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Items: 41

1.

An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber.

Meral D, Provasi D, Filizola M.

J Chem Phys. 2018 Dec 14;149(22):224101. doi: 10.1063/1.5060960.

PMID:
30553249
2.

Single Proteoliposome High-Content Analysis Reveals Differences in the Homo-Oligomerization of GPCRs.

Walsh SM, Mathiasen S, Christensen SM, Fay JF, King C, Provasi D, Borrero E, Rasmussen SGF, Fung JJ, Filizola M, Hristova K, Kobilka B, Farrens DL, Stamou D.

Biophys J. 2018 Jul 17;115(2):300-312. doi: 10.1016/j.bpj.2018.05.036.

PMID:
30021106
3.

Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations.

Meral D, Provasi D, Prada-Gracia D, Möller J, Marino K, Lohse MJ, Filizola M.

Sci Rep. 2018 May 16;8(1):7705. doi: 10.1038/s41598-018-26070-8.

4.

Development of novel biosensors to study receptor-mediated activation of the G-protein α subunits Gs and Golf.

Yano H, Provasi D, Cai NS, Filizola M, Ferré S, Javitch JA.

J Biol Chem. 2017 Dec 8;292(49):19989-19998. doi: 10.1074/jbc.M117.800698. Epub 2017 Oct 17.

5.

Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity.

Kapoor A, Martinez-Rosell G, Provasi D, de Fabritiis G, Filizola M.

Sci Rep. 2017 Sep 12;7(1):11255. doi: 10.1038/s41598-017-11483-8.

6.

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model.

Marino KA, Prada-Gracia D, Provasi D, Filizola M.

PLoS Comput Biol. 2016 Dec 13;12(12):e1005240. doi: 10.1371/journal.pcbi.1005240. eCollection 2016 Dec.

7.

Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability.

Crowley RS, Riley AP, Sherwood AM, Groer CE, Shivaperumal N, Biscaia M, Paton K, Schneider S, Provasi D, Kivell BM, Filizola M, Prisinzano TE.

J Med Chem. 2016 Dec 22;59(24):11027-11038. doi: 10.1021/acs.jmedchem.6b01235. Epub 2016 Dec 13.

8.
9.

Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors.

Shang Y, Yeatman HR, Provasi D, Alt A, Christopoulos A, Canals M, Filizola M.

ACS Chem Biol. 2016 May 20;11(5):1220-9. doi: 10.1021/acschembio.5b00712. Epub 2016 Feb 17.

10.

The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics.

Schneider S, Provasi D, Filizola M.

Methods Mol Biol. 2015;1335:277-94. doi: 10.1007/978-1-4939-2914-6_18.

11.

Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association.

Provasi D, Boz MB, Johnston JM, Filizola M.

PLoS Comput Biol. 2015 Mar 30;11(3):e1004148. doi: 10.1371/journal.pcbi.1004148. eCollection 2015 Mar.

12.

Computational structural biology of opioid receptors.

Provasi D.

Methods Mol Biol. 2015;1230:13-38. doi: 10.1007/978-1-4939-1708-2_2.

PMID:
25293313
13.

Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multimicrosecond, all-atom molecular dynamics simulations.

Provasi D, Negri A, Coller BS, Filizola M.

Proteins. 2014 Dec;82(12):3231-3240. doi: 10.1002/prot.24540. Epub 2014 Sep 25.

14.

Bioactive conformations of two seminal delta opioid receptor penta-peptides inferred from free-energy profiles.

Scarabelli G, Provasi D, Negri A, Filizola M.

Biopolymers. 2014 Jan;101(1):21-7. doi: 10.1002/bip.22251.

15.

Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.

Coudray N, Valvo S, Hu M, Lasala R, Kim C, Vink M, Zhou M, Provasi D, Filizola M, Tao J, Fang J, Penczek PA, Ubarretxena-Belandia I, Stokes DL.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2140-5. doi: 10.1073/pnas.1215455110. Epub 2013 Jan 22.

16.

Assessing the relative stability of dimer interfaces in g protein-coupled receptors.

Johnston JM, Wang H, Provasi D, Filizola M.

PLoS Comput Biol. 2012;8(8):e1002649. doi: 10.1371/journal.pcbi.1002649. Epub 2012 Aug 16.

17.

Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs.

Fribourg M, Moreno JL, Holloway T, Provasi D, Baki L, Mahajan R, Park G, Adney SK, Hatcher C, Eltit JM, Ruta JD, Albizu L, Li Z, Umali A, Shim J, Fabiato A, MacKerell AD Jr, Brezina V, Sealfon SC, Filizola M, González-Maeso J, Logothetis DE.

Cell. 2011 Nov 23;147(5):1011-23. doi: 10.1016/j.cell.2011.09.055.

18.

Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques.

Provasi D, Artacho MC, Negri A, Mobarec JC, Filizola M.

PLoS Comput Biol. 2011 Oct;7(10):e1002193. doi: 10.1371/journal.pcbi.1002193. Epub 2011 Oct 13.

19.

Molecular determinants and thermodynamics of the amyloid precursor protein transmembrane domain implicated in Alzheimer's disease.

Wang H, Barreyro L, Provasi D, Djemil I, Torres-Arancivia C, Filizola M, Ubarretxena-Belandia I.

J Mol Biol. 2011 May 20;408(5):879-95. doi: 10.1016/j.jmb.2011.03.028. Epub 2011 Mar 31.

20.

Making structural sense of dimerization interfaces of delta opioid receptor homodimers.

