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Items: 1 to 50 of 63

1.

Coevolutionary Analysis of Protein Sequences for Molecular Modeling.

Malinverni D, Barducci A.

Methods Mol Biol. 2019;2022:379-397. doi: 10.1007/978-1-4939-9608-7_16.

PMID:
31396912
2.

Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H-13C Labeling and Fast Magic-Angle Spinning NMR.

Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P.

J Am Chem Soc. 2019 Jul 17;141(28):11183-11195. doi: 10.1021/jacs.9b04219. Epub 2019 Jul 5.

PMID:
31199882
3.

Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression.

Cordeiro TN, Sibille N, Germain P, Barthe P, Boulahtouf A, Allemand F, Bailly R, Vivat V, Ebel C, Barducci A, Bourguet W, le Maire A, Bernadó P.

Structure. 2019 Aug 6;27(8):1270-1285.e6. doi: 10.1016/j.str.2019.05.001. Epub 2019 Jun 6.

PMID:
31178221
4.

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes.

Marko JF, De Los Rios P, Barducci A, Gruber S.

Nucleic Acids Res. 2019 Jul 26;47(13):6956-6972. doi: 10.1093/nar/gkz497.

5.

Insights into the activation mechanism of human estrogen-related receptor γ by environmental endocrine disruptors.

Thouennon E, Delfosse V, Bailly R, Blanc P, Boulahtouf A, Grimaldi M, Barducci A, Bourguet W, Balaguer P.

Cell Mol Life Sci. 2019 May 24. doi: 10.1007/s00018-019-03129-x. [Epub ahead of print]

PMID:
31127318
6.

Structural basis for chemically-induced homodimerization of a single domain antibody.

Lesne J, Chang HJ, De Visch A, Paloni M, Barthe P, Guichou JF, Mayonove P, Barducci A, Labesse G, Bonnet J, Cohen-Gonsaud M.

Sci Rep. 2019 Feb 12;9(1):1840. doi: 10.1038/s41598-019-38752-y.

7.

Function, evolution, and structure of J-domain proteins.

Kampinga HH, Andreasson C, Barducci A, Cheetham ME, Cyr D, Emanuelsson C, Genevaux P, Gestwicki JE, Goloubinoff P, Huerta-Cepas J, Kirstein J, Liberek K, Mayer MP, Nagata K, Nillegoda NB, Pulido P, Ramos C, De Los Rios P, Rospert S, Rosenzweig R, Sahi C, Taipale M, Tomiczek B, Ushioda R, Young JC, Zimmermann R, Zylicz A, Zylicz M, Craig EA, Marszalek J.

Cell Stress Chaperones. 2019 Jan;24(1):7-15. doi: 10.1007/s12192-018-0948-4. Epub 2018 Nov 26.

8.

Emerging fields in chaperone proteins: A French workshop.

Mileo E, Ilbert M, Barducci A, Bordes P, Castanié-Cornet MP, Garnier C, Genevaux P, Gillet R, Goloubinoff P, Ochsenbein F, Richarme G, Iobbi-Nivol C, Giudici-Orticoni MT, Gontero B, Genest O.

Biochimie. 2018 Aug;151:159-165. doi: 10.1016/j.biochi.2018.06.004. Epub 2018 Jun 8.

9.

Lipid tempering simulation of model biological membranes on parallel platforms.

Cardelli C, Barducci A, Procacci P.

Biochim Biophys Acta Biomembr. 2018 Jul;1860(7):1480-1488. doi: 10.1016/j.bbamem.2018.04.013. Epub 2018 May 1.

10.

Clinical biomarkers for cancer recognition and prevention: A novel approach with optical measurements.

Latini G, De Felice C, Barducci A, Dipaola L, Gentile M, Andreassi MG, Correale M, Bianciardi G.

Cancer Biomark. 2018;22(2):179-198. doi: 10.3233/CBM-170050. Review.

PMID:
29689703
11.

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins.

Goloubinoff P, Sassi AS, Fauvet B, Barducci A, De Los Rios P.

Nat Chem Biol. 2018 Apr;14(4):388-395. doi: 10.1038/s41589-018-0013-8. Epub 2018 Mar 5.

PMID:
29507388
12.

Catch bond drives stator mechanosensitivity in the bacterial flagellar motor.

Nord AL, Gachon E, Perez-Carrasco R, Nirody JA, Barducci A, Berry RM, Pedaci F.

Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):12952-12957. doi: 10.1073/pnas.1716002114. Epub 2017 Nov 28.

13.

Prion protein β2-α2 loop conformational landscape.

