Pyramidalization of backbone carbonyl carbon atoms in proteins (449 views)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2000 Oct; 9(10): 2038-2042.
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Paper type: Journal Article,
Impact factor: 3.869, 5-year impact factor: 3.029
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-0033773831&partnerID=40&md5=e30f16e6642e50902fa71b92b495433b
Keywords: Carbon Pyramidalization, Peptide Planarity, Protein Geometry-Conformation, Protein Structure-Function, Ultra-High Resolution, Carbonyl Derivative, Polypeptide, Article, Nuclear Magnetic Resonance Spectroscopy, Peptide Analysis, Priority Journal, Protein Folding, Structure Analysis, X Ray Analysis, Animals, Cattle, Crystallography, X-Ray, Protein Conformation, Reproducibility Of Results, Ribonuclease, Pancreatic, Sensitivity And Specificity,
Affiliations:
Centro di Studio di Biocristallografia, Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Via Mezzocannone 4, I-80134 Napoli, Italy
References:
Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Motherwell, W.D.S., The Cambridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information (1979) Acta Crystallogr Sect B, 35, pp. 2331-233
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Tasumi, M., The Protein Data Bank: A computer-based archival file for macromolecular structures (1977) J Mol Biol, 112, pp. 535-542
Bode, W., Huber, R., Natural protein proteinase inhibitors and their interaction with proteinases (1992) Eur J Biochem, 204, pp. 433-451
Brown, R.D., Godfrey, P.D., Kleibomer, B., The conformation of formamide (1987) J Mol Spectrosc, 124, pp. 34-45
Burgi, H.B., Dunitz, J.D., Shefter, E., Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group (1973) J Am Chem Soc, 95, pp. 5065-5067
Burton, N.A., Chiu, S.S.-L., Davidson, M.M., Green, D.V.S., Hillier, I.H., McDouall, J.J.W., Vincent, M.A., Rotation about the C-N bond in formamide: An ab initio molecular orbital study of structure and energetics in the gas phase and in solution (1993) J Chem Soc Faraday Trans, 89, pp. 2631-2635
Caramella, P., Rondan, N.G., Paddon-Row, M.N., Houk, K.N., Origin of π-facial stereoselectivity in additions to π-bonds: Generality of the anti-periplanar effect (1981) J Am Chem Soc, 103, pp. 2438-2440
Cieplak, A.S., Solid-state conformations of linear oligopeptides and aliphatic amides. A model of chiral perturbation of a conjugated system (1985) J Am Chem Soc, 107, pp. 271-273
Costain, C.C., Dowling, J.M., Microwave spectrum and molecular structure of formamide (1960) J Chem Phys, 32, pp. 158-165
Dauter, Z., Lamzin, V.S., Wilson, K.S., The benefits of atomic resolution (1997) Curr Opin Struct Biol, 7, pp. 681-688
Deane, C.M., Blundell, T.L., Examination of the less favoured regions of the Ramachandran plot (1999), pp. 196-208. , Yathindra N, Kolashar AS, Vijayan M, eds. Perspectives in structural biology. Bangalore University, India: Indian Academy of SciencesEsposito, L., Vitagliano, L., Sica, F., Sorrentino, G., Zagari, A., Mazzarella, L., The ultrahigh resolution crystal structure of RNase A containing an isoaspartyl residue
hydration and stereochemical analysis (2000) J Mol Biol, 297, pp. 713-732
Fogarasi, G., Szalay, P.G., High-level electron correlation calculations on formamide and the resonance model (1997) J Phys Chem, 101, pp. 1400-1408
Hansen, E.L., Larsen, N.W., Nicolaisen, F.M., An infrared investigation of formamide, acetamide and thioacetamide in the vapour phase. Inversion of the amino group (1980) Chem Phys Lett, 69, pp. 327-331
Hu, J.S., Bax, A., Determination of φ and χ1 angles in proteins from 13C-13C three bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond? (1997) J Am Chem Soc, 119, pp. 6360-6368
