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Items: 32

1.

Self-assembly of lobed particles into amorphous and crystalline porous structures.

Paul S, Vashisth H.

Soft Matter. 2019 Dec 9. doi: 10.1039/c9sm01878f. [Epub ahead of print]

PMID:
31815274
2.

An Interhelical Salt Bridge Controls Flexibility and Inhibitor Potency for Regulators of G-protein Signaling Proteins 4, 8, and 19.

Shaw VS, Mohammadi M, Quinn JA, Vashisth H, Neubig RR.

Mol Pharmacol. 2019 Dec;96(6):683-691. doi: 10.1124/mol.119.117176. Epub 2019 Sep 22.

PMID:
31543506
3.

Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes.

Liu Y, Vashisth H.

Phys Chem Chem Phys. 2019 Oct 24;21(41):22711-22721. doi: 10.1039/c9cp04408f.

PMID:
31454001
4.

Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes.

Schuster KD, Mohammadi M, Cahill KB, Matte SL, Maillet AD, Vashisth H, Cote RH.

PLoS One. 2019 Mar 27;14(3):e0214554. doi: 10.1371/journal.pone.0214554. eCollection 2019.

5.

Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein.

Mohammadi M, Mohammadiarani H, Shaw VS, Neubig RR, Vashisth H.

Proteins. 2019 Feb;87(2):146-156. doi: 10.1002/prot.25642. Epub 2018 Dec 26.

PMID:
30521141
6.

Diffusion network of CO in FeFe-Hydrogenase.

Liu Y, Mohammadi M, Vashisth H.

J Chem Phys. 2018 Nov 28;149(20):204108. doi: 10.1063/1.5054877.

PMID:
30501239
7.

Biomimetic water channels: general discussion.

Baaden M, Barboiu M, Bill RM, Chen CL, Davis J, Di Vincenzo M, Freger V, Fröba M, Gale PA, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hou JL, Hummer G, Kumar M, Legrand YM, Lokesh M, Mi B, Murail S, Pohl P, Sansom M, Song Q, Song W, Törnroth-Horsefield S, Vashisth H, Vögele M.

Faraday Discuss. 2018 Sep 28;209(0):205-229. doi: 10.1039/c8fd90020e. No abstract available.

PMID:
30225508
8.

Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins.

Mohammadiarani H, Shaw VS, Neubig RR, Vashisth H.

J Phys Chem B. 2018 Oct 11;122(40):9314-9323. doi: 10.1021/acs.jpcb.8b07494. Epub 2018 Oct 1.

9.

Structure and function of natural proteins for water transport: general discussion.

Baaden M, Barboiu M, Bill RM, Casanova S, Chen CL, Conner M, Freger V, Gong B, Góra A, Hinds B, Horner A, Hummer G, Kumar M, Lokesh M, Mitra S, Noy A, Pohl P, Sadet A, Sansom M, Törnroth-Horsefield S, Vashisth H.

Faraday Discuss. 2018 Sep 28;209(0):83-95. doi: 10.1039/c8fd90019a. No abstract available.

PMID:
30215655
10.

The modelling and enhancement of water hydrodynamics: general discussion.

Baaden M, Borthakur MP, Casanova S, Coalson R, Freger V, Gonzalez M, Góra A, Hinds B, Hirunpinyopas W, Hummer G, Kumar M, Lynch C, Murail S, Noy A, Sansom M, Song Q, Vashisth H, Vögele M.

Faraday Discuss. 2018 Sep 28;209(0):273-285. doi: 10.1039/c8fd90021c. No abstract available.

PMID:
30215654
11.

Applications to water transport systems: general discussion.

Baaden M, Barboiu M, Borthakur MP, Chen CL, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hirunpinyopas W, Horner A, Hou JL, Hummer G, Iamprasertkun P, Kazushi K, Kumar M, Legrand YM, Lokesh M, Mi B, Mitra S, Murail S, Noy A, Nunes S, Pohl P, Song Q, Song W, Tornroth-Horsefield S, Vashisth H.

Faraday Discuss. 2018 Sep 28;209(0):389-414. doi: 10.1039/c8fd90022a. No abstract available.

PMID:
30215649
12.

Publisher Correction: Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes.

Shen YX, Song W, Barden DR, Ren T, Lang C, Feroz H, Henderson CB, Saboe PO, Tsai D, Yan H, Butler PJ, Bazan GC, Phillip WA, Hickey RJ, Cremer PS, Vashisth H, Kumar M.

Nat Commun. 2018 Aug 14;9(1):3304. doi: 10.1038/s41467-018-05447-3.

13.

Parameterization and atomistic simulations of biomimetic membranes.

Barden DR, Vashisth H.

