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Accuracy in Predicting Secondary Structure of Ionic Channels [chapter]

Bogumil Konopka, Witold Dyrka, Jean-Christophe Nebel, Malgorzata Kotulska
2009 Studies in Computational Intelligence  
Prediction quality showed dependence on the ratio of secondary structures in the ionic channel.  ...  In the paper, prediction quality of ionic channel secondary structure is evaluated. The tests were carried out with general protein predictors and predictors only for transmembrane segments.  ...  This work was in part supported by Erasmus grant for B.K. and Young Scientist grants of Wroclaw University of Technology and of British Council Programme (WAR/342/108) for W.D.  ... 
doi:10.1007/978-3-642-03958-4_27 fatcat:3t2xcg2tpbfknc4sjxgpe66hwa

Predictions Suggesting a Participation of β-Sheet Configuration in the M2 Domain of the P2X7 Receptor: A Novel Conformation?

Pedro Celso Nogueira Teixeira, Cristina Alves Magalhães de Souza, Mônica Santos de Freitas, Débora Foguel, Ernesto Raul Caffarena, Luiz Anastacio Alves
2009 Biophysical Journal  
However, none has identified an a-helix structure, the paradigmatic secondary structure of ion channels in mammalian cells.  ...  Thus, we investigated the hydrophobic M2 domain with the aim of predicting the fitted position and the secondary structure of the TM2 segment from human P2X 7 R (hP2X 7 R).  ...  Each program is rated in % accuracy (1). (-) represents negative prediction.  ... 
doi:10.1016/j.bpj.2008.10.043 pmid:19186133 pmcid:PMC2716642 fatcat:g3nh2tit2rd6hleajdil3kywdi

Identification of a Tetramerization Domain in the C Terminus of the Vanilloid Receptor

N. Garcia-Sanz
2004 Journal of Neuroscience  
Together, these findings are consistent with the tenet that the TRP-like domain in TRPV1 is a molecular determinant of the tetramerization of receptor subunits into functional channels.  ...  Structurally, TRPV1 appears to be a tetramer formed by the assembly of four identical subunits around a central aqueous pore.  ...  Secondary structure prediction was performed by the consensus secondary structure prediction method ( B, Coiled-coil prediction of the C terminus of TRPV1.  ... 
doi:10.1523/jneurosci.0202-04.2004 pmid:15190102 fatcat:y4525swrijfydnixk5d5ui576u

Structure-function of cyanobacterial outer-membrane protein, Slr1270: Homolog ofEscherichia colidrug export/colicin import protein, TolC

Rachna Agarwal, Stanislav Zakharov, S. Saif Hasan, Christopher M. Ryan, Julian P. Whitelegge, William A. Cramer
2014 FEBS Letters  
Refolded Slr1270 displays a single band in native-electrophoresis, has an a-helical content of 50-60%, as in E. coli TolC with which it has significant secondary-structure similarity, and an ion-channel  ...  The pH-dependence of channel conductance implies a role for carboxylate residues in channel gating, analogous to that in TolC.  ...  Notably, the helical content of $50-60% is similar to that of $57% in the predicted secondary structure (Supplementary Fig. S1 ).  ... 
doi:10.1016/j.febslet.2014.08.028 pmid:25218435 pmcid:PMC4288923 fatcat:jppjvepcrvb6vahnljjvbvzpz4

Computational modeling of membrane proteins

Julia Koehler Leman, Martin B. Ulmschneider, Jeffrey J. Gray
2014 Proteins: Structure, Function, and Bioinformatics  
In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology.  ...  Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed.  ...  (TMPred) and prediction of protein secondary structure (SSPred).  ... 
doi:10.1002/prot.24703 pmid:25355688 pmcid:PMC4270820 fatcat:lk7ku2koqnfi5axp7luxq6e44e