Jeffrey, G.A., Houk, K.N., Paddon-Row, M.N., Rondan, N.G., Mitra, J., Pyramidalization of carbonyl carbons in asymmetric environments: Carboxilates, amides and amino acids (1985) J Am Chem Soc, 107, pp. 321-326
Jiang, X., Cao, M., Teppen, B., Newton, S., Schafer, L., Predictions of protein backbone structural parameters from first principles: Systematic comparisons of calculated N-Calpha-C' angles with high-resolution protein crystallographic results (1995) J Phys Chem, 99, pp. 10521-10525
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Karplus, P.A., Experimentally observed conformation-dependent geometry and hidden strain in proteins (1996) Protein Sci, 5, pp. 1406-1420
Lamzin, V.S., Morris, R.J., Dauter, Z., Wilson, K.S., Teeter, M.M., Experimental observation of bonding electrons in proteins (1999) J Biol Chem, 274, pp. 20753-20755
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J Appl Crystallogr, 26, pp. 283-291
MacArthur, M.W., Thornton, J.M., Deviations from planarity of the peptide bond in peptides and proteins (1996) J Mol Biol, 264, pp. 1180-1195
Mack, H., Oberhammer, H., Planarity of N,N-dimethylacetamide, (CH3)2NC(O)CH3 (1997) J Am Chem Soc, 119, pp. 3567-3570
Marquardt, M., Walter, J., Deisenhofer, J., Bode, W., Huber, R., The geometry of the reactive site of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors (1983) Acta Crystallogr Sect B, 39, pp. 480-490
Merritt, E.A., Kuhn, P., Sarfaty, S., Erbe, J.L., Holmes, R.K., Hol, W.G.J., The 1.25 Å resolution refinement of the cholera toxin B-pentamer: Evidence of peptide backbone strain at the receptor-binding site (1998) J Mol Biol, 282, pp. 1043-1059
Sevcik, J., Dauter, Z., Lamzin, V.S., Wilson, K.S., Ribonuclease from Streptomyces aurofaciens at atomic resolution (1996) Acta Crystallogr Sect D, 52, pp. 327-344
Sheldrick, G.M., Schneider, T.R., SHELXL: High resolution refinement (1997) Methods Enzymol, 277, pp. 319-343
Sulzbach, H.M., Schleyer, P.V.R., Schaefer, H.F., Influence of nonplanarity of the amide moiety on computed chemical shifts in peptide analogs. Is the amide nitrogen pyramidal? (1995) J Am Chem Soc, 117, pp. 2632-2637
Wong, M.W., Wiberg, K.B., Structure of acetamide: Planar or nonplanar? (1992) J Phys Chem, 96, pp. 668-671
Wright, G.M., Simmonds, R.J., Parry, D.E., Ab initio studies of the ground-state potential energy surface of formamide (1988) J Comput Chem, 9, pp. 600-603
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Motherwell, W. D. S., The Cambridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information (1979) Acta Crystallogr Sect B, 35, pp. 2331-233
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Tasumi, M., The Protein Data Bank: A computer-based archival file for macromolecular structures (1977) J Mol Biol, 112, pp. 535-542
Brown, R. D., Godfrey, P. D., Kleibomer, B., The conformation of formamide (1987) J Mol Spectrosc, 124, pp. 34-45
Burgi, H. B., Dunitz, J. D., Shefter, E., Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group (1973) J Am Chem Soc, 95, pp. 5065-5067
Burton, N. A., Chiu, S. S. -L., Davidson, M. M., Green, D. V. S., Hillier, I. H., McDouall, J. J. W., Vincent, M. A., Rotation about the C-N bond in formamide: An ab initio molecular orbital study of structure and energetics in the gas phase and in solution (1993) J Chem Soc Faraday Trans, 89, pp. 2631-2635
Cieplak, A. S., Solid-state conformations of linear oligopeptides and aliphatic amides. A model of chiral perturbation of a conjugated system (1985) J Am Chem Soc, 107, pp. 271-273
Costain, C. C., Dowling, J. M., Microwave spectrum and molecular structure of formamide (1960) J Chem Phys, 32, pp. 158-165
