1
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Seo J, Singh R, Ryu J, Choi JH. Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions. J Chem Inf Model 2024; 64:138-149. [PMID: 37983534 DOI: 10.1021/acs.jcim.3c01382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Osmolytes, small organic compounds, play a key role in modulating the protein stability in aqueous solutions, but the operating mechanism of the osmolyte remains inconclusive. Here, we attempt to clarify the mode of osmolyte action by quantitatively estimating the microheterogeneity of osmolyte-water mixtures with the aid of molecular dynamics simulation, graph theoretical analysis, and spatial distribution measurement in the four osmolyte solutions of trimethylamine-N-oxide (TMAO), tetramethylurea (TMU), dimethyl sulfoxide, and urea. TMAO, acting as a protecting osmolyte, tends to remain isolated with no formation of osmolyte aggregates while preferentially interacting with water, but there is a strong aggregation propensity in the denaturant TMU solution, characterized by favored hydrophobic interactions between TMU molecules. Taken together, the mechanism of osmolyte action on protein stability is proposed as a comprehensive one that encompasses the direct interactions between osmolytes and proteins and indirect interactions through the regulation of water properties in the osmolyte-water mixtures.
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Affiliation(s)
- Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Ravi Singh
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jonghyuk Ryu
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
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2
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Pérez-Trejo I, Dominguez L. GaMD simulations as an alternative in the TFE-water mixture description. J Mol Model 2023; 29:352. [PMID: 37906368 PMCID: PMC10618327 DOI: 10.1007/s00894-023-05749-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
CONTEXT 2,2,2-Trifluoroethanol has been widely used to study the structure and dynamic properties of intrinsically disordered proteins. Experimentally, it is known that TFE-water mixtures stabilize secondary structures of IDPs, and therefore, it allows the studying of conformational ensembles of these proteins. In the last decades, molecular dynamic simulations have helped study the IDPs' conformational ensemble. Unfortunately, conventional MD requires very long simulation times to describe the properties of IDPs. Therefore, a variety of accelerated sampling techniques have been developed and employed. The TFE-water mixture arrangement description through MD has faced substantial difficulties since emulating the TFE nanocrowding at certain TFE:H[Formula: see text]O ratios (around 15-40% of TFE). In this work, we determine the most suitable conditions that reproduce experimentally reported properties of TFE-water mixtures. We compared the employment of conventional MD and GaMD simulations and various water parameters. Our results show that the combination of parameters that better reproduce the experimental information is the combination of the TIP4PD water model and GaMD simulations. Therefore, these conditions help accurately describe the structural ensemble of IDPs in TFE-water mixtures. METHODS Conventional MD and GaMD simulations were performed under AMBER 18 software. The TFE and water molecules were described using GAFF2 and a variety of water models, such as TIP3P, TIP4P2005, TIP4PD, and TIP5P, respectively. The systems were simulated a 100 ns at 298 K.
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Affiliation(s)
- Itzel Pérez-Trejo
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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3
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Biswas S, Kaur S, Myers CA, Chen AA, Welch JT. Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ 6-sulfanyl-ethan-1-ol (CF 3SF 4-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments. ACS OMEGA 2023; 8:30037-30047. [PMID: 37636933 PMCID: PMC10448670 DOI: 10.1021/acsomega.3c02019] [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: 03/25/2023] [Accepted: 06/26/2023] [Indexed: 08/29/2023]
Abstract
2-Tetrafluoro(trifluoromethyl)-λ6-sulfanylethan-1-ol (CF3SF4-ethanol) combines the polar hydrophobicity of tetrafluoro(trifluoromethyl)-λ6-sulfanyl (CF3SF4) group with the polarity of simple alcohols. The properties of aqueous solutions of the well-known fluorinated alcohols 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) were compared with those of aqueous solutions of the novel CF3SF4-ethanol. Those properties were computed using all atom molecular dynamics simulations with OPLS-compatible parameters. DFT ab initio calculations were used to accurately describe the nonsymmetrical, hypervalent sulfur in CF3SF4-ethanol. Although the molecular and conformational characteristics of CF3SF4-ethanol are like those of both TFE and HFIP, the greater hydrophobicity and lower polarity of CF3SF4-ethanol resulted in solution phase aggregation at a much lower concentration. The properties computed for TFE and HFIP in this work were consistent with published computational and experimental studies. CF3SF4-ethanol is predicted to be environmentally benign and hence an excellent green solvent candidate while possessing many of the same properties as TFE or HFIP.
