Abstract:
:We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Shell MS,Ozkan SB,Voelz V,Wu GA,Dill KAdoi
10.1016/j.bpj.2008.11.009subject
Has Abstractpub_date
2009-02-01 00:00:00pages
917-24issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(08)00446-3journal_volume
96pub_type
杂志文章abstract::Mechanosensitive ion channels (MSCs) which could provide for fast osmoregulatory responses in bacteria, remain unidentified as molecular entities. MSCs from Escherichia coli (strain AW740) were examined using the patch-clamp technique, either (a) in giant spheroplasts, (b) after reconstitution by fusing native membran...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81044-0
更新日期:1993-07-01 00:00:00
abstract::Cartilage stiffness was measured ex vivo at the micrometer and nanometer scales to explore structure-mechanical property relationships at smaller scales than has been done previously. A method was developed to measure the dynamic elastic modulus, |E(*)|, in compression by indentation-type atomic force microscopy (IT A...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74375-1
更新日期:2004-05-01 00:00:00
abstract::Lateral tension in cell plasma membranes plays an essential role in regulation of a number of membrane-related intracellular processes and cell motion. Understanding the physical factors generating the lateral tension and quantitative determination of the tension distribution along the cell membrane is an emerging top...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.11.009
更新日期:2014-01-07 00:00:00
abstract::We present a molecular model of a chromatophore vesicle from Rhodobacter sphaeroides. These vesicles are ideal benchmark systems for molecular and systemic simulations, because they have been well studied, they are small, and they are naturally separated from their cellular environment. To set up a photosynthetic chai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.067561
更新日期:2006-08-01 00:00:00
abstract::The reaction of c-cytochromes with iron hexacyanides is similar in mechanism to the interaction of cytochromes with their physiological oxidants and reductants in that the formation of complexes precedes electron transfer. Analysis of the kinetics of oxidation and reduction of a number of c-cytochromes by solving the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84754-6
更新日期:1981-12-01 00:00:00
abstract::Segmentation of the Drosophila melanogaster embryo results from the dynamic establishment of spatial mRNA and protein patterns. Here, we exploit recent temporal mRNA and protein expression measurements on the full surface of the blastoderm to calibrate a dynamical model of the gap gene network on the entire embryo cor...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.060
更新日期:2011-07-20 00:00:00
abstract::Steady-state and time-resolved fluorescence spectroscopy was used to follow the local and global changes in structure and dynamics during chemical and thermal denaturation of unlabeled human serum albumin (HSA) and HSA with an acrylodan moiety bound to Cys34. Acrylodan fluorescence was monitored to obtain information ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77598-8
更新日期:1998-08-01 00:00:00
abstract::Rhodobacter sphaeroides can swim toward a wide range of attractants (a process known as taxis), propelled by a single rotating flagellum. The reversals of motor direction that cause tumbles in Eschericia coli taxis are replaced by brief motor stops, and taxis is controlled by a complex sensory system with multiple hom...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76678-1
更新日期:2000-03-01 00:00:00
abstract::Coarse-grained molecular dynamics simulations are applied to explore the experimentally observed ability of the liquid-ordered (lo)/liquid-disordered (ld) phase boundary to facilitate viral membrane fusion. Surprisingly, a formed fusion stalk can be both attracted (i.e., stalkophilic) and repelled (i.e., stalkophobic)...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2017.04.031
更新日期:2017-06-20 00:00:00
abstract::L-type (alpha(1C)) calcium channels inactivate rapidly in response to localized elevation of intracellular Ca(2+), providing negative Ca(2+) feedback in a diverse array of biological contexts. The dominant Ca(2+) sensor for such Ca(2+)-dependent inactivation has recently been identified as calmodulin, which appears to...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76739-7
更新日期:2000-04-01 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::Protein kinases are key players in signal transduction pathways where they are crafted into two functional states. In response to growth factor binding stimulus, epidermal growth factor receptor (EGFR), which is physiologically populated in an autoinhibited inactive state, becomes active. Here, we outline a simple all...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2019.05.021
更新日期:2019-07-09 00:00:00
abstract::Some plant leaves display complex, orientation-dependent, proton nuclear magnetic resonance (1H NMR) spectra. The spectral patterns vary as the angle between the leaf surface and the applied magnetic field is varied. They also vary with temperature and with the quantity of absorbed manganous ions, but they are indepen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83826-1
更新日期:1985-11-01 00:00:00
abstract::In rat mesenteric arteries, smooth muscle cells exhibit intercellular calcium waves in response to local phenylephrine stimulation. These waves have a velocity of approximately 20 cells/s and a range of approximately 80 cells. We analyze these waves in a theoretical model of a population of coupled smooth muscle cells...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.04.031
更新日期:2010-07-21 00:00:00
