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Molecular dynamics studies of the P pilus rod subunit PapA (100 visite)

Vitagliano L, Ruggiero A, Pedone C, Berisio R

J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2009 Mar; 15(3): 192-199.

Tipo di articolo: Journal Article, Research Support, Non-U. S. Gov'T,

Impact factor: 1.807

Impact factor a 5 anni: 1.872


Parole chiave: Adhesive Proteins, Chaperone, Donor-Strand Exchange, Molecular Dynamics, Protein-Protein Interactions, Bacterial Protein, Protein Papa, Unclassified Drug, Atpa Protein, E Coli, Escherichia Coli Protein, Fimbria Protein, Bacterium Pilus, Binding Site, Complex Formation, Conference Paper, Controlled Study, Molecular Model, Nonhuman, Priority Journal, Protein Domain, Protein Protein Interaction, Uropathogenic Escherichia Coli, Article, Chemistry, Computer Simulation, Protein Secondary Structure, Protein Tertiary Structure, Thermodynamics, Bacteria (microorganisms), Fimbriae Proteins, Protein Structure,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-63449138207&partnerID=40&md5=3221e7d0d77e45dc87f20a31d40306d7

Adhesion of uropathogenic Escherichia coli to host tissues is mediated by pili, which extend from the outer cell membrane of the bacterium. Here we report molecular dynamics (MD) characterizations of the major constituent of P pili from the uropathogenic E. coli, PapA, in unliganded state and in complex with the G1 strand of the chaperone PapD. To mimic the PapA response to the gradual dissociation of the PapD G1 strand and to evaluate the role of PapA chaperone recognition sites, we also carried out MD simulations of complexes of PapA with fragments of PapD G1 strand, that leave either the P4 or both P3 and P4 sites unoccupied. Data on the unbound form of PapA indicate that, upon release of the chaperone, PapA evolves toward compact states that are likely not prone to subunit-subunit association. In line with recent experimental reports, this finding implies that chaperone release and subunit-subunit association must be concerted. Our data also indicated that the gradual unbinding of the chaperone from the PapA groove has increasingly strong structural consequences. Indeed, the release of the chaperone from the site P4, which is closest to the initiation site (P5), does not have dramatic effects on the domain structure, whereas its release from both the P4 and the adjacent P3 sites induces a quick structural transition toward a collapsed state, where the subunit groove is obstructed. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
*** IBB - CNR ***

Istituto di Biostrutture e Bioimmagini, CNR, Università degli Studi di Napoli Federico II, via Mezzocannone 16, I-80134 Napoli, Italy

Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, via Mezzocannone 16, I-80134 Napoli, Italy
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Sauer, F.G., Knight, S.D., Waksman, G.J., Hultgren, S.J., Papd-like chaperones and pilus biogenesis (2000) Semin. Cell Dev. Biol, 11, pp. 27-34

Sauer, F.G., Remaut, H., Hultgren, S.J., Waksman, G., Fiber assembly by the chaperone-usher pathway (2004) Biochim. Biophys. Acta, 1694, pp. 259-267

Zavialov, A.V., Kersley, J., Korpela, T., Zav'yalov, V.P., MacIntyre, S., Knight, S.D., Donor strand complementation mechanism in the biogenesis of non-pilus systems (2002) Mol. Microbiol, 45, pp. 983-995

Zavialov, A., Zav'yalova, G., Korpela, T., Zav'yalov, V., Fgl chaperone-assembled fimbrial polyadhesins: Anti-immune armament of gram-negative bacterial pathogens (2007) FEMS Microbiol. Rev, 31, pp. 478-514

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Dodson, K.W., Jacob-Dubuisson, F., Striker, R.T., Hultgren, S.J., Outermembrane papc molecular usher discriminately recognizes periplasmic chaperone-pilus subunit complexes (1993) Proc. Natl. Acad. Sci. U.S.A, 90, pp. 3670-3674

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Zavialov, A.V., Berglund, J., Pudney, A.F., Fooks, L.J., Ibrahim, T.M., MacIntyre, S., Knight, S.D., Structure and biogenesis of the capsular f1 antigen from yersinia pestis: Preserved folding energy drives fiber formation (2003) Cell, 113, pp. 587-596

Zavialov, A.V., Tischenko, V.M., Fooks, L.J., Brandsdal, B.O., Aqvist, J., Zav'yalov, V.P., Macintyre, S., Knight, S.D., Resolving the energy paradox of chaperone/ usher-mediated fibre assembly (2005) Biochem. J, 389, pp. 685-694

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Verger, D., Bullitt, E., Hultgren, S.J., Waksman, G., Crystal structure of the p pilus rod subunit papa (2007) PLoS Pathog, 3, pp. e73

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107: 5064-5073Vetsch, M., Erilov, D., Moliere, N., Nishiyama, M., Ignatov, O., Glockshuber, R., Mechanism of fibre assembly through the chaperone-usher pathway (2006) EMBO Rep, 7, pp. 734-738

Verger, D., Miller, E., Remaut, H., Waksman, G., Hultgren, S., Molecular mechanism of p pilus termination in uropathogenic escherichia coli (2006) EMBO Rep, 7, pp. 1228-1232

Hooton, T. M., Stamm, W. E., Diagnosis and treatment of uncomplicated urinary tract infection (1997) Infect. Dis. Clin. North Am, 11, pp. 551-58

Sauer, F. G., Knight, S. D., Waksman, G. J., Hultgren, S. J., Papd-like chaperones and pilus biogenesis (2000) Semin. Cell Dev. Biol, 11, pp. 27-34

