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Items: 47

1.

Exploring Allosteric Pathways of a V-Type Enzyme with Dynamical Perturbation Networks.

Gheeraert A, Pacini L, Batista VS, Vuillon L, Lesieur C, Rivalta I.

J Phys Chem B. 2019 Apr 25;123(16):3452-3461. doi: 10.1021/acs.jpcb.9b01294. Epub 2019 Apr 15.

PMID:
30943726
2.

Allostery in Its Many Disguises: From Theory to Applications.

Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T.

Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. Review.

PMID:
30744993
3.

Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA.

Q Rev Biophys. 2018;51. pii: e91. doi: 10.1017/S0033583518000070. Epub 2018 Aug 3.

4.

Eigenvector centrality for characterization of protein allosteric pathways.

Negre CFA, Morzan UN, Hendrickson HP, Pal R, Lisi GP, Loria JP, Rivalta I, Ho J, Batista VS.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12201-E12208. doi: 10.1073/pnas.1810452115. Epub 2018 Dec 10.

PMID:
30530700
5.

COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.

Weingart O, Nenov A, Altoè P, Rivalta I, Segarra-Martí J, Dokukina I, Garavelli M.

J Mol Model. 2018 Sep 3;24(9):271. doi: 10.1007/s00894-018-3769-6.

PMID:
30178229
6.

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy.

Segatta F, Gdor I, Réhault J, Taioli S, Friedman N, Sheves M, Rivalta I, Ruhman S, Cerullo G, Garavelli M.

Chemistry. 2018 Aug 14;24(46):12084-12092. doi: 10.1002/chem.201803525. Epub 2018 Aug 2.

PMID:
30048017
7.

Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols.

Gholami S, Nenov A, Rivalta I, Bocola M, Bordbar AK, Schwaneberg U, Davari MD, Garavelli M.

J Phys Chem B. 2018 Aug 9;122(31):7668-7681. doi: 10.1021/acs.jpcb.8b04231. Epub 2018 Jul 30.

PMID:
29996651
8.

Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy.

Segarra-Martí J, Mukamel S, Garavelli M, Nenov A, Rivalta I.

Top Curr Chem (Cham). 2018 Jun 1;376(3):24. doi: 10.1007/s41061-018-0201-8. Review.

PMID:
29858697
9.

Resolving the Singlet Excited State Manifold of Benzophenone by First-Principles Simulations and Ultrafast Spectroscopy.

Segarra-Martí J, Zvereva E, Marazzi M, Brazard J, Dumont E, Assfeld X, Haacke S, Garavelli M, Monari A, Léonard J, Rivalta I.

J Chem Theory Comput. 2018 May 8;14(5):2570-2585. doi: 10.1021/acs.jctc.7b01208. Epub 2018 Apr 11.

10.

UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level.

Pepino AJ, Segarra-Martí J, Nenov A, Rivalta I, Improta R, Garavelli M.

Phys Chem Chem Phys. 2018 Mar 7;20(10):6877-6890. doi: 10.1039/c7cp08235e.

11.

The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone.

Zvereva E, Segarra-Martí J, Marazzi M, Brazard J, Nenov A, Weingart O, Léonard J, Garavelli M, Rivalta I, Dumont E, Assfeld X, Haacke S, Monari A.

Photochem Photobiol Sci. 2018 Mar 14;17(3):323-331. doi: 10.1039/c7pp00439g.

12.

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates.

Segarra-Martí J, Jaiswal VK, Pepino AJ, Giussani A, Nenov A, Mukamel S, Garavelli M, Rivalta I.

Faraday Discuss. 2018 Apr 17;207(0):233-250. doi: 10.1039/c7fd00201g.

PMID:
29359207
13.

Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA.

Q Rev Biophys. 2018 Jan;51:e9. doi: 10.1017/S0033583518000070.

PMID:
30912489
14.

Fine Tuning of Retinal Photoinduced Decay in Solution.

Demoulin B, Altavilla SF, Rivalta I, Garavelli M.

J Phys Chem Lett. 2017 Sep 21;8(18):4407-4412. doi: 10.1021/acs.jpclett.7b01780. Epub 2017 Sep 5.

PMID:
28853582
15.

Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9.

Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA.

J Am Chem Soc. 2017 Nov 15;139(45):16028-16031. doi: 10.1021/jacs.7b05313. Epub 2017 Aug 7.

16.

Characterization of Protein Tyrosine Phosphatase 1B Inhibition by Chlorogenic Acid and Cichoric Acid.

Lipchock JM, Hendrickson HP, Douglas BB, Bird KE, Ginther PS, Rivalta I, Ten NS, Batista VS, Loria JP.

Biochemistry. 2017 Jan 10;56(1):96-106. doi: 10.1021/acs.biochem.6b01025. Epub 2016 Dec 27.

17.

Allosteric Communication Disrupted by a Small Molecule Binding to the Imidazole Glycerol Phosphate Synthase Protein-Protein Interface.

Rivalta I, Lisi GP, Snoeberger NS, Manley G, Loria JP, Batista VS.

Biochemistry. 2016 Nov 29;55(47):6484-6494. Epub 2016 Nov 11.