Deane, C. M., Blundell, T. L., Examination of the less favoured regions of the Ramachandran plot (1999), pp. 196-208. , Yathindra N, Kolashar AS, Vijayan M, eds. Perspectives in structural biology. Bangalore University, India: Indian Academy of SciencesEsposito, L., Vitagliano, L., Sica, F., Sorrentino, G., Zagari, A., Mazzarella, L., The ultrahigh resolution crystal structure of RNase A containing an isoaspartyl residue
Hansen, E. L., Larsen, N. W., Nicolaisen, F. M., An infrared investigation of formamide, acetamide and thioacetamide in the vapour phase. Inversion of the amino group (1980) Chem Phys Lett, 69, pp. 327-331
Hu, J. S., Bax, A., Determination of and 1 angles in proteins from 13C-13C three bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond? (1997) J Am Chem Soc, 119, pp. 6360-6368
Jeffrey, G. A., Houk, K. N., Paddon-Row, M. N., Rondan, N. G., Mitra, J., Pyramidalization of carbonyl carbons in asymmetric environments: Carboxilates, amides and amino acids (1985) J Am Chem Soc, 107, pp. 321-326
Karplus, P. A., Experimentally observed conformation-dependent geometry and hidden strain in proteins (1996) Protein Sci, 5, pp. 1406-1420
Lamzin, V. S., Morris, R. J., Dauter, Z., Wilson, K. S., Teeter, M. M., Experimental observation of bonding electrons in proteins (1999) J Biol Chem, 274, pp. 20753-20755
Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J Appl Crystallogr, 26, pp. 283-291
MacArthur, M. W., Thornton, J. M., Deviations from planarity of the peptide bond in peptides and proteins (1996) J Mol Biol, 264, pp. 1180-1195
Merritt, E. A., Kuhn, P., Sarfaty, S., Erbe, J. L., Holmes, R. K., Hol, W. G. J., The 1. 25 resolution refinement of the cholera toxin B-pentamer: Evidence of peptide backbone strain at the receptor-binding site (1998) J Mol Biol, 282, pp. 1043-1059
Sheldrick, G. M., Schneider, T. R., SHELXL: High resolution refinement (1997) Methods Enzymol, 277, pp. 319-343
Sulzbach, H. M., Schleyer, P. V. R., Schaefer, H. F., Influence of nonplanarity of the amide moiety on computed chemical shifts in peptide analogs. Is the amide nitrogen pyramidal? (1995) J Am Chem Soc, 117, pp. 2632-2637
Wong, M. W., Wiberg, K. B., Structure of acetamide: Planar or nonplanar? (1992) J Phys Chem, 96, pp. 668-671
Wright, G. M., Simmonds, R. J., Parry, D. E., Ab initio studies of the ground-state potential energy surface of formamide (1988) J Comput Chem, 9, pp. 600-603
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2000 Oct; 9(10): 2038-2042.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 3.869, 5-year impact factor: 3.029
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-0033773831&partnerID=40&md5=e30f16e6642e50902fa71b92b495433b
Keywords: Carbon Pyramidalization, Peptide Planarity, Protein Geometry-Conformation, Protein Structure-Function, Ultra-High Resolution, Carbonyl Derivative, Polypeptide, Article, Nuclear Magnetic Resonance Spectroscopy, Peptide Analysis, Priority Journal, Protein Folding, Structure Analysis, X Ray Analysis, Animals, Cattle, Crystallography, X-Ray, Protein Conformation, Reproducibility Of Results, Ribonuclease, Pancreatic, Sensitivity And Specificity,
Affiliations:
Centro di Studio di Biocristallografia, Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Via Mezzocannone 4, I-80134 Napoli, Italy
References:
Allen, F.H., Bellard, S., Brice, M.D., Cartwright, B.A., Doubleday, A., Higgs, H., Hummelink, T., Motherwell, W.D.S., The Cambridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information (1979) Acta Crystallogr Sect B, 35, pp. 2331-233
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Tasumi, M., The Protein Data Bank: A computer-based archival file for macromolecular structures (1977) J Mol Biol, 112, pp. 535-542
