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Items: 1 to 50 of 89

1.

The Pore-Lipid Interface: Role of Amino-Acid Determinants of Lipophilic Access by Ivabradine to the hERG1 Pore Domain.

Perissinotti L, Guo J, Kudaibergenova M, Lees-Miller J, Ol'khovich M, Sharapova A, Perlovich GL, Muruve DA, Gerull B, Noskov SY, Duff HJ.

Mol Pharmacol. 2019 Aug;96(2):259-271. doi: 10.1124/mol.118.115642. Epub 2019 Jun 10.

PMID:
31182542
2.

Editorial.

Noskov SY, Yarov-Yarovoy V.

Neurosci Lett. 2019 May 1;700:1-2. doi: 10.1016/j.neulet.2019.02.040. Epub 2019 Feb 26. No abstract available.

PMID:
30822438
3.

Emerging Diversity in Lipid-Protein Interactions.

Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP.

Chem Rev. 2019 May 8;119(9):5775-5848. doi: 10.1021/acs.chemrev.8b00451. Epub 2019 Feb 13.

4.

Structure of voltage-dependent anion channel-tethered bilayer lipid membranes determined using neutron reflectivity.

Hoogerheide DP, Noskov SY, Kuszak AJ, Buchanan SK, Rostovtseva TK, Nanda H.

Acta Crystallogr D Struct Biol. 2018 Dec 1;74(Pt 12):1219-1232. doi: 10.1107/S2059798318011749. Epub 2018 Nov 30.

PMID:
30605136
5.

Molecular Mechanism of Conductance Enhancement in Narrow Cation-Selective Membrane Channels.

Miranda WE, Ngo VA, Wang R, Zhang L, Chen SRW, Noskov SY.

J Phys Chem Lett. 2018 Jun 21;9(12):3497-3502. doi: 10.1021/acs.jpclett.8b01005. Epub 2018 Jun 13.

PMID:
29886737
6.

Performance of Machine Learning Algorithms for Qualitative and Quantitative Prediction Drug Blockade of hERG1 channel.

Wacker S, Noskov SY.

Comput Toxicol. 2018 May;6:55-63. doi: 10.1016/j.comtox.2017.05.001. Epub 2017 May 13.

7.

Lipid roles in hERG function and interactions with drugs.

Kudaibergenova M, Perissinotti LL, Noskov SY.

Neurosci Lett. 2019 May 1;700:70-77. doi: 10.1016/j.neulet.2018.05.019. Epub 2018 May 27. Review.

PMID:
29758301
8.

Determinants of Isoform-Specific Gating Kinetics of hERG1 Channel: Combined Experimental and Simulation Study.

Perissinotti LL, De Biase PM, Guo J, Yang PC, Lee MC, Clancy CE, Duff HJ, Noskov SY.

Front Physiol. 2018 Apr 12;9:207. doi: 10.3389/fphys.2018.00207. eCollection 2018.

9.

Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations.

DeMarco KR, Bekker S, Clancy CE, Noskov SY, Vorobyov I.

Front Pharmacol. 2018 Feb 1;9:26. doi: 10.3389/fphar.2018.00026. eCollection 2018.

10.

Computational membrane biophysics: From ion channel interactions with drugs to cellular function.

Miranda WE, Ngo VA, Perissinotti LL, Noskov SY.

Biochim Biophys Acta Proteins Proteom. 2017 Nov;1865(11 Pt B):1643-1653. doi: 10.1016/j.bbapap.2017.08.008. Epub 2017 Aug 26. Review.

11.

A multiscale computational modelling approach predicts mechanisms of female sex risk in the setting of arousal-induced arrhythmias.

Yang PC, Perissinotti LL, López-Redondo F, Wang Y, DeMarco KR, Jeng MT, Vorobyov I, Harvey RD, Kurokawa J, Noskov SY, Clancy CE.

J Physiol. 2017 Jul 15;595(14):4695-4723. doi: 10.1113/JP273142. Epub 2017 Jun 14.

12.

First universal pharmacophore model for hERG1 K+ channel activators: acthER.

Durdagi S, Erol I, Salmas RE, Patterson M, Noskov SY.

J Mol Graph Model. 2017 Jun;74:153-170. doi: 10.1016/j.jmgm.2017.03.020. Epub 2017 Apr 5.

PMID:
28499268
13.

Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptors.

Ngo VA, Perissinotti LL, Miranda W, Chen SRW, Noskov SY.

Biophys J. 2017 Apr 25;112(8):1645-1653. doi: 10.1016/j.bpj.2017.03.014.

14.

Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes.

Hoogerheide DP, Noskov SY, Jacobs D, Bergdoll L, Silin V, Worcester DL, Abramson J, Nanda H, Rostovtseva TK, Bezrukov SM.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):E3622-E3631. doi: 10.1073/pnas.1619806114. Epub 2017 Apr 18.

15.

Computational Models for Understanding of Structure, Function and Pharmacology of the Cardiac Potassium Channel Kv11.1 (hERG).

Wacker S, Noskov SY, Perissinotti LL.

Curr Top Med Chem. 2017;17(23):2681-2702. doi: 10.2174/1568026617666170414143430. Review.

PMID:
28413954
16.

Characterization of the Cation Binding Sites in the NCKX2 Na+/Ca2+-K+ Exchanger.

Zhekova H, Zhao C, Schnetkamp PP, Noskov SY.

Biochemistry. 2016 Nov 22;55(46):6445-6455. Epub 2016 Nov 10.

PMID:
27805378
17.

Role of the pH in state-dependent blockade of hERG currents.

Wang Y, Guo J, Perissinotti LL, Lees-Miller J, Teng G, Durdagi S, Duff HJ, Noskov SY.

Sci Rep. 2016 Oct 12;6:32536. doi: 10.1038/srep32536.

18.

Molecular mechanism of Zn2+ inhibition of a voltage-gated proton channel.

Qiu F, Chamberlin A, Watkins BM, Ionescu A, Perez ME, Barro-Soria R, González C, Noskov SY, Larsson HP.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):E5962-E5971. Epub 2016 Sep 19.

19.

Improved QM/MM Linear-Interaction Energy Model for Substrate Recognition in Zinc-Containing Metalloenzymes.

Miranda WE, Ngo VA, Valiente PA, Noskov SY.

J Phys Chem B. 2016 Aug 18;120(32):7824-35. doi: 10.1021/acs.jpcb.6b05628. Epub 2016 Aug 4.

PMID:
27448039
20.

What controls open-pore and residual currents in the first sensing zone of alpha-hemolysin nanopore? Combined experimental and theoretical study.

De Biase PM, Ervin EN, Pal P, Samoylova O, Markosyan S, Keehan MG, Barrall GA, Noskov SY.

Nanoscale. 2016 Jun 2;8(22):11571-9. doi: 10.1039/c6nr00164e.

PMID:
27210516
21.

BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms.

Solano CJ, Pothula KR, Prajapati JD, De Biase PM, Noskov SY, Kleinekathöfer U.

J Chem Theory Comput. 2016 May 10;12(5):2401-17. doi: 10.1021/acs.jctc.5b01196. Epub 2016 Apr 28.

PMID:
27088446
22.

Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC).

Noskov SY, Rostovtseva TK, Chamberlin AC, Teijido O, Jiang W, Bezrukov SM.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1778-90. doi: 10.1016/j.bbamem.2016.02.026. Epub 2016 Mar 3. Review.

23.

Estimation of Potentials of Mean Force from Nonequilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method.

Ngo VA, Kim I, Allen TW, Noskov SY.

J Chem Theory Comput. 2016 Mar 8;12(3):1000-10. doi: 10.1021/acs.jctc.5b01050. Epub 2016 Feb 10.

PMID:
26799775
24.

LiCl solvation in N-methyl-acetamide (NMA) as a model for understanding Li(+) binding to an amide plane.

Manin N, da Silva MC, Zdravkovic I, Eliseeva O, Dyshin A, Yaşar O, Salahub DR, Kolker AM, Kiselev MG, Noskov SY.

Phys Chem Chem Phys. 2016 Feb 7;18(5):4191-200. doi: 10.1039/c5cp04847h.

PMID:
26784370
25.

K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Na(v) Channels.

Ngo V, Wang Y, Haas S, Noskov SY, Farley RA.

PLoS Comput Biol. 2016 Jan 4;12(1):e1004482. doi: 10.1371/journal.pcbi.1004482. eCollection 2016 Jan.

26.

Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra.

Singh G, Chamberlin AC, Zhekova HR, Noskov SY, Tieleman DP.