18.

Dissecting Dynamic Allosteric Pathways Using Chemically Related Small-Molecule Activators.

Lisi GP, Manley GA, Hendrickson H, Rivalta I, Batista VS, Loria JP.

Structure. 2016 Jul 6;24(7):1155-66. doi: 10.1016/j.str.2016.04.010. Epub 2016 May 26.

19.

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate.

Li Q, Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Voityuk AA, Mukamel S, Roca-Sanjuán D, Garavelli M, Blancafort L.

Chemistry. 2016 May 23;22(22):7497-507. doi: 10.1002/chem.201505086. Epub 2016 Apr 26.

20.

Allosteric Pathways in the PPARγ-RXRα nuclear receptor complex.

Ricci CG, Silveira RL, Rivalta I, Batista VS, Skaf MS.

Sci Rep. 2016 Jan 29;6:19940. doi: 10.1038/srep19940.

21.

Two-Dimensional Electronic Spectroscopy of Benzene, Phenol, and Their Dimer: An Efficient First-Principles Simulation Protocol.

Nenov A, Mukamel S, Garavelli M, Rivalta I.

J Chem Theory Comput. 2015 Aug 11;11(8):3755-71. doi: 10.1021/acs.jctc.5b00443.

PMID:
26574458
22.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

Aquilante F, Autschbach J, Carlson RK, Chibotaru LF, Delcey MG, De Vico L, Fdez Galván I, Ferré N, Frutos LM, Gagliardi L, Garavelli M, Giussani A, Hoyer CE, Li Manni G, Lischka H, Ma D, Malmqvist PÅ, Müller T, Nenov A, Olivucci M, Pedersen TB, Peng D, Plasser F, Pritchard B, Reiher M, Rivalta I, Schapiro I, Segarra-Martí J, Stenrup M, Truhlar DG, Ungur L, Valentini A, Vancoillie S, Veryazov V, Vysotskiy VP, Weingart O, Zapata F, Lindh R.

J Comput Chem. 2016 Feb 15;37(5):506-41. doi: 10.1002/jcc.24221. Epub 2015 Nov 12.

PMID:
26561362
23.

Spectral lineshapes in nonlinear electronic spectroscopy.

Nenov A, Giussani A, Fingerhut BP, Rivalta I, Dumont E, Mukamel S, Garavelli M.

Phys Chem Chem Phys. 2015 Dec 14;17(46):30925-36. doi: 10.1039/c5cp01167a.

24.

Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy.

Nenov A, Giussani A, Segarra-Martí J, Jaiswal VK, Rivalta I, Cerullo G, Mukamel S, Garavelli M.

J Chem Phys. 2015 Jun 7;142(21):212443. doi: 10.1063/1.4921016.

25.

Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate.

Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M.

Front Chem. 2015 Apr 20;3:29. doi: 10.3389/fchem.2015.00029. eCollection 2015.

26.

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back.

Conti I, Nenov A, Höfinger S, Flavio Altavilla S, Rivalta I, Dumont E, Orlandi G, Garavelli M.

Phys Chem Chem Phys. 2015 Mar 21;17(11):7291-302. doi: 10.1039/c4cp05546b.

PMID:
25695904
27.

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations.

Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF, Mukamel S, Garavelli M.

Faraday Discuss. 2015;177:345-62. doi: 10.1039/c4fd00175c.

PMID:
25607949
28.

Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy.

Polli D, Rivalta I, Nenov A, Weingart O, Garavelli M, Cerullo G.

Photochem Photobiol Sci. 2015 Feb;14(2):213-28. doi: 10.1039/c4pp00370e. Review.

PMID:
25429920
29.

Tracking conformational dynamics of polypeptides by nonlinear electronic spectroscopy of aromatic residues: a first-principles simulation study.

Nenov A, Beccara S, Rivalta I, Cerullo G, Mukamel S, Garavelli M.

Chemphyschem. 2014 Oct 20;15(15):3282-90. doi: 10.1002/cphc.201402374. Epub 2014 Aug 21.

30.

Disentangling Peptide Configurations via Two-Dimensional Electronic Spectroscopy: Ab Initio Simulations Beyond the Frenkel Exciton Hamiltonian.

Nenov A, Rivalta I, Cerullo G, Mukamel S, Garavelli M.

J Phys Chem Lett. 2014 Feb 20;5(4):767-771. Epub 2014 Feb 7.

31.

Modelling time-resolved two-dimensional electronic spectroscopy of the primary photoisomerization event in rhodopsin.

Rivalta I, Nenov A, Weingart O, Cerullo G, Garavelli M, Mukamel S.

J Phys Chem B. 2014 Jul 17;118(28):8396-405. doi: 10.1021/jp502538m. Epub 2014 May 8.

32.

Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins.

Rivalta I, Nenov A, Garavelli M.

Phys Chem Chem Phys. 2014 Aug 28;16(32):16865-79. doi: 10.1039/c3cp55211j. Epub 2014 Apr 2.

PMID:
24691216
33.

Spectral tuning of ultraviolet cone pigments: an interhelical lock mechanism.

