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Hope M, Šebestík J, Kapitán J, Bouř P. Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides. J Phys Chem A 2020; 124:674-683. [DOI: 10.1021/acs.jpca.9b10557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Hope
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Norwegian University of Science and Technology NO-7491 Trondheim, Norway
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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2
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Bünnemann K, Merten C. Solvation of N,C-Protected Valine: Interactions with DMSO and a Chiral Solvating Agent. J Phys Chem B 2016; 120:9434-42. [DOI: 10.1021/acs.jpcb.6b05897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Christian Merten
- Organische
Chemie 2, Ruhr Universität Bochum, 44801 Bochum, Germany
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3
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MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 2014; 102:3586-616. [PMID: 24889800 DOI: 10.1021/jp973084f] [Citation(s) in RCA: 10914] [Impact Index Per Article: 1091.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.
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Affiliation(s)
- A D MacKerell
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, and Laboratoire de Chimie Biophysique, ISIS, Institut Le Bel, Université Louis Pasteur, 67000 Strasbourg, France
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4
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Knapp K, Górecki M, Frelek J, Luboradzki R, Hollósi M, Majer Z, Vass E. Comprehensive Chiroptical Study of Proline-Containing Diamide Compounds. Chirality 2014; 26:228-42. [DOI: 10.1002/chir.22305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/13/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Krisztina Knapp
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Marcin Górecki
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Jadwiga Frelek
- Institute of Organic Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Roman Luboradzki
- Institute of Physical Chemistry; Polish Academy of Sciences; Warsaw Poland
| | - Miklós Hollósi
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Zsuzsa Majer
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Elemér Vass
- Laboratory for Chiroptical Structure Analysis, Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
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5
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Quesada-Moreno MM, Márquez-García AÁ, Avilés-Moreno JR, López-González JJ. Conformational landscape of l-threonine in neutral, acid and basic solutions from vibrational circular dichroism spectroscopy and quantum chemical calculations. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.tetasy.2013.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Parchaňský V, Kapitán J, Kaminský J, Šebestík J, Bouř P. Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity. J Phys Chem Lett 2013; 4:2763-2768. [PMID: 26706714 DOI: 10.1021/jz401366j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accessible values of the φ and ψ torsional angles determining peptide main chain conformation are traditionally displayed in the form of Ramachandran plots. The number of experimental methods making it possible to determine such conformational distribution is limited. In the present study, Raman optical activity (ROA) spectra of Ac-Ala-NHMe were measured and fit by theoretical curves. This revealed the most favored conformers and a large part of the potential energy surface (PES) of this model dipeptide. Such experimental PES compares well to quantum chemical computations, whereas molecular dynamics (MD) modeling reproduces it less faithfully. The surface shape is consistent with the temperature dependence of the spectra, as observed experimentally and predicted by MD. Despite errors associated with spectral modeling and the measurement, the results are likely to facilitate future applications of ROA spectroscopy.
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Affiliation(s)
- Václav Parchaňský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
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7
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Pazderková M, Profant V, Hodačová J, Šebestík J, Pazderka T, Novotná P, Urbanová M, Šafařík M, Buděšínský M, Tichý M, Bednárová L, Baumruk V, Maloň P. Nonplanar Tertiary Amides in Rigid Chiral Tricyclic Dilactams. Peptide Group Distortions and Vibrational Optical Activity. J Phys Chem B 2013; 117:9626-42. [DOI: 10.1021/jp405226k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
- Charles University in Prague, 121 16 Prague 2, Czech Republic
| | - Václav Profant
- Charles University in Prague, 121 16 Prague 2, Czech Republic
| | - Jana Hodačová
- Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Tomáš Pazderka
- Charles University in Prague, 121 16 Prague 2, Czech Republic
| | - Pavlína Novotná
- Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Marie Urbanová
- Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Miloš Tichý
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | | | - Petr Maloň
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
- Charles University in Prague, 121 16 Prague 2, Czech Republic
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8
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l-Serine in aqueous solutions at different pH: Conformational preferences and vibrational spectra of cationic, anionic and zwitterionic species. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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10
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Putz MV, Putz AM. DFT Chemical Reactivity Driven by Biological Activity: Applications for the Toxicological Fate of Chlorinated PAHs. STRUCTURE AND BONDING 2012. [DOI: 10.1007/978-3-642-32750-6_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Teramae H, Ishimoto T, Nagashima U. Mixing parameters for geometry optimization using the Hamiltonian algorithm. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1010-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Larsen KL, Barsberg S. Environmental effects on the lignin model monomer, vanillyl alcohol, studied by Raman spectroscopy. J Phys Chem B 2011; 115:11470-80. [PMID: 21830768 DOI: 10.1021/jp203910h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Structural analysis of plant materials, i.e., lignin, cellulose, hemicellulose, etc., supports the growing interest of their uses, e.g., as sources for biofuels or materials. Lignin is a main polymer formed from three phenolic presursors, containing none, one, or two OMe groups, i.e., H, G, and S units, respectively. Raman spectroscopy gives valuable knowledge on lignin and has a large potential for further developments. Thus in the present work we show how the use of electronic structure theory can support the study of environmental effects on lignin Raman bands. Raman spectra of the lignin model monomer, vanillyl alcohol (G type), dissolved in different solvents were compared to investigate such effects on the Raman band shapes and positions. Density functional theory combined with the polarizable continuum model were applied to assign the observed bands and tested for prediction accuracy. Two ring deformation modes at ∼1600 cm(-1) showed strong dependency on solvent ability to act as hydrogen bond donor, and this has to be considered in addition to substitutional effects on these modes.