Johnston JM, Aburi M, Provasi D, Bortolato A, Urizar E, Lambert NA, Javitch JA, Filizola M.

Biochemistry. 2011 Mar 15;50(10):1682-90. doi: 10.1021/bi101474v. Epub 2011 Feb 9.

21.

Closed headpiece of integrin αIIbβ3 and its complex with an αIIbβ3-specific antagonist that does not induce opening.

Zhu J, Zhu J, Negri A, Provasi D, Filizola M, Coller BS, Springer TA.

Blood. 2010 Dec 2;116(23):5050-9. doi: 10.1182/blood-2010-04-281154. Epub 2010 Aug 2.

22.

Lessons from free energy simulations of delta-opioid receptor homodimers involving the fourth transmembrane helix.

Provasi D, Johnston JM, Filizola M.

Biochemistry. 2010 Aug 10;49(31):6771-6. doi: 10.1021/bi100686t.

23.

Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics.

Provasi D, Filizola M.

Biophys J. 2010 May 19;98(10):2347-55. doi: 10.1016/j.bpj.2010.01.047.

24.

Progress in elucidating the structural and dynamic character of G Protein-Coupled Receptor oligomers for use in drug discovery.

Bortolato A, Mobarec JC, Provasi D, Filizola M.

Curr Pharm Des. 2009;15(35):4017-25. Review.

25.

Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics.

Provasi D, Bortolato A, Filizola M.

Biochemistry. 2009 Oct 27;48(42):10020-9. doi: 10.1021/bi901494n.

26.

Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing-out in beta3 integrins.

Provasi D, Murcia M, Coller BS, Filizola M.

Proteins. 2009 Nov 1;77(2):477-89. doi: 10.1002/prot.22463.

27.

Identification and characterization of folding inhibitors of hen egg lysozyme: an example of a new paradigm of drug design.

Caldarini M, Vasile F, Provasi D, Longhi R, Tiana G, Broglia RA.

Proteins. 2009 Feb 1;74(2):390-9. doi: 10.1002/prot.22161.

PMID:
18623063
28.

Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm.

Marini F, Camilloni C, Provasi D, Broglia RA, Tiana G.

Gene. 2008 Oct 1;422(1-2):37-40. doi: 10.1016/j.gene.2008.06.003. Epub 2008 Jun 6.

PMID:
18593595
29.

Early events in protein folding: Is there something more than hydrophobic burst?

Camilloni C, Sutto L, Provasi D, Tiana G, Broglia RA.

Protein Sci. 2008 Aug;17(8):1424-33. doi: 10.1110/ps.035105.108. Epub 2008 May 29.

30.

Atomistic simulations of the HIV-1 protease folding inhibition.

Verkhivker G, Tiana G, Camilloni C, Provasi D, Broglia RA.

Biophys J. 2008 Jul;95(2):550-62. doi: 10.1529/biophysj.107.127621. Epub 2008 Mar 28.

31.

Exploring the protein G helix free-energy surface by solute tempering metadynamics.

Camilloni C, Provasi D, Tiana G, Broglia RA.

Proteins. 2008 Jun;71(4):1647-54.

PMID:
18076039
32.

Optical absorption of a green fluorescent protein variant: environment effects in a density functional study.

Camilloni C, Provasi D, Tiana G, Broglia RA.

J Phys Chem B. 2007 Sep 13;111(36):10807-12. Epub 2007 Aug 22.

PMID:
17713940
33.

Insight into the folding inhibition of the HIV-1 protease by a small peptide.

Bonomi M, Gervasio FL, Tiana G, Provasi D, Broglia RA, Parrinello M.

Biophys J. 2007 Oct 15;93(8):2813-21. Epub 2007 Jun 15.

34.

Low-throughput model design of protein folding inhibitors.

Broglia RA, Tiana G, Sutto L, Provasi D, Perelli V.

Proteins. 2007 May 1;67(2):469-78.

PMID:
17295323
35.

A folding inhibitor of the HIV-1 protease.

Broglia RA, Provasi D, Vasile F, Ottolina G, Longhi R, Tiana G.

Proteins. 2006 Mar 1;62(4):928-33.

PMID:
16385559
36.

Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers.

Broglia RA, Tiana G, Sutto L, Provasi D, Simona F.

Protein Sci. 2005 Oct;14(10):2668-81.

37.

Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins.

Tiana G, Provasi D, Broglia RA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 May;67(5 Pt 1):051909. Epub 2003 May 14.

PMID:
12786180
38.

Off-label use of drugs in Italy: a prospective, observational and multicentre study.

Pandolfini C, Impicciatore P, Provasi D, Rocchi F, Campi R, Bonati M; Italian Paediatric Off-label Collaborative Group.

Acta Paediatr. 2002;91(3):339-47.

PMID:
12022310
39.

Designability of lattice model heteropolymers.

Tiana G, Broglia RA, Provasi D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jul;64(1 Pt 1):011904. Epub 2001 Jun 13.

PMID:
11461285
40.

Incidence of adverse drug reactions in paediatric in/out-patients: a systematic review and meta-analysis of prospective studies.

Impicciatore P, Choonara I, Clarkson A, Provasi D, Pandolfini C, Bonati M.

Br J Clin Pharmacol. 2001 Jul;52(1):77-83. Review.

41.

Nasal delivery progesterone powder formulations comparison with oral administration.

Provasi D, De Ascentiis A, Minutello A, Colombo P, Catellani PL.

Boll Chim Farm. 1993 Nov;132(10):402-4. No abstract available.

PMID:
8054196

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