51
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Kang YK, Park HS, Byun BJ. Puckering transitions of pseudoproline residues. Biopolymers 2009; 91:444-55. [DOI: 10.1002/bip.21150] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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52
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Kang YK, Kang NS. Conformational preferences ofN-methoxycarbonyl proline dipeptide. J Comput Chem 2009; 30:1116-27. [DOI: 10.1002/jcc.21136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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53
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Flores-Ortega A, Casanovas J, Assfeld X, Alemán C. Protonation of the Side Group in β- and γ-Aminated Proline Analogues: Effects on the Conformational Preferences. J Org Chem 2009; 74:3101-8. [DOI: 10.1021/jo900169s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Jordi Casanovas
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Xavier Assfeld
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
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54
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Yonezawa Y, Nakata K, Sakakura K, Takada T, Nakamura H. Intra- and Intermolecular Interaction Inducing Pyramidalization on Both Sides of a Proline Dipeptide during Isomerization: An Ab Initio QM/MM Molecular Dynamics Simulation Study in Explicit Water. J Am Chem Soc 2009; 131:4535-40. [DOI: 10.1021/ja807814x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasushige Yonezawa
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Kazuto Nakata
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Kota Sakakura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Toshikazu Takada
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan, CREST, Japan Science and Technology Agency, HPC Marketing Promotion Division, NEC Corporation, 1-10, Nisshin-Cho, Fuchu, Tokyo 183-8501, Japan, and RIKEN, Research Program for Computational Science, 2-1-1 Marunouchi, Chiyodaku, Tokyo 100-0005, Japan
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55
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Flores-Ortega A, Casanovas J, Nussinov R, Alemán C. Conformational preferences of beta- and gamma-aminated proline analogues. J Phys Chem B 2008; 112:14045-55. [PMID: 18842022 PMCID: PMC2836598 DOI: 10.1021/jp807638p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cbeta- or Cgamma-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N'-methylamide derivatives of four isomers of aminoproline, which differ not only in the beta- or gamma-position of the substituent but also in its cis or trans relative disposition, has been performed. To further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of (dimethylamino)proline. In addition, the effects of solvation on aminoproline and (dimethylamino)proline dipeptides have been evaluated using a self-consistent reaction field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone...side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cgamma-position with a cis relative disposition is the most stable in the gas phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated (dimethylamino)proline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
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56
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Li QG, Xue Y, Yan GS. Water-assisted enol-to-keto tautomerism of a simple peptide model: A computational investigation. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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57
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58
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Lee JY, Byun BJ, Kang YK. Conformational preferences and pKa value of cysteine residue. J Phys Chem B 2008; 112:11189-93. [PMID: 18700737 DOI: 10.1021/jp8052423] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational preferences of the Cys dipeptides with thiol and thiolate groups (Ac-Cys-NHMe and Ac-Cys (-)-NHMe, respectively) and the apparent (i.e., macroscopic) p K a value of the Cys dipeptide have been studied at the hybrid density functional B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d) level with the conductor-like polarizable continuum model in the gas phase and in water. The hydrogen bonds and/or favorable interactions between the backbone and the thiol group of the side chain resulted in the different conformational preferences of the Cys and Cys (-) dipeptides from those of the Ala dipeptide in the gas phase and in water, although the preferred conformations of the Cys dipeptide are in part similar to those of the Ala dipeptide. In particular, the interactions between the thiolate group and the backbone amide groups appear to play a role in stabilizing the alpha- or 3 10-helical conformations for the Cys (-) dipeptide in the gas phase and in water. The p K a value of the Cys residue is estimated to be 8.58 at 25 degrees C using the statistically weighted free energies of all feasible conformations for the Cys and Cys (-) dipeptides in the gas phase and solvation free energies, which is consistent with the observed values of 8.3 and 8.22 +/- 0.16.
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Affiliation(s)
- Joo Yun Lee
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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59
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Jamet H, Jourdan M, Dumy P. NMR and Theoretical Calculations: A Unified View of the Cis/Trans Isomerization of 2-Substituted Thiazolidines Containing Peptides. J Phys Chem B 2008; 112:9975-81. [DOI: 10.1021/jp7118982] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helene Jamet
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Muriel Jourdan
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Pascal Dumy
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
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60
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Kang YK, Byun BJ. Conformational Preferences and Cis−Trans Isomerization of l-Lactic Acid Residue. J Phys Chem B 2008; 112:9126-34. [DOI: 10.1021/jp801200m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Byung Jin Byun
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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61
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Kwac K, Lee KK, Han JB, Oh KI, Cho M. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra. J Chem Phys 2008; 128:105106. [PMID: 18345930 DOI: 10.1063/1.2837461] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.
