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Items: 47

1.

Transmembrane Prolines Mediate Signal Sensing and Decoding in Bacillus subtilis DesK Histidine Kinase.

Fernández P, Porrini L, Albanesi D, Abriata LA, Dal Peraro M, de Mendoza D, Mansilla MC.

MBio. 2019 Nov 26;10(6). pii: e02564-19. doi: 10.1128/mBio.02564-19.

2.

pH-Induced Binding of the Axial Ligand in an Engineered CuA Site Favors the πu State.

Morgada MN, Emiliani F, Chacón KN, Álvarez-Paggi D, Murgida DH, Blackburn NJ, Abriata LA, Vila AJ.

Inorg Chem. 2019 Dec 2;58(23):15687-15691. doi: 10.1021/acs.inorgchem.9b01868. Epub 2019 Nov 11.

PMID:
31710470
3.

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments.

Abriata LA, Tamò GE, Dal Peraro M.

Proteins. 2019 Dec;87(12):1100-1112. doi: 10.1002/prot.25787. Epub 2019 Aug 7.

PMID:
31344267
4.

Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States.

Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA.

MBio. 2019 Jul 2;10(4). pii: e00405-19. doi: 10.1128/mBio.00405-19.

5.

Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes.

Mayorov A, Dal Peraro M, Abriata LA.

Mol Biol Evol. 2019 Aug 1;36(8):1728-1733. doi: 10.1093/molbev/msz096.

PMID:
31004173
6.

Electron transfer in an acidophilic bacterium: interaction between a diheme cytochrome and a cupredoxin.

Wang X, Roger M, Clément R, Lecomte S, Biaso F, Abriata LA, Mansuelle P, Mazurenko I, Giudici-Orticoni MT, Lojou E, Ilbert M.

Chem Sci. 2018 May 1;9(21):4879-4891. doi: 10.1039/c8sc01615a. eCollection 2018 Jun 7.

7.

Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway.

Bologna NG, Iselin R, Abriata LA, Sarazin A, Pumplin N, Jay F, Grentzinger T, Dal Peraro M, Voinnet O.

Mol Cell. 2018 Feb 15;69(4):709-719.e5. doi: 10.1016/j.molcel.2018.01.007. Epub 2018 Feb 1.

8.

Augmenting Research, Education, and Outreach with Client-Side Web Programming.

Abriata LA, Rodrigues JPGLM, Salathé M, Patiny L.

Trends Biotechnol. 2018 May;36(5):473-476. doi: 10.1016/j.tibtech.2017.11.009. Epub 2017 Dec 15.

9.
10.

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods.

Abriata LA, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M.

Proteins. 2018 Mar;86 Suppl 1:97-112. doi: 10.1002/prot.25423. Epub 2017 Nov 29.

PMID:
29139163
11.

Structural, physicochemical and dynamic features conserved within the aerolysin pore-forming toxin family.

Cirauqui N, Abriata LA, van der Goot FG, Dal Peraro M.

Sci Rep. 2017 Oct 24;7(1):13932. doi: 10.1038/s41598-017-13714-4.

12.

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics.

Abriata LA, Kinch LN, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M.

Proteins. 2018 Mar;86 Suppl 1:16-26. doi: 10.1002/prot.25403. Epub 2017 Oct 24.

PMID:
29044714
13.

Functional assays for the assessment of the pathogenicity of variants of GOSR2, an ER-to-Golgi SNARE involved in progressive myoclonus epilepsies.

Völker JM, Dergai M, Abriata LA, Mingard Y, Ysselstein D, Krainc D, Dal Peraro M, Fischer von Mollard G, Fasshauer D, Koliwer J, Schwake M.

Dis Model Mech. 2017 Dec 19;10(12):1391-1398. doi: 10.1242/dmm.029132.

14.

Mitochondrial cytochrome c oxidase biogenesis: Recent developments.

Timón-Gómez A, Nývltová E, Abriata LA, Vila AJ, Hosler J, Barrientos A.

Semin Cell Dev Biol. 2018 Apr;76:163-178. doi: 10.1016/j.semcdb.2017.08.055. Epub 2017 Sep 8. Review.

15.

Signal Sensing and Transduction by Histidine Kinases as Unveiled through Studies on a Temperature Sensor.

Abriata LA, Albanesi D, Dal Peraro M, de Mendoza D.

Acc Chem Res. 2017 Jun 20;50(6):1359-1366. doi: 10.1021/acs.accounts.6b00593. Epub 2017 May 5. Review.