CAVD, towards better characterization of void space for ionic transport analysis

Bing He, Anjiang Ye, Shuting Chi, Penghui Mi, Yunbing Ran, Liwen Zhang, Xinxin Zou, Bowei Pu, Qian Zhao, Zheyi Zou, Da Wang, Wenqing Zhang (+3 others)
2020 Scientific Data  
Its effectiveness is demonstrated by 99% recovery rate for the lattice sites of mobile ions in 6,955 Li-, Na-, Mg- and Al-containing ionic compounds extracted from the Inorganic Crystal Structure Database  ...  Geometric crystal structure analysis using three-dimensional Voronoi tessellation provides intuitive insights into the ionic transport behavior of metal-ion electrode materials or solid electrolytes by  ...  structure prediction possible 85 .  ... 
doi:10.1038/s41597-020-0491-x pmid:32444597 fatcat:tc7bd3niozfbhd6karhxoxv7wu

An Alternative Approach to Protein Folding

Yeona Kang, Charles M. Fortmann
2013 BioMed Research International  
The drift-diffusion model predicted tertiary structures with RMSD values in the 3–5 Angstroms range for proteins ranging 30 to 150 amino acids.  ...  Greater than 70% of the secondary core structures with over 80% alpha helices were correctly identified on protein ranging from 30 to 200 amino-acid sequence.  ...  The kinetic model demonstrated state-of-the-art accuracy in overall secondary structure prediction and excellent alpha helix prediction.  ... 
doi:10.1155/2013/583045 pmid:24078920 pmcid:PMC3775432 fatcat:rveh72vkzzbb7kadr6j6fgz75u

Candidate structures for inorganic lithium solid-state electrolytes identified by high-throughput bond-valence calculations

Ruijuan Xiao, Hong Li, Liquan Chen
2015 Journal of Materiomics  
The promising structures are selected to be further optimized in the future.  ...  As an important prerequisite for developing all-solid-state lithium secondary batteries, the materials with high lithium ionic conductivity and inhibited electronic conductivity must be found.  ...  Acknowledgment We acknowledge the National Natural Science Foundation of China (Grant Nos. 11234013 and 51172274), "863" Project (Grant No. 2015AA034201), and Beijing S&T Project (Grant No.  ... 
doi:10.1016/j.jmat.2015.08.001 fatcat:u2ncxomlwrhh5adlvftslucctm

Multiscale modelling of saliva secretion

James Sneyd, Edmund Crampin, David Yule
2014 Mathematical Biosciences  
relative unimportance of acinar spatial structure for isotonic water transport, (vi) the prediction that duct cells are highly depolarised, (vii) the prediction that the secondary saliva takes at least  ...  need for the periodic Ca 2+ waves to be as fast as possible in order to maximise water transport, (iv) the presence of functional K + channels in the apical membrane increases saliva secretion, (v) the  ...  channels are situated in the apical membrane. • We predict that saliva secretion is most efficient in the isoosmotic regime. • Acinar spatial structure might be unimportant.  ... 
doi:10.1016/j.mbs.2014.06.017 pmid:25014770 pmcid:PMC4252247 fatcat:wf645ugnqrbi3eufsj6ir4eog4

Dissociation Energies of Silicon Clusters: A Depth Gauge for the Global Minimum on the Potential Energy Surface

Alexandre A. Shvartsburg, Martin F. Jarrold, Bei Liu, Zhong-Yi Lu, Cai-Zhuang Wang, Kai-Ming Ho
1998 Physical Review Letters  
We have modeled the dissociation of Si n neutrals and cations in the n # 26 range.  ...  This indicates that our search of configuration space for the silicon clusters in this size range has indeed found the global minima -a family of "stacked Si 9 tricapped trigonal prisms."  ...  Ionic mobilities calculated for the stacked TTP structures are in good agreement with the values for Si n cations in helium [3, 4] .  ... 
doi:10.1103/physrevlett.81.4616 fatcat:ohn6svkshvhuni62do75soq5te

Electrical Characteristics and Electrohydrodynamic Flows in Electrostatic Precipitator of Six Shaped Discharge Electrodes

