1
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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2
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Welte H, Zhou T, Mihajlenko X, Mayans O, Kovermann M. What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein. Sci Rep 2020; 10:2640. [PMID: 32060391 PMCID: PMC7021800 DOI: 10.1038/s41598-020-59446-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/29/2020] [Indexed: 11/21/2022] Open
Abstract
Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.
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Affiliation(s)
- Hannah Welte
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.,Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Tiankun Zhou
- Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Xenia Mihajlenko
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Olga Mayans
- Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.,Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. .,Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. .,Zukunftskolleg, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.
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3
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Betush RJ, Urban JM, Nilsson BL. Balancing hydrophobicity and sequence pattern to influence self-assembly of amphipathic peptides. Biopolymers 2018; 110. [PMID: 29292825 DOI: 10.1002/bip.23099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 01/25/2023]
Abstract
Amphipathic peptides with alternating polar and nonpolar amino acid sequences efficiently self-assemble into functional β-sheet fibrils as long as the nonpolar residues have sufficient hydrophobicity. For example, the Ac-(FKFE)2 -NH2 peptide rapidly self-assembles into β-sheet bilayer nanoribbons, while Ac-(AKAE)2 -NH2 fails to self-assemble under similar conditions due to the significantly reduced hydrophobicity and β-sheet propensity of Ala relative to Phe. Herein, we systematically explore the effect of substituting only two of the four Ala residues at various positions in the Ac-(AKAE)2 -NH2 peptide with amino acids of increasing hydrophobicity, β-sheet potential, and surface area (including Phe, 1-naphthylalanine (1-Nal), 2-naphthylalanine (2-Nal), cyclohexylalanine (Cha), and pentafluorophenylalanine (F5 -Phe)) on the self-assembly propensity of the resulting sequences. It was found that double Phe variants, regardless of the position of substitution, failed to self-assemble under the conditions used in this study. In contrast, all double 1-Nal and 2-Nal variants readily self-assembled, albeit at differing rates depending on the substitution patterns. To determine whether this was due to hydrophobicity or side chain surface area, we also prepared double Cha and F5 -Phe variant peptides (both side chain groups are more hydrophobic than Phe). Each of these variants also underwent effective self-assembly, with the aromatic F5 -Phe peptides doing so with greater efficiency. These findings provide insight into the role of amino acid hydrophobicity and sequence pattern on self-assembly proclivity of amphipathic peptides and on how targeted substitutions of nonpolar residues in these sequences can be exploited to tune the characteristics of the resulting self-assembled materials.
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Affiliation(s)
- Ria J Betush
- Department of Chemistry, Gannon University, Erie, Pennsylvania
| | - Jennifer M Urban
- Department of Chemistry, University of Rochester, Rochester, New York
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York
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4
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Abstract
An efficient route for the synthesis of enantiopure 3,3-difluoroproline on multigram-scale is described herein. The deoxofluorination can be achieved with DAST on the corresponding racemic pyrrolidinone in good yield. Resolution of the racemate by crystallization with D- and L-tyrosine hydrazide provides both enantiomers of 3,3-difluoroproline in high yield and ee%.
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Affiliation(s)
- Christelle Doebelin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Yuanjun He
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
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5
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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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6
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Matsuzaki K, Okuyama K, Tokunaga E, Shiro M, Shibata N. Sterically Demanding Unsymmetrical Diaryl-λ(3)-iodanes for Electrophilic Pentafluorophenylation and an Approach to α-Pentafluorophenyl Carbonyl Compounds with an All-Carbon Stereocenter. ChemistryOpen 2015; 3:233-7. [PMID: 25558441 PMCID: PMC4280821 DOI: 10.1002/open.201402045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Indexed: 01/09/2023] Open
Abstract
A sterically demanding unsymmetrical pentafluorophenyl-triisopropylphenyl-λ(3)-iodane was developed as an effective reagent for the electrophilic pentafluorophenylation of various β-keto esters and a β-keto amide. 17 examples of α-pentafluorophenylated 1,3-dicarbonyl compounds 3 having a quaternary carbon center are provided. The resulting compounds were nicely transformed into chiral α-pentafluorophenyl ketones with an all-carbon stereogenic center in high yields and high enantioselectivities using asymmetric organocatalysis (up to 98 % ee) or asymmetric metal catalysis (up to 82 % ee).
