1
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Majumdar BB, Pyne P, Mitra RK, Das Mahanta D. Impact of hydrophobicity on local solvation structures and its connection with the global solubilization thermodynamics of amphiphilic molecules. Phys Chem Chem Phys 2023; 25:27161-27169. [PMID: 37789695 DOI: 10.1039/d3cp02741d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The relationship between the local solvation structures and global thermodynamics, specifically in the case of amphiphilic molecules, is a complex phenomenon and is not yet fully understood. With the prior knowledge that local solvation structures can impose a significant impact on the overall solvation process, we here combine THz spectroscopic analysis with MD simulations to investigate the impact of the altered hydrophobicity and polarity of amphiphilic solute molecules on the local solvation configurations. We use two water soluble alcohols: ethanol (EtOH) and its fluorinated counterpart, 2,2,2-trifluoroethanol (TFE), as model solutes. Our study is aimed to determine the relative abundance of different hydrogen bonded conformers and to establish a correlation between the spectral signatures (as obtained from THz spectroscopic measurements) and microscopic solute-solvent interactions associated with the local solvation structures (as obtained from MD simulations). Finally, we estimate the possible energetic parameters associated with the alcohol solubilization process. We found that while both the alcohols are completely water soluble, they receive a contrasting solvation energy share in terms of entropy and enthalpy. We understand that these findings are not limited to the specific system studied here but can be broadly extrapolated to other amphiphilic aqueous solutions.
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Affiliation(s)
- Bibhab Bandhu Majumdar
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
| | - Partha Pyne
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
| | - Rajib Kumar Mitra
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
| | - Debasish Das Mahanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th 4 Street, Austin, TX 78712, USA.
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2
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Hohmann T, Dubatouka P, Pfeifer K, Koksch B. Establishing Fluorine-Containing Amino Acids as an Orthogonal Tool in Coiled Coil Assembly. Biomacromolecules 2023. [PMID: 37379337 DOI: 10.1021/acs.biomac.3c00427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The α-helical coiled coil (CC) is one of the best-characterized folding motifs in the protein world. In this context, fluorinated amino acids have been shown to be capable of tuning the properties of CC assemblies, and especially fluorinated derivatives of aliphatic amino acids can significantly increase the stability of this folding motif when placed in the hydrophobic a and d positions. However, it has not been shown yet whether fluorinated amino acids, by means of rational design, can be used as an orthogonal tool to control CC assembly processes. In the current work, we approached this question by creating a combinatorial peptide library based on a VPE/VPK heteromeric CC system previously established and characterized in our group. This CC model allowed us to screen fluorinated amino acids for interaction with different potential binding partners in position a of the VPE/VPK model with a particular emphasis on studying the impact of stereochemistry within the side chain of α-branched aliphatic fluorinated amino acids on CC properties such as oligomerization state, thermodynamic stability, and orientation. 28 combinations of library members were characterized regarding structure, oligomerization, and thermal stability utilizing circular dichroism, size exclusion chromatography, and Förster resonance energy transfer measurements. This detailed approach showed that the stability and oligomerization state of the motif were not only dependent on the steric demand and the fluorination of corresponding amino acids but also on the stereochemistry within the side chain. The results were applied for a rational design of the fluorine-driven orthogonal assembly, and we could show that CC dimer formation occurred based on specific interactions between fluorinated amino acids. These results demonstrate the potential of fluorinated amino acids as an orthogonal tool besides classical electrostatic and hydrophobic interactions for the fine-tuning and direction of peptide-peptide interactions. Furthermore, within the space of fluorinated amino acids, we could demonstrate the specificity of interactions between differently fluorinated side chains.
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Affiliation(s)
- Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Palina Dubatouka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Katharina Pfeifer
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
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3
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Ghosh P, Nandy T, Singh PC, Ghosh D. Substitution enables significant new decay channels for a non-canonical amino acid. Phys Chem Chem Phys 2022; 24:17695-17702. [PMID: 35838114 DOI: 10.1039/d2cp00465h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-Vis absorption spectra and emission peaks of indole and 7-fluoroindole are measured and it is observed that 7-fluoroindole quenches the fluorescence signals significantly compared to indole. This observation is elucidated via reconstruction of the potential energy surfaces, determination of the conical intersections, and dynamical studies. It is observed that a single fluorine substitution on indole leads to the appearance of several accessible low-energy conical intersections that cause fast nonradiative decay. In this paper, we have investigated the nonradiative processes of Ind and 7F-Ind theoretically using high-level methods, such as EOM-EE-CCSD, SA-CASSCF, MS-CASPT2/6-311++G(d,p) levels of theory, to study these pathways and their feasibility.