PMID:
28475313
17.

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

Abriata LA, Spiga E, Peraro MD.

Biophys J. 2016 Aug 23;111(4):743-755. doi: 10.1016/j.bpj.2016.07.011.

18.

Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins.

Song AS, Poor TA, Abriata LA, Jardetzky TS, Dal Peraro M, Lamb RA.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):E3844-51. doi: 10.1073/pnas.1608349113. Epub 2016 Jun 22.

20.

Structural database resources for biological macromolecules.

Abriata LA.

Brief Bioinform. 2017 Jul 1;18(4):659-669. doi: 10.1093/bib/bbw049.

PMID:
27273290
21.

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory.

González MM, Abriata LA, Tomatis PE, Vila AJ.

Mol Biol Evol. 2016 Jul;33(7):1768-76. doi: 10.1093/molbev/msw052. Epub 2016 Mar 15.

22.

XacFhaB adhesin, an important Xanthomonas citri ssp. citri virulence factor, is recognized as a pathogen-associated molecular pattern.

Garavaglia BS, Zimaro T, Abriata LA, Ottado J, Gottig N.

Mol Plant Pathol. 2016 Dec;17(9):1344-1353. doi: 10.1111/mpp.12364. Epub 2016 Jun 9.

23.

GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis.

Kolly GS, Mukherjee R, Kilacsková E, Abriata LA, Raccaud M, Blaško J, Sala C, Dal Peraro M, Mikušová K, Cole ST.

J Bacteriol. 2015 Dec;197(23):3686-97. doi: 10.1128/JB.00628-15. Epub 2015 Sep 14.

24.

Loop recognition and copper-mediated disulfide reduction underpin metal site assembly of CuA in human cytochrome oxidase.

Morgada MN, Abriata LA, Cefaro C, Gajda K, Banci L, Vila AJ.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11771-6. doi: 10.1073/pnas.1505056112. Epub 2015 Sep 8.

25.

A coiled coil switch mediates cold sensing by the thermosensory protein DesK.

Saita E, Abriata LA, Tsai YT, Trajtenberg F, Lemmin T, Buschiazzo A, Dal Peraro M, de Mendoza D, Albanesi D.

Mol Microbiol. 2015 Oct;98(2):258-71. doi: 10.1111/mmi.13118. Epub 2015 Aug 3.

26.

Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in Cu(A) Sites of Cytochrome c Oxidase.

Zitare U, Alvarez-Paggi D, Morgada MN, Abriata LA, Vila AJ, Murgida DH.

Angew Chem Int Ed Engl. 2015 Aug 10;54(33):9555-9. doi: 10.1002/anie.201504188. Epub 2015 Jun 26.

PMID:
26118421
27.
28.

The importance of dynamics in integrative modeling of supramolecular assemblies.

Tamò GE, Abriata LA, Dal Peraro M.

Curr Opin Struct Biol. 2015 Apr;31:28-34. doi: 10.1016/j.sbi.2015.02.018. Epub 2015 Mar 18. Review.

PMID:
25795087
29.

How structural and physicochemical determinants shape sequence constraints in a functional enzyme.

Abriata LA, Palzkill T, Dal Peraro M.

PLoS One. 2015 Feb 23;10(2):e0118684. doi: 10.1371/journal.pone.0118684. eCollection 2015.

30.

A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP.

Abriata LA, Pontel LB, Vila AJ, Dal Peraro M, Soncini FC.

J Inorg Biochem. 2014 Nov;140:199-201. doi: 10.1016/j.jinorgbio.2014.07.022. Epub 2014 Aug 7.

PMID:
25151035
31.

Control of the electronic ground state on an electron-transfer copper site by second-sphere perturbations.

Morgada MN, Abriata LA, Zitare U, Alvarez-Paggi D, Murgida DH, Vila AJ.

Angew Chem Int Ed Engl. 2014 Jun 10;53(24):6188-92. doi: 10.1002/anie.201402083. Epub 2014 Apr 28.

PMID:
24777732
32.

Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics.

Spiga E, Abriata LA, Piazza F, Dal Peraro M.

J Phys Chem B. 2014 May 22;118(20):5310-21. doi: 10.1021/jp4126705. Epub 2014 May 9.

PMID:
24773474
33.

Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control.

Abriata LA, Vila AJ, Dal Peraro M.

J Biol Inorg Chem. 2014 Jun;19(4-5):565-75. doi: 10.1007/s00775-014-1108-7. Epub 2014 Jan 30.