abstract::We present a theoretical model for aqueous solutions of double-stranded (ds) DNA with explicit consideration of electrostatic interactions, excluded-volume effects, van der Waals attractions, and salt ions. With reasonable parameters estimated from the DNA structure and experimental data for electrolytes, we are able ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.112508
更新日期:2008-02-01 00:00:00
abstract::We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacolo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.11.009
更新日期:2010-12-15 00:00:00
abstract::Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.051169
更新日期:2005-02-01 00:00:00
abstract::The pore-forming alpha 1 subunit of L-type calcium (Ca2+) channels is the molecular target of Ca2+ channel blockers such as phenylalkylamines (PAAs). Association and dissociation rates of (-)devapamil were compared for a highly PAA-sensitive L-type Ca2+ channel chimera (Lh) and various class A Ca2+ channel mutants. Th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78056-1
更新日期:1997-07-01 00:00:00
abstract::The reported rates of thermal 13-cis to all-trans isomerization of the protonated Schiff base of retinal (PSBR) in solution and in bacteriorhodopsin (BR) are shown to be correlated with the red shift in the absorption maximum of the chromophore, though the linear fit is different for BR and for a model PSBR in solutio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82070-7
更新日期:1991-08-01 00:00:00
abstract::Actin dynamics is important in determining cell shape, tension, and migration. Methods such as fluorescent speckle microscopy and spatial temporal image correlation spectroscopy have been used to capture high-resolution actin turnover dynamics within cells in two dimensions. However, these methods are not directly app...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.07.057
更新日期:2013-10-15 00:00:00
abstract::We find evidence for a direct transition of insulin monomers into amyloid fibrils without measurable concentrations of oligomers or protofibrils, suggesting that fibrillogenesis may occur directly from assembly of denaturing insulin monomers rather than by successive transitions through protofibril nuclei. To support ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.10.010
更新日期:2010-12-15 00:00:00
abstract::The molecular basis of the activation of G-proteins by the G-protein coupled receptor for parathyroid hormone (PTH) is unknown. Employing a combination of NMR methods and computer-based structural refinement, structural features involved in the activation of Galpha(s) by the PTH receptor (PTH1R) have been determined. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.094813
更新日期:2007-01-15 00:00:00
abstract::The cardiac muscle protein titin, responsible for developing passive elasticity and extensibility of muscle, possesses about 40 immunoglobulin-like (Ig) domains in its I-band region. Atomic force microscopy (AFM) and steered molecular dynamics (SMD) have been successfully combined to investigate the reversible unfoldi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75343-5
更新日期:2002-12-01 00:00:00
abstract::Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.05.001
更新日期:2015-06-16 00:00:00
abstract::A mean-field statistical mechanical theory has been developed to describe molecular distributions in interphases. The excluded volume interaction has been modeled in terms of a reversible work that is required to create a cavity of the solute size against a pressure tensor exerted by the surrounding interphase molecul...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(94)80833-1
更新日期:1994-03-01 00:00:00
abstract::Sarcoplasmic reticulum (SR) Ca2+ ATPase was derivatized with 4,4'-diisothiocyanatostilbene-2,2'-sulfonic acid (DIDS), and complete enzyme inactivation was produced with a molecular stoichiometry of one DIDS per ATPase. It was determined by peptide analysis and sequencing that Lys492 and Lys515 were the ATPase residues...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78245-6
更新日期:1997-10-01 00:00:00
abstract::A new method for measuring the mechanical forces exerted by cells on the substratum and through the substratum to act on other cells is described. This method depends upon the growth of cells on a photoelastic substratum, polydimethylsiloxane coated with a near monolayer of fibronectin. Changes in the forces applied b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.088849
更新日期:2007-03-15 00:00:00
abstract::The hydrophobic surfactant proteins, SP-B and SP-C, greatly accelerate the adsorption of the surfactant lipids to an air/water interface. Previous studies of factors that affect curvature suggest that vesicles may adsorb via a rate-limiting structure with prominent negative curvature, in which the hydrophilic face of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.12.041
更新日期:2013-02-05 00:00:00
abstract::Quantitative characterization of protein interactions under physiological conditions is vital for systems biology. Fluorescence photobleaching/activation experiments of GFP-tagged proteins are frequently used for this purpose, but robust analysis methods to extract physicochemical parameters from such data are lacking...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.071241
更新日期:2006-03-15 00:00:00
abstract::Xenopus oocytes are widely employed for heterologous expression of cloned proteins, particularly electrogenic molecules such as ion channels and transporters. The high levels of expression readily obtained permit detailed investigations without interference from endogenous conductances. Injection of min K mRNA into Xe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79964-7
更新日期:1995-09-01 00:00:00