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Affiliation(s)
- Kiki L Larsen
- Faculty of Life Sciences, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark
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13
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Yamabe S, Kawagishi N. A computational study on the relationship between formation and electrolytic dissociation of carbonic acid. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0929-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Effect of regular hydration on gas phase structural stability of [zwitterionic alanine+M+] (M+=Li+, Na+, K+) complexes: A quantum chemical study. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2010.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Biswal HS, Loquais Y, Tardivel B, Gloaguen E, Mons M. Isolated monohydrates of a model peptide chain: effect of a first water molecule on the secondary structure of a capped phenylalanine. J Am Chem Soc 2011; 133:3931-42. [PMID: 21361380 DOI: 10.1021/ja108643p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.
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Affiliation(s)
- Himansu S Biswal
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
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16
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Liu Z, Ensing B, Moore PB. Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space. J Chem Theory Comput 2010; 7:402-19. [PMID: 26596162 DOI: 10.1021/ct100395n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.
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Affiliation(s)
- Zhiwei Liu
- West Center for Computational Chemistry and Drug Design, Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States and Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Bernd Ensing
- West Center for Computational Chemistry and Drug Design, Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States and Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Preston B Moore
- West Center for Computational Chemistry and Drug Design, Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States and Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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17
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Zhang RB, Eriksson LA. Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group. Phys Chem Chem Phys 2010; 12:3690-7. [PMID: 20358065 DOI: 10.1039/b921646d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.
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Affiliation(s)
- Ru bo Zhang
- Institute for Chemical Physics, School of Science, Beijing Institute of Technology, Beijing 100081, China
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18
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Qiu S, Li G, Liu P, Wang C, Feng Z, Li C. Chirality transition in the epoxidation of (−)-α-pinene and successive hydrolysis studied by Raman optical activity and DFT. Phys Chem Chem Phys 2010; 12:3005-13. [DOI: 10.1039/b919993d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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19
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20
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Berhanu WM, Mikhailov IA, Masunov AE. Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation? J Mol Model 2009; 16:1093-101. [PMID: 19924452 DOI: 10.1007/s00894-009-0610-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
Abstract
We report density functional theory (DFT) calculations of the Raman spectra for hexapeptides of glutamic acid and lysine in three different conformations (alpha, beta and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.
