Home Research Locations About us Organization Staff Contacts Education Login Documents IT
Projects highlights

INCIPIT
(External link)

ISTAPCA
(964 views)

 INMiND
(980 views)

Fondo Europeo Pesca
(343 views)

Fondazione Veronesi
(External link)

Instruct-IT
(External link)

Euro-BioImaging
(External link)

 PRIN
(1107 views)

 eHealthNet
(909 views)

  Ponrec
(858 views)

MFAG Grant
(939 views)

(110 views)

MERIT
(External link)


Links

 |<  < >  >| 

    Export to BibTeX    Export to EndNote

Bond distances in polypeptide backbones depend on the local conformation (60 views)

Improta R, Vitagliano L, Esposito L

Acta Crystallogr Sect D Biol Crystallogr Acta Crystallographica Section D Biological Crystallography (ISSN: 0907-4449), 2015; 71: 1272-1283.

Abstract
By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C-O and C-N) and those bonds centred on the Cα atom. All of these bond lengths indeed display a systematic variability in the ψ angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of Cα distances on ψ is governed by interactions between the σ system of the Cα moiety and the C-O π system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C-O and C-N distances is related to the strength of the interactions between the lone pair of the N atom and the C-O π∗ system, which is modulated by the ψ angle. The C-O and C-N distances are related but their trends are not strictly connected to peptide-bond planarity, although a correlation amongst all of these parameters is expected on the basis of the classical resonance model. © 2015 International Union of Crystallography.

Affiliations ▼
*** IBB - CNR Affiliation

Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, Napoli, Italy

Details ▼
Impact factor: 2.51, 5-year impact factor: 8.75

Paper type: Journal Article,

Keywords: Backbone Geometry, Bond Distances, Conformational Dependences, Peptide-Bond Resonance,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84931074135&partnerID=40&md5=475f4c2a85cbf45ef566e849526f6f38

References ▼
Adamo, C., Scuseria, G.E., Barone, V., (1999) J. Chem. Phys., 111, pp. 2889-289

Benzi, C., Improta, R., Scalmani, G., Barone, V., (2002) J. Comput. Chem., 23, pp. 341-350

Berkholz, D.S., Krenesky, P.B., Davidson, J.R., Karplus, P.A., (2010) Nucleic Acids Res., 38, pp. 320-325

Berkholz, D.S., Shapovalov, M.V., Dunbrack, R.L., Jr., Karplus, P.A., (2009) Structure, 17, pp. 1316-1325

Berman, H., Henrick, K., Nakamura, H., Markley, J.L., (2007) Nucleic Acids Res., 35, pp. D301-D303

Bönisch, H., Schmidt, C.L., Bianco, P., Ladenstein, R., (2005) Acta Cryst. D, 61, pp. 990-1004

Carugo, O., (2003) Acta Chim. Slov., 50, pp. 505-511

Cruickshank, D.W.J., (1999) Acta Cryst. D, 55, pp. 583-601

Edison, A.S., (2001) Nature Struct. Biol., 8, pp. 201-202

Elias, M., Wellner, A., Goldin-Azulay, K., Chabriere, E., Vorholt, J.A., Erb, T.J., Tawfik, D.S., (2012) Nature (London), 491, pp. 134-137

Esposito, L., Balasco, N., De Simone, A., Berisio, R., Vitagliano, L., (2013) Biomed. Res. Int., 2013, p. 326914

Esposito, L., De Simone, A., Zagari, A., Vitagliano, L., (2005) J. Mol. Biol., 347, pp. 483-487

Esposito, L., Vitagliano, L., Mazzarella, L., (2002) Protein Pept. Lett., 9, pp. 95-105

EU 3-D Validation Network, (1998) J. Mol. Biol., 276, pp. 417-436

Foster, J.P., Weinhold, F., (1980) J. Am. Chem. Soc., 102, pp. 7211-7218

Frisch, M.J., (2004) Gaussian 03, Version C.02, , Gaussian Inc., Wallingford, Connecticut, USA

Glendening, E.D., Weinhold, F., (1998) J. Comput. Chem., 19, pp. 593-609

Howard, E.I., Sanishvili, R., Cachau, R.E., Mitschler, A., Chevrier, B., Barth, P., Lamour, V., Podjarny, A., (2004) Proteins, 55, pp. 792-804

