Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures(734 views) Improta R, Vitagliano L, Esposito L
Keywords: Amide, Carbon, Peptide, Protein, Accuracy, Aqueous Solution, Article, Chemical Bond, Chemical Interaction, Crystal Structure, Density Functional Theory, Molecular Interaction, Prediction, Protein Analysis, Protein Conformation, Protein Structure, Quantum Mechanics, Chemical Structure, Chemistry, Protein Database, Quantum Theory, X Ray Crystallography, X-Ray, Models, Erratum,
Affiliations: *** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche (CNR), Napoli, Italy
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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
Rondan, N. G., Paddon-Row, M. N., Caramella, P., Houk, K. N., Nonplanar alkenes and carbonyls: a molecular distortion which parallels addition stereoselectivity (1981) J Am Chem Soc, 103, pp. 2436-2438
Jeffrey, G. A., Houk, K. N., Paddon-Row, M. N., Rondan, N. G., Mitra, J., Pyramidalization of carbonyl carbons in asymmetric environments: carboxylates, amides, and amino acids (1985) J Am Chem Soc, 107, pp. 321-326
Ulmer, T. S., Ramirez, B. E., Delaglio, F., Bax, A., Evaluation of Backbone Proton Positions and Dynamics in a Small Protein by Liquid Crystal NMR Spectroscopy (2003) J Am Chem Soc, 125, pp. 9179-9191
Edison, A. S., Linus Pauling and the planar peptide bond (2001) Nat Struct Biol, 8, pp. 201-202
Dunitz, J. D., Winkler, F. K., Amide group deformation in medium-ring lactams (1975) Acta Crystallogr B, 31, pp. 251-263
Ramachandran, G. N., Kolaskar, A. S., The non-planar peptide unit. Comparison of theory with crystal structure data (1973) Biochim Biophys Acta, 303, pp. 385-388
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
Ramek, M., Yu, C. -H., Sakon, J., Schaefer, L., Ab initio study of the conformational dependence of the nonplanarity of the peptide group (2000) J Phys Chem A, 104, pp. 9636-9645
Rick, S. W., Cachau, R. E., The nonplanarity of the peptide group: Molecular dynamics simulations with a polarizable two-state model for the peptide bond (2000) J Chem Phys, 112, pp. 5230-5241
Hu, J. S., Bax, A., Determination of j and c1 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
Burton, N. A., Chiu, S. S. L., Davidson, M. M., Green, D. V. S., Hiller, I. H., Rotation about the carbon-nitrogen 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
Wiberg, K. B., Rablen, P. R., Rush, D. J., Keith, T. A., Amides. 3. Experimental and Theoretical Studies of the Effect of the Medium on the Rotational Barriers for N, N-Dimethylformamide and N, N-Dimethylacetamide (1995) J Am Chem Soc, 117, pp. 4261-4270
Mujika, J. I., Matxain, J. M., Eriksson, L. A., Lopez, X., Resonance structures of the amide bond: the advantages of planarity (2006) Chemistry, 12, pp. 7215-7224
Wiberg, K. B., Breneman, C. M., Resonance interactions in acyclic systems. 3. Formamide internal rotation revisited. Charge and energy redistribution along the C-N bond rotational pathway (1992) J Am Chem Soc, 114, pp. 831-840
Milner-White, E. J., The partial charge of the nitrogen atom in peptide bonds (1997) Protein Sci, 6, pp. 2477-2482
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., The Protein Data Bank (2002) Acta Crystallogr D Biol Crystallogr, 58, pp. 899-907
Allen, F. H., The Cambridge Structural Database: a quarter of a million crystal structures and rising (2002) Acta Crystallogr B, 58, pp. 380-388
Tsai, M. I., Xu, Y., Dannenberg, J. J., Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution (2009) J Phys Chem B, 113, pp. 309-318
Poon, C. D., Samulski, E. T., Weise, C. F., Weisshaar, J. C., Do Bridging Water Molecules Dictate the Structure of a Model Dipeptide in Aqueous Solution? (2000) J Am Chem Soc, 122, pp. 5642-5643
Jalkanen, K. J., Degtyarenko, I. M., Nieminen, R. M., Cao, X., Nafie, L. A., Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N -methylamide in aqueous solution: a combined theoretical and experimental approach (2008) Theor Chem Acc, 119, pp. 191-210
Bartlett, G. J., Choudhary, A., Raines, R. T., Woolfson, D. N., n pi* interactions in proteins (2011) Nat Chem Biol, 6, pp. 615-620
Lamzin, V. S., Wilson, K. S., Automated refinement for protein crystallography (1997) Methods Enzymol, 277, pp. 269-305
Karplus, P. A., Shapovalov, M. V., Dunbrack Jr., R. L., Berkholz, D. S., A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions (2008) Acta Crystallogr D Biol Crystallogr, 64, pp. 335-336
Berkholz, D. S., Krenesky, P. B., Davidson, J. R., Karplus, P. A., Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry (2010) Nucleic Acids Res, 38, pp. 320-325
Berkholz, D. S., Shapovalov, M. V., Dunbrack Jr., R. L., Karplus, P. A., Conformation dependence of backbone geometry in proteins (2009) Structure, 17, pp. 1316-1325
Network, E. -D. V., Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network (1998) J Mol Biol, 276, pp. 417-436
Rohl, C. A., Strauss, C. E., Misura, K. M., Baker, D., Protein structure prediction using Rosetta (2004) Methods Enzymol, 383, pp. 66-93
Tronrud, D. E., Karplus, P. A., A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution (2011) Acta Crystallogr D Biol Crystallogr, 67, pp. 699-706
Foster, J. P., Weinhold, F., Natural hybrid orbitals (1980) J Am Chem Soc, 102, pp. 7211-7218
Glendening, E. D., Weinhold, F., Natural resonance theory. I. General formalism (1998) J Comput Chem, 19, pp. 593-609
Frisch, M. J., (2004) Gaussian 03, , Revision C. 02 Ed, Wallingford CT, Gaussian Inc
Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures
Kállay C, Dávid A, Timári S, Nagy EM, Sanna D, Garribba E, Micera G, De Bona P, Pappalardo G, Rizzarelli E, Sóvágó I * Copper(II) complexes of rat amylin fragments(357 views) Dalton T (ISSN: 1477-9234, 1477-9226, 1477-9234electronic), 2011 Oct 14; 40(38): 9711-9721. Impact Factor:3.838 ViewExport to BibTeXExport to EndNote