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The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis (32 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


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,

Url: 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.
*** IBB - CNR ***

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


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* Chemistry of Peptidoglycan in Mycobacterium tuberculosis life style: an off-the-wall balance of synthesis and degradation (115 visite) (PDF 73 visite)
Squeglia F, Ruggiero A, Berisio R
Chemistry (ISSN: 1521-3765electronic, 0947-6539linking), 2018; 24: 2533-2546.
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* Inhibition of Abeta Amyloid Growth and Toxicity by Silybins: The Crucial Role of Stereochemistry (59 visite) (PDF 61 visite)
Sciacca MFM, Romanucci V, Zarrelli A, Monaco I, Lolicato F, Spinella N, Galati C, Grasso G, D'Urso L, Romeo M, Diomede L, Salmona M, Bongiorno C, Di Fabio G, La Rosa C, Milardi D
Acs Chem Neurosci (ISSN: 1948-7193electronic, 1948-7193linking), 2017 Jun 09; N/D: N/D-N/D.
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* A new cryptic host defense peptide identified in human 11-hydroxysteroid dehydrogenase-1 beta-like: from in silico identification to experimental evidence (60 visite)
Bosso A, Pirone L, Gaglione R, Pane K, Del Gatto A, Zaccaro L, Di Gaetano S, Diana D, Fattorusso R, Pedone E, Cafaro V, Haagsman HP, Van Dijk A, Scheenstra MR, Zanfardino A, Crescenzi O, Arciello A, Varcamonti M, Veldhuizen EJA, Di Donato A, Notomista E, Pizzo E
Biochim Biophys Acta (ISSN: 0006-3002print, 0006-3002linking, 0005-2728), 2017 Apr 25; N/D: N/D-N/D.
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* L-Histidinol Dehydrogenase as a New Target for Old Diseases (95 visite)
Monti SM, De Simone G, D'Ambrosio K
Curr Top Med Chem (ISSN: 1568-0266linking, 1873-4294electronic), 2016 Apr 13; 16(21): 2369-2378.
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* 1, 2, 3-Triazole Bridge as Conformational Constrain in beta-Hairpin Peptides: Analysis of Hydrogen-Bonded Positions (39 visite)
Celentano V, Diana D, Di Salvo C, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD
Chemistry (ISSN: 1521-3765electronic, 0947-6539linking), 2016 Apr 11; 22(16): 5534-5537.
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* Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases (100 visite)
Improta R, Santoro F, Blancafort L
Chemical Reviews (ISSN: 0009-2665), 2016; 116(6): 3540-3593.
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* The Role of the Amino Protecting Group during Parahydrogenation of Protected Dehydroamino Acids (58 visite)
Cerutti E, Viale A, Nervi C, Gobetto R, Aime S
J Phys Chem A (ISSN: 1520-5215electronic, 1089-5639linking), 2015 Nov 19; 119(46): 11271-11279.
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* Crystal structure of the most catalytically effective carbonic anhydrase enzyme known, SazCA from the thermophilic bacterium Sulfurihydrogenibium azorense (79 visite)
De Simone G, Monti SM, Alterio V, Buonanno M, De Luca V, Rossi M, Carginale V, Supuran CT, Capasso C, Di Fiore A
Bioorganic And Medicinal Chemistry Letters (ISSN: 0960-894x), 2015 May 1; 25(9): 2002-2006.
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* Chemistry of lipid a: At the heart of innate immunity (147 visite) (PDF 156 visite)
Molinaro A, Holst O, Lorenzo FD, Callaghan M, Nurisso A, D'Errico G, Zamyatina A, Peri F, Berisio R, Jerala R, Jiménez-Barbero J, Silipo A, Martín-Santamarí S
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2015 Jan 7; 21(2): 500-519.
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* The chemistry of carnosine derivatives (45 visite)
Bellia F, Rizzarelli E, Vecchio G
Food And Nutritional Components In Focus (ISSN: 2045-1695), 2015; 2015-January(8): 61-83.
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* Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis (105 visite)
D'Ambrosio K, Lopez M, Dathan NA, Ouahrani-bettache S, Köhler S, Ascione G, Monti SM, Winum JY, De Simone G
Biochimie (ISSN: 0300-9084, 1638-6183, 1638-6183electronic), 2014 Feb; 97(1): 114-120.
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* The Copper (ii) And Zinc (ii) Coordination Mode Of Hexxh And Hxxeh Motif In Small Peptides: The Role Of Carboxylate Location And Hydrogen Bonding Network (91 visite)
GrassoG, Magrì A, Bellia F, Pietropaolo A, La Mendola D, Rizzarelli E
J Chem Res (ISSN: 1873-3344electronic, 0162-0134linking, 0162-0134print), 2014 Jan; 130(1): 92-102.
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* Gastric emptying after sleeve gastrectomy: Statistical evidence of a controlled prospective study with gastric scintigraphy (87 visite)
Pilone V, Tramontano S, Di Micco R, Monda A, Hasani A, Izzo G, Vitiello A, Caprio MG, Cuocolo A, Forestieri P
Minerva Chir (ISSN: 0026-4733), 2013 Sep; 68(4): 385-392.
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* X-ray structure of the first 'extremo-alpha-carbonic anhydrase', a dimeric enzyme from the thermophilic bacterium Sulfurihydrogenibium yellowstonense YO3AOP1 (97 visite)