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Affiliation(s)
- Workalemahu Mikre Berhanu
- NanoScience Technology Center and Department of Chemistry, University of Central Florida, Orlando, FL 32826, USA
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21
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Yang S, Cho M. Direct calculations of vibrational absorption and circular dichroism spectra of alanine dipeptide analog in water: Quantum mechanical/molecular mechanical molecular dynamics simulations. J Chem Phys 2009; 131:135102. [DOI: 10.1063/1.3243078] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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22
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23
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Role of quantum chemical calculations in molecular biophysics with a historical perspective. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0622-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Liégeois V. A Vibrational Raman Optical Activity Study of 1,1′-Binaphthyl Derivatives. Chemphyschem 2009; 10:2017-25. [DOI: 10.1002/cphc.200900115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Agnihotri N, Mishra PC. Mutagenic Product Formation Due to Reaction of Guanine Radical Cation with Nitrogen Dioxide. J Phys Chem B 2009; 113:3129-38. [DOI: 10.1021/jp805942y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Neha Agnihotri
- Department of Physics, Banaras Hindu University, Varanasi - 221 005, India
| | - P. C. Mishra
- Department of Physics, Banaras Hindu University, Varanasi - 221 005, India
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26
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A quantum chemical study of reactions of DNA bases with sulphur mustard: a chemical warfare agent. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0514-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Svistunenko DA, Jones GA. Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters. Phys Chem Chem Phys 2009; 11:6600-13. [DOI: 10.1039/b905522c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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David C, Foley S, Enescu M. Protein S–S bridge reduction: a Raman and computational study of lysozyme interaction with TCEP. Phys Chem Chem Phys 2009; 11:2532-42. [DOI: 10.1039/b815492a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Jena B, Manoharan SS. Blue to green shifted fluorescence in inter- and intramolecular hydrogen bonded di(benzimidazol-2-yl)benzene. Chem Commun (Camb) 2009:4426-8. [DOI: 10.1039/b907745f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations. Biophys J 2008; 95:5574-86. [PMID: 18805935 DOI: 10.1529/biophysj.108.137596] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N'-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (alpha(R)) and left-handed (alpha(L)) helical conformations. The computed ROA spectra based on MC-sampled alpha(R) and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the alpha(L)- and beta-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the alpha(R) and PPII conformations but no substantial population of alpha(L)- or beta-structures, despite sampling alpha(L)- and beta-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.
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31
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Grdadolnik J, Grdadolnik SG, Avbelj F. Determination of conformational preferences of dipeptides using vibrational spectroscopy. J Phys Chem B 2008; 112:2712-8. [PMID: 18260662 DOI: 10.1021/jp7096313] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The NMR coupling constants ((3)J(H(N), H(alpha))) of dipeptides indicate that the backbone conformational preferences vary strikingly among dipeptides. These preferences are similar to those of residues in small peptides, denatured proteins, and the coil regions of native proteins. Detailed characterization of the conformational preferences of dipeptides is therefore of fundamental importance for understanding protein structure and folding. Here, we studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. The main advantage of vibrational spectroscopy over NMR spectroscopy is in its much shorter time scale, which enables the determination of the conformational preferences of short-lived states. Accuracy of structure determination using vibrational spectroscopy depends critically on identification of the vibrational parameters that are sensitive to changes in conformation. We show that the frequencies of the amide I band and the A12 ratio of the amide I components of dipeptides correlate with the (3)J(H(N), H(alpha)). These two infrared vibrational parameters are thus analogous to (3)J(H(N), H(alpha)), indicators for the preference for the dihedral angle phi. We also show that the intensities of the components of the amide III bands in infrared spectra and the intensities of the skeletal vibrations in Raman spectra are indicators of populations of the P(II), beta, and alpha(R) conformations. The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the beta conformation increases in valine dipeptides. The populations of the alpha(R) conformation are generally small. These data are in accord with the electrostatic screening model of conformational preferences.
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Affiliation(s)
- Joze Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI 1000 Ljubljana, Slovenia.
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32
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Jalkanen KJ, Gale JD, Lassen PR, Hemmingsen L, Rodarte A, Degtyarenko IM, Nieminen RM, Brøgger Christensen S, Knapp-Mohammady M, Suhai S. A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0390-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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34
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Jalkanen KJ, Degtyarenko IM, Nieminen RM, Cao X, Nafie LA, Zhu F, Barron LD. 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. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0361-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Ramnarayan K, Bohr HG, Jalkanen KJ. Classification of protein fold classes by knot theory and prediction of folds by neural networks: A combined theoretical and experimental approach. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0285-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0276-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Abstract
The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and Basic Science Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea.
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38
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Takekiyo T, Imai T, Kato M, Taniguchi Y. Understanding high pressure stability of helical conformation of oligopeptides and helix bundle protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:355-63. [PMID: 16478681 DOI: 10.1016/j.bbapap.2005.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 11/13/2005] [Accepted: 11/18/2005] [Indexed: 11/27/2022]
Abstract
The pressure effect on conformational equilibria of simple organic compounds and the pressure denaturation of proteins have been well investigated by using vibrational spectroscopy. However, there was no systematic investigation of the pressure effect on conformational equilibria of oligopeptides, which are located between the simple organic compounds and proteins. Here, we review the recent vibrational spectroscopic and theoretical studies of the pressure effect on conformational equilibria of model oligopeptides and helix bundle protein in aqueous solution.
