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Items: 37

1.

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics.

Fiorin G, Marinelli F, Faraldo-Gómez JD.

J Comput Chem. 2019 Oct 11. doi: 10.1002/jcc.26075. [Epub ahead of print]

PMID:
31602694
2.

Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements.

Marinelli F, Fiorin G.

Structure. 2019 Feb 5;27(2):359-370.e12. doi: 10.1016/j.str.2018.10.013. Epub 2018 Dec 6.

PMID:
30528595
3.

Suppression of Plant Immunity by Fungal Chitinase-like Effectors.

Fiorin GL, Sanchéz-Vallet A, Thomazella DPT, do Prado PFV, do Nascimento LC, Figueira AVO, Thomma BPHJ, Pereira GAG, Teixeira PJPL.

Curr Biol. 2018 Sep 24;28(18):3023-3030.e5. doi: 10.1016/j.cub.2018.07.055. Epub 2018 Sep 13.

4.

No evidence for cerebellar abnormality in adults with developmental dyslexia.

van Oers CAMM, Goldberg N, Fiorin G, van den Heuvel MP, Kappelle LJ, Wijnen FNK.

Exp Brain Res. 2018 Nov;236(11):2991-3001. doi: 10.1007/s00221-018-5351-y. Epub 2018 Aug 16.

5.

Mechanically Strong Polymer Sheets from Aligned Ultrahigh-Molecular-Weight Polyethylene Nanocomposites.

Zhang Z, Mogurampelly S, Percec S, Hu Y, Fiorin G, Klein ML, Ren S.

J Phys Chem Lett. 2018 May 17;9(10):2652-2658. doi: 10.1021/acs.jpclett.8b00790. Epub 2018 May 7.

PMID:
29703081
6.

Difficulties in Comprehending Affirmative and Negative Sentences: Evidence From Chinese Children With Reading Difficulties.

Hu S, Vender M, Fiorin G, Delfitto D.

J Learn Disabil. 2018 Mar/Apr;51(2):181-193. doi: 10.1177/0022219417714775. Epub 2017 Jun 27.

PMID:
28653560
7.

Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel.

Markiewicz BN, Lemmin T, Zhang W, Ahmed IA, Jo H, Fiorin G, Troxler T, DeGrado WF, Gai F.

Phys Chem Chem Phys. 2016 Oct 19;18(41):28939-28950.

8.

The semantics of person and de se effects in free indirect discourse.

Delfitto D, Fiorin G, Reboul A.

Springerplus. 2016 Aug 30;5(1):1451. doi: 10.1186/s40064-016-3102-8. eCollection 2016.

9.

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes.

MacDermaid CM, Kashyap HK, DeVane RH, Shinoda W, Klauda JB, Klein ML, Fiorin G.

J Chem Phys. 2015 Dec 28;143(24):243144. doi: 10.1063/1.4937153.

PMID:
26723629
10.

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.

Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF.

Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):14260-5. doi: 10.1073/pnas.1518493112. Epub 2015 Nov 2. Erratum in: Proc Natl Acad Sci U S A. 2016 May 3;113(18):E2548.

11.

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

Shen R, Han W, Fiorin G, Islam SM, Schulten K, Roux B.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004368. doi: 10.1371/journal.pcbi.1004368. eCollection 2015 Oct.

12.

How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields?

Oh KI, Fiorin G, Gai F.

Chemphyschem. 2015 Dec 1;16(17):3595-8. doi: 10.1002/cphc.201500777. Epub 2015 Oct 12.

13.

Dehydration of multilamellar fatty acid membranes: towards a computational model of the stratum corneum.

MacDermaid CM, DeVane RH, Klein ML, Fiorin G.

J Chem Phys. 2014 Dec 14;141(22):22D526. doi: 10.1063/1.4902363.

PMID:
25494797
14.

Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel.

Wu Y, Canturk B, Jo H, Ma C, Gianti E, Klein ML, Pinto LH, Lamb RA, Fiorin G, Wang J, DeGrado WF.

J Am Chem Soc. 2014 Dec 31;136(52):17987-95. doi: 10.1021/ja508461m. Epub 2014 Dec 18.

15.

High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa.

Teixeira PJ, Thomazella DP, Reis O, do Prado PF, do Rio MC, Fiorin GL, José J, Costa GG, Negri VA, Mondego JM, Mieczkowski P, Pereira GA.

Plant Cell. 2014 Nov;26(11):4245-69. doi: 10.1105/tpc.114.130807. Epub 2014 Nov 4.

16.

Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors.

Gianti E, Carnevale V, DeGrado WF, Klein ML, Fiorin G.

J Phys Chem B. 2015 Jan 22;119(3):1173-83. doi: 10.1021/jp506807y. Epub 2014 Nov 11.

17.

Proton release from the histidine-tetrad in the M2 channel of the influenza A virus.

Dong H, Fiorin G, DeGrado WF, Klein ML.

J Phys Chem B. 2014 Nov 6;118(44):12644-51. doi: 10.1021/jp5102225. Epub 2014 Oct 27.

18.

Counterion-assisted cation transport in a biological calcium channel.

Dong H, Klein ML, Fiorin G.

J Phys Chem B. 2014 Aug 14;118(32):9668-76. doi: 10.1021/jp5059897. Epub 2014 Aug 5.

PMID:
25068680
19.

