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Items: 1 to 50 of 86

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.

Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores.

Cao C, Cirauqui N, Marcaida MJ, Buglakova E, Duperrex A, Radenovic A, Dal Peraro M.

Nat Commun. 2019 Oct 29;10(1):4918. doi: 10.1038/s41467-019-12690-9.

3.

Editorial overview: The future after the cryo-EM resolution revolution.

Dal Peraro M, Song JJ.

Curr Opin Struct Biol. 2019 Oct;58:iii-iv. doi: 10.1016/j.sbi.2019.07.007. Epub 2019 Aug 31. No abstract available.

PMID:
31481281
4.

KAP1 is an antiparallel dimer with a functional asymmetry.

Fonti G, Marcaida MJ, Bryan LC, Träger S, Kalantzi AS, Helleboid PJ, Demurtas D, Tully MD, Grudinin S, Trono D, Fierz B, Dal Peraro M.

Life Sci Alliance. 2019 Aug 19;2(4). pii: e201900349. doi: 10.26508/lsa.201900349. Print 2019 Aug.

5.

Modelling structures in cryo-EM maps.

Malhotra S, Träger S, Dal Peraro M, Topf M.

Curr Opin Struct Biol. 2019 Oct;58:105-114. doi: 10.1016/j.sbi.2019.05.024. Epub 2019 Aug 5. Review.

PMID:
31394387
6.

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
7.

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
8.

An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis.

Lohman DC, Aydin D, Von Bank HC, Smith RW, Linke V, Weisenhorn E, McDevitt MT, Hutchins P, Wilkerson EM, Wancewicz B, Russell J, Stefely MS, Beebe ET, Jochem A, Coon JJ, Bingman CA, Dal Peraro M, Pagliarini DJ.

Mol Cell. 2019 Feb 21;73(4):763-774.e10. doi: 10.1016/j.molcel.2018.11.033. Epub 2019 Jan 17.

PMID:
30661980
9.

Mapping the sensing spots of aerolysin for single oligonucleotides analysis.

Cao C, Li MY, Cirauqui N, Wang YQ, Dal Peraro M, Tian H, Long YT.

Nat Commun. 2018 Jul 19;9(1):2823. doi: 10.1038/s41467-018-05108-5.

10.

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.

11.
12.

Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family.

Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, Pagliarini DJ.

Cell Chem Biol. 2018 Feb 15;25(2):154-165.e11. doi: 10.1016/j.chembiol.2017.11.001. Epub 2017 Nov 30.

13.

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
14.

Recruitment of the amyloid precursor protein by γ-secretase at the synaptic plasma membrane.

Audagnotto M, Kengo Lorkowski A, Dal Peraro M.

Biochem Biophys Res Commun. 2018 Mar 29;498(2):334-341. doi: 10.1016/j.bbrc.2017.10.164. Epub 2017 Oct 31.

PMID:
29097209
15.

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.

16.

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
17.

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.

18.

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
19.

Protein post-translational modifications: In silico prediction tools and molecular modeling.

Audagnotto M, Dal Peraro M.

Comput Struct Biotechnol J. 2017 Mar 31;15:307-319. doi: 10.1016/j.csbj.2017.03.004. eCollection 2017. Review.

20.

Transcriptional regulatory logic of the diurnal cycle in the mouse liver.

Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F; CycliX consortium.

PLoS Biol. 2017 Apr 17;15(4):e2001069. doi: 10.1371/journal.pbio.2001069. eCollection 2017 Apr.

21.

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies.

Tamò G, Maesani A, Träger S, Degiacomi MT, Floreano D, Dal Peraro M.

Sci Rep. 2017 Mar 22;7(1):235. doi: 10.1038/s41598-017-00266-w.

22.

A Biologically-validated HCV E1E2 Heterodimer Structural Model.

Castelli M, Clementi N, Pfaff J, Sautto GA, Diotti RA, Burioni R, Doranz BJ, Dal Peraro M, Clementi M, Mancini N.

Sci Rep. 2017 Mar 16;7(1):214. doi: 10.1038/s41598-017-00320-7.

23.

Evolution of Acid-Sensing Olfactory Circuits in Drosophilids.

Prieto-Godino LL, Rytz R, Cruchet S, Bargeton B, Abuin L, Silbering AF, Ruta V, Dal Peraro M, Benton R.

Neuron. 2017 Feb 8;93(3):661-676.e6. doi: 10.1016/j.neuron.2016.12.024. Epub 2017 Jan 19.

24.

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria.

Murima P, Zimmermann M, Chopra T, Pojer F, Fonti G, Dal Peraro M, Alonso S, Sauer U, Pethe K, McKinney JD.

Nat Commun. 2016 Aug 24;7:12527. doi: 10.1038/ncomms12527.

25.

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
26.

Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity.

Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJP, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ.

Mol Cell. 2016 Aug 18;63(4):608-620. doi: 10.1016/j.molcel.2016.06.030. Epub 2016 Aug 4.

27.

Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process.

Iacovache I, De Carlo S, Cirauqui N, Dal Peraro M, van der Goot FG, Zuber B.

Nat Commun. 2016 Jul 13;7:12062. doi: 10.1038/ncomms12062.

28.

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.

30.

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.

Genna V, Gaspari R, Dal Peraro M, De Vivo M.

Nucleic Acids Res. 2016 Apr 7;44(6):2827-36. doi: 10.1093/nar/gkw128. Epub 2016 Mar 1.

31.

Pore-forming toxins: ancient, but never really out of fashion.

Dal Peraro M, van der Goot FG.

Nat Rev Microbiol. 2016 Feb;14(2):77-92. doi: 10.1038/nrmicro.2015.3. Epub 2015 Dec 7. Review.

PMID:
26639780
32.

LipidBuilder: A Framework To Build Realistic Models for Biological Membranes.

Bovigny C, Tamò G, Lemmin T, Maïno N, Dal Peraro M.

J Chem Inf Model. 2015 Dec 28;55(12):2491-9. doi: 10.1021/acs.jcim.5b00501. Epub 2015 Dec 10.

PMID:
26606666
33.

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.

34.

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.

35.
36.

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp. 1519.

Modarres HP, Dorokhov BD, Popov VO, Ravin NV, Skryabin KG, Dal Peraro M.

Biochemistry. 2015 May 19;54(19):3076-85.

PMID:
25900264
37.

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
38.

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.

39.

Catalytic metal ions and enzymatic processing of DNA and RNA.

Palermo G, Cavalli A, Klein ML, Alfonso-Prieto M, Dal Peraro M, De Vivo M.

Acc Chem Res. 2015 Feb 17;48(2):220-8. doi: 10.1021/ar500314j. Epub 2015 Jan 15. Review.

PMID:
25590654
40.

New strategies for integrative dynamic modeling of macromolecular assembly.

Spiga E, Degiacomi MT, Dal Peraro M.

Adv Protein Chem Struct Biol. 2014;96:77-111. doi: 10.1016/bs.apcsb.2014.06.008. Epub 2014 Sep 30. Review.

PMID:
25443955
41.

HCV E2 core structures and mAbs: something is still missing.

Castelli M, Clementi N, Sautto GA, Pfaff J, Kahle KM, Barnes T, Doranz BJ, Dal Peraro M, Clementi M, Burioni R, Mancini N.

Drug Discov Today. 2014 Dec;19(12):1964-70. doi: 10.1016/j.drudis.2014.08.011. Epub 2014 Aug 27. Review.

42.

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
43.

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase.

Bovigny C, Degiacomi MT, Lemmin T, Dal Peraro M, Stenta M.

J Phys Chem B. 2014 Jul 10;118(27):7457-7466. doi: 10.1021/jp411786z. Epub 2014 Jun 10.

PMID:
24914486
44.

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
45.

Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2.

Vestergaard AL, Coleman JA, Lemmin T, Mikkelsen SA, Molday LL, Vilsen B, Molday RS, Dal Peraro M, Andersen JP.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):E1334-43. doi: 10.1073/pnas.1321165111. Epub 2014 Mar 24. Erratum in: Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16629.

46.

Functional dissection of intersubunit interactions in the EspR virulence regulator of Mycobacterium tuberculosis.

Blasco B, Japaridze A, Stenta M, Wicky BI, Dietler G, Dal Peraro M, Pojer F, Cole ST.

J Bacteriol. 2014 May;196(10):1889-900. doi: 10.1128/JB.00039-14. Epub 2014 Mar 14.

47.

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
48.

Perturbations of the straight transmembrane α-helical structure of the amyloid precursor protein affect its processing by γ-secretase.

Lemmin T, Dimitrov M, Fraering PC, Dal Peraro M.

J Biol Chem. 2014 Mar 7;289(10):6763-74. doi: 10.1074/jbc.M113.470781. Epub 2014 Jan 27.

49.

ComEA is essential for the transfer of external DNA into the periplasm in naturally transformable Vibrio cholerae cells.

Seitz P, Pezeshgi Modarres H, Borgeaud S, Bulushev RD, Steinbock LJ, Radenovic A, Dal Peraro M, Blokesch M.

PLoS Genet. 2014 Jan;10(1):e1004066. doi: 10.1371/journal.pgen.1004066. Epub 2014 Jan 2.

50.

TAL effectors specificity stems from negative discrimination.

Wicky BI, Stenta M, Dal Peraro M.

PLoS One. 2013 Nov 25;8(11):e80261. doi: 10.1371/journal.pone.0080261. eCollection 2013.

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