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Affiliation(s)
- Kijeong Kwac
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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62
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Mathieu S, Poteau R, Trinquier G. Estimating the "steric clash" at cis peptide bonds. J Phys Chem B 2008; 112:7894-902. [PMID: 18543981 DOI: 10.1021/jp711082d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.
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Affiliation(s)
- Simon Mathieu
- Laboratoire de Chimie et Physique Quantique, IRSAMC, Université Paul-Sabatier, Toulouse Cedex 9, France
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63
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Flores-Ortega A, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Casanovas J. Conformational preferences of alpha-substituted proline analogues. J Org Chem 2008; 73:3418-27. [PMID: 18351745 PMCID: PMC2679371 DOI: 10.1021/jo702710x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the alpha hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N'-methylamide derivatives of L-proline, L-alpha-methylproline, and L-alpha-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated by using a Self-Consistent Reaction Field model. As expected, tetrasubstitution at the alpha carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at C (alpha) may play a significant role in modulating the conformational preferences of proline.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
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64
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Lee JY, Kang YK. The rate enhancement for prolyl cis-to-trans isomerization of cyclic CPFC peptide is caused by an increase in the vibrational entropy of the transition state. J Phys Chem B 2008; 112:3287-9. [PMID: 18302366 DOI: 10.1021/jp711715j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformational preferences and prolyl cis-trans isomerization of oxidized and reduced Ac-Cys-Pro-Phe-Cys-NH2 (CPFC peptides) have been carried out using the ab initio HF/6-31+G(d) and hybrid density functional B3LYP/6-311++G(d,p) levels of theory. The most preferred conformations of oxidized and reduced CPFC peptides with the trans prolyl peptide bond have a type-I beta-turn for the Pro-Phe sequence in common. In particular, the transition states for both forms are stabilized by the intramolecular hydrogen bonds between the prolyl nitrogen and the N-H group of the Phe3 residue. The rotational barrier DeltaGct to the cis-to-trans isomerization for the oxidized CPFC peptide is calculated to be 19.37 kcal/mol at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory, which is lower by 0.88 kcal/mol than that of the reduced CPFC peptide. This may indicate that the rate constant kc-->t of the prolyl cis-to-trans isomerization for the oxidized form is about 4 times larger than that of the reduced form, which is reasonably consistent with the value deduced from NMR experiments. In particular, the increase in vibrational entropy for the transition state of the oxidized form over that of the reduced form contributes to enhance the rate constant for the prolyl cis-to-trans isomerization of the oxidized form.
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Affiliation(s)
- Joo Yun Lee
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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65
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A matrix isolation study on Ac–l-Pro–NH2: a frequent structural element of β- and γ-turns of peptides and proteins. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.12.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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66
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Kang YK, Park HS. Conformational Preferences of Pseudoproline Residues. J Phys Chem B 2007; 111:12551-62. [DOI: 10.1021/jp074128f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
| | - Hae Sook Park
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
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67
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Abstract
The puckering transition of the proline residue with trans and cis prolyl peptide bonds was explored by optimizations along the torsion angle chi1 of the prolyl ring using quantum-chemical methods in water. By analyzing the potential energy surfaces and local minima in water, it is observed that the puckering transition of the proline residue proceeds from a down-puckered conformation to an up-puckered one and vice versa through the transition state with an envelope form having the N atom at the top of the envelope and not a planar one, as seen in the gas phase, although the backbone conformations are different in the gas phase and in water. The barriers to the puckering transition DeltaGup-->down are estimated to be 3.12 and 3.00 kcal/mol for trans and cis conformers at the B3LYP/6-311++G(d,p) level of theory in water, respectively, which are about 1.7 kcal/mol higher than those in the gas phase. Out of 2197 prolines from the 241 high-resolution PDB chains, four transition-state-like structures with the envelope ring puckering are identified. Three of them have the trans prolyl peptide bonds and one has the cis one. The favorable or steric interactions by neighboring residues may be responsible for the stabilization of these transition-state-like ring structures in the proteins.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea.
