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Items: 1 to 20 of 22

1.

Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining.

Garate JA, Bernardin A, Escalona Y, Yanez C, English NJ, Perez-Acle T.

J Phys Chem B. 2019 Mar 28;123(12):2599-2608. doi: 10.1021/acs.jpcb.8b09374. Epub 2019 Mar 15.

PMID:
30831028
2.

Controlling ionic conductivity through transprotein electropores in human aquaporin 4: a non-equilibrium molecular-dynamics study.

Bernardi M, Marracino P, Liberti M, Gárate JA, Burnham CJ, Apollonio F, English NJ.

Phys Chem Chem Phys. 2019 Feb 6;21(6):3339-3346. doi: 10.1039/c8cp06643d.

PMID:
30688325
3.

Human aquaporin 4 gating dynamics under axially oriented electric-field impulses: A non-equilibrium molecular-dynamics study.

Bernardi M, Marracino P, Ghaani MR, Liberti M, Del Signore F, Burnham CJ, Gárate JA, Apollonio F, English NJ.

J Chem Phys. 2018 Dec 28;149(24):245102. doi: 10.1063/1.5044665.

PMID:
30599740
4.

RIP-MD: a tool to study residue interaction networks in protein molecular dynamics.

Contreras-Riquelme S, Garate JA, Perez-Acle T, Martin AJM.

PeerJ. 2018 Dec 7;6:e5998. doi: 10.7717/peerj.5998. eCollection 2018.

5.

Transprotein-Electropore Characterization: A Molecular Dynamics Investigation on Human AQP4.

Marracino P, Bernardi M, Liberti M, Del Signore F, Trapani E, Gárate JA, Burnham CJ, Apollonio F, English NJ.

ACS Omega. 2018 Nov 30;3(11):15361-15369. doi: 10.1021/acsomega.8b02230. Epub 2018 Nov 13.

6.

Disaccharide-Based Anionic Amphiphiles as Potent Inhibitors of Lipopolysaccharide-Induced Inflammation.

Borio A, Holgado A, Garate JA, Beyaert R, Heine H, Zamyatina A.

ChemMedChem. 2018 Nov 6;13(21):2317-2331. doi: 10.1002/cmdc.201800505. Epub 2018 Oct 23.

PMID:
30276970
7.

Human Aquaporin 4 Gating Dynamics under Perpendicularly-Oriented Electric-Field Impulses: A Molecular Dynamics Study.

Marracino P, Liberti M, Trapani E, Burnham CJ, Avena M, Garate JA, Apollonio F, English NJ.

Int J Mol Sci. 2016 Jul 14;17(7). pii: E1133. doi: 10.3390/ijms17071133.

8.

Exploration of graphene oxide as an intelligent platform for cancer vaccines.

Yue H, Wei W, Gu Z, Ni D, Luo N, Yang Z, Zhao L, Garate JA, Zhou R, Su Z, Ma G.

Nanoscale. 2015 Dec 21;7(47):19949-57. doi: 10.1039/c5nr04986e. Epub 2015 Sep 30.

PMID:
26419315
9.

Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane.

Duan G, Kang SG, Tian X, Garate JA, Zhao L, Ge C, Zhou R.

Nanoscale. 2015 Oct 7;7(37):15214-24. doi: 10.1039/c5nr01839k.

PMID:
26315610
10.

Reduced Cytotoxicity of Graphene Nanosheets Mediated by Blood-Protein Coating.

Chong Y, Ge C, Yang Z, Garate JA, Gu Z, Weber JK, Liu J, Zhou R.

ACS Nano. 2015 Jun 23;9(6):5713-24. doi: 10.1021/nn5066606. Epub 2015 Jun 9.

PMID:
26040772
11.

Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene.

Liu J, Yang Z, Li H, Gu Z, Garate JA, Zhou R.

J Chem Phys. 2014 Dec 14;141(22):22D520. doi: 10.1063/1.4901113.

PMID:
25494791
12.

Anti-endotoxic activity and structural basis for human MD-2·TLR4 antagonism of tetraacylated lipid A mimetics based on βGlcN(1↔1)αGlcN scaffold.

Garate JA, Stöckl J, Fernández-Alonso Mdel C, Artner D, Haegman M, Oostenbrink C, Jiménez-Barbero J, Beyaert R, Heine H, Kosma P, Zamyatina A.

Innate Immun. 2015 Jul;21(5):490-503. doi: 10.1177/1753425914550426. Epub 2014 Nov 13.

13.

Characterization of a novel water pocket inside the human Cx26 hemichannel structure.

Araya-Secchi R, Perez-Acle T, Kang SG, Huynh T, Bernardin A, Escalona Y, Garate JA, Martínez AD, García IE, Sáez JC, Zhou R.

Biophys J. 2014 Aug 5;107(3):599-612. doi: 10.1016/j.bpj.2014.05.037.

14.

On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations.

Garate JA, Perez-Acle T, Oostenbrink C.

Phys Chem Chem Phys. 2014 Mar 21;16(11):5119-28. doi: 10.1039/c3cp54554g.

PMID:
24477412
15.

Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods.

Lai B, Nagy G, Garate JA, Oostenbrink C.

J Chem Inf Model. 2014 Jan 27;54(1):151-8. doi: 10.1021/ci4006657. Epub 2014 Jan 9.

16.

Human aquaporin 4 gating dynamics under and after nanosecond-scale static and alternating electric-field impulses: a molecular dynamics study of field effects and relaxation.

Reale R, English NJ, Garate JA, Marracino P, Liberti M, Apollonio F.

J Chem Phys. 2013 Nov 28;139(20):205101. doi: 10.1063/1.4832383.

PMID:
24289379
17.

Conformationally constrained lipid A mimetics for exploration of structural basis of TLR4/MD-2 activation by lipopolysaccharide.

Artner D, Oblak A, Ittig S, Garate JA, Horvat S, Arrieumerlou C, Hofinger A, Oostenbrink C, Jerala R, Kosma P, Zamyatina A.

ACS Chem Biol. 2013 Nov 15;8(11):2423-32. doi: 10.1021/cb4003199. Epub 2013 Sep 26.

18.

Free-energy differences between states with different conformational ensembles.

Garate JA, Oostenbrink C.

J Comput Chem. 2013 Jun 15;34(16):1398-408. doi: 10.1002/jcc.23276. Epub 2013 Mar 23.

PMID:
23526629
19.

Lipid A from lipopolysaccharide recognition: structure, dynamics and cooperativity by molecular dynamics simulations.

Garate JA, Oostenbrink C.

Proteins. 2013 Apr;81(4):658-74. doi: 10.1002/prot.24223. Epub 2013 Jan 15.

PMID:
23184816
20.

Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: molecular dynamics and quantum chemical studies.

El-Hendawy MM, Garate JA, English NJ, O'Reilly S, Mooney DA.

J Chem Phys. 2012 Oct 14;137(14):145103. doi: 10.1063/1.4757021.

PMID:
23061867

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