2020 Journal of Applied Fluid Mechanics  
For the high inlet velocity, the local recirculation and high turbulence by the secondary flow near the collecting plate in the all six channels disappear but still remain in the downstream of the discharge  ...  electrodes, and the airflow in the central region of the six channels would be accelerated.  ...  APPENDIX Supplementary UDF code regarding the interaction between the gas flow and the electric field was used for the simulations accompanies this paper, and is available for download from the Journal of  ... 
doi:10.36884/jafm.13.06.31085 fatcat:b6smmsqwcnfhpaonhtpwuxgrle

Human In Silico Drug Trials Demonstrate Higher Accuracy than Animal Models in Predicting Clinical Pro-Arrhythmic Cardiotoxicity

Elisa Passini, Oliver J. Britton, Hua Rong Lu, Jutta Rohrbacher, An N. Hermans, David J. Gallacher, Robert J. H. Greig, Alfonso Bueno-Orovio, Blanca Rodriguez
2017 Frontiers in Physiology  
Our results demonstrate that human in silico drug trials constitute a powerful methodology for prediction of clinical pro-arrhythmic cardiotoxicity, ready for integration in the existing drug safety assessment  ...  Integrative Physiology, a section of the journal Frontiers in Physiology upstroke velocity captures variations in rabbit QRS complex.  ...  Early prediction of cardiotoxicity is critical for drug development. Current animal models raise ethical and translational questions, and have limited accuracy in clinical risk prediction.  ... 
doi:10.3389/fphys.2017.00668 pmid:28955244 pmcid:PMC5601077 fatcat:dm2ftk655rcrjpgvhfwshcc7ya

Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types [article]

Jingqi Q. X. Gong, Eric A. Sobie
2017 bioRxiv   pre-print
We found that quantitatively accurate predictions of responses to selective or non-selective drugs could be generated based on iPSC-CM responses and that the method can be extended to predict drug responses  ...  We addressed this issue, in the context of cardiac electrophysiology, through mechanistic mathematical modeling combined with statistical analyses.  ...  Quantification of these effects in Fig. 7E verifies the accuracy 192 .  ... 
doi:10.1101/176321 fatcat:plg5wf5uazbs3eqigxkk2l33hq

Improved Secondary Structure Predictions for a Nicotinic Receptor Subunit: Incorporation of Solvent Accessibility and Experimental Data into a Two-Dimensional Representation

Nicolas Le Novère, Pierre-Jean Corringer, Jean-Pierre Changeux
1999 Biophysical Journal  
A refined prediction of the nicotinic acetylcholine receptor (nAChR) subunits' secondary structure was computed with third-generation algorithms.  ...  This led to a proposed twodimensional representation of the secondary structure in which the peptide chain of the extracellular domain winds alternatively between the two interfaces of the subunit.  ...  We thank Marc Delarue, Stuart Edelstein, and Clément Léna for critical reading of the manuscript, and Burkhard Rost for his comments.  ... 
doi:10.1016/s0006-3495(99)77390-x pmid:10233052 pmcid:PMC1300207 fatcat:anfxpte2zzg5xophljw33qu5si

Electrostatics of Nanoparticle–Wall Interactions within Nanochannels: Role of Double-Layer Structure and Ion–Ion Correlations

Inderbir S. Sidhu, Amalie L. Frischknecht, Paul J. Atzberger
2018 ACS Omega  
We find there are energy barriers and energy minima giving preferred nanoparticle locations in the channel near the center and at a distance near to but separated from the channel walls.  ...  We discuss the implications of our results for phenomena in nanoscale devices.  ...  Ionic Double-Layer Structure: BD Simulations. Typical distributions for the counterions and coions as the nanoparticle position is varied in the case of σ = −6 and C m = 8 are shown in Figure 2 .  ... 
doi:10.1021/acsomega.8b01393 pmid:31459242 pmcid:PMC6644950 fatcat:7rkbw4f3irgx5lvolu65taaqqm
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