Bode, W., Huber, R., Natural protein proteinase inhibitors and their interaction with proteinases (1992) Eur J Biochem, 204, pp. 433-451
Brown, R.D., Godfrey, P.D., Kleibomer, B., The conformation of formamide (1987) J Mol Spectrosc, 124, pp. 34-45
Burgi, H.B., Dunitz, J.D., Shefter, E., Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group (1973) J Am Chem Soc, 95, pp. 5065-5067
Burton, N.A., Chiu, S.S.-L., Davidson, M.M., Green, D.V.S., Hillier, I.H., McDouall, J.J.W., Vincent, M.A., Rotation about the C-N bond in formamide: An ab initio molecular orbital study of structure and energetics in the gas phase and in solution (1993) J Chem Soc Faraday Trans, 89, pp. 2631-2635
Caramella, P., Rondan, N.G., Paddon-Row, M.N., Houk, K.N., Origin of π-facial stereoselectivity in additions to π-bonds: Generality of the anti-periplanar effect (1981) J Am Chem Soc, 103, pp. 2438-2440
Cieplak, A.S., Solid-state conformations of linear oligopeptides and aliphatic amides. A model of chiral perturbation of a conjugated system (1985) J Am Chem Soc, 107, pp. 271-273
Costain, C.C., Dowling, J.M., Microwave spectrum and molecular structure of formamide (1960) J Chem Phys, 32, pp. 158-165
Dauter, Z., Lamzin, V.S., Wilson, K.S., The benefits of atomic resolution (1997) Curr Opin Struct Biol, 7, pp. 681-688
Deane, C.M., Blundell, T.L., Examination of the less favoured regions of the Ramachandran plot (1999), pp. 196-208. , Yathindra N, Kolashar AS, Vijayan M, eds. Perspectives in structural biology. Bangalore University, India: Indian Academy of SciencesEsposito, L., Vitagliano, L., Sica, F., Sorrentino, G., Zagari, A., Mazzarella, L., The ultrahigh resolution crystal structure of RNase A containing an isoaspartyl residue
hydration and stereochemical analysis (2000) J Mol Biol, 297, pp. 713-732
Fogarasi, G., Szalay, P.G., High-level electron correlation calculations on formamide and the resonance model (1997) J Phys Chem, 101, pp. 1400-1408
Hansen, E.L., Larsen, N.W., Nicolaisen, F.M., An infrared investigation of formamide, acetamide and thioacetamide in the vapour phase. Inversion of the amino group (1980) Chem Phys Lett, 69, pp. 327-331
Hu, J.S., Bax, A., Determination of φ and χ1 angles in proteins from 13C-13C three bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond? (1997) J Am Chem Soc, 119, pp. 6360-6368
Jeffrey, G.A., Houk, K.N., Paddon-Row, M.N., Rondan, N.G., Mitra, J., Pyramidalization of carbonyl carbons in asymmetric environments: Carboxilates, amides and amino acids (1985) J Am Chem Soc, 107, pp. 321-326
Jiang, X., Cao, M., Teppen, B., Newton, S., Schafer, L., Predictions of protein backbone structural parameters from first principles: Systematic comparisons of calculated N-Calpha-C' angles with high-resolution protein crystallographic results (1995) J Phys Chem, 99, pp. 10521-10525
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Karplus, P.A., Experimentally observed conformation-dependent geometry and hidden strain in proteins (1996) Protein Sci, 5, pp. 1406-1420
Lamzin, V.S., Morris, R.J., Dauter, Z., Wilson, K.S., Teeter, M.M., Experimental observation of bonding electrons in proteins (1999) J Biol Chem, 274, pp. 20753-20755
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J Appl Crystallogr, 26, pp. 283-291
MacArthur, M.W., Thornton, J.M., Deviations from planarity of the peptide bond in peptides and proteins (1996) J Mol Biol, 264, pp. 1180-1195
Mack, H., Oberhammer, H., Planarity of N,N-dimethylacetamide, (CH3)2NC(O)CH3 (1997) J Am Chem Soc, 119, pp. 3567-3570
Marquardt, M., Walter, J., Deisenhofer, J., Bode, W., Huber, R., The geometry of the reactive site of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors (1983) Acta Crystallogr Sect B, 39, pp. 480-490