Sekharan S, Mooney VL, Rivalta I, Kazmi MA, Neitz M, Neitz J, Sakmar TP, Yan EC, Batista VS.

J Am Chem Soc. 2013 Dec 26;135(51):19064-7. doi: 10.1021/ja409896y. Epub 2013 Dec 12.

34.

Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II.

Amin M, Vogt L, Vassiliev S, Rivalta I, Sultan MM, Bruce D, Brudvig GW, Batista VS, Gunner MR.

J Phys Chem B. 2013 May 23;117(20):6217-26. doi: 10.1021/jp403321b. Epub 2013 May 15.

35.

Solution NMR and computational methods for understanding protein allostery.

Manley G, Rivalta I, Loria JP.

J Phys Chem B. 2013 Mar 21;117(11):3063-73. doi: 10.1021/jp312576v. Epub 2013 Mar 12.

36.

Characterization of an amorphous iridium water-oxidation catalyst electrodeposited from organometallic precursors.

Blakemore JD, Mara MW, Kushner-Lenhoff MN, Schley ND, Konezny SJ, Rivalta I, Negre CF, Snoeberger RC, Kokhan O, Huang J, Stickrath A, Tran LA, Parr ML, Chen LX, Tiede DM, Batista VS, Crabtree RH, Brudvig GW.

Inorg Chem. 2013 Feb 18;52(4):1860-71. doi: 10.1021/ic301968j. Epub 2013 Feb 5.

PMID:
23383971
37.

Allosteric pathways in imidazole glycerol phosphate synthase.

Rivalta I, Sultan MM, Lee NS, Manley GA, Loria JP, Batista VS.

Proc Natl Acad Sci U S A. 2012 May 29;109(22):E1428-36. doi: 10.1073/pnas.1120536109. Epub 2012 May 14.

38.

Oxomanganese complexes for natural and artificial photosynthesis.

Rivalta I, Brudvig GW, Batista VS.

Curr Opin Chem Biol. 2012 Apr;16(1-2):11-8. doi: 10.1016/j.cbpa.2012.03.003. Epub 2012 Apr 3. Review.

39.

Reengineering rate-limiting, millisecond enzyme motions by introduction of an unnatural amino acid.

Watt ED, Rivalta I, Whittier SK, Batista VS, Loria JP.

Biophys J. 2011 Jul 20;101(2):411-20. doi: 10.1016/j.bpj.2011.05.039.

40.

Structural-functional role of chloride in photosystem II.

Rivalta I, Amin M, Luber S, Vassiliev S, Pokhrel R, Umena Y, Kawakami K, Shen JR, Kamiya N, Bruce D, Brudvig GW, Gunner MR, Batista VS.

Biochemistry. 2011 Jul 26;50(29):6312-5. doi: 10.1021/bi200685w. Epub 2011 Jun 27.

41.

S1-state model of the O2-evolving complex of photosystem II.

Luber S, Rivalta I, Umena Y, Kawakami K, Shen JR, Kamiya N, Brudvig GW, Batista VS.

Biochemistry. 2011 Jul 26;50(29):6308-11. doi: 10.1021/bi200681q. Epub 2011 Jun 27.

42.

Adsorption of Ethylene, Vinyl, Acetic Acid, and Acetate Species on PdAu(111) and PdAu(100) Surface Alloys: A Cluster Model Study.

Rivalta I, Mazzone G, Russo N, Sicilia E.

J Chem Theory Comput. 2009 May 12;5(5):1350-60. doi: 10.1021/ct9000137. Epub 2009 Apr 20.

PMID:
26609724
43.

The geometric effect in palladium-gold catalysis. Is the coupling the rate-determining step in the vinyl-acetate synthesis?

Mazzone G, Rivalta I, Russo N, Sicilia E.

Chem Commun (Camb). 2009 Apr 14;(14):1852-4. doi: 10.1039/b823207e. Epub 2009 Feb 20.

PMID:
19319423
44.

Theoretical Investigation of the Mechanism of Acid-Catalyzed Oxygenation of a Pd(II)-Hydride To Produce a Pd(II)-Hydroperoxide.

Chowdhury S, Rivalta I, Russo N, Sicilia E.

J Chem Theory Comput. 2008 Aug;4(8):1283-92. doi: 10.1021/ct8001442.

PMID:
26631704
45.

Activation of methane by the iron dimer cation. A theoretical study.

Chiodo S, Rivalta I, Michelini Mdel C, Russo N, Sicilia E, Ugalde JM.

J Phys Chem A. 2006 Nov 16;110(45):12501-11.

PMID:
17091956
46.

Acetylene cyclotrimerization by early second-row transition metals in the gas phase. A theoretical study.

Martinez M, del Carmen Michelini M, Rivalta I, Russo N, Sicilia E.

Inorg Chem. 2005 Dec 26;44(26):9807-16.

PMID:
16363850
47.

Methane activation by chromium oxide cations in the gas phase: a theoretical study.

Rivalta I, Russo N, Sicilia E.

J Comput Chem. 2006 Jan 30;27(2):174-87.

PMID:
16323159

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