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Casoria M, Macchiagodena M, Rovero P, Andreini C, Papini AM, Cardini G, Pagliai M. Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation. J Pept Sci 2024; 30:e3543. [PMID: 37734745 DOI: 10.1002/psc.3543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/16/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
The standard GAFF2 force field parameterization has been refined for the fluorinated alcohols 2,2,2-trifluoroethanol (TFE), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), and 1,1,1,3,3,3-hexafluoropropan-2-one (HFA), which are commonly used to study proteins and peptides in biomimetic media. The structural and dynamic properties of both proteins and peptides are significantly influenced by the biomimetic environment created by the presence of these cosolvents in aqueous solutions. Quantum mechanical calculations on stable conformers were used to parameterize the atomic charges. Different systems, such as pure liquids, aqueous solutions, and systems formed by melittin protein and cosolvent/water solutions, have been used to validate the new models. The calculated macroscopic and structural properties are in agreement with experimental findings, supporting the validity of the newly proposed models.
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Affiliation(s)
- Michele Casoria
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Department of NeuroFarBa, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Claudia Andreini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Sesto Fiorentino, Italy
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2
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De Ricco R, Valensin D, Gaggelli E, Valensin G. Conformation propensities of des-acyl-ghrelin as probed by CD and NMR. Peptides 2013; 43:62-7. [PMID: 23470254 DOI: 10.1016/j.peptides.2013.02.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/20/2013] [Accepted: 02/20/2013] [Indexed: 12/30/2022]
Abstract
Des-acyl-ghrelin is a 28 amino acid peptide secreted by both human and rat stomach. Together with ghrelin and obestatin, it is obtained by post-translational modification of a 117 aminoacid prepropeptide mainly expressed in distinct endocrine cell type in the stomach. Although its receptor has not been unambiguously identified so far, des-acyl-ghrelin is considered one of the strongest antagonists of ghrelin in activating the growth hormone secretagogue receptor (GHS-R). Here the secondary structure of des-acyl-ghrelin in different experimental conditions has been investigated and compared with that of obestatin, a bioactive peptide having similar biological functions. CD and NMR techniques have been combined for gaining the desired conformational features. The obtained structures support a steady alpha-helix structure spanning residues from 7 to 14, very similar to that observed for obestatin at the same experimental conditions, leading to suggest that a similar secondary structure can be associated with the similar biological role.
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Affiliation(s)
- Riccardo De Ricco
- Department of Biotechnology, University of Siena, Via A. Moro 2, 53100 Siena, Italy
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3
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Gerig JT. Investigation of Methanol–Peptide Nuclear Overhauser Effects through Molecular Dynamics Simulations. J Phys Chem B 2012; 116:1965-73. [DOI: 10.1021/jp211098v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- J. T. Gerig
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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4
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Chagolla DP, Gerig JT. Conformations of Betanova in aqueous trifluoroethanol. Biopolymers 2010; 93:893-903. [DOI: 10.1002/bip.21498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Suzuki Y, Gerig JT, Asakura T. NMR Study of Interactions between Silk Model Peptide and Fluorinated Alcohols for Preparation of Regenerated Silk Fiber. Macromolecules 2010. [DOI: 10.1021/ma902544c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Suzuki
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - J. T. Gerig
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
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6
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Saielli G, Bagno A. Preferential solvation of glucose and talose in water-acetonitrile mixtures: a molecular dynamics simulation study. Phys Chem Chem Phys 2010; 12:2981-8. [PMID: 20449390 DOI: 10.1039/b922550a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the preferential solvation of four carbohydrates, namely alpha- and beta-glucose and alpha- and beta-talose, in mixtures of water and acetonitrile. The structure of the solvation shell, obtained by means of molecular dynamics simulation, has been analyzed using radial and spatial distribution functions. In agreement with available experimental data, water is found to preferentially solvate the sugars. The micro-heterogeneity of the mixture, with clusters of hydrogen-bonded water molecules and clusters of dipole-dipole interacting acetonitrile molecules, favours the solvation of the carbohydrates by the water clusters. This, in turn, causes a stronger intermolecular NOE of the alkyl sugar protons with water than with acetonitrile.
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Affiliation(s)
- Giacomo Saielli
- Istituto per la Tecnologia delle Membrane del CNR, Sezione di Padova, Via Marzolo, 1 35131, Padova, Italy.
