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Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (62 views)

Improta R, Vitagliano L, Esposito L

Plos One (ISSN: 1932-6203, 1932-6203electronic), 2011 Sep 16; 6(9): e24533-e24533.

Abstract
By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of C α substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed. © 2011 Improta et al.

Affiliations ▼
*** IBB - CNR Affiliation

Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche (CNR), Napoli, Italy

Details ▼
Impact factor: 3.534, 5-year impact factor: 4.015

Paper type: Erratum, Research Support, Non-U. S. Gov'T, Abstract,

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,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-80052850167&partnerID=40&md5=d5e36aea476bda084e7f391da1983b79

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Shoulders, M. D., Satyshur, K. A., Forest, K. T., Raines, R. T., Stereoelectronic and steric effects in side chains preorganize a protein main chain (2010) Proc Natl Acad Sci U S A, 107, pp. 559-564

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


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6 Records (6 excluding Abstracts and Conferences).
Total impact factor: 17.808 (17.808 excluding Abstracts and Conferences).
Total 5-year impact factor: 17.779 (17.779 excluding Abstracts and Conferences).



Your bibliography query: (([btitle, keywords, abstract] AMIDE AND [btitle, keywords, abstract] CARBON AND [btitle, keywords, abstract] PEPTIDE AND [btitle, keywords, abstract] PROTEIN)) AND NOT [id] = 50957



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