PMID:
24477946
34.

Redox-state sensing by hydrogen bonds in the CuA center of cytochrome c oxidase.

Abriata LA, Vila AJ.

J Inorg Biochem. 2014 Mar;132:18-20. doi: 10.1016/j.jinorgbio.2013.07.032. Epub 2013 Jul 31.

PMID:
24012017
35.

All-atom simulations of crowding effects on ubiquitin dynamics.

Abriata LA, Spiga E, Dal Peraro M.

Phys Biol. 2013 Aug;10(4):045006. doi: 10.1088/1478-3975/10/4/045006. Epub 2013 Aug 2.

PMID:
23911977
36.

Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank.

Abriata LA.

Acta Crystallogr B Struct Sci Cryst Eng Mater. 2013 Apr;69(Pt 2):176-83. doi: 10.1107/S2052519213002959. Epub 2013 Feb 26.

PMID:
23719704
37.

Native Cu(A) redox sites are largely resilient to pH variations within a physiological range.

Alvarez-Paggi D, Abriata LA, Murgida DH, Vila AJ.

Chem Commun (Camb). 2013 Jun 14;49(47):5381-3. doi: 10.1039/c3cc40457a.

PMID:
23652317
38.

Electron spin density on the axial His ligand of high-spin and low-spin nitrophorin 2 probed by heteronuclear NMR spectroscopy.

Abriata LA, Zaballa ME, Berry RE, Yang F, Zhang H, Walker FA, Vila AJ.

Inorg Chem. 2013 Feb 4;52(3):1285-95. doi: 10.1021/ic301805y. Epub 2013 Jan 17.

39.

Off-the-Vine Ripening of Tomato Fruit Causes Alteration in the Primary Metabolite Composition.

Sorrequieta A, Abriata LA, Boggio SB, Valle EM.

Metabolites. 2013 Oct 16;3(4):967-78. doi: 10.3390/metabo3040967.

40.

Alternative ground states enable pathway switching in biological electron transfer.

Abriata LA, Álvarez-Paggi D, Ledesma GN, Blackburn NJ, Vila AJ, Murgida DH.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17348-53. doi: 10.1073/pnas.1204251109. Epub 2012 Oct 10.

41.

Analysis of copper-ligand bond lengths in X-ray structures of different types of copper sites in proteins.

Abriata LA.

Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1223-31. doi: 10.1107/S0907444912026054. Epub 2012 Aug 18.

PMID:
22948924
42.

Sequence-function-stability relationships in proteins from datasets of functionally annotated variants: the case of TEM β-lactamases.

Abriata LA, Salverda ML, Tomatis PE.

FEBS Lett. 2012 Sep 21;586(19):3330-5. doi: 10.1016/j.febslet.2012.07.010. Epub 2012 Jul 28.

43.

Flexibility of the metal-binding region in apo-cupredoxins.

Zaballa ME, Abriata LA, Donaire A, Vila AJ.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9254-9. doi: 10.1073/pnas.1119460109. Epub 2012 May 29.

44.

Electronic structure of the ground and excited states of the Cu(A) site by NMR spectroscopy.

Abriata LA, Ledesma GN, Pierattelli R, Vila AJ.

J Am Chem Soc. 2009 Feb 11;131(5):1939-46. doi: 10.1021/ja8079669.

45.

Nitration of solvent-exposed tyrosine 74 on cytochrome c triggers heme iron-methionine 80 bond disruption. Nuclear magnetic resonance and optical spectroscopy studies.

Abriata LA, Cassina A, Tórtora V, Marín M, Souza JM, Castro L, Vila AJ, Radi R.

J Biol Chem. 2009 Jan 2;284(1):17-26. doi: 10.1074/jbc.M807203200. Epub 2008 Oct 29.

46.

Mechanism of Cu(A) assembly.

Abriata LA, Banci L, Bertini I, Ciofi-Baffoni S, Gkazonis P, Spyroulias GA, Vila AJ, Wang S.

Nat Chem Biol. 2008 Oct;4(10):599-601. doi: 10.1038/nchembio.110. Epub 2008 Aug 31.

47.

Engineered mononuclear variants in Bacillus cereus metallo-beta-lactamase BcII are inactive.

Abriata LA, González LJ, Llarrull LI, Tomatis PE, Myers WK, Costello AL, Tierney DL, Vila AJ.

Biochemistry. 2008 Aug 19;47(33):8590-9. doi: 10.1021/bi8006912. Epub 2008 Jul 25.

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