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Affiliation(s)
- Paulami Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Tonima Nandy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Prashant C Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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4
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Santhouse JR, Rao SR, Horne WS. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Methods Enzymol 2021; 656:93-122. [PMID: 34325801 PMCID: PMC8392274 DOI: 10.1016/bs.mie.2021.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent years have seen a growing number of examples of designed oligomeric molecules with artificial backbone connectivity that are capable of adopting complex folded tertiary structures analogous to those seen in natural proteins. A range of experimental techniques from structural biology and biophysics have been brought to bear in the study of these proteomimetic agents. Here, we discuss some considerations encountered in the characterization of high-resolution folded structure as well as folding thermodynamics of protein-like artificial backbones. We provide an overview of the use of X-ray crystallography and NMR spectroscopy in such systems and review example applications of these methods in the primary literature. Further, we provide detailed protocols for two experiments that have proved useful in our prior and ongoing efforts to compare folding thermodynamics between natural protein domains and heterogeneous-backbone counterparts.
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Affiliation(s)
| | - Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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5
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Miller MA, Sletten EM. Perfluorocarbons in Chemical Biology. Chembiochem 2020; 21:3451-3462. [PMID: 32628804 PMCID: PMC7736518 DOI: 10.1002/cbic.202000297] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Indexed: 01/10/2023]
Abstract
Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.
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Affiliation(s)
- Margeaux A Miller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
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6
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Feskov IO, Golub BO, Vashchenko BV, Levterov VV, Kondratov IS, Grygorenko OO, Haufe G. GABA Analogues and Related Mono-/Bifunctional Building Blocks Derived from the Fluorocyclobutane Scaffold. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Illia O. Feskov
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry; NAS of Ukraine; Murmanska Street 1 02660 Kyiv Ukraine
| | | | - Bohdan V. Vashchenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | | | - Ivan S. Kondratov
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Günter Haufe
- Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Corrensstraße 40 48149 Münster Germany
- Cells-in-Motion Cluster of Excellence; Westfälische Wilhelms-Universität Münster; Waldeyerstraße 15 48149 Münster Germany
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7
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Biswas B, Singh PC. The role of fluorocarbon group in the hydrogen bond network, photophysical and solvation dynamics of fluorinated molecules. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2019.109414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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8
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Improved enantioselective gram scale synthesis route to N-Fmoc-protected monofluoroethylglycine. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2020.109453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Brewitz L, Noda H, Kumagai N, Shibasaki M. (
2R
,
3S
)‐3,4,4,4‐Tetrafluorovaline: A Fluorinated Bioisostere of Isoleucine. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lennart Brewitz
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
| | - Naoya Kumagai
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
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10
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Robalo JR, Mendes de Oliveira D, Imhof P, Ben-Amotz D, Vila Verde A. Quantifying how step-wise fluorination tunes local solute hydrophobicity, hydration shell thermodynamics and the quantum mechanical contributions of solute–water interactions. Phys Chem Chem Phys 2020; 22:22997-23008. [DOI: 10.1039/d0cp04205f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Locally tuning solute–water interactions with fluorination.
