate lasers, a phenomenon we call "light quenching." We now describe the theory of light quenching and some of its effects on the steady-state and time-resolved intensity and ani...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80686-1
更新日期:1994-11-01 00:00:00
abstract::For many cell types, growth, differentiation, and motility are dependent on receptor-mediated adhesion to ligand-coated surfaces. Focal contacts are strong, specialized, adhesive connections between cell and substrate in which receptors aggregate and connect extracellular ligand to intracellular cytoskeletal molecules...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81456-5
更新日期:1993-03-01 00:00:00
abstract::Both the solution and the oriented film absorption and circular dichroic spectra of the bacteriorhodopsin (bR(568)) and M(412) intermediate of the purple membrane photocycle were compared over the wavelength region 800-183 nm to assess structural changes during this photocycle. The main findings are (a) loss of the ex...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83943-6
更新日期:1985-04-01 00:00:00
abstract::Xenopus oocytes express mechanosensitive (MS(XO)) channels that can be studied in excised patches of membrane with the patch-clamp technique. This study examines the steady-state kinetic gating properties of MS(XO) channels using detailed single-channel analysis. The open and closed one-dimensional dwell-time distribu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75857-2
更新日期:2001-10-01 00:00:00
abstract::The interpretation of phi-values has led to an understanding of the folding transition state ensemble of a variety of proteins. Although the main guidelines and equations for calculating phi are well established, there remains some controversy about the quality of the numerical values obtained. By analyzing a complete...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.113241
更新日期:2008-06-01 00:00:00
abstract::We provide evidence that the onset of functional dynamics of folded proteins with elevated temperatures is associated with the effective sampling of its energy landscape under physiological conditions. The analysis is based on data describing the relaxation phenomena governing the backbone dynamics of bovine pancreati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.050252
更新日期:2005-03-01 00:00:00
abstract::We investigate the conditions under which nonideality in solution influences the Donnan equilibrium. Of the various parameters that characterize this equilibrium, the osmotic pressure established across the Donnan membrane is found to be particularly sensitive to intermolecular interactions between the diffusible and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83526-3
更新日期:1986-11-01 00:00:00
abstract::Voltage-sensing dyes and voltage-sensing fluorescence proteins have been continually improved and as a result have provided a wealth of insights into neuronal circuits. Further improvements in voltage-sensing dyes and voltage-sensing fluorescence proteins are needed, however, for routine detection of single action pot...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.12.047
更新日期:2017-02-28 00:00:00
abstract::The Green's function technique is applied to a study of breathing modes in a DNA double helix which contains a region of different base pairs from the rest of the double helix. The calculation is performed on a G-C helix in the B conformation with four consecutive base pairs replaced by A-T. The average stretch in hyd...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82570-4
更新日期:1990-03-01 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::We have obtained clear evidence for the flexibility of native scallop adductor thin filaments by studying the temperature and ionic strength dependence of the average decay constants obtained from intensity fluctuation spectroscopic (IFS) measurements. The low-angle (10-25 degrees ), average decay constants obtained f...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85116-2
更新日期:1980-01-01 00:00:00
abstract::Biological spread cells exist in a perpetually fluctuating state and therefore cannot be described in terms of a unique deterministic system. For modeling approaches to provide novel insight and uncover new mechanisms that drive cell behavior, a framework is required that progresses from traditional deterministic meth...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.11.007
更新日期:2018-12-18 00:00:00