Faraday Discuss. 2018 Sep 28;209(0):161-178. doi: 10.1039/c8fd00047f.

PMID:
29974902
14.

Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes.

Shen YX, Song W, Barden DR, Ren T, Lang C, Feroz H, Henderson CB, Saboe PO, Tsai D, Yan H, Butler PJ, Bazan GC, Phillip WA, Hickey RJ, Cremer PS, Vashisth H, Kumar M.

Nat Commun. 2018 Jun 12;9(1):2294. doi: 10.1038/s41467-018-04604-y. Erratum in: Nat Commun. 2018 Aug 14;9(1):3304.

15.

Differential Protein Dynamics of Regulators of G-Protein Signaling: Role in Specificity of Small-Molecule Inhibitors.

Shaw VS, Mohammadiarani H, Vashisth H, Neubig RR.

J Am Chem Soc. 2018 Mar 7;140(9):3454-3460. doi: 10.1021/jacs.7b13778. Epub 2018 Feb 26.

16.

Pathways and Thermodynamics of Oxygen Diffusion in [FeFe]-Hydrogenase.

Mohammadi M, Vashisth H.

J Phys Chem B. 2017 Nov 2;121(43):10007-10017. doi: 10.1021/acs.jpcb.7b06489. Epub 2017 Oct 18.

PMID:
28975788
17.

Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review.

Dickson A, Tiwary P, Vashisth H.

Curr Top Med Chem. 2017;17(23):2626-2641. doi: 10.2174/1568026617666170414142908. Review.

PMID:
28413946
18.

Insulin mimetic peptide S371 folds into a helical structure.

Mohammadiarani H, Vashisth H.

J Comput Chem. 2017 Jun 5;38(15):1158-1166. doi: 10.1002/jcc.24746. Epub 2017 Feb 12.

PMID:
28190265
19.

All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors.

Mohammadiarani H, Vashisth H.

Front Endocrinol (Lausanne). 2016 Jun 20;7:68. doi: 10.3389/fendo.2016.00068. eCollection 2016.

20.

Theoretical and computational studies of peptides and receptors of the insulin family.

Vashisth H.

Membranes (Basel). 2015 Feb 11;5(1):48-83. doi: 10.3390/membranes5010048. Review.

21.
22.

Collective variable approaches for single molecule flexible fitting and enhanced sampling.

Vashisth H, Skiniotis G, Brooks CL 3rd.

Chem Rev. 2014 Mar 26;114(6):3353-65. doi: 10.1021/cr4005988. Epub 2014 Jan 21. Review. No abstract available.

23.

Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule.

Vashisth H, Storaska AJ, Neubig RR, Brooks CL 3rd.

ACS Chem Biol. 2013 Dec 20;8(12):2778-84. doi: 10.1021/cb400568g. Epub 2013 Oct 24.

24.

Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.

Vashisth H, Skiniotis G, Brooks CL 3rd.

J Phys Chem B. 2013 Apr 11;117(14):3738-46. doi: 10.1021/jp3126297. Epub 2013 Apr 1.

25.

All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.

Vashisth H, Abrams CF.

Proteins. 2013 Jun;81(6):1017-30. doi: 10.1002/prot.24255. Epub 2013 Feb 27.

26.
27.

Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps.

Vashisth H, Skiniotis G, Brooks CL 3rd.

Structure. 2012 Sep 5;20(9):1453-62. doi: 10.1016/j.str.2012.08.007.

28.

"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop.

Vashisth H, Maragliano L, Abrams CF.

Biophys J. 2012 Apr 18;102(8):1979-87. doi: 10.1016/j.bpj.2012.03.031.

29.

Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.

Strunk BS, Loucks CR, Su M, Vashisth H, Cheng S, Schilling J, Brooks CL 3rd, Karbstein K, Skiniotis G.

Science. 2011 Sep 9;333(6048):1449-53. doi: 10.1126/science.1208245. Epub 2011 Aug 11.

30.

All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.

Vashisth H, Abrams CF.

J Mol Biol. 2010 Jul 16;400(3):645-58. doi: 10.1016/j.jmb.2010.05.025. Epub 2010 May 19.

PMID:
20488191
31.

Docking of insulin to a structurally equilibrated insulin receptor ectodomain.

Vashisth H, Abrams CF.

Proteins. 2010 May 1;78(6):1531-43. doi: 10.1002/prot.22670. Erratum in: Proteins. 2010 Aug 1;78(10):2403.

PMID:
20112420
32.

Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex.

Vashisth H, Abrams CF.

Biophys J. 2008 Nov 1;95(9):4193-204. doi: 10.1529/biophysj.108.139675. Epub 2008 Aug 1.

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