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Affiliation(s)
- Kohei Matsuzaki
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
| | - Kenta Okuyama
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
| | - Etsuko Tokunaga
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
| | - Motoo Shiro
- Rigaku Corporation 3-9-12 Mastubara-cho, Akishima, Tokyo 196-8666 (Japan)
| | - Norio Shibata
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
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7
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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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8
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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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9
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Lence E, Tizón L, Otero JM, Peón A, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, González-Bello C. Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. ACS Chem Biol 2013. [PMID: 23198883 DOI: 10.1021/cb300493s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural changes caused by the substitution of the aromatic moiety in (2S)-2-benzyl-3-dehydroquinic acids and its epimers in C2 by electron-withdrawing or electron-donating groups in type II dehydroquinase enzyme from M. tuberculosis and H. pylori has been investigated by structural and computational studies. Both compounds are reversible competitive inhibitors of this enzyme, which is essential in these pathogenic bacteria. The crystal structures of M. tuberculosis and H. pylori in complex with (2S)-2-(4-methoxy)benzyl- and (2S)-2-perfluorobenzyl-3-dehydroquinic acids have been solved at 2.0, 2.3, 2.0, and 1.9 Å, respectively. The crystal structure of M. tuberculosis in complex with (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid is also reported at 1.55 Å. These crystal structures reveal key differences in the conformation of the flexible loop of the two enzymes, a difference that depends on the presence of electron-withdrawing or electron-donating groups in the aromatic moiety of the inhibitors. This loop closes over the active site after substrate binding, and its flexibility is essential for the function of the enzyme. These differences have also been investigated by molecular dynamics simulations in an effort to understand the significant inhibition potency differences observed between some of these compounds and also to obtain more information about the possible movements of the loop. These computational studies have also allowed us to identify key structural factors of the H. pylori loop that could explain its reduced flexibility in comparison to the M. tuberculosis loop, specifically by the formation of a key salt bridge between the side chains of residues Asp18 and Arg20.
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Affiliation(s)
| | | | | | | | | | | | - Gavin C. Fox
- Proxima 2, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, F-91192
Gif-sur-Yvette, France
| | - Mark J. van Raaij
- Departamento de Estructura de
Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Heather Lamb
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
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10
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Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle. Chem Sci 2013. [DOI: 10.1039/c2sc21117c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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11
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Buer BC, Meagher JL, Stuckey JA, Marsh ENG. Comparison of the structures and stabilities of coiled-coil proteins containing hexafluoroleucine and t-butylalanine provides insight into the stabilizing effects of highly fluorinated amino acid side-chains. Protein Sci 2012; 21:1705-15. [PMID: 22930450 PMCID: PMC3527707 DOI: 10.1002/pro.2150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/08/2022]
Abstract
Highly fluorinated analogs of hydrophobic amino acids are well known to increase the stability of proteins toward thermal unfolding and chemical denaturation, but there is very little data on the structural consequences of fluorination. We have determined the structures and folding energies of three variants of a de novo designed 4-helix bundle protein whose hydrophobic cores contain either hexafluoroleucine (hFLeu) or t-butylalanine (tBAla). Although the buried hydrophobic surface area is the same for all three proteins, the incorporation of tBAla causes a rearrangement of the core packing, resulting in the formation of a destabilizing hydrophobic cavity at the center of the protein. In contrast, incorporation of hFLeu, causes no changes in core packing with respect to the structure of the nonfluorinated parent protein which contains only leucine in the core. These results support the idea that fluorinated residues are especially effective at stabilizing proteins because they closely mimic the shape of the natural residues they replace while increasing buried hydrophobic surface area.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - Jennifer L Meagher
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
| | - Jeanne A Stuckey
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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12
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Mortenson DE, Satyshur KA, Guzei IA, Forest KT, Gellman SH. Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations. J Am Chem Soc 2012; 134:2473-6. [PMID: 22280019 PMCID: PMC3351109 DOI: 10.1021/ja210045s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Quasiracemic crystallization has been used to obtain high-resolution structures of two variants of the villin headpiece subdomain (VHP) that contain a pentafluorophenylalanine (F(5)Phe) residue in the hydrophobic core. In each case, the crystal contained the variant constructed from l-amino acids and the native sequence constructed from d-amino acids. We were motivated to undertake these studies by reports that racemic proteins crystallize more readily than homochiral forms and the prospect that quasiracemic crystallization would enable us to determine whether a polypeptide containing a noncanonical residue can closely mimic the tertiary structure of the native sequence. The results suggest that quasiracemic crystallization may prove to be generally useful for assessing mimicry of naturally evolved protein folding patterns by polypeptides that contain unnatural side-chain or backbone subunits.
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Affiliation(s)
- David E. Mortenson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
| | - Kenneth A. Satyshur
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 (