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Neuman RC, Gerig JT. Interactions of 2,2,2-trifluoroethanol with melittin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:925-931. [PMID: 19634131 DOI: 10.1002/mrc.2489] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Melittin dissolved in 42% trifluoroethanol-water at pH 2 has been shown to be alpha-helical between residues 6 and 12 and between residues 13 and 25, with the two helical regions separated by a bend at the Leu13 residue. The inter-helix angle was found to be 154 +/- 3 degrees at 0 degrees C and 135 +/- 3 degrees at 25 degrees C. The dominant conformation of the peptide is thus similar to those observed by previous workers for the peptide in a variety of media. At 25 degrees C, intermolecular nuclear Overhauser effects arising from nuclear spin dipole-dipole interactions between melittin hydrogens and fluorines of the solvent are essentially those expected for a system that is homogeneous as regards concentration and translational diffusion of the peptide and fluoroalcohol components. However, at 0 degrees C, peptide-trifluoroethanol cross-relaxation terms are negative, a result consistent with the conclusion that fluoroalcohol molecules associate with the peptide for times (approximately 1 ns) that are long compared to the time of a typical peptide-fluoroalcohol diffusive encounter (approximately 0.2 ns). Such interactions may be responsible for the reduction of the translational diffusion coefficient of trifluoroethanol produced by dissolved peptides.
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Affiliation(s)
- Robert C Neuman
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106, USA
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Gerig JT. Solvent Interactions with [Val5]angiotensin II in Ethanol−Water. J Phys Chem B 2008; 112:7967-76. [DOI: 10.1021/jp801489q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John T. Gerig
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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Tanizaki S, Clifford J, Connelly BD, Feig M. Conformational sampling of peptides in cellular environments. Biophys J 2007; 94:747-59. [PMID: 17905846 PMCID: PMC2186233 DOI: 10.1529/biophysj.107.116236] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over alpha-helical conformations at the dipeptide level at and below dielectric constants of 5-10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at epsilon = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response.
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Affiliation(s)
- Seiichiro Tanizaki
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Jacob Clifford
- Department of Physics, Michigan State University, East Lansing, Michigan
| | - Brian D. Connelly
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan
- Department of Chemistry, Michigan State University, East Lansing, Michigan
- Address reprint requests to Michael Feig, Tel.: 517-432-7439; Fax: 517-353-9334.
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Chatterjee C, Martinez D, Gerig JT. Interactions of Trifluoroethanol with [val5]angiotensin II. J Phys Chem B 2007; 111:9355-62. [PMID: 17630790 DOI: 10.1021/jp0711343] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intermolecular 1H{19F} NOE experiments have been used to explore the interactions of trifluoroethanol (TFE) with the octapeptide hormone [val5]angiotensin II at temperatures from 5 to 25 degrees C. Circular dichroism spectra indicate that 40% trifluoroethanol has an influence on the conformations of the peptide, probably leading to beta-structures. Diffusion experiments show that the mean hydrodynamic radius of the peptide in 40% trifluoroethanol-water is about 8 A, consistent with significant folding of the peptide in this medium. Distance constraints derived from intramolecular NOESY data along with observed vicinal coupling constants (3JCalphaHNH) were used to develop conformations consistent with available data. Assuming that intermolecular 1H{19F} NOEs are the result of diffusive encounters of TFE and peptide molecules, it is shown that no single conformation is consistent with the experimental values of the sigmaHF cross-relaxation parameters. It is argued that the disagreements between observed and expected values of sigmaHF are the result of formation of long-lived (approximately 0.5 ns) fluoroalcohol-peptide complexes, a conclusion consonant with similar studies of other peptide-fluoroalcohol systems. Complex formation appears to be especially prevalent near the charged amino acid side chains of the hormone.
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Affiliation(s)
- Chiradip Chatterjee
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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Nordstierna L, Yushmanov PV, Furó I. Solute-solvent contact by intermolecular cross relaxation. I. The nature of the water-hydrophobic interface. J Chem Phys 2006; 125:074704. [PMID: 16942361 DOI: 10.1063/1.2336199] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Intermolecular cross-relaxation rates between solute and solvent were measured by {1H} 19F nuclear magnetic resonance experiments in aqueous molecular solutions of ammonium perfluoro-octanoate and sodium trifluoroacetate. The experiments performed at three different magnetic fields provide frequency-dependent cross-relaxation rates which demonstrate clearly the lack of extreme narrowing for nuclear spin relaxation by diffusionally modulated intermolecular interactions. Supplemented by suitable intramolecular cross-relaxation, longitudinal relaxation, and self-diffusion data, the obtained cross-relaxation rates are evaluated within the framework of recent relaxation models and provide information about the hydrophobic hydration. In particular, water dynamics around the trifluoromethyl group in ammonium perfluoro-octanoate are more retarded than that in the smaller trifluoroacetate.
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Affiliation(s)
- Lars Nordstierna
- Division of Physical Chemistry and Industrial NMR Center, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden
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