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Affiliation(s)
- João R. Robalo
- Department of Theory & Bio-Systems
- Max Planck Institute for Colloids and Interfaces
- Science Park
- Potsdam 14476
- Germany
| | | | - Petra Imhof
- Institute for Theoretical Physics
- Free University of Berlin
- 14195 Berlin
- Germany
| | - Dor Ben-Amotz
- Purdue University
- Department of Chemistry
- West Lafayette
- USA
| | - Ana Vila Verde
- Department of Theory & Bio-Systems
- Max Planck Institute for Colloids and Interfaces
- Science Park
- Potsdam 14476
- Germany
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11
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Robalo JR, Streacker LM, Mendes de Oliveira D, Imhof P, Ben-Amotz D, Verde AV. Hydrophobic but Water-Friendly: Favorable Water–Perfluoromethyl Interactions Promote Hydration Shell Defects. J Am Chem Soc 2019; 141:15856-15868. [DOI: 10.1021/jacs.9b06862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- João R. Robalo
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
| | - Louis M. Streacker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Petra Imhof
- Institute for Theoretical Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ana Vila Verde
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
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12
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Ikeda A, Capellan A, Welch JT. The secondary structure of a heptapeptide containing trifluoromethyl-λ 6-tetrafluorosulfanyl substituted amino acids. Org Biomol Chem 2019; 17:8079-8082. [PMID: 31454017 DOI: 10.1039/c9ob01797f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Site specific introduction of the polar hydrophobic trifluoromethyl-λ6-tetrafluorosulfanyl (CF3SF4) group can effectively control the secondary structure of a heptapeptide, the minimum repeat unit of an α-helix. The structural influence of CF3SF4-containing amino acid on the heptapeptide was established using NMR methods.
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Affiliation(s)
- Akari Ikeda
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Aimée Capellan
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - John T Welch
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
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13
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Nandy T, Mondal S, Singh PC. Solvent organization around the noncanonical part of tyrosine modulates its fluorescence properties. Phys Chem Chem Phys 2019; 21:6042-6050. [DOI: 10.1039/c8cp06410e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Solvent interactions with the fluorocarbon group of noncanonical amino acids are the cause of their diverse fluorescence behaviors, which implies their usefulness as solvent-sensitive environmental sensors in many biological processes.
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Affiliation(s)
- Tonima Nandy
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Saptarsi Mondal
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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14
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Lou YG, Wang AJ, Zhao L, He LF, Li XF, He CY, Zhang X. Palladium-catalyzed cross-coupling of unactivated alkylzinc reagents with 2-bromo-3,3,3-trifluoropropene and its application in the synthesis of fluorinated amino acids. Chem Commun (Camb) 2019; 55:3705-3708. [DOI: 10.1039/c8cc10212k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A palladium-catalyzed cross-coupling of unactivated alkylzinc reagents with 2-bromo-3,3,3-trifluoropropene (BTP) has been developed, which was used as a key step to prepare a series of trifluoromethylated and difluoromethylated amino acids.
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Affiliation(s)
- Yue-Guang Lou
- Generic Drug Research Center of Guizhou Province
- School of Pharmacy
- Zunyi Medical University
- Zunyi
- P. R. China
| | - An-Jun Wang
- Generic Drug Research Center of Guizhou Province
- School of Pharmacy
- Zunyi Medical University
- Zunyi
- P. R. China
| | - Liang Zhao
- Generic Drug Research Center of Guizhou Province
- School of Pharmacy
- Zunyi Medical University
- Zunyi
- P. R. China
| | - Lin-Feng He
- Generic Drug Research Center of Guizhou Province
- School of Pharmacy
- Zunyi Medical University
- Zunyi
- P. R. China
| | - Xiao-Fei Li
- Generic Drug Research Center of Guizhou Province
- School of Pharmacy
- Zunyi Medical University
- Zunyi
- P. R. China
| | - Chun-Yang He
- Generic Drug Research Center of Guizhou Province
- School of Pharmacy
- Zunyi Medical University
- Zunyi
- P. R. China
| | - Xingang Zhang
- Key Laboratory of Organofluorine Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
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15
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Haney CM, Werner HM, McKay JJ, Horne WS. Thermodynamic origin of α-helix stabilization by side-chain cross-links in a small protein. Org Biomol Chem 2018; 14:5768-73. [PMID: 27006192 DOI: 10.1039/c6ob00475j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Peptide cross-linking has been widely explored as a means of constraining short sequences into stable folded conformations, most commonly α-helices. The prevailing hypothesis for the origin of helix stabilization is an entropic effect resulting from backbone pre-organization; however, obtaining direct evidence bearing on this hypothesis is challenging. Here, we compare the folding thermodynamics of a small helix-rich protein domain and analogues containing one of three common cross-linking motifs. Analysis of the folding free energy landscapes of linear vs. cyclized species reveal consistent trends in the effect of cyclization on folding energetics, as well as subtle differences based on the chemistry of the cross link. Stabilization in all three systems arises entirely from a reduction in the entropic penalty of folding that more than compensates for an enthalpic destabilization of the folded state.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - James J McKay
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA.