Caldarulo E, Barducci A, Wüthrich K, Parrinello M.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9617-9622. doi: 10.1073/pnas.1712155114. Epub 2017 Aug 21.

14.

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.

Nillegoda NB, Stank A, Malinverni D, Alberts N, Szlachcic A, Barducci A, De Los Rios P, Wade RC, Bukau B.

Elife. 2017 May 15;6. pii: e24560. doi: 10.7554/eLife.24560.

15.

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis.

Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A.

Elife. 2017 May 12;6. pii: e23471. doi: 10.7554/eLife.23471.

16.

Communication: Role of explicit water models in the helix folding/unfolding processes.

Palazzesi F, Salvalaglio M, Barducci A, Parrinello M.

J Chem Phys. 2016 Sep 28;145(12):121101.

PMID:
27782670
17.

Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer.

Audagnotto M, Lemmin T, Barducci A, Dal Peraro M.

J Phys Chem Lett. 2016 Sep 15;7(18):3572-8. doi: 10.1021/acs.jpclett.6b01721. Epub 2016 Aug 29.

PMID:
27518597
18.

Accuracy of current all-atom force-fields in modeling protein disordered states.

Palazzesi F, Prakash MK, Bonomi M, Barducci A.

J Chem Theory Comput. 2015 Jan 13;11(1):2-7. doi: 10.1021/ct500718s. Epub 2014 Dec 18.

PMID:
26574197
19.

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones.

Malinverni D, Marsili S, Barducci A, De Los Rios P.

PLoS Comput Biol. 2015 Jun 5;11(6):e1004262. doi: 10.1371/journal.pcbi.1004262. eCollection 2015 Jun.

20.

Quantifying the role of chaperones in protein translocation by computational modeling.

Assenza S, De Los Rios P, Barducci A.

Front Mol Biosci. 2015 Mar 23;2:8. doi: 10.3389/fmolb.2015.00008. eCollection 2015.

21.

Non-equilibrium conformational dynamics in the function of molecular chaperones.

Barducci A, De Los Rios P.

Curr Opin Struct Biol. 2015 Feb;30:161-169. doi: 10.1016/j.sbi.2015.02.008. Epub 2015 Mar 13. Review.

PMID:
25771489
22.

Tackling sampling challenges in biomolecular simulations.

Barducci A, Pfaendtner J, Bonomi M.

Methods Mol Biol. 2015;1215:151-71. doi: 10.1007/978-1-4939-1465-4_8.

PMID:
25330963
23.

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein.

Kellner R, Hofmann H, Barducci A, Wunderlich B, Nettels D, Schuler B.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13355-60. doi: 10.1073/pnas.1407086111. Epub 2014 Aug 27.

24.

Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption.

De Los Rios P, Barducci A.

Elife. 2014 May 27;3:e02218. doi: 10.7554/eLife.02218.

25.

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P.

Chem Soc Rev. 2014 Jul 7;43(13):4871-93. doi: 10.1039/c4cs00048j. Epub 2014 Apr 23. Review.

26.

Free-energy landscape of protein oligomerization from atomistic simulations.

Barducci A, Bonomi M, Prakash MK, Parrinello M.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4708-13. doi: 10.1073/pnas.1320077110. Epub 2013 Nov 18.

27.

Structural and energetic basis for hybridization limits in high-density DNA monolayers.

Doni G, Nkoua Ngavouka MD, Barducci A, Parisse P, De Vita A, Scoles G, Casalis L, Pavan GM.

Nanoscale. 2013 Oct 21;5(20):9988-93. doi: 10.1039/c3nr01799k.

PMID:
23996015
28.

The allosteric communication pathways in KIX domain of CBP.

Palazzesi F, Barducci A, Tollinger M, Parrinello M.

Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14237-42. doi: 10.1073/pnas.1313548110. Epub 2013 Aug 12.

29.

Oral mucosal color changes as a clinical biomarker for cancer detection.

Latini G, De Felice C, Barducci A, Chitano G, Pignatelli A, Grimaldi L, Tramacere F, Laurini R, Andreassi MG, Portaluri M.

Eur J Cancer Prev. 2012 Jul;21(4):360-6. doi: 10.1097/CEJ.0b013e328350de51.

PMID:
22634938
30.

Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.

Berteotti A, Barducci A, Parrinello M.

J Am Chem Soc. 2011 Nov 2;133(43):17200-6. doi: 10.1021/ja202849a. Epub 2011 Oct 6.

PMID:
21854002
31.

Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations.

Prakash MK, Barducci A, Parrinello M.