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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* Biochemical and structural characterization of recombinant short-chain NAD(H)-dependent dehydrogenase/reductase from Sulfolobus acidocaldarius highly enantioselective on diaryl diketone benzil (106 visite)
Pennacchio A, Sannino V, Sorrentino G, Rossi M, Raia CA,  Esposito L
Applied Microbiology And Biotechnology (ISSN: 0175-7598), 2013 May; 97(9): 1-16.
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* UV-light-induced hydrogen transfer in guanosine-guanosine aggregates (99 visite)
Hunger K, Buschhaus L, Biemann L, Braun M, Kovalenko S, Improta R, Kleinermanns K
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2013 Apr; 19(17): 5425-5431.
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* Liposomes derivatized with tetrabranched neurotensin peptides via click chemistry reactions (83 visite)
Accardo A, Ringhieri P, Tesauro D, Morelli G
New Journal Of Chemistry (ISSN: 1144-0546), 2013; 37(11): 3528-3534.
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* Photophysics and photochemistry of thymine deoxy-dinucleotide in water: A PCM/TD-DFT quantum mechanical study (86 visite)
Improta R
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2012 Dec 13; 116(49): 14261-14274.
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Pitfalls in statistical methods (71 visite)
Petretta M, Cuocolo A
J Nucl Cardiol (ISSN: 1532-6551, 1071-3581, 1532-6551electronic), 2012 Sep; 19(4): 818-818.
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* Proteins as sponges: A statistical journey along protein structure organization principles (101 visite)
Paola LD, Paci P, Santoni D, Ruvo MD, Giuliani A
J Chem Inf Model American Chemical Society (ISSN: 1549-9596), 2012 Feb 27; 52(2): 474-482.
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* Development of an efficient and low-cost protocol for the manual PNA synthesis by Fmoc chemistry (95 visite)
Avitabile C, Moggio L, D'Andrea LD, Pedone C, Romanelli A
Tetrahedron Letters (ISSN: 0040-4039), 2010 Jul 21; 51(29): 3716-3718.
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* Nobel prize in chemistry 2009: When biology turns into chemistry (51 visite)
Berisio R, Baram D, Keinan E
Isr J Chem (ISSN: 0021-2148), 2010 Jun; 50(1): 24-26.
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* Insight into the stereospecificity of short-chain Thermus thermophilus alcohol dehydrogenase showing pro-S hydride transfer and Prelog enantioselectivity (102 visite)
Pennacchio A, Giordano A, Esposito L, Langella E, Rossi M, Raia CA
Protein And Peptide Letters (ISSN: 0929-8665, 1875-5305), 2010 Apr; 17(4): 437-443.
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* Crystal And Molecular Structure Of Beta-Cyclodextrins Functionalized With The Anti-Inflammatory Drug Etodolac (113 visite)
Puglisi A, Rizzarelli E, Vecchio G, Iacovino R, Benedetti E, Pedone C, Saviano M
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1227-1235.
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* Role of Tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase (78 visite)
Pennacchio A, Esposito L, Zagari A, Rossi M, Raia CA
Extremophilesextremophiles (ISSN: 1431-0651, 1433-4909), 2009 Sep; 13(5): 751-761.
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* Sterochemistry And Thermodynamics Of The Inclusion Of Aliphatic And Aromatic Anionic Guests In A Tetracationic Calix [4] Arene In Acidic And Neutral Aqueous Solutions (51 visite)
Sgarlata C, Bonaccorso C, Gulino FG, Zito V, Arena G, Sciotto D
New Journal Of Chemistry, 2009; 33: 991-991.
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* Supramolecular structure of extrinsically chiral porphyrin hetero-assemblies and achiral analogues (104 visite)
Matassa R, Carbone M, Lauceri R, Purrello R, Caminiti R
Adv Mater (ISSN: 0935-9648), 2007; 19(22): 3961-3967.
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* Invariant Thr(244) is essential for the efficient acylation step of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans (74 visite)
Pailot A, D'Ambrosio K, Corbier C, Talfournier F, Branlant G
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2006 Dec 15; 400: 521-530.
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* Polyproline helices in protein structures: A statistical survey (71 visite)
Berisio R, Loguercio S, De Simone A, Zagari A, Vitagliano L
Protein And Peptide Letters (ISSN: 0929-8665, 1875-5305), 2006; 13(8): 847-854.
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* Crystal structure of a ternary complex of the alcohol dehydrogenase from Sulfolobus solfataricus (90 visite)
Esposito L, Bruno I, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2003 Dec 16; 42(49): 14397-14407.
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* Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity (76 visite)
Esposito L, Bruno I, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic), 2003 Mar 27; 539(1-3): 14-18.