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Affiliation(s)
- Samadrita Biswas
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave, Albany, New York 12222, United States
| | - Simi Kaur
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave, Albany, New York 12222, United States
- RNA
Institute, University at Albany, State University
of New York, 1400 Washington Ave, Albany, New York 12222, United States
| | - Christopher A. Myers
- RNA
Institute, University at Albany, State University
of New York, 1400 Washington Ave, Albany, New York 12222, United States
- Department
of Physics, University at Albany, State
University of New York, 1400 Washington Ave, Albany, New York 12222, United States
| | - Alan A. Chen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave, Albany, New York 12222, United States
- RNA
Institute, University at Albany, State University
of New York, 1400 Washington Ave, Albany, New York 12222, United States
| | - John T. Welch
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave, Albany, New York 12222, United States
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4
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Koszinowski K, Rahrt R. Anionic Dimers of Fluorinated Alcohols. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1411-1418. [PMID: 35609237 DOI: 10.1021/jasms.2c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Negative-ion mode electrospray ionization of solutions of ethanol (RF0OH), 2-fluoroethanol (RF1OH), 2,2-difluoroethanol (RF2OH), and/or 2,2,2-trifluoroethanol (RF3OH) produces anionic dimers of the types (RFnO)2H- and (RFnO)(RFn+1O)H-. The exchange reactions of these anionic dimers with the neutral alcohols are examined in a quadrupole-ion trap to extract kinetic data, from which the reaction Gibbs energies are obtained. In all cases, the formation of anionic dimers containing the more highly fluorinated alcohols is favored. Quantum chemical calculations confirm this trend and, besides affording structural data, also determine the dissociation energies of the anionic dimers. These dissociation energies are much higher than those of the corresponding neutral dimers and increase further for the more highly fluorinated alcohols due to the stronger hydrogen-bond donor ability of the latter. The present results on the interaction of individual alkoxide anions and neutral alcohol molecules contribute to a better understanding of the association of the fluorinated alcohols in solution.
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Affiliation(s)
- Konrad Koszinowski
- Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077 Göttingen, Germany
| | - Rene Rahrt
- Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077 Göttingen, Germany
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5
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Lui LH, Egbu R, Graver T, Williams GR, Brocchini S, Velayudhan A. Computational and Experimental Evaluation of the Stability of a GLP-1-like Peptide in Ethanol–Water Mixtures. Pharmaceutics 2022; 14:pharmaceutics14071462. [PMID: 35890357 PMCID: PMC9321252 DOI: 10.3390/pharmaceutics14071462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Aggregation resulting from the self-association of peptide molecules remains a major challenge during preformulation. Whereas certain organic solvents are known to promote aggregation, ethanol (EtOH) is capable of disrupting interactions between peptide molecules. It is unclear whether it is beneficial or counterproductive to include EtOH in formulations of short peptides. Here, we employed molecular dynamics simulations using the DAFT protocol and MARTINI force field to predict the formation of self-associated dimers and to estimate the stability of a GLP-1-like peptide (G48) in 0–80% aqueous EtOH solutions. Both simulation and experimental data reveal that EtOH leads to a remarkable increase in the conformational stability of the peptide when stored over 15 days at 27 °C. In the absence of EtOH, dimerisation and subsequent loss in conformational stability (α-helix → random coil) were observed. EtOH improved conformational stability by reducing peptide–peptide interactions. The data suggest that a more nuanced approach may be applied in formulation decision making and, if the native state of the peptide is an α-helix organic solvent, such as EtOH, may enhance stability and improve prospects of long-term storage.
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Affiliation(s)
- Lok Hin Lui
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK; (L.H.L.); (R.E.); (T.G.); (G.R.W.); (S.B.)
| | - Raphael Egbu
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK; (L.H.L.); (R.E.); (T.G.); (G.R.W.); (S.B.)
| | - Thomas Graver
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK; (L.H.L.); (R.E.); (T.G.); (G.R.W.); (S.B.)
| | - Gareth R. Williams
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK; (L.H.L.); (R.E.); (T.G.); (G.R.W.); (S.B.)
| | - Steve Brocchini
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK; (L.H.L.); (R.E.); (T.G.); (G.R.W.); (S.B.)
| | - Ajoy Velayudhan
- Department of Biochemical Engineering, University College London, London WC1E 6BT, UK
- Correspondence:
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6
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Guan X, Huang Z, Lu H, Sun D. Microheterogeneity and CO 2 Switchability of N, N-Dimethylcyclohexylamine-Water Binary Mixtures. J Phys Chem B 2019; 123:3096-3102. [PMID: 30883124 DOI: 10.1021/acs.jpcb.8b12060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Binary mixtures of water and organic solvents are described as the aqueous solutions of organic solvents, which are usually spatially heterogeneous on the scale of a few molecular sizes but homogeneous on longer length scales, that is, microheterogeneity. For the water-organic solvent binary mixtures with microheterogeneity, most organic solvents are miscible with water at any ratio. Interestingly, some slightly water-miscible organic solvents can also be used to prepare binary mixtures with microheterogeneity. In this study, N, N-dimethylcyclohexylamine (DMCHA) was used to prepare binary mixtures with microheterogeneity and CO2 switchability. With the help of conductivity, Fourier-transform infrared spectroscopy, ultraviolet-visible spectroscopy, and dynamic light scattering measurements, we found that water molecules are hydrogen-bonded together to form clusters over the water content range of 9 to 27 wt %, exhibiting microheterogeneity in the binary mixture. The size of the water clusters increases slightly with increasing water content. What is more, the DMCHA-water mixtures can be reversibly split into two phases by alternate bubbling of CO2 and N2, exhibiting excellent CO2 switchability. The binary mixtures can be used as reaction media for the synthesis of CaCO3 nanoparticles. Binary mixtures with microheterogeneity can also be formed under high salinity or high temperature conditions or be prepared using other slightly water-miscible organic solvents, opening up more interesting possibilities for binary mixtures with microheterogeneity.