J Chem Theory Comput. 2011 Jul 12;7(7):2025-7. doi: 10.1021/ct200208h. Epub 2011 Jun 22.

PMID:
26606473
32.

Assessing the Quality of the OPEP Coarse-Grained Force Field.

Barducci A, Bonomi M, Derreumaux P.

J Chem Theory Comput. 2011 Jun 14;7(6):1928-34. doi: 10.1021/ct100646f. Epub 2011 May 19.

PMID:
26596453
33.

The hyperspectral irradiometer, a new instrument for long-term and unattended field spectroscopy measurements.

Meroni M, Barducci A, Cogliati S, Castagnoli F, Rossini M, Busetto L, Migliavacca M, Cremonese E, Galvagno M, Colombo R, di Cella UM.

Rev Sci Instrum. 2011 Apr;82(4):043106. doi: 10.1063/1.3574360.

PMID:
21528994
34.

Multiple routes and milestones in the folding of HIV-1 protease monomer.

Bonomi M, Barducci A, Gervasio FL, Parrinello M.

PLoS One. 2010 Oct 13;5(10):e13208. doi: 10.1371/journal.pone.0013208.

35.

Radiometric and signal-to-noise ratio properties of multiplex dispersive spectrometry.

Barducci A, Guzzi D, Lastri C, Nardino V, Marcoionni P, Pippi I.

Appl Opt. 2010 Oct 1;49(28):5366-73. doi: 10.1364/AO.49.005366.

PMID:
20885473
36.

Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations.

Prakash MK, Barducci A, Parrinello M.

Biophys J. 2010 Jul 21;99(2):588-94. doi: 10.1016/j.bpj.2010.04.024.

37.

Theoretical aspects of Fourier Transform Spectrometry and common path triangular interferometers.

Barducci A, Guzzi D, Lastri C, Marcoionni P, Nardino V, Pippi I.

Opt Express. 2010 May 24;18(11):11622-49. doi: 10.1364/OE.18.011622.

PMID:
20589022
38.

Linking well-tempered metadynamics simulations with experiments.

Barducci A, Bonomi M, Parrinello M.

Biophys J. 2010 May 19;98(9):L44-6. doi: 10.1016/j.bpj.2010.01.033.

39.

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

Bonomi M, Barducci A, Parrinello M.

J Comput Chem. 2009 Aug;30(11):1615-21. doi: 10.1002/jcc.21305.

PMID:
19421997
40.

Di-(2-ethylhexyl)phthalate leakage and color changes in endotracheal tubes after application in high-risk newborns.

Latini G, De Felice C, Del Vecchio A, Barducci A, Ferri M, Chiellini F.

Neonatology. 2009;95(4):317-23. doi: 10.1159/000181161. Epub 2008 Dec 11.

PMID:
19077392
41.

Aerospace wetland monitoring by hyperspectral imaging sensors: a case study in the coastal zone of San Rossore Natural Park.

Barducci A, Guzzi D, Marcoionni P, Pippi I.

J Environ Manage. 2009 May;90(7):2278-86. doi: 10.1016/j.jenvman.2007.06.033. Epub 2008 Apr 21.

PMID:
18423842
42.
43.

Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

Barducci A, Bussi G, Parrinello M.

Phys Rev Lett. 2008 Jan 18;100(2):020603. Epub 2008 Jan 18.

PMID:
18232845
44.

Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations.

Chelli R, Marsili S, Barducci A, Procacci P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):050101. Epub 2007 May 7.

PMID:
17677005
45.

Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations.

Chelli R, Marsili S, Barducci A, Procacci P.

J Chem Phys. 2007 Jul 21;127(3):034110.

PMID:
17655434
46.
47.

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.

Procacci P, Marsili S, Barducci A, Signorini GF, Chelli R.

J Chem Phys. 2006 Oct 28;125(16):164101.

PMID:
17092057
48.

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations.

Marsili S, Barducci A, Chelli R, Procacci P, Schettino V.

J Phys Chem B. 2006 Jul 27;110(29):14011-3.

PMID:
16854090
49.

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding.

Barducci A, Chelli R, Procacci P, Schettino V, Gervasio FL, Parrinello M.

J Am Chem Soc. 2006 Mar 1;128(8):2705-10.

PMID:
16492057
50.

Abnormal oral mucosal light reflectance: a new clinical marker of high risk for colorectal cancer.

De Felice C, Gentile M, Barducci A, Bellosi A, Parrini S, Chitano G, Latini G.

Gut. 2006 Oct;55(10):1436-9. Epub 2006 Feb 9.

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