J Chem Theory Comput. 2016 Jan 12;12(1):364-71. doi: 10.1021/acs.jctc.5b00520. Epub 2015 Dec 4.

PMID:
26579726
27.

Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins.

Ngo V, da Silva MC, Kubillus M, Li H, Roux B, Elstner M, Cui Q, Salahub DR, Noskov SY.

J Chem Theory Comput. 2015 Oct 13;11(10):4992-5001. doi: 10.1021/acs.jctc.5b00524. Epub 2015 Oct 5.

28.

In silico prediction of drug therapy in catecholaminergic polymorphic ventricular tachycardia.

Yang PC, Moreno JD, Miyake CY, Vaughn-Behrens SB, Jeng MT, Grandi E, Wehrens XH, Noskov SY, Clancy CE.

J Physiol. 2016 Feb 1;594(3):567-93. doi: 10.1113/JP271282. Epub 2015 Dec 30.

29.

Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors.

Salmas RE, Mestanoglu M, Yurtsever M, Noskov SY, Durdagi S.

Biophys J. 2015 Sep 15;109(6):1163-8. doi: 10.1016/j.bpj.2015.08.001. Epub 2015 Sep 1.

30.

In response to Melgari et al. "hERG potassium channel inhibition by ivabradine requires channel gating".

Lees-Miller JP, Guo J, Wang Y, Perissinotti LL, Noskov SY, Duff HJ.

J Mol Cell Cardiol. 2015 Oct;87:192-3. doi: 10.1016/j.yjmcc.2015.08.003. Epub 2015 Aug 20. No abstract available.

PMID:
26299838
31.

Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.

Miranda WE, Noskov SY, Valiente PA.

J Chem Inf Model. 2015 Sep 28;55(9):1867-77. doi: 10.1021/acs.jcim.5b00012. Epub 2015 Aug 18.

PMID:
26180998
32.

In silico investigation of PARP-1 catalytic domains in holo and apo states for the design of high-affinity PARP-1 inhibitors.

Salmas RE, Unlu A, Yurtsever M, Noskov SY, Durdagi S.

J Enzyme Inhib Med Chem. 2016;31(1):112-20. doi: 10.3109/14756366.2015.1005011. Epub 2015 Jun 17.

PMID:
26083304
33.

Ivabradine prolongs phase 3 of cardiac repolarization and blocks the hERG1 (KCNH2) current over a concentration-range overlapping with that required to block HCN4.

Lees-Miller JP, Guo J, Wang Y, Perissinotti LL, Noskov SY, Duff HJ.

J Mol Cell Cardiol. 2015 Aug;85:71-8. doi: 10.1016/j.yjmcc.2015.05.009. Epub 2015 May 16.

PMID:
25986146
34.

Elucidating factors important for monovalent cation selectivity in enzymes: E. coli β-galactosidase as a model.

Wheatley RW, Juers DH, Lev BB, Huber RE, Noskov SY.

Phys Chem Chem Phys. 2015 Apr 28;17(16):10899-909. doi: 10.1039/c4cp04952g.

PMID:
25820412
35.

Kinetic model for NS1643 drug activation of WT and L529I variants of Kv11.1 (hERG1) potassium channel.

Perissinotti LL, Guo J, De Biase PM, Clancy CE, Duff HJ, Noskov SY.

Biophys J. 2015 Mar 24;108(6):1414-1424. doi: 10.1016/j.bpj.2014.12.056.

36.

NS1643 interacts around L529 of hERG to alter voltage sensor movement on the path to activation.

Guo J, Cheng YM, Lees-Miller JP, Perissinotti LL, Claydon TW, Hull CM, Thouta S, Roach DE, Durdagi S, Noskov SY, Duff HJ.

Biophys J. 2015 Mar 24;108(6):1400-1413. doi: 10.1016/j.bpj.2014.12.055.

37.

QM/MM calculations with deMon2k.

Salahub DR, Noskov SY, Lev B, Zhang R, Ngo V, Goursot A, Calaminici P, Köster AM, Alvarez-Ibarra A, Mejía-Rodríguez D, Řezáč J, Cailliez F, de la Lande A.

Molecules. 2015 Mar 16;20(3):4780-812. doi: 10.3390/molecules20034780. Review.

38.

Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.