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16
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17
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Mondal S, Chaterjee S, Halder R, Jana B, Singh PC. Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules. J Phys Chem B 2017; 121:7681-7688. [PMID: 28737391 DOI: 10.1021/acs.jpcb.7b03420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Soumit Chaterjee
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Ritaban Halder
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Biman Jana
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
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18
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Mondal S, Halder R, Biswas B, Jana B, Singh PC. Solvent organization around the perfluoro group of coumarin 153 governs its photophysical properties: An experimental and simulation study of coumarin dyes in ethanol as well as fluorinated ethanol solvents. J Chem Phys 2017; 144:184504. [PMID: 27179492 DOI: 10.1063/1.4948704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The self-aggregation property of the perfluoro group containing molecules makes it important in the research fields of biology and polymer and organic synthesis. In the quest of understanding the role of the perfluoro group on the photophysical properties of perfluoro-containing molecules in biologically important fluoroethanol solvents, we have applied photophysical as well as molecular dynamics simulation techniques to explore the properties of perfluoro groups containing molecule coumarin-153 (C153) in ethanol (ETH), monofluoroethanol (MFE), difluoroethanol (DFE), and trifluoroethanol (TFE) and compared them with the molecules without perfluoro moiety, namely coumarin-6H (C6H) and coumarin-480 (C480). In contrast to C6H and C480, the excited state lifetime of C153 in fluorinated ETHs is not monotonic. The excited state lifetime of C153 decreases in MFE and DFE as compared to ETH, whereas in TFE, it increases as compared to MFE and DFE. Molecular dynamics simulation reveals that the carbon terminal away from the OH group of fluorinated ETHs has a preferential orientation near the perfluoro (CF3) group of C153. In MFE and DFE, the CF3 group of C153 prefers to have a CF2-F⋯H -(CHF) type of electrostatic interaction over CF2-F⋯F -(CH2) kind of dispersion interaction which increases the rate of nonradiative decay, probably due to the electrostatic nature of the CF2-F⋯H -(CHF) hydrogen bond. On the other hand, in TFE, C-F⋯ F-C type of dispersion interaction, also known as fluorous interaction, takes place between the CF3 groups of C153 and TFE which decreases the rate of nonradiative rate as compared to MFE and DFE, leading to the increased lifetime of C153 in TFE. Photophysical and MD simulation studies clearly depict that the structural organization of solvents and their interaction with the fluorocarbon group are crucial factors for the photophysical behavior of the fluorocarbon containing molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Ritaban Halder
- Department of Physical Chemistry, 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
| | - Biman Jana
- Department of Physical Chemistry, 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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19
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Völler JS, Dulic M, Gerling-Driessen UIM, Biava H, Baumann T, Budisa N, Gruic-Sovulj I, Koksch B. Discovery and Investigation of Natural Editing Function against Artificial Amino Acids in Protein Translation. ACS CENTRAL SCIENCE 2017; 3:73-80. [PMID: 28149956 PMCID: PMC5269655 DOI: 10.1021/acscentsci.6b00339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 05/24/2023]
Abstract
Fluorine being not substantially present in the chemistry of living beings is an attractive element in tailoring novel chemical, biophysical, and pharmacokinetic properties of peptides and proteins. The hallmark of ribosome-mediated artificial amino acid incorporation into peptides and proteins is a broad substrate tolerance, which is assumed to rely on the absence of evolutionary pressure for efficient editing of artificial amino acids. We used the well-characterized editing proficient isoleucyl-tRNA synthetase (IleRS) from Escherichia coli to investigate the crosstalk of aminoacylation and editing activities against fluorinated amino acids. We show that translation of trifluoroethylglycine (TfeGly) into proteins is prevented by hydrolysis of TfeGly-tRNAIle in the IleRS post-transfer editing domain. The remarkable observation is that dissociation of TfeGly-tRNAIle from IleRS is significantly slowed down. This finding is in sharp contrast to natural editing reactions by tRNA synthetases wherein fast editing rates for the noncognate substrates are essential to outcompete fast aa-tRNA dissociation rates. Using a post-transfer editing deficient mutant of IleRS (IleRSAla10), we were able to achieve ribosomal incorporation of TfeGly in vivo. Our work expands the knowledge of ribosome-mediated artificial amino acid translation with detailed analysis of natural editing function against an artificial amino acid providing an impulse for further systematic investigations and engineering of the translation and editing of unusual amino acids.