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* The role of segment 32-47 of cholecystokinin receptor type A in CCK8 binding: Synthesis, nuclear magnetic resonance, circular dichroism and fluorescence studies (70 visite)
De Luca S, Ragone R, Bracco C, Digilio G, Tesauro D, Saviano M, Pedone C, Morelli G
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2003 Mar; 9(3): 156-169.
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* Crystal Structure Of The Alcohol Dehydrogenase From The Hyperthermophilic Archaeon Sulfolobus Solfataricus At 1. 85 Angstrom Resolution (85 visite)
Esposito L, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
J Mol Biol Journal Of Molecular Biology (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2002 Apr 26; 318(2): 463-477.
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* Identification of tissue transglutaminase-reactive lysine residues in glyceraldehyde-3-phosphate dehydrogenase (78 visite)
Orru S, Ruoppolo M, Francese S, Vitagliano L, Marino G, Esposito C
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2002 Jan; 11(1): 137-146.
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* Comparison of control of Listeria by nitric oxide redox chemistry from murine macrophages and no donors: Insights into listeriocidal activity of oxidative and nitrosative stress (83 visite)
Ogawa R, Pacelli R, Espey MG, Miranda KM, Friedman N, Kim SM, Cox G, Mitchell JB, Wink DA, Russo A
Free Radic Biol Med Free Radical Biology And Medicine (ISSN: 0891-5849, 0891-5849linking), 2001 Feb 1; 30(3): 268-276.
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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)) (88 visite)
Impellizzeri G, Pappalardo G, D'Alessandro F, Rizzarelli E, Saviano M, Iacovino R, Benedetti E, Pedone C
Eur J Org Chem (ISSN: 1434-193x), 2000; (12): 2345-2345.
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Protein Crystal Growth In The Advance Protein Crystallisation Facility On The Lms Mission: A Comparison Of Sulfolobus Solfataricus Alchool Dehydrogenase Crystals Grown On The Ground And In Microgravity (48 visite)
 Esposito L, Sica F, Sorrentino G, Berisio R, Carotenuto L, Giordano A, Raia C, Rossi M, Lamzin VS, Willson KS, Zagari A
Acta Crystallogr D Biol Crystallogr, 1998; 54: 386-390.
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Protein crystal growth in the advanced protein crystallization facility on the LMS mission: A comparison of Sulfolobus solfataricus alcohol dehydrogenase crystals grown on the ground and in microgravity (74 visite)
Esposito L, Sica F, Sorrentino G, Berisio R, Carotenuto L, Giordano A, Raia CA, Rossi M, Lamzin VS, Wilson KS, Zagari A
Acta Crystallogr Sect D Biol Crystallogr Acta Crystallographica Section D Biological Crystallography (ISSN: 0907-4449), 1998; 54(3): 386-390.
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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 (77 visite)
Bonomo RP, Di Blasio B, Maccarrone G, Pavone V, Pedone C, Rizzarelli E, Saviano M, Vecchio G
Inorg Chem (ISSN: 0020-1669, 1520-510x, 1520-510xelectronic), 1996 Jul 17; 35(15): 4497-4504.
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The effect of various nitric oxide-donor agents on hydrogen peroxide-mediated toxicity: A direct correlation between nitric oxide formation and protection (75 visite)
Wink DA, Cook JA, Pacelli R, DeGraff W, Gamson J, Liebmann J, Krishna MC, Mitchell JB
Arch Biochem Biophys (ISSN: 0003-9861), 1996 Jul 15; 331(2): 241-248.
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NITRIC-OXIDE POTENTIATES HYDROGEN PEROXIDE-INDUCED KILLING OF ESCHERICHIA-COLI (54 visite)
Pacelli R, Wink DA, Cook JA, Krishna MC, DeGraff W, Friedman N, Tsokos M, Samuni A, Mitchell JB
Journal Of Experimental Medicine (ISSN: 0022-1007), 1995 Nov 1; 182(5): 1469-1479.
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Molecular structure and conformation of the (Z) and (E) geometric isomers of 2-(2-phenylbenzylidene)-3 quinuclidinone (73 visite)
SANTINI A, BENEDETTI E, PEDONE C, GIORDANO M, CALIENDO G, SANTAGADA V, GRIECO P, GRECO G
Tetrahedron (ISSN: 0040-4020), 1995 Feb 13; 51(7): 1995-2008.
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CRYSTALLIZATION AND PRELIMINARY-X-RAY ANALYSIS OF AN NAD+-DEPENDENT ALCOHOL-DEHYDROGENASE FROM THE EXTREME THERMOPHILIC ARCHAEBACTERIUM SULFOLOBUS-SOLFATARICUS (66 visite)
PEARL L, DEMASI D, HEMMINGS A, SICA F, MAZZARELLA L, RAIA C, DAURIA S, ROSSI M
J Mol Biol Journal Of Molecular Biology (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 1993 Feb 5; 229(3): 782-784.
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43 Records (40 escludendo Abstract e Conferenze).
Impact factor totale: 200.655 (192.463 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 207.76 (199.213 escludendo Abstract e Conferenze).

Interrogazione bibliografica effettuata: (([btitle] "Chemistry" OR [btitle] "Hydrogen" OR [btitle] "Statistical" OR [btitle] "Molecular Structure" OR [btitle] "Nuclear Magnetic Resonance") AND NOT [id] = 53473)







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