Improta, R., Barone, V., (2004) J. Comput. Chem., 25, pp. 1333-1341

Improta, R., Benzi, C., Barone, V., (2001) J. Am. Chem. Soc., 123, pp. 12568-12577

Improta, R., Vitagliano, L., Esposito, L., (2011) PLoS One, 6

Jaskolski, M., Gilski, M., Dauter, Z., Wlodawer, A., (2007) Acta Cryst. D, 63, pp. 611-620

Jiang, X., Yu, C.-H., Cao, M., Newton, S.Q., Paulus, E.F., Schäfer, L., (1997) J. Mol. Struct., 403, pp. 83-93

Karplus, P.A., (1996) Protein Sci., 5, pp. 1406-1420

Kleywegt, G.J., (2009) Acta Cryst. D, 65, pp. 134-139

Langella, E., Improta, R., Barone, V., (2002) J. Am. Chem. Soc., 124, pp. 11531-11540

Milner-White, E.J., (1997) Protein Sci., 6, pp. 2477-2482

Moriarty, N.W., Tronrud, D.E., Adams, P.D., Karplus, P.A., (2014) FEBS J., 281, pp. 4061-4071

Mujika, J.I., Matxain, J.M., Eriksson, L.A., Lopez, X., (2006) Chem. Eur. J., 12, pp. 7215-7224

Pauling, L., Corey, R.B., (1951) Proc. Natl Acad. Sci. USA, 37, pp. 251-256

Reed, A.E., Weinhold, F., (1983) J. Chem. Phys., 78, pp. 4066-4073

Schaftenaar, G., Noordik, J.H., (2000) J. Comput. Aided Mol. Des., 14, pp. 123-134

Tomasi, J., Mennucci, B., Cammi, R., (2005) Chem. Rev., 105, pp. 2999-3094

Tronrud, D.E., Berkholz, D.S., Karplus, P.A., (2010) Acta Cryst. D, 66, pp. 834-842

Tronrud, D.E., Karplus, P.A., (2011) Acta Cryst. D, 67, pp. 699-706

Van Alsenoy, C., Yu, C.-H., Peeters, A., Martin, J.M.L., Schäfer, L., (1998) J. Phys. Chem. A, 102, pp. 2246-2251

Wiberg, K.B., Breneman, C.M., (1992) J. Am. Chem. Soc., 114, pp. 831-840


Related activities ▼
No results.

Related papers ▼
Cationic porphyrins are tunable gatekeepers of the 20S proteasome (restricted access) (101 views)
Copper ion interaction with the RNase catalytic site fragment of the angiogenin protein: an experimental and theoretical investigation (public domain) (32 views)
Designing Covalently Linked Heterodimeric Four-Helix Bundles (public domain) (49 views)

Related bibliography ▼

Content: [X]
Extended

Authors: [X]
AND Paper type: [X]

AND Start date: End date: [X]   AND Site:    AND  IBB affiliation

[Clear form]

<=2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018   ALL YEARS

Sort by: date    title    journal    authors      impact factor

* Dissection of Factors Affecting the Variability of the Peptide Bond Geometry and Planarity (4 views)
Balasco N, Esposito L, Thind AS, Guarracino MR, Vitagliano L
Biomed Res Int (ISSN: 2314-6141electronic), 2017; 2017: 2617629-2617629.
View    Export to BibTeX    Export to EndNote

* Interplay between peptide bond geometrical parameters in nonglobular structural contexts (64 views)
Esposito L, Balasco N, De Simone A, Berisio R, Vitagliano L
Biomed Res Int (ISSN: 2314-6133, 2314-6141, 2314-6141electronic), 2013; 2013: N/D-N/D.
View    Export to BibTeX    Export to EndNote



4 Records (3 excluding Abstracts and Conferences).
Total impact factor: 10.3 (6.208 excluding Abstracts and Conferences).
Total 5-year impact factor: 10.991 (6.454 excluding Abstracts and Conferences).



Your bibliography query: (([btitle, keywords, abstract] BACKBONE AND [btitle, keywords, abstract] GEOMETRY AND [btitle, keywords, abstract] BOND)) AND NOT [id] = 52880



Last modified by Luciana Esposito on Thursday 21 July 2016, 19:11:54
60 views. Last viewed on Tuesday 20 February 2018, 19:24:59

Webmaster and developer: Marco Comerci
For problems and suggestions: adminibb.cnr.it
Last updated: Thursday 22 February 2018, 11:53:02