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Affiliation(s)
- Jan-Stefan Völler
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Morana Dulic
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
| | - Ulla I. M. Gerling-Driessen
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hernan Biava
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Tobias Baumann
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Nediljko Budisa
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Ita Gruic-Sovulj
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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20
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Chernykh AV, Feskov IO, Chernykh AV, Kondratov IS, Tolmachova N, Radchenko DS, Daniliuc CG, Haufe G. Synthesis and Physical-Chemical Properties ofcis- andtrans-1-Amino-3-fluoro-3-methylcyclobutanecarboxylic Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anton V. Chernykh
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry; National Academy of Sciences of Ukraine; Murmanska Str. 5 02660 Kyiv Ukraine
| | - Illia O. Feskov
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | | | - Ivan S. Kondratov
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | - Nataliya Tolmachova
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut; Universität Münster; Corrensstraße 40 48149 Münster Germany
| | - Günter Haufe
- Organisch-Chemisches Institut; Universität Münster; Corrensstraße 40 48149 Münster Germany
- Cells-in-Motion Cluster of Excellence; Universität Münster; Waldeyerstraße 15 48149 Münster Germany
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21
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Abstract
As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.
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Affiliation(s)
- E N G Marsh
- University of Michigan, Ann Arbor, MI, United States.
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22
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Huhmann S, Nyakatura EK, Erdbrink H, Gerling UI, Czekelius C, Koksch B. Effects of single substitutions with hexafluoroleucine and trifluorovaline on the hydrophobic core formation of a heterodimeric coiled coil. J Fluor Chem 2015. [DOI: 10.1016/j.jfluchem.2015.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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24
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Appel R, Tacke S, Klingauf J, Besenius P. Tuning the pH-triggered self-assembly of dendritic peptide amphiphiles using fluorinated side chains. Org Biomol Chem 2015; 13:1030-9. [DOI: 10.1039/c4ob02185a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the synthesis of a series of anionic dendritic peptide amphiphiles of increasing hydrophobic character and describe their self-assembly into supramolecular nanorods using pH and ionic strength dependent state diagrams.
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Affiliation(s)
- Ralph Appel
- Organic Chemistry Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
- Center for Nanotechnology (CeNTech)
| | - Sebastian Tacke
- Department of Cellular Biophysics
- Institute of Medical Physics and Biophysics
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jürgen Klingauf
- Department of Cellular Biophysics
- Institute of Medical Physics and Biophysics
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Pol Besenius
- Organic Chemistry Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
- Center for Nanotechnology (CeNTech)
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25
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Marsh ENG. Fluorinated proteins: from design and synthesis to structure and stability. Acc Chem Res 2014; 47:2878-86. [PMID: 24883933 DOI: 10.1021/ar500125m] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fluorine is all but absent from biology; however, it has proved to be a remarkably useful element with which to modulate the activity of biological molecules and to study their mechanism of action. Our laboratory's interest in incorporating fluorine into proteins was stimulated by the unusual physicochemical properties exhibited by perfluorinated small molecules. These include extreme chemical inertness and thermal stability, properties that have made them valuable as nonstick coatings and fire retardants. Fluorocarbons also exhibit an unusual propensity to phase segregation. This phenomenon, which has been termed the "fluorous effect", has been effectively exploited in organic synthesis to purify compounds from reaction mixtures by extracting fluorocarbon-tagged molecules into fluorocarbon solvents. As biochemists, we were curious to explore whether the unusual physicochemical properties of perfluorocarbons could be engineered into proteins. To do this, we developed a synthesis of a highly fluorinated amino acid, hexafluoroleucine, and designed a model 4-helix bundle protein, α4H, in which the hydrophobic core was packed exclusively with leucine. We then investigated the effects of repacking the