Structure of water at charged interfaces: a molecular dynamics study.

Dewan S, Carnevale V, Bankura A, Eftekhari-Bafrooei A, Fiorin G, Klein ML, Borguet E.

Langmuir. 2014 Jul 15;30(27):8056-65. doi: 10.1021/la5011055. Epub 2014 Jun 30.

PMID:
24979659
20.

Supramolecular polymerization of benzene-1,3,5-tricarboxamide: a molecular dynamics simulation study.

Bejagam KK, Fiorin G, Klein ML, Balasubramanian S.

J Phys Chem B. 2014 May 15;118(19):5218-28. doi: 10.1021/jp502779z. Epub 2014 May 6.

PMID:
24780060
21.

Binding of the antitubercular pro-drug isoniazid in the heme access channel of catalase-peroxidase (KatG). A combined structural and metadynamics investigation.

Vidossich P, Loewen PC, Carpena X, Fiorin G, Fita I, Rovira C.

J Phys Chem B. 2014 Mar 20;118(11):2924-31. doi: 10.1021/jp4123425. Epub 2014 Mar 7.

PMID:
24568093
22.

Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus.

Ma C, Fiorin G, Carnevale V, Wang J, Lamb RA, Klein ML, Wu Y, Pinto LH, DeGrado WF.

Structure. 2013 Nov 5;21(11):2033-41. doi: 10.1016/j.str.2013.08.029. Epub 2013 Oct 17.

23.

Pore waters regulate ion permeation in a calcium release-activated calcium channel.

Dong H, Fiorin G, Carnevale V, Treptow W, Klein ML.

Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17332-7. doi: 10.1073/pnas.1316969110. Epub 2013 Oct 7.

24.

Exploring Histidine Conformations in the M2 Channel Lumen of the Influenza A Virus at Neutral pH via Molecular Simulations.

Dong H, Fiorin G, Degrado WF, Klein ML.

J Phys Chem Lett. 2013 Sep 19;4(18):3067-3071. Epub 2013 Aug 28.

25.

Novel receptor-like kinases in cacao contain PR-1 extracellular domains.

Teixeira PJ, Costa GG, Fiorin GL, Pereira GA, Mondego JM.

Mol Plant Pathol. 2013 Aug;14(6):602-9. doi: 10.1111/mpp.12028. Epub 2013 Apr 10.

26.

Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus.

Wang J, Ma C, Wang J, Jo H, Canturk B, Fiorin G, Pinto LH, Lamb RA, Klein ML, DeGrado WF.

J Med Chem. 2013 Apr 11;56(7):2804-12. doi: 10.1021/jm301538e. Epub 2013 Mar 27.

27.

Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus.

Wang J, Wu Y, Ma C, Fiorin G, Wang J, Pinto LH, Lamb RA, Klein ML, Degrado WF.

Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1315-20. doi: 10.1073/pnas.1216526110. Epub 2013 Jan 9.

28.

Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2.

Wang J, Ma C, Fiorin G, Carnevale V, Wang T, Hu F, Lamb RA, Pinto LH, Hong M, Klein ML, DeGrado WF.

J Am Chem Soc. 2011 Aug 17;133(32):12834-41. doi: 10.1021/ja204969m. Epub 2011 Jul 21.

29.

Multiple Proton Confinement in the M2 Channel from the Influenza A Virus.

Carnevale V, Fiorin G, Levine BG, Degrado WF, Klein ML.

J Phys Chem C Nanomater Interfaces. 2010 Oct 21;114(48):20856-20863.

30.

Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion.

Donald JE, Zhang Y, Fiorin G, Carnevale V, Slochower DR, Gai F, Klein ML, DeGrado WF.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3958-63. doi: 10.1073/pnas.1019668108. Epub 2011 Feb 14.

31.

Structural biology. The flu's proton escort.

Fiorin G, Carnevale V, DeGrado WF.

Science. 2010 Oct 22;330(6003):456-8. doi: 10.1126/science.1197748. No abstract available.

32.

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus.

Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, Klein ML.

Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15075-80. doi: 10.1073/pnas.1007071107. Epub 2010 Aug 5.

33.

On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation.

Vidossich P, Fiorin G, Alfonso-Prieto M, Derat E, Shaik S, Rovira C.

J Phys Chem B. 2010 Apr 22;114(15):5161-9. doi: 10.1021/jp911170b.

PMID:
20345187
34.

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.

Hénin J, Fiorin G, Chipot C, Klein ML.

J Chem Theory Comput. 2010 Jan 12;6(1):35-47. doi: 10.1021/ct9004432. Epub 2009 Dec 3.

PMID:
26614317
35.

Functional studies and modeling of pore-lining residue mutants of the influenza a virus M2 ion channel.

Balannik V, Carnevale V, Fiorin G, Levine BG, Lamb RA, Klein ML, Degrado WF, Pinto LH.

Biochemistry. 2010 Feb 2;49(4):696-708. doi: 10.1021/bi901799k.

36.

Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail.

Fiorin G, Pastore A, Carloni P, Parrinello M.

Biophys J. 2006 Oct 15;91(8):2768-77. Epub 2006 Jul 28.

37.

Unwinding the helical linker of calcium-loaded calmodulin: a molecular dynamics study.

Fiorin G, Biekofsky RR, Pastore A, Carloni P.

Proteins. 2005 Dec 1;61(4):829-39.

PMID:
16193483

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