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Park HS, Byun BJ, Kang YK. Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations. ACS OMEGA 2022; 7:27755-27768. [PMID: 35967045 PMCID: PMC9366962 DOI: 10.1021/acsomega.2c03942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol-1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a βII'-bend-like motif at the Gly3-Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double β-bends such as a βII' bend at the Gly2-Gly3 sequence and a βI bend at the Gly3-Phe4 sequence. The calculated ensemble-averaged distance between CGly2 α and CLeu5 α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double β-bends isolated in water into the "bioactive conformation" like an extended structure when binding to δOR.
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Affiliation(s)
- Hae Sook Park
- Department
of Nursing, Cheju Halla University, 38 Halladaehak-ro, Jeju, Jeju-do 63092, Republic of Korea
| | - Byung Jin Byun
- Drug
Discovery Center, JW Pharmaceutical Co.
Ltd., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic
of Korea
| | - Young Kee Kang
- Department
of Chemistry, Chungbuk National University, 1 Chungdae-ro,
Seowon-gu, Cheongju, Chungbuk 28644, Republic of Korea
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2
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Teodoro TQ, Koenis MAJ, Rüger R, Galembeck SE, Buma WJ, Nicu VP, Visscher L. Use of Density Functional Based Tight Binding Methods in Vibrational Circular Dichroism. J Phys Chem A 2018; 122:9435-9445. [PMID: 30452264 DOI: 10.1021/acs.jpca.8b08218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vibrational circular dichroism (VCD) is a spectroscopic technique used to resolve the absolute configuration of chiral systems. Obtaining a theoretical VCD spectrum requires computing atomic polar and axial tensors on top of the computationally demanding construction of the force constant matrix. In this study we evaluated a VCD model in which all necessary quantities are obtained with density functional based tight binding (DFTB) theory. The analyzed DFTB parametrizations fail at providing accurate vibrational frequencies and electric dipole gradients but yield reasonable normal modes at a fraction of the computational cost of density functional theory (DFT). Thus, by applying DFTB in composite methods along with DFT, we show that it is possible to obtain accurate VCD spectra at a much lower computational demand.
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Affiliation(s)
- T Q Teodoro
- Departamento de Química , FFCLRP, Universidade de São Paulo , Avenida Bandeirantes 3900 , Ribeirão Preto , 14040-901 São Paulo Brazil.,Amsterdam Center for Multiscale Modeling, Faculty of Science , Vrije Universiteit Amsterdam , de Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - M A J Koenis
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - R Rüger
- Software for Chemistry & Materials BV , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - S E Galembeck
- Departamento de Química , FFCLRP, Universidade de São Paulo , Avenida Bandeirantes 3900 , Ribeirão Preto , 14040-901 São Paulo Brazil
| | - W J Buma
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - V P Nicu
- Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street, Nr. 7-9 , 550012 Sibiu , Romania
| | - L Visscher
- Amsterdam Center for Multiscale Modeling, Faculty of Science , Vrije Universiteit Amsterdam , de Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
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3
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Xiong J, Xu D. Insights into the Catalytic Mechanism of Unsaturated Glucuronyl Hydrolase of Bacillus sp. GL1. J Phys Chem B 2017; 121:931-941. [DOI: 10.1021/acs.jpcb.6b10501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
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4
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Wahiduzzaman M, Oliveira AF, Philipsen P, Zhechkov L, van Lenthe E, Witek HA, Heine T. DFTB Parameters for the Periodic Table: Part 1, Electronic Structure. J Chem Theory Comput 2013; 9:4006-17. [DOI: 10.1021/ct4004959] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohammad Wahiduzzaman
- School of
Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
- Scientific Computing & Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Augusto F. Oliveira
- School of
Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
- Scientific Computing & Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Pier Philipsen
- Scientific Computing & Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lyuben Zhechkov
- School of
Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
| | - Erik van Lenthe
- Scientific Computing & Modelling NV, Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Henryk A. Witek
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Thomas Heine
- School of
Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
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5
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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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6
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Pomogaev V, Pomogaeva A, Avramov P, Jalkanen KJ, Kachin S. Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum–mechanical methods. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0936-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Gaigeot MP. Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase. Phys Chem Chem Phys 2010; 12:3336-59. [PMID: 20336243 DOI: 10.1039/b924048a] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France.
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8
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Hughes TF, Flocke N, Bartlett RJ. Natural Linear-Scaled Coupled-Cluster Theory with Local Transferable Triple Excitations: Applications to Peptides. J Phys Chem A 2008; 112:5994-6003. [DOI: 10.1021/jp800516q] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas F. Hughes
- University of Florida, Department of Chemistry, Quantum Theory Project, Gainesville, Florida 32611
| | - Norbert Flocke
- University of Florida, Department of Chemistry, Quantum Theory Project, Gainesville, Florida 32611
| | - Rodney J. Bartlett
- University of Florida, Department of Chemistry, Quantum Theory Project, Gainesville, Florida 32611
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9
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Cai ZL, Lopez P, Reimers JR, Cui Q, Elstner M. Application of the Computationally Efficient Self-Consistent-Charge Density-Functional Tight-Binding Method to Magnesium-Containing Molecules. J Phys Chem A 2007; 111:5743-50. [PMID: 17555305 DOI: 10.1021/jp071701m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometric properties, ionization potentials, heats of formation, incremental binding energies, and protonation energies for up to 75 magnesium-containing compounds have been studied using the self-consistent-charge density-functional tight-binding method (SCC-DFTB), the complete-basis set (CBS-QB3) method, traditional B3LYP density-functional theory, and a number of modern semiempirical methods such as Austin Model 1 (AM1), modified neglect of diatomic overlap without and with inclusion of d functions (MNDO, MNDO/d), and the Parametric Method 3 (PM3) and its modification (PM5). The test set contains some widely varying chemical motifs including ionic or covalent, closed-shell or radical compounds, and many biologically relevant complexes. Geometric data are compared to experiment, if available, and otherwise to previous high-level ab initio calculations or the present B3LYP results. SCC-DFTB is found to predict bond lengths to high accuracy, with the root-mean-square (RMS) error being less than half that found for the other semiempirical methods. However, SCC-DFTB performs very poorly for absolute heats of formation, giving an RMS error of 29 kcal mol(-1), but for this property B3LYP and the other semiempirical methods also yield poor but useful results with errors of 12-22 kcal mol(-1). Nevertheless, SCC-DFTB does provide useful results for biologically relevant chemical-process energies such as protonation energies (RMS error 10 kcal mol(-1), with the range 6-19 kcal mol(-1) found for the other semiempirical methods) and ligation energies (RMS error 9 kcal mol(-1), less than the errors of 12-23 kcal mol(-1) found for the other semiempirical methods). SCC-DFTB is shown to provide a computationally expedient means of calculating properties of magnesium compounds, providing results with at most double the inaccuracy of the high-quality but dramatically more-expensive B3LYP method.
