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
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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.
Pyramidalization of backbone carbonyl carbon atoms in proteins
No results.
Pyramidalization of backbone carbonyl carbon atoms in proteins