Li H, Ngo V, Da Silva MC, Salahub DR, Callahan K, Roux B, Noskov SY.

J Phys Chem B. 2015 Jul 23;119(29):9401-16. doi: 10.1021/jp510560k. Epub 2015 Feb 4.

39.

Magic angle spinning nuclear magnetic resonance characterization of voltage-dependent anion channel gating in two-dimensional lipid crystalline bilayers.

Eddy MT, Andreas L, Teijido O, Su Y, Clark L, Noskov SY, Wagner G, Rostovtseva TK, Griffin RG.

Biochemistry. 2015 Feb 3;54(4):994-1005. doi: 10.1021/bi501260r. Epub 2015 Jan 16.

40.

Mapping the gating and permeation pathways in the voltage-gated proton channel Hv1.

Chamberlin A, Qiu F, Wang Y, Noskov SY, Larsson HP.

J Mol Biol. 2015 Jan 16;427(1):131-45. doi: 10.1016/j.jmb.2014.11.018. Epub 2014 Dec 4.

41.

Structure driven design of novel human ether-a-go-go-related-gene channel (hERG1) activators.

Guo J, Durdagi S, Changalov M, Perissinotti LL, Hargreaves JM, Back TG, Noskov SY, Duff HJ.

PLoS One. 2014 Sep 5;9(9):e105553. doi: 10.1371/journal.pone.0105553. eCollection 2014.

42.

A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity.

Anwar-Mohamed A, Barakat KH, Bhat R, Noskov SY, Tyrrell DL, Tuszynski JA, Houghton M.

Toxicol Lett. 2014 Nov 4;230(3):382-92. doi: 10.1016/j.toxlet.2014.08.007. Epub 2014 Aug 13.

PMID:
25127758
43.

Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore.

Markosyan S, De Biase PM, Czapla L, Samoylova O, Singh G, Cuervo J, Tieleman DP, Noskov SY.

Nanoscale. 2014 Aug 7;6(15):9006-16. doi: 10.1039/c3nr06559f.

PMID:
24968858
44.

Acidification asymmetrically affects voltage-dependent anion channel implicating the involvement of salt bridges.

Teijido O, Rappaport SM, Chamberlin A, Noskov SY, Aguilella VM, Rostovtseva TK, Bezrukov SM.

J Biol Chem. 2014 Aug 22;289(34):23670-82. doi: 10.1074/jbc.M114.576314. Epub 2014 Jun 24.

45.

Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches.

Buturak B, Durdagi S, Noskov SY, Ildeniz AT.

J Mol Graph Model. 2014 May;50:16-34. doi: 10.1016/j.jmgm.2014.02.007. Epub 2014 Mar 6.

PMID:
24699019
46.

Rehabilitating drug-induced long-QT promoters: in-silico design of hERG-neutral cisapride analogues with retained pharmacological activity.

Durdagi S, Randall T, Duff HJ, Chamberlin A, Noskov SY.

BMC Pharmacol Toxicol. 2014 Mar 8;15:14. doi: 10.1186/2050-6511-15-14.

47.

Molecular strategies to achieve selective conductance in NaK channel variants.

Wang Y, Chamberlin AC, Noskov SY.

J Phys Chem B. 2014 Feb 27;118(8):2041-9. doi: 10.1021/jp4107537. Epub 2014 Feb 18.

PMID:
24506283
48.

Sodium channel selectivity and conduction: prokaryotes have devised their own molecular strategy.

Finol-Urdaneta RK, Wang Y, Al-Sabi A, Zhao C, Noskov SY, French RJ.

J Gen Physiol. 2014 Feb;143(2):157-71. doi: 10.1085/jgp.201311037. Epub 2014 Jan 13.

49.

Hydrophobic plug functions as a gate in voltage-gated proton channels.

Chamberlin A, Qiu F, Rebolledo S, Wang Y, Noskov SY, Larsson HP.

Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):E273-82. doi: 10.1073/pnas.1318018111. Epub 2013 Dec 30.

50.

ATP transport through VDAC and the VDAC-tubulin complex probed by equilibrium and nonequilibrium MD simulations.

Noskov SY, Rostovtseva TK, Bezrukov SM.

Biochemistry. 2013 Dec 23;52(51):9246-56. doi: 10.1021/bi4011495. Epub 2013 Nov 25.

PMID:
24245503

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