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The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis (69 visite)

Improta R, Vitagliano L, Esposito L

Proteins (ISSN: 1097-0134electronic, 0887-3585linking), 2015 Nov; 83(11): 1973-1986.

Tipo di articolo: Journal Article, Research Support, Non-U. S. Gov'T, , Impact factor: 2.499, Impact factor a 5 anni: 2.725, Url: Non disponibile.

Parole chiave: Carbon, Chemistry, Hydrogen, Models, Statistical, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Peptides, Proteins, Ramachandran Plot, Backbone Angles, Conformational Energetics, Context-Dependent Geometry, Local Effects,

Affiliazioni: *** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche (CNR), Napoli, I-80134, Italy.,


Riferimenti: Non disponibile.

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of psi and/or phi. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(alpha) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations.
Nessun risultato.

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GrassoG, Magrì A, Bellia F, Pietropaolo A, La Mendola D, Rizzarelli E
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Pailot A, D'Ambrosio K, Corbier C, Talfournier F, Branlant G
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Berisio R, Loguercio S, De Simone A, Zagari A, Vitagliano L
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Esposito L, Bruno I, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
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Impact Factor: 3.922
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Esposito L, Bruno I, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
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Impact Factor: 3.609
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De Luca S, Ragone R, Bracco C, Digilio G, Tesauro D, Saviano M, Pedone C, Morelli G
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Esposito L, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
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Orru S, Ruoppolo M, Francese S, Vitagliano L, Marino G, Esposito C
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Ogawa R, Pacelli R, Espey MG, Miranda KM, Friedman N, Kim SM, Cox G, Mitchell JB, Wink DA, Russo A
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Impellizzeri G, Pappalardo G, D'Alessandro F, Rizzarelli E, Saviano M, Iacovino R, Benedetti E, Pedone C
Erratum: Solid state and solution conformation of 6-{4-[N-tert- butoxycarbonyl-N-(N'-ethyl)propanamide]imidazolyl}-6- deoxycyclomaltoheptaose: Evidence of self-inclusion of the boc group within the β-cyclodextrin cavity (European Journal of Organic Chemistry (2000) (1065-1076)) (115 visite)
Eur J Org Chem (ISSN: 1434-193x), 2000; (12): 2345-2345.
Impact Factor: 2.15
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 Esposito L, Sica F, Sorrentino G, Berisio R, Carotenuto L, Giordano A, Raia C, Rossi M, Lamzin VS, Willson KS, Zagari A
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Acta Crystallogr D Biol Crystallogr, 1998; 54: 386-390.
Impact Factor: 0
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Esposito L, Sica F, Sorrentino G, Berisio R, Carotenuto L, Giordano A, Raia CA, Rossi M, Lamzin VS, Wilson KS, Zagari A
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Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 1998; 54(3): 386-390.
Impact Factor: 2.244
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Bonomo RP, Di Blasio B, Maccarrone G, Pavone V, Pedone C, Rizzarelli E, Saviano M, Vecchio G
Crystal and Molecular Structure of the [6-Deoxy-6-[(2-(4-imidazolyl)ethyl)amino]cyclomaltoheptaose]copper(II) Ternary Complex with L-Tryptophanate. Role of Weak Forces in the Chiral Recognition Process Assisted by a Metallocyclodextrin (157 visite)
Inorg Chem (ISSN: 0020-1669, 1520-510x, 1520-510xelectronic), 1996 Jul 17; 35(15): 4497-4504.
Impact Factor: 2.736
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Wink DA, Cook JA, Pacelli R, DeGraff W, Gamson J, Liebmann J, Krishna MC, Mitchell JB
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Arch Biochem Biophys (ISSN: 0003-9861), 1996 Jul 15; 331(2): 241-248.
Impact Factor: 2.649
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Pacelli R, Wink DA, Cook JA, Krishna MC, DeGraff W, Friedman N, Tsokos M, Samuni A, Mitchell JB
NITRIC-OXIDE POTENTIATES HYDROGEN PEROXIDE-INDUCED KILLING OF ESCHERICHIA-COLI (78 visite)
Journal Of Experimental Medicine (ISSN: 0022-1007), 1995 Nov 1; 182(5): 1469-1479.
Impact Factor: 14.384
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SANTINI A, BENEDETTI E, PEDONE C, GIORDANO M, CALIENDO G, SANTAGADA V, GRIECO P, GRECO G
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Tetrahedron (ISSN: 0040-4020), 1995 Feb 13; 51(7): 1995-2008.
Impact Factor: 2.327
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PEARL L, DEMASI D, HEMMINGS A, SICA F, MAZZARELLA L, RAIA C, DAURIA S, ROSSI M
CRYSTALLIZATION AND PRELIMINARY-X-RAY ANALYSIS OF AN NAD+-DEPENDENT ALCOHOL-DEHYDROGENASE FROM THE EXTREME THERMOPHILIC ARCHAEBACTERIUM SULFOLOBUS-SOLFATARICUS (116 visite)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 1993 Feb 5; 229(3): 782-784.
Impact Factor: 5.673
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45 Records (42 escludendo Abstract e Conferenze).
Impact factor totale: 208.754 (200.562 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 216.03 (207.483 escludendo Abstract e Conferenze).







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