hydrophobic core of α4H with various combinations of leucine and hexafluoroleucine. These initial studies demonstrated that fluorination is a general and effective strategy for enhancing the stability of proteins against chemical and thermal denaturation and proteolytic degradation. We had originally envisaged that the "fluorous interactions", postulated from the self-segregating properties of fluorous solvents, might be used to mediate specific protein-protein interactions orthogonal to those of natural proteins. However, various lines of evidence indicate that no special, favorable fluorine-fluorine interactions occur in the core of the fluorinated α4 protein. This makes it unlikely that fluorinated amino acids can be used to direct protein-protein interactions. More recent detailed thermodynamic and structural studies in our laboratory have uncovered the basis for the remarkably general ability of fluorinated side chains to stabilize protein structure. Crystal structures of α4H and its fluorinated analogues show that the fluorinated residues fit into the hydrophobic core with remarkably little perturbation to the structure. This is explained by the fact that fluorinated side chains, although larger, very closely preserve the shape of the hydrophobic amino acids they replace. Thus, an increase in buried hydrophobic surface area in the folded state is responsible for the additional thermodynamic stability of the fluorinated protein. Measurements of ΔG°, ΔH°, ΔS°, and ΔCp° for unfolding demonstrate that the "fluorous" stabilization of these protein arises from the hydrophobic effect in the same way that hydrophobic partitioning stabilizes natural proteins.
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Affiliation(s)
- E. Neil G. Marsh
- Departments
of Chemistry
and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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26
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Budisa N, Kubyshkin V, Schulze-Makuch D. Fluorine-rich planetary environments as possible habitats for life. Life (Basel) 2014; 4:374-85. [PMID: 25370378 PMCID: PMC4206852 DOI: 10.3390/life4030374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 11/16/2022] Open
Abstract
In polar aprotic organic solvents, fluorine might be an element of choice for life that uses selected fluorinated building blocks as monomers of choice for self-assembling of its catalytic polymers. Organofluorine compounds are extremely rare in the chemistry of life as we know it. Biomolecules, when fluorinated such as peptides or proteins, exhibit a "fluorous effect", i.e., they are fluorophilic (neither hydrophilic nor lipophilic). Such polymers, capable of creating self-sorting assemblies, resist denaturation by organic solvents by exclusion of fluorocarbon side chains from the organic phase. Fluorous cores consist of a compact interior, which is shielded from the surrounding solvent. Thus, we can anticipate that fluorine-containing "teflon"-like or "non-sticking" building blocks might be monomers of choice for the synthesis of organized polymeric structures in fluorine-rich planetary environments. Although no fluorine-rich planetary environment is known, theoretical considerations might help us to define chemistries that might support life in such environments. For example, one scenario is that all molecular oxygen may be used up by oxidation reactions on a planetary surface and fluorine gas could be released from F-rich magma later in the history of a planetary body to result in a fluorine-rich planetary environment.
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Affiliation(s)
- Nediljko Budisa
- Department of Chemistry, Technical University of Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Vladimir Kubyshkin
- Department of Chemistry, Technical University of Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Dirk Schulze-Makuch
- School of the Environment, Washington State University, Webster Hall 1148, Pullman, WA 99164, USA.
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27
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Trifluoromethyl-modified dipeptides by ZrCl4-promoted aza-Henry reactions. Amino Acids 2014; 46:1961-70. [PMID: 24802246 DOI: 10.1007/s00726-014-1749-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/10/2014] [Indexed: 10/25/2022]
Abstract
Chiral (R)-1-phenylethylamine was successfully employed in a tandem aza-Henry addition-reduction reaction to give chiral β-nitro α-trifluoromethyl amines. A subsequent coupling reaction with N-Boc-protected amino acids leads to obtain optically pure CF3-modified dipeptides carrying two different N-protecting groups. These peptidomimetic units are characterized by the presence of the [CH(CF3)NH] group as mimetic of the natural [CONH] peptidic bond and can be used for the synthesis of more complex CF3-modified peptides after selective deprotection of one of the two amine functions. 2D NMR spectral analyses were employed to determine the absolute configurations of all newly synthesized chiral compounds.