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Affiliation(s)
- Xueqian Guan
- College of Chemistry and Chemical Engineering , Southwest Petroleum University , Chengdu 610500 , P. R. China
| | - Zhiyu Huang
- College of Chemistry and Chemical Engineering , Southwest Petroleum University , Chengdu 610500 , P. R. China
| | - Hongsheng Lu
- College of Chemistry and Chemical Engineering , Southwest Petroleum University , Chengdu 610500 , P. R. China
| | - Dejun Sun
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education , Shandong University , Jinan 250100 , P. R. China
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7
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Gerig JT. Examination of Trifluoroethanol Interactions with Trp-Cage in Trifluoroethanol-Water at 298 K through Molecular Dynamics Simulations and Intermolecular Nuclear Overhauser Effects. J Phys Chem B 2019; 123:3248-3258. [PMID: 30916962 DOI: 10.1021/acs.jpcb.9b01171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular dynamics simulations of the protein model Trp-cage in 42% trifluoroethanol (TFE)-water at 298 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The TFE5 model of TFE developed in a previous work was used with the TIP5P-Ew model of water. System densities and component translational diffusion coefficients predicted by the simulations were within 20% of the experimental values. Consideration of the calculated relative amounts of TFE and water surrounding the hydrogens of Trp-cage indicated that the composition of the solvent mixture beyond ∼1.5 nm from the van der Waals surface of the peptide is close to the composition of the bulk solvent, but as observed by others, TFE accumulates preferentially near the peptide surface. In the simulations, both TFE and water molecules make contacts with the peptide surface; water molecules predominate in contacts with the peptide backbone atoms and TFE molecules generally preferentially interact with side chains. Translational diffusion of solvent molecules appears to be slowed near the surface of the peptide. Depending on the location in the structure, TFE molecules form complexes with the peptide that may persist for up to ∼7 ns. Many of the peptide spin-solvent fluorine cross-relaxation parameters (ΣHF) for which experimental values are available are reasonably well-predicted from the simulations. However, the calculated ΣHF values were too small for some hydrogens of the 6Trp indole ring and the amino acid hydrogens near this residue in the native structure, whereas ΣHF values for hydrogens on the side chains of 1Asn, 4Ile, and 7Leu are too large. In 42% TFE-water, persistent conformations of Trp-cage are found, which differ from the conformation found in water by the orientation of the 3Tyr ring.
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Affiliation(s)
- J T Gerig
- Department of Chemistry & Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
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8
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Mondal S, Biswas B, Nandy T, Singh PC. Understanding the Role of Hydrophobic Terminal in the Hydrogen Bond Network of the Aqueous Mixture of 2,2,2-Trifluoroethanol: IR, Molecular Dynamics, Quantum Chemical as Well as Atoms in Molecules Studies. J Phys Chem B 2018; 122:6616-6626. [DOI: 10.1021/acs.jpcb.8b04365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biswajit Biswas
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Tonima Nandy
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
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9
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Gerig JT. Examination of Trifluoroethanol Interactions with Trp-Cage through MD Simulations and Intermolecular Nuclear Overhauser Effects. J Phys Chem B 2016; 120:11256-11265. [DOI: 10.1021/acs.jpcb.6b08430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. T. Gerig
- Department of Chemistry and
Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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10
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Culik RM, Abaskharon RM, Pazos IM, Gai F. Experimental validation of the role of trifluoroethanol as a nanocrowder. J Phys Chem B 2014; 118:11455-61. [PMID: 25215518 PMCID: PMC4183368 DOI: 10.1021/jp508056w] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Trifluoroethanol
(TFE) is commonly used to induce protein secondary
structure, especially α-helix formation. Due to its amphiphilic
nature, however, TFE can also self-associate to form micellelike,
nanometer-sized clusters. Herein, we hypothesize that such clusters
can act as nanocrowders to increase protein folding rates via the
excluded volume effect. To test this hypothesis, we measure the conformational
relaxation kinetics of an intrinsically disordered protein, the phosphorylated
kinase inducible domain (pKID), which forms a helix–turn–helix
in TFE solutions. We find that the conformational relaxation rate
of pKID displays a rather complex dependence on TFE percentage (v/v):
while it first decreases between 0 and 5%, between 5 and 15% the rate
increases and then remains relatively unchanged between 15 and 30%
and finally decreases again at higher percentages (i.e., 50%). This
trend coincides with the fact that TFE clustering is maximized in
the range of 15–30%, thus providing validation of our hypothesis.