Sauer, F. G., Remaut, H., Hultgren, S. J., Waksman, G., Fiber assembly by the chaperone-usher pathway (2004) Biochim. Biophys. Acta, 1694, pp. 259-267

Zavialov, A. V., Kersley, J., Korpela, T., Zav'yalov, V. P., MacIntyre, S., Knight, S. D., Donor strand complementation mechanism in the biogenesis of non-pilus systems (2002) Mol. Microbiol, 45, pp. 983-995

Soto, G. E., Hultgren, S. J., Bacterial adhesins: Common themes and variations in architecture and assembly (1999) J. Bacteriol, 181, pp. 1059-1071

Dodson, K. W., Jacob-Dubuisson, F., Striker, R. T., Hultgren, S. J., Outermembrane papc molecular usher discriminately recognizes periplasmic chaperone-pilus subunit complexes (1993) Proc. Natl. Acad. Sci. U. S. A, 90, pp. 3670-3674

Knight, S. D., Structure and assembly of yersinia pestis f1 antigen (2007) Adv. Exp. Med. Biol, 603, pp. 74-87

Sauer, F. G., Mulvey, M. A., Schilling, J. D., Martinez, J. J., Hultgren, S. J., Bacterial pili: Molecular mechanisms of pathogenesis (2000) Curr. Opin. Microbiol, 3, pp. 65-72

Sauer, F. G., Pinkner, J. S., Waksman, G., Hultgren, S. J., Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation (2002) Cell, 111, pp. 543-551

Sauer, F. G., Futterer, K., Pinkner, J. S., Dodson, K. W., Hultgren, S. J., Waksman, G., Structural basis of chaperone function and pilus biogenesis (1999) Science, 285, pp. 1058-1061

Zavialov, A. V., Berglund, J., Pudney, A. F., Fooks, L. J., Ibrahim, T. M., MacIntyre, S., Knight, S. D., Structure and biogenesis of the capsular f1 antigen from yersinia pestis: Preserved folding energy drives fiber formation (2003) Cell, 113, pp. 587-596

Zavialov, A. V., Tischenko, V. M., Fooks, L. J., Brandsdal, B. O., Aqvist, J., Zav'yalov, V. P., Macintyre, S., Knight, S. D., Resolving the energy paradox of chaperone/ usher-mediated fibre assembly (2005) Biochem. J, 389, pp. 685-694

Rose, R. J., Welsh, T. S., Waksman, G., Ashcroft, A. E., Radford, S. E., Paci, E., Donor-strand exchange in chaperone-assisted pilus assembly revealed in atomic detail by molecular dynamics (2008) J. Mol. Biol, 375, pp. 908-919

Jones, T. A., Interactive electron-density map interpretation: Frominter to o (2004) Acta Crystallogr. D Biol. Crystallogr, 60, pp. 2115-2125

Scott, W. R. P., Huenenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., van Gunsteren, W. F., The gromos biomolecular simulation program package (1999) J. Phys. Chem. A, 103, pp. 3596-3607

Jorgensen, W. L., Tirado-Rives, T., The opls forcefield for proteins. Energy minimizations for crystals of cyclic peptides and crambin (1988) J. Am. Chem. Soc, 110, pp. 1657-1666

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Langella E, Improta R, Crescenzi O, Barone V
* Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations (148 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.
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Merlino A, Esposito L, Vitagliano L
* Polyglutamine Repeats And Beta-Helix Structure: Molecular Dynamics Study (119 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jun 1; 63(4): 918-927.
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De Capua A, Goodman M, Amino Y, Saviano M, Benedetti E
* Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies (171 visite)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2006 Feb; 7(2): 377-387.
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Merlino A, Mazzarella L, Carannante A, Di Fiore A, Di Donato A, Notomista E, Sica F
* The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants (108 visite)
J Biol Chem Journal Of Biological Chemistry (ISSN: 0021-9258, 1083-351x), 2005 May 6; 280(18): 17953-17960.
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Esposito L, Daggett V
* Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations (94 visite)
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2005 Mar 8; 44(9): 3358-3368.
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Merlino A, Ceruso MA, Vitagliano L, Mazzarella L
* Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease (124 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2005 Mar; 88(3): 2003-2012.
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Langella E, Improta R, Barone V
* Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues (113 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2004 Dec; 87(6): 3623-3632.
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Pappalardo M, Milardi D, La Rosa C, Zannoni C, Rizzarelli E, Grasso D
* A molecular dynamics study on the conformational stability of PrP 180-193 helix II prion fragment (97 visite)
Chemical Physics Letters (ISSN: 0009-2614), 2004 Jun 1; 390(4-6): 511-516.
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Pappalardo M, Milardi D, Grasso DM, La Rosa C
* Free energy perturbation and molecular dynamics calculations of copper binding to azurin (103 visite)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2003 Apr 30; 24(6): 779-785.
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Merlino A, Vitagliano L, Ceruso M, Di Nola A, Mazzarella L
* Global and local motions in ribonuclease A: A molecular dynamics study (97 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002 Nov 15; 65(4): 274-283.
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Saviano M, Rossi F, Pavone V, Di Blasio B, Pedone C
Molecular dynamics simulation in vacuo and in solution of [Aib5, 6-D- Ala8] Cyclolinopeptide A: A conformational and comparative study (102 visite)
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 1992 Jun; 9(6): 1045-1060.
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45 Records (40 escludendo Abstract e Conferenze).
Impact factor totale: 172.373 (152.52 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 168.662 (145.87 escludendo Abstract e Conferenze).







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