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68
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de M. Seabra G, Walker RC, Elstner M, Case DA, Roitberg AE. Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A 2007; 111:5655-64. [PMID: 17521173 PMCID: PMC3197852 DOI: 10.1021/jp070071l] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-consistent charge density functional tight-binding (SCC-DFTB) is a semiempirical method based on density functional theory and has in many cases been shown to provide relative energies and geometries comparable in accuracy to full DFT or ab initio MP2 calculations using large basis sets. This article shows an implementation of the SCC-DFTB method as part of the new QM/MM support in the AMBER 9 molecular dynamics program suite. Details of the implementation and examples of applications are shown.
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Affiliation(s)
- Gustavo de M. Seabra
- Department of Chemistry and Quantum Theory Project, University of Florida; P.O. Box 118435; Gainesville, FL, 32611-8435. USA
| | - Ross C. Walker
- Dept. of Molecular Biology, TPC15, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037 USA
| | - Marcus Elstner
- Institut für Physikalische und Theoretische Chemie. Technische Universität Braunschweig. Hans-Sommer-Straße 10. D-38106 Braunschweig. Germany
| | - David A. Case
- Dept. of Molecular Biology, TPC15, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037 USA
| | - Adrian E. Roitberg
- Department of Chemistry and Quantum Theory Project, University of Florida; P.O. Box 118435; Gainesville, FL, 32611-8435. USA
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69
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Flores-Ortega A, Casanovas J, Zanuy D, Nussinov R, Alemán C. Conformations of proline analogues having double bonds in the ring. J Phys Chem B 2007; 111:5475-82. [PMID: 17458993 DOI: 10.1021/jp0712001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intrinsic conformational preferences of proline analogues having double bonds between carbon atoms in their rings have been investigated using quantum mechanical calculations at the B3LYP/6-31+G(d,p) level. For this purpose, the potential energy surface of the N-acety-N'-methylamide derivatives of three dehydroprolines (proline analogues unsaturated at alpha,beta; beta,gamma; and gamma,delta) and pyrrole (proline analogue with unsaturations at both alpha,beta and gamma,delta) have been explored, and the results are compared with those obtained for the derivative of the nonmodified proline. We found that the double bonds affect the ring puckering and the geometric internal parameters, even though the backbone conformation was influenced the most. Results indicate that the formation of double bonds between carbon atoms in the pyrrolidine ring should be considered as an effective procedure to restrict the conformational flexibility of prolines. Interestingly, we also found that the N-acetyl-N'-methylamide derivative of pyrrole shows a high probability of having a cis peptide bond preceding the proline analogue.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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70
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Kang YK, Byun BJ. Conformational Preferences and cis−trans Isomerization of Azaproline Residue. J Phys Chem B 2007; 111:5377-85. [PMID: 17439267 DOI: 10.1021/jp067826t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea
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Jhon JS, Kang YK. Conformational Preferences of Proline Analogues with Different Ring Size. J Phys Chem B 2007; 111:3496-507. [PMID: 17388495 DOI: 10.1021/jp066835z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational study on L-azetidine-2-carboxylic acid (Ac-Aze-NHMe, the Aze dipeptide) and (S)-piperidine-2-carboxylic acid (Ac-Pip-NHMe, the Pip dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in conformational preferences and cis-trans isomerization for proline residue and its analogues with different ring size in the gas phase and in solution (chloroform and water). The change of ring size by deleting a CH2 group from or adding a CH2 group to the prolyl ring results the remarkable changes in backbone and ring structures compared with those of the Pro dipeptide, especially in the C'-N imide bond length and the bond angles around the N-C(alpha) bond. The four-membered azetidine ring can have either puckered structure depending on the backbone structure because of the less puckered structure. The six-membered piperidine ring can adopt chair and boat conformations, but the chair conformation is more preferred than the boat conformation. These calculated preferences for puckering are consistent with experimental results from analysis of X-ray structures of Aze- and Pip-containing peptides. On going from Pro to Aze to Pip, the axiality (i.e., a tendency to adopt the axial orientation) of the NHMe group becomes stronger, which can be ascribed to reduce the steric hindrances between 1,2-substituted Ac and NHMe groups. As the solvent polarity increases, the polyproline II-like conformation becomes more populated and the relative stability of conformation tC with a C7 hydrogen bond between C'=O of the amino group and N-H of the carboxyl group decreases for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. The cis population and rotational barriers for the imide bond increase with the increase of solvent polarity for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. In particular, the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about azetyl and piperidyl peptide bonds in the gas phase and in solution, as seen for alanyl and prolyl peptide bonds. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure, but the lower rotational barriers for the Aze and Pip dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized.
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Affiliation(s)
- Jong Suk Jhon
- Department of Chemistry and Basic Science Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea
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