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28
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Cormanich RA, Ducati LC, Tormena CF, Rittner R. Phenylalanine and tyrosine methyl ester intramolecular interactions and conformational analysis by (1)H NMR and infrared spectroscopies and theoretical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 123:482-489. [PMID: 24434201 DOI: 10.1016/j.saa.2013.12.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/29/2013] [Accepted: 12/21/2013] [Indexed: 06/03/2023]
Abstract
Amino acid conformational analysis in solution are scarce, since these compounds present a bipolar zwitterionic structure ((+)H3NCHRCOO(-)) in these media. Also, intramolecular hydrogen bonds have been classified as the sole interactions governing amino acid conformational behavior in the literature. In the present work we propose phenylalanine and tyrosine methyl ester conformational studies in different solvents by (1)H NMR and infrared spectroscopies and theoretical calculations. Both experimental and theoretical results are in agreement and suggest that the conformational behavior of the phenylalanine and tyrosine methyl esters are similar and are dictated by the interplay between steric and hyperconjugative interactions.
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Affiliation(s)
- Rodrigo A Cormanich
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, Brazil
| | - Lucas C Ducati
- Chemistry Institute, University of São Paulo, P.O. Box 26077, 05508-900 São Paulo, Brazil
| | - Cláudio F Tormena
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, Brazil
| | - Roberto Rittner
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, Brazil.
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29
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Biava H, Budisa N. Evolution of fluorinated enzymes: An emerging trend for biocatalyst stabilization. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Hernan Biava
- Department of Biocatalysis, Institute of Chemistry Berlin Institute of Technology/TU Berlin Berlin Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Institute of Chemistry Berlin Institute of Technology/TU Berlin Berlin Germany
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30
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Reinert ZE, Horne WS. Folding Thermodynamics of Protein-Like Oligomers with Heterogeneous Backbones. Chem Sci 2014; 5:3325-3330. [PMID: 25071931 DOI: 10.1039/c4sc01094a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The thermodynamics of protein folding are dictated by a complex interplay of interatomic interactions and physical forces. A variety of unnatural protein-like oligomers have the capacity to manifest defined folding patterns. While the energetics of folding in natural proteins is well studied, little is known about the forces that govern folding in modified backbones. Here, we explore the thermodynamic consequences of backbone alteration on protein folding, focusing on two types of chemical changes made in different structural contexts of a compact tertiary fold. Our results reveal a surprising favorable impact on folding entropy that accompanies modifications that increase disorder in the ensemble of unfolded states, due to differences in the solvation of natural and unnatural backbones.
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Affiliation(s)
- Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15217, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15217, USA
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31
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Abstract
Highly fluorinated analogs of hydrophobic amino acids have proven to be generally effective in increasing the thermodynamic stability of proteins. These non-proteogenic amino acids can be incorporated into both α-helix and β-sheet structural motifs and generally enhance protein stability towards unfolding by heat and chemical denaturants, and retard their degradation by proteases. Recent detailed structural and thermodynamic studies have demonstrated that the increase in buried hydrophobic surface area that accompanies fluorination is primarily responsible for the stabilizing properties of fluorinated side chains. Fluorination appears to be a particularly useful strategy for increasing protein stability because fluorinated amino acids closely retain the shape of the side chain, and are thus minimally perturbing to protein structure and function. The first part of this chapter discusses some examples of highly fluorinated model proteins designed by our laboratory and protocols for their synthesis. In the second part, methods for determining their thermodynamic stability, along with conditions that have proven to be useful for crystallizing these proteins, are presented.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
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32
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Gerling UIM, Salwiczek M, Cadicamo CD, Erdbrink H, Czekelius C, Grage SL, Wadhwani P, Ulrich AS, Behrends M, Haufe G, Koksch B. Fluorinated amino acids in amyloid formation: a symphony of size, hydrophobicity and α-helix propensity. Chem Sci 2014. [DOI: 10.1039/c3sc52932k] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Cormanich RA, Ducati LC, Tormena CF, Rittner R. A theoretical investigation of the dictating forces in small amino acid conformational preferences: The case of glycine, sarcosine and N,N-dimethylglycine. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Nyakatura EK, Reimann O, Vagt T, Salwiczek M, Koksch B. Accommodating fluorinated amino acids in a helical peptide environment. RSC Adv 2013. [DOI: 10.1039/c3ra41110a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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