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Affiliation(s)
- Zheng-Li Cai
- School of Chemistry, The University of Sydney, NSW 2006, Australia
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10
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Reimers JR, Solomon GC, Gagliardi A, Bilić A, Hush NS, Frauenheim T, Di Carlo A, Pecchia A. The Green's Function Density Functional Tight-Binding (gDFTB) Method for Molecular Electronic Conduction. J Phys Chem A 2007; 111:5692-702. [PMID: 17530826 DOI: 10.1021/jp070598y] [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
A review is presented of the nonequilibrium Green's function (NEGF) method "gDFTB" for evaluating elastic and inelastic conduction through single molecules employing the density functional tight-binding (DFTB) electronic structure method. This focuses on the possible advantages that DFTB implementations of NEGF have over conventional methods based on density functional theory, including not only the ability to treat large irregular metal-molecule junctions with high nonequilibrium thermal distributions but perhaps also the ability to treat dispersive forces, bond breakage, and open-shell systems and to avoid large band lineup errors. New results are presented indicating that DFTB provides a useful depiction of simple gold-thiol interactions. Symmetry is implemented in DFTB, and the advantages it brings in terms of large savings of computational resources with significant increase in numerical stability are described. The power of DFTB is then harnessed to allow the use of gDFTB as a real-time tool to discover the nature of the forces that control inelastic charge transport through molecules and the role of molecular symmetry in determining both elastic and inelastic transport. Future directions for the development of the method are discussed.
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11
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Dolgonos G, Lukin O, Elstner M, Peslherbe GH, Leszczynski J. Toward a Reversible Isolation of a C20 Fullerene Inside a Tetraureacalix[4]arene Dimer. A Theoretical Study. J Phys Chem A 2006; 110:9405-10. [PMID: 16869690 DOI: 10.1021/jp0574201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential stabilization of normally unstable C20, the smallest fullerene, via its encapsulation inside a tetraureacalix[4]arene dimer has been analyzed using molecular mechanics calculations with different force fields, the self-consistent-charge density-functional tight-binding with dispersion correction (SCC-DFTB-D) model, and standard density-functional-theory (DFT) calculations. The interaction energies obtained for the C20 complex have been compared with analogous values calculated for numerous complexes of the tetraureacalix[4]arene dimer with other guests. Results of the calculations with all force fields and SCC-DFTB-D predict that the binding of C20 occurs with the highest selectivity. On the other hand, standard DFT calculations fail to correctly describe the stabilization of the complexes under study as standard DFT generally does not treat dispersion interactions properly. Predicted relative stabilities of the complexes are discussed in conjunction with available experimental data. Molecular dynamics simulations reveal the instability of the guest-free capsular dimer, which decomposes on a 1-ns time scale, while dimeric complexes with guests remained intact during the 5-ns simulation time, indicating the guest-driven formation of the molecular capsule.
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Affiliation(s)
- Grygoriy Dolgonos
- Centre for Research in Molecular Modeling, Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada, H3G 1M8
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12
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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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13
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Takekiyo T, Kato M, Taniguchi Y. FT-IR spectroscopic study on conformational equilibria of [Leu]5-enkephalin in DMSO and 2H2O solutions. J Mol Liq 2005. [DOI: 10.1016/j.molliq.2004.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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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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15
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Kalinowski JA, Lesyng B, Thompson JD, Cramer CJ, Truhlar DG. Class IV Charge Model for the Self-Consistent Charge Density-Functional Tight-Binding Method. J Phys Chem A 2004. [DOI: 10.1021/jp037288+] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Abdali S, Refstrup P, Nielsen OF, Bohr H. Enkephalins: Raman spectral analysis and comparison as function of pH 1-13. Biopolymers 2003; 72:318-28. [PMID: 12949822 DOI: 10.1002/bip.10404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Raman spectral studies are carried out on Leu- and Met-enkephalin as a function of the pH value in the range of 1-13. The molecules are dissolved in KCl solvent and the pH is controlled at each value. Spectral analyses reveal the dependence of the structural conformation on the pH, and a comparison of the two molecules is made in three frequency regions: the tyrosine Fermi doublet (850-830 cm(-1)), aromatic side chains (1650-1550 cm(-1)), and carboxylate (1430-1400 cm(-1)). All regions and frequencies are presented, discussed, and compared for the two molecules.
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Affiliation(s)
- S Abdali
- Quantum Protein Centre QUP, Department of Physics, Building 309, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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