Merritt, E.A., Kuhn, P., Sarfaty, S., Erbe, J.L., Holmes, R.K., Hol, W.G.J., The 1.25 Å resolution refinement of the cholera toxin B-pentamer: Evidence of peptide backbone strain at the receptor-binding site (1998) J Mol Biol, 282, pp. 1043-1059
Sevcik, J., Dauter, Z., Lamzin, V.S., Wilson, K.S., Ribonuclease from Streptomyces aurofaciens at atomic resolution (1996) Acta Crystallogr Sect D, 52, pp. 327-344
Sheldrick, G.M., Schneider, T.R., SHELXL: High resolution refinement (1997) Methods Enzymol, 277, pp. 319-343
Sulzbach, H.M., Schleyer, P.V.R., Schaefer, H.F., Influence of nonplanarity of the amide moiety on computed chemical shifts in peptide analogs. Is the amide nitrogen pyramidal? (1995) J Am Chem Soc, 117, pp. 2632-2637
Wong, M.W., Wiberg, K.B., Structure of acetamide: Planar or nonplanar? (1992) J Phys Chem, 96, pp. 668-671
Wright, G.M., Simmonds, R.J., Parry, D.E., Ab initio studies of the ground-state potential energy surface of formamide (1988) J Comput Chem, 9, pp. 600-603
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Motherwell, W. D. S., The Cambridge Crystallographic Data Centre: Computer-based search, retrieval, analysis and display of information (1979) Acta Crystallogr Sect B, 35, pp. 2331-233
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Tasumi, M., The Protein Data Bank: A computer-based archival file for macromolecular structures (1977) J Mol Biol, 112, pp. 535-542
Brown, R. D., Godfrey, P. D., Kleibomer, B., The conformation of formamide (1987) J Mol Spectrosc, 124, pp. 34-45
Burgi, H. B., Dunitz, J. D., Shefter, E., Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group (1973) J Am Chem Soc, 95, pp. 5065-5067
Burton, N. A., Chiu, S. S. -L., Davidson, M. M., Green, D. V. S., Hillier, I. H., McDouall, J. J. W., Vincent, M. A., Rotation about the C-N bond in formamide: An ab initio molecular orbital study of structure and energetics in the gas phase and in solution (1993) J Chem Soc Faraday Trans, 89, pp. 2631-2635
Cieplak, A. S., Solid-state conformations of linear oligopeptides and aliphatic amides. A model of chiral perturbation of a conjugated system (1985) J Am Chem Soc, 107, pp. 271-273
Costain, C. C., Dowling, J. M., Microwave spectrum and molecular structure of formamide (1960) J Chem Phys, 32, pp. 158-165
Deane, C. M., Blundell, T. L., Examination of the less favoured regions of the Ramachandran plot (1999), pp. 196-208. , Yathindra N, Kolashar AS, Vijayan M, eds. Perspectives in structural biology. Bangalore University, India: Indian Academy of SciencesEsposito, L., Vitagliano, L., Sica, F., Sorrentino, G., Zagari, A., Mazzarella, L., The ultrahigh resolution crystal structure of RNase A containing an isoaspartyl residue
Hansen, E. L., Larsen, N. W., Nicolaisen, F. M., An infrared investigation of formamide, acetamide and thioacetamide in the vapour phase. Inversion of the amino group (1980) Chem Phys Lett, 69, pp. 327-331
Hu, J. S., Bax, A., Determination of and 1 angles in proteins from 13C-13C three bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond? (1997) J Am Chem Soc, 119, pp. 6360-6368
Jeffrey, G. A., Houk, K. N., Paddon-Row, M. N., Rondan, N. G., Mitra, J., Pyramidalization of carbonyl carbons in asymmetric environments: Carboxilates, amides and amino acids (1985) J Am Chem Soc, 107, pp. 321-326
Karplus, P. A., Experimentally observed conformation-dependent geometry and hidden strain in proteins (1996) Protein Sci, 5, pp. 1406-1420
Lamzin, V. S., Morris, R. J., Dauter, Z., Wilson, K. S., Teeter, M. M., Experimental observation of bonding electrons in proteins (1999) J Biol Chem, 274, pp. 20753-20755
Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J Appl Crystallogr, 26, pp. 283-291
MacArthur, M. W., Thornton, J. M., Deviations from planarity of the peptide bond in peptides and proteins (1996) J Mol Biol, 264, pp. 1180-1195
Merritt, E. A., Kuhn, P., Sarfaty, S., Erbe, J. L., Holmes, R. K., Hol, W. G. J., The 1. 25 resolution refinement of the cholera toxin B-pentamer: Evidence of peptide backbone strain at the receptor-binding site (1998) J Mol Biol, 282, pp. 1043-1059
Sheldrick, G. M., Schneider, T. R., SHELXL: High resolution refinement (1997) Methods Enzymol, 277, pp. 319-343
Sulzbach, H. M., Schleyer, P. V. R., Schaefer, H. F., Influence of nonplanarity of the amide moiety on computed chemical shifts in peptide analogs. Is the amide nitrogen pyramidal? (1995) J Am Chem Soc, 117, pp. 2632-2637
Wong, M. W., Wiberg, K. B., Structure of acetamide: Planar or nonplanar? (1992) J Phys Chem, 96, pp. 668-671
Wright, G. M., Simmonds, R. J., Parry, D. E., Ab initio studies of the ground-state potential energy surface of formamide (1988) J Comput Chem, 9, pp. 600-603
Pyramidalization of backbone carbonyl carbon atoms in proteins
The high accuracy of X-ray analyses at atomic resolution is now able to display subtle deformations from standard geometry of building blocks in proteins. From the analysis of nine ultra-high resolution protein structures, we derived the first experimental evidence that a significant pyramidalization at the main-chain carbonyl carbon atom occurs in proteins. Our findings also show that this pyramidalisation is related to the main-chain psi torsion angle. The carbonyl carbon atoms of residues that adopt alpha (R) and extended conformations show a clear preference for positive and negative pyramidalization, respectively. The agreement between our data and those previously obtained from small molecule structures demonstrates that carbon pyramidalization is an intrinsic property of the peptide structure. Although small in magnitude, the pyramidalization is well preserved in the complex folded state of a macromolecular structure that results from the interplay of many different forces. In addition, this property of the peptide group may have interesting implications for the enzymatic reactions involving the carbonyl carbon atoms.
The high accuracy of X-ray analyses at atomic resolution is now able to display subtle deformations from standard geometry of building blocks in proteins. From the analysis of nine ultra-high resolution protein structures, we derived the first experimental evidence that a significant pyramidalization at the main-chain carbonyl carbon atom occurs in proteins. Our findings also show that this pyramidalisation is related to the main-chain psi torsion angle. The carbonyl carbon atoms of residues that adopt alpha (R) and extended conformations show a clear preference for positive and negative pyramidalization, respectively. The agreement between our data and those previously obtained from small molecule structures demonstrates that carbon pyramidalization is an intrinsic property of the peptide structure. Although small in magnitude, the pyramidalization is well preserved in the complex folded state of a macromolecular structure that results from the interplay of many different forces. In addition, this property of the peptide group may have interesting implications for the enzymatic reactions involving the carbonyl carbon atoms.
Pyramidalization of backbone carbonyl carbon atoms in proteins
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Pyramidalization of backbone carbonyl carbon atoms in proteins
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Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2000 Jun; 9(6): 1217-1225.
