Bond distances in polypeptide backbones depend on the local conformation (212 views visite)
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2015; 71: 1272-1283.
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Paper type Tipo di articolo: Journal Article,
Impact factor: 2.51, 5-year impact factor Impact factor a 5 anni: 8.75
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84931074135&partnerID=40&md5=475f4c2a85cbf45ef566e849526f6f38
Keywords Parole chiave: Backbone Geometry, Bond Distances, Conformational Dependences, Peptide-Bond Resonance,
Affiliations Affiliazioni:
*** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, Napoli, Italy
References Riferimenti:
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
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2015; 71: 1272-1283.
Export to Esporta in BibTeX Export to Esporta in EndNote
Paper type Tipo di articolo: Journal Article,
Impact factor: 2.51, 5-year impact factor Impact factor a 5 anni: 8.75
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84931074135&partnerID=40&md5=475f4c2a85cbf45ef566e849526f6f38
Keywords Parole chiave: Backbone Geometry, Bond Distances, Conformational Dependences, Peptide-Bond Resonance,
Affiliations Affiliazioni:
*** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, Napoli, Italy
References Riferimenti:
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
Bond distances in polypeptide backbones depend on the local conformation
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.
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.
Bond distances in polypeptide backbones depend on the local conformation
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Bond distances in polypeptide backbones depend on the local conformation
Esposito L, Vitagliano L, Zagari A, Mazzarella L
Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures (216 visite)
Protein Eng (ISSN: 0269-2139, 0269-2139print, 0269-2139linking), 2000 Dec; 13(12): 825-828.
Impact Factor: 2.442
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Esposito L, Vitagliano L, Zagari A, Mazzarella L
Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures (216 visite)
Protein Eng (ISSN: 0269-2139, 0269-2139print, 0269-2139linking), 2000 Dec; 13(12): 825-828.
Impact Factor: 2.442
Dettagli Esporta in BibTeX Esporta in EndNote
1 Records (1 escludendo Abstract e Conferenze).
Impact factor totale: 2.442 (2.442 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 2.604 (2.604 escludendo Abstract e Conferenze).
Impact factor totale: 2.442 (2.442 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 2.604 (2.604 escludendo Abstract e Conferenze).
Last modified by Ultima modifica di Luciana Esposito on in data Sunday 12 July 2020, 13:14:50
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