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The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis (15 views)

Improta R, Vitagliano L, Esposito L

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

Abstract
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.

Affiliations ▼
*** IBB - CNR Affiliation

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

Details ▼
Impact factor: 2.499, 5-year impact factor: 2.725

Paper type: Journal Article, Research Support, Non-U. S. Gov'T,

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

Url: Not available.

References ▼
Not available.

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* Out of the active site binding pocket for carbonic anhydrase inhibitors (114 views) (PDF 87 views)
D'Ambrosio K, Carradori S, Monti SM, Buonanno M, Secci D, Vullo D, Supuran CT, De Simone G
Chem Commun (ISSN: 1359-7345, 1364-548x, 1364-548xelectronic), 2015 Jan 7; 51(2): 302-305.
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* The role of copper(II) in the aggregation of human amylin (105 views)
Sinopoli A, Magri A, Milardi D, Pappalardo M, Pucci P, Flagiello A, Titman JJ, Nicoletti VG, Caruso G, Pappalardo G, GrassoG
Metallomics (ISSN: 1756-591xelectronic, 1756-5901linking), 2014 Oct; 6(10): 1841-1852.
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* X-ray structure of the first 'extremo-alpha-carbonic anhydrase', a dimeric enzyme from the thermophilic bacterium Sulfurihydrogenibium yellowstonense YO3AOP1 (80 views)
Di Fiore A, Capasso C, De Luca V, Monti SM, Carginale V, Supuran CT, Scozzafava A, Pedone C, Rossi M, De Simone G
Acta Crystallogr Sect D Biol Crystallogr Acta Crystallographica Section D Biological Crystallography (ISSN: 0907-4449), 2013 Jun; 69(6): 1150-1159.
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* Carbonic anhydrase inhibitors: X-ray and molecular modeling study for the interaction of a fluorescent antitumor sulfonamide with isozyme II and IX (67 views)
Alterio V, Vitale RM, Monti SM, Pedone C, Scozzafava A, Cecchi A, De Simone G, Supuran CT
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2006 Jun 28; 128(25): 8329-8335.
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* Benzophenone photophore flexibility and proximity: Molecular and crystal-state structure of a Bpa-containing trichogin dodecapeptide analogue (54 views)
Saviano M, Improta R, Benedetti E, Carrozzini B, Cascarano GL, Didierjean C, Toniolo C, Crisma M
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2004 Apr 2; 5(4): 541-544.
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* Atomic resolution structures of ribonuclease A at six pH values (70 views)
Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L
Acta Crystallogr Sect D Biol Crystallogr Acta Crystallographica Section D Biological Crystallography (ISSN: 0907-4449), 2002; 58(3): 441-450.
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6 Records (6 excluding Abstracts and Conferences).
Total impact factor: 30.314 (30.314 excluding Abstracts and Conferences).
Total 5-year impact factor: 43.762 (43.762 excluding Abstracts and Conferences).



Your bibliography query: (([btitle, keywords, abstract] CARBON AND [btitle, keywords, abstract] CHEMISTRY AND [btitle, keywords, abstract] HYDROGEN AND [btitle, keywords, abstract] MODELS)) AND NOT [id] = 53473



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