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Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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39
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Abstract
The structures of one conformer of the nonionic neutral and zwitterionic species of L-serinyl L-serinyl L-serine (SSS or tri-L-serine), together with its cationic and anionic species and the capped N-acetyl tri-L-serine N'-methylamide analog were optimized with density functional theory with the Becke 3LYP hybrid exchange correlation (XC) functional and the PW91 GGA XC functional and the 6-31G* and aug-cc-pVDZ basis sets. Subsequently, the vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra were simulated in order to compare them to experimentally measured spectra. In addition, we compare to previously reported studies for both structural determination and spectral simulations and measurements. A comparison of the various ways to treat the effects of the environment and solvation on both the structure and the spectral properties is thoroughly investigated for one conformer, with the goal to determine which level of theory is appropriate to use in the systematic search of the conformational space. In addition, the effects of the counterion, here Cl- anion, are also investigated. Here we present the current state of the art in nanobiology, where the latest methods in experimental and theoretical vibrational spectroscopy are used to gain useful information about the coupling of the nuclear, electronic and magnetic degrees of freedom and structure of tri-L-serine and its capped peptide analog with the environment.
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Affiliation(s)
- V Würtz Jürgensen
- Quantum Protein Centre, Department of Physics, Technical University of Denmark, Bldg 309, DK-2800 Kgs Lyngby, Denmark
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40
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Linear Response Properties Required to Simulate Vibrational Spectra of Biomolecules in Various Media: (R)-Phenyloxirane (A Comparative Theoretical and Spectroscopic Vibrational Study). ADVANCES IN QUANTUM CHEMISTRY 2005. [DOI: 10.1016/s0065-3276(05)50006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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41
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Wang ZX, Duan Y. Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water. J Comput Chem 2004; 25:1699-716. [PMID: 15362127 DOI: 10.1002/jcc.20092] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.
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Affiliation(s)
- Zhi-Xiang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 222 S. Chapel St., Newark, Delaware 19716, USA
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42
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Jalkanen K, Elstner M, Suhai S. Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2003.12.045] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Shi Z, Woody RW, Kallenbach NR. Is polyproline II a major backbone conformation in unfolded proteins? ADVANCES IN PROTEIN CHEMISTRY 2004; 62:163-240. [PMID: 12418104 DOI: 10.1016/s0065-3233(02)62008-x] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, New York 10003, USA
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44
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Takekiyo T, Imai T, Kato M, Taniguchi Y. Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution. Biopolymers 2004; 73:283-90. [PMID: 14755584 DOI: 10.1002/bip.10548] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We investigated the temperature and pressure effects on conformational equilibria of N-acetyl-L-alanine-N'-methylamide (AAlaMA) in aqueous solution by Raman spectroscopy. Scattering intensities in the skeletal stretching mode of AAlaMA in aqueous solution were decomposed into some component bands by the spectra analysis. Our results indicate that each component band for AAlaMA adopts not only the P(II) and alpha(R) conformations but also the C(7eq) conformation. From temperature and pressure dependencies of the band intensities, we determined the enthalpy differences and the volume differences between the conformers. The C(7eq) conformer is enthalpically most stable due to the intramolecular hydrogen bond. The partial molar volume of the C(7eq) conformer is the smallest through the solvent-exclusion effect rather than the solute-solvent electrostatic interaction effect.
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Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
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45
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Weise CF, Weisshaar JC. Conformational Analysis of Alanine Dipeptide from Dipolar Couplings in a Water-Based Liquid Crystal. J Phys Chem B 2003. [DOI: 10.1021/jp026854i] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph F. Weise
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396
| | - James C. Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396
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46
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Bouř P, Kapitán J, Baumruk V. Simulation of the Raman Optical Activity of l-Alanyl−l-Alanine. J Phys Chem A 2001. [DOI: 10.1021/jp002572b] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 16610, Prague, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 16610, Prague, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 16610, Prague, Czech Republic, and Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
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47
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Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations. Chem Phys 2001. [DOI: 10.1016/s0301-0104(00)00375-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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49
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Frimand K, Bohr H, Jalkanen K, Suhai S. Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study. Chem Phys 2000. [DOI: 10.1016/s0301-0104(00)00069-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Elstner M, Jalkanen K, Knapp-Mohammady M, Frauenheim T, Suhai S. DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20. Chem Phys 2000. [DOI: 10.1016/s0301-0104(00)00100-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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