Impact Factor: 3.869
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Berisio R, Vitagliano L, Mazzarella L, Zagari A
Crystal Structure Of A Collagen-Like Polypeptide With Repeating Sequence Pro-Hyp-Gly At 1. 4 Ang Resolution: Implications For Collagen Hydration (437 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2000; 56(1): 8-13.
Impact Factor: 2.405
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Vitagliano L, Adinolfi S, Sica F, Merlino A, Zagari A, Mazzarella L
A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease (381 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 1999 Oct 29; 293(3): 569-577.
Impact Factor: 5.501
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Vitagliano L, Adinolfi S, Riccio A, Sica F, Zagari A, Mazzarella L
Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2 ', 5 ')adenosine (425 views)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 1998 Sep; 7(8): 1691-1699.
Impact Factor: 4.44
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* Crystallographic and spectroscopic characterizations of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability (300 views)
J Struct Biol (ISSN: 1047-8477, 1047-8477linking), 2012 Feb; 177(2): 506-512.
Impact Factor: 3.361
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Ruggiero A, Masullo M, Marasco D, Ruocco MR, Grimaldi P, Arcari P, Zagari A, Vitagliano L
* The dimeric structure of Sulfolobus solfataricus thioredoxin A2 and the basis of its thermostability (316 views)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2009 Dec; 77(4): 1004-1008.
Impact Factor: 3.085
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Esposito L, De Simone A, Zagari A, Vitagliano L
* Correlation Between Omega And Psi Dihedral Angles In Protein Structures (592 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2005 Apr 1; 347(3): 483-487.
Impact Factor: 5.229
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Merlino A, Vitagliano L, Sica F, Zagari A, Mazzarella L
* Population shift vs induced fit: The case of bovine seminal ribonuclease swapping dimer (384 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2004 Apr 15; 73(6): 689-695.
Impact Factor: 2.863
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Merlino A, Vitagliano L, Ceruso M, Di Nola A, Mazzarella L
* Global and local motions in ribonuclease A: A molecular dynamics study (411 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002 Nov 15; 65(4): 274-283.
Impact Factor: 2.372
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Vitagliano L, Merlino A, Zagari A, Mazzarella L
* Reversible substrate-induced domain motions in ribonuclease (336 views)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2002 Jan 1; 46(1): 97-104.
Impact Factor: 4.096
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Orru S, Vitagliano L, Esposito L, Mazzarella L, Marino G, Ruoppolo M
Effect of deamidation on folding of ribonuclease (387 views)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2000 Dec; 9(12): 2577-2582.
Impact Factor: 3.869
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Vitagliano L, Merlino A, Zagari A, Mazzarella L
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2 ', 5 ')guanosine (552 views)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2000 Jun; 9(6): 1217-1225.
Impact Factor: 3.869
View Export to BibTeX Export to EndNote
Berisio R, Vitagliano L, Mazzarella L, Zagari A
Crystal Structure Of A Collagen-Like Polypeptide With Repeating Sequence Pro-Hyp-Gly At 1. 4 Ang Resolution: Implications For Collagen Hydration (437 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2000; 56(1): 8-13.
Impact Factor: 2.405
View Export to BibTeX Export to EndNote
Vitagliano L, Adinolfi S, Sica F, Merlino A, Zagari A, Mazzarella L
A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease (381 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 1999 Oct 29; 293(3): 569-577.
Impact Factor: 5.501
View Export to BibTeX Export to EndNote
Vitagliano L, Adinolfi S, Riccio A, Sica F, Zagari A, Mazzarella L
Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2 ', 5 ')adenosine (425 views)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 1998 Sep; 7(8): 1691-1699.
Impact Factor: 4.44
View Export to BibTeX Export to EndNote
11 Records (11 excluding Abstracts).
Total impact factor: 41.09 (41.09 excluding Abstracts).
Total 5 year impact factor: 36.105 (36.105 excluding Abstracts).
Total impact factor: 41.09 (41.09 excluding Abstracts).
Total 5 year impact factor: 36.105 (36.105 excluding Abstracts).
449 views. Last view on Friday 17 February 2023, 15:30:32
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