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Items: 1 to 20 of 43

1.

Role of Urea-Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State.

Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD.

J Am Chem Soc. 2017 Oct 25;139(42):14931-14946. doi: 10.1021/jacs.7b05463. Epub 2017 Oct 17.

PMID:
28975780
2.

Microsecond simulation of human aquaporin 2 reveals structural determinants of water permeability and selectivity.

Padhi S, Priyakumar UD.

Biochim Biophys Acta. 2017 Jan;1859(1):10-16. doi: 10.1016/j.bbamem.2016.10.011. Epub 2016 Oct 26.

3.

Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions.

Suresh G, Padhi S, Patil I, Priyakumar UD.

Biochemistry. 2016 Oct 11;55(40):5653-5664. Epub 2016 Sep 29.

PMID:
27657980
4.

Urea-Aromatic Stacking and Concerted Urea Transport: Conserved Mechanisms in Urea Transporters Revealed by Molecular Dynamics.

Padhi S, Priyakumar UD.

J Chem Theory Comput. 2016 Oct 11;12(10):5190-5200. Epub 2016 Sep 9.

PMID:
27576044
5.

Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch.

Suresh G, Srinivasan H, Nanda S, Priyakumar UD.

Biochemistry. 2016 Jun 21;55(24):3349-60. doi: 10.1021/acs.biochem.5b00973. Epub 2016 Jun 13.

PMID:
27249101
6.

Cooperation of Hydrophobic Gating, Knock-on Effect, and Ion Binding Determines Ion Selectivity in the p7 Channel.

Padhi S, Priyakumar UD.

J Phys Chem B. 2016 May 19;120(19):4351-6. doi: 10.1021/acs.jpcb.6b00684. Epub 2016 May 5.

PMID:
27111292
7.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers.

Kanchi S, Suresh G, Priyakumar UD, Ayappa KG, Maiti PK.

J Phys Chem B. 2015 Oct 15;119(41):12990-3001. doi: 10.1021/acs.jpcb.5b07124. Epub 2015 Oct 6.

PMID:
26378813
8.

Sumoylation of Sir2 differentially regulates transcriptional silencing in yeast.

Hannan A, Abraham NM, Goyal S, Jamir I, Priyakumar UD, Mishra K.

Nucleic Acids Res. 2015 Dec 2;43(21):10213-26. doi: 10.1093/nar/gkv842. Epub 2015 Aug 28.

9.

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

Suresh G, Priyakumar UD.

J Mol Graph Model. 2015 Sep;61:150-9. doi: 10.1016/j.jmgm.2015.07.009. Epub 2015 Jul 29.

PMID:
26254870
10.

Ion hydration dynamics in conjunction with a hydrophobic gating mechanism regulates ion permeation in p7 viroporin from hepatitis C virus.

Padhi S, Priyakumar UD.

J Phys Chem B. 2015 May 21;119(20):6204-10. doi: 10.1021/acs.jpcb.5b02759. Epub 2015 May 8.

PMID:
25933117
11.

Dynamics based pharmacophore models for screening potential inhibitors of mycobacterial cyclopropane synthase.

Choudhury C, Priyakumar UD, Sastry GN.

J Chem Inf Model. 2015 Apr 27;55(4):848-60. doi: 10.1021/ci500737b. Epub 2015 Mar 16.

PMID:
25751016
12.

Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf.

Samadani R, Zhang J, Brophy A, Oashi T, Priyakumar UD, Raman EP, St John FJ, Jung KY, Fletcher S, Pozharski E, MacKerell AD Jr, Shapiro P.

Biochem J. 2015 May 1;467(3):425-38. doi: 10.1042/BJ20131571.

13.

Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution.

Kasavajhala K, Bikkina S, Patil I, MacKerell AD Jr, Priyakumar UD.

J Phys Chem B. 2015 Mar 5;119(9):3755-61. doi: 10.1021/jp512414f. Epub 2015 Feb 23.

14.

Prediction of the structures of helical membrane proteins based on a minimum unfavorable contacts approach.

Padhi S, Ramakrishna S, Priyakumar UD.

J Comput Chem. 2015 Mar 30;36(8):539-52. doi: 10.1002/jcc.23828. Epub 2015 Jan 6.

PMID:
25565454
15.

Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.

Padhi S, Burri RR, Jameel S, Priyakumar UD.

PLoS One. 2014 Nov 13;9(11):e112983. doi: 10.1371/journal.pone.0112983. eCollection 2014.

16.

Double zipper helical assembly of deoxyoligonucleotides: mutual templating and chiral imprinting to form hybrid DNA ensembles.

Narayanaswamy N, Suresh G, Priyakumar UD, Govindaraju T.

Chem Commun (Camb). 2015 Mar 28;51(25):5493-6. doi: 10.1039/c4cc06759b.

PMID:
25233941
17.
19.

Solvent-induced helical assembly and reversible chiroptical switching of chiral cyclic-dipeptide-functionalized naphthalenediimides.

Manchineella S, Prathyusha V, Priyakumar UD, Govindaraju T.

Chemistry. 2013 Dec 2;19(49):16615-24. doi: 10.1002/chem.201303123. Epub 2013 Nov 4.

PMID:
24281809
20.

Molecular dynamics simulations reveal the HIV-1 Vpu transmembrane protein to form stable pentamers.

Padhi S, Khan N, Jameel S, Priyakumar UD.

PLoS One. 2013 Nov 6;8(11):e79779. doi: 10.1371/journal.pone.0079779. eCollection 2013.

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