Another line of supporting evidence comes from the observation that
the relaxation rate of a monomeric helical peptide, which due to its
predominantly local interactions in the folded state is less affected
by crowding, does not show a similar TFE dependence.
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Affiliation(s)
- Robert M Culik
- Department of Biochemistry & Biophysics and ‡Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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11
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Migliolo L, Silva ON, Silva PA, Costa MP, Costa CR, Nolasco DO, Barbosa JARG, Silva MRR, Bemquerer MP, Lima LMP, Romanos MTV, Freitas SM, Magalhães BS, Franco OL. Structural and functional characterization of a multifunctional alanine-rich peptide analogue from Pleuronectes americanus. PLoS One 2012; 7:e47047. [PMID: 23056574 PMCID: PMC3466273 DOI: 10.1371/journal.pone.0047047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023] Open
Abstract
Recently, defense peptides that are able to act against several targets have been characterized. The present work focuses on structural and functional evaluation of the peptide analogue Pa-MAP, previously isolated as an antifreeze peptide from Pleuronectes americanus. Pa-MAP showed activities against different targets such as tumoral cells in culture (CACO-2, MCF-7 and HCT-116), bacteria (Escherichia coli ATCC 8739 and Staphylococcus aureus ATCC 25923), viruses (HSV-1 and HSV-2) and fungi (Candida parapsilosis ATCC 22019, Trichophyton mentagrophytes (28d&E) and T. rubrum (327)). This peptide did not show toxicity against mammalian cells such as erythrocytes, Vero and RAW 264.7 cells. Molecular mechanism of action was related to hydrophobic residues, since only the terminal amino group is charged at pH 7 as confirmed by potentiometric titration. In order to shed some light on its structure-function relations, in vitro and in silico assays were carried out using circular dichroism and molecular dynamics. Furthermore, Pa-MAP showed partial unfolding of the peptide changes in a wide pH (3 to 11) and temperature (25 to 95°C) ranges, although it might not reach complete unfolding at 95°C, suggesting a high conformational stability. This peptide also showed a conformational transition with a partial α-helical fold in water and a full α-helical core in SDS and TFE environments. These results were corroborated by spectral data measured at 222 nm and by 50 ns dynamic simulation. In conclusion, data reported here show that Pa-MAP is a potential candidate for drug design against pathogenic microorganisms due to its structural stability and wide activity against a range of targets.
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Affiliation(s)
- Ludovico Migliolo
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Osmar N. Silva
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- Programa de Pós-Graduação em Genética e Biotecnologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Paula A. Silva
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- Departamento de Virologia-Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maysa P. Costa
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Carolina R. Costa
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Diego O. Nolasco
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - João A. R. G. Barbosa
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- Laboratório de Biofísica-Departamento de Biologia Celular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria R. R. Silva
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcelo P. Bemquerer
- Laboratório de Sîntese de Peptídeos, EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Lidia M. P. Lima
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria T. V. Romanos
- Departamento de Virologia-Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sonia M. Freitas
- Laboratório de Biofísica-Departamento de Biologia Celular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Beatriz S. Magalhães
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Octavio L. Franco
- Centro de Análises Proteômicas e Bioquímicas-Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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12
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Shao Q, Fan Y, Yang L, Qin Gao Y. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J Chem Phys 2012; 136:115101. [DOI: 10.1063/1.3692801] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Dupradeau FY, Pigache A, Zaffran T, Savineau C, Lelong R, Grivel N, Lelong D, Rosanski W, Cieplak P. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Phys Chem Chem Phys 2010; 12:7821-39. [PMID: 20574571 PMCID: PMC2918240 DOI: 10.1039/c0cp00111b] [Citation(s) in RCA: 677] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.
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Affiliation(s)
- François-Yves Dupradeau
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Adrien Pigache
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Thomas Zaffran
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Corentin Savineau
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Rodolphe Lelong
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Nicolas Grivel
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Dimitri Lelong
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Wilfried Rosanski
- CNRS UMR 6219 & Faculté de Pharmacie, Université de Picardie - Jules Verne, 1, rue des Louvels, F-80037 Amiens cedex 1, France
| | - Piotr Cieplak
- Sanford|Burnham Institute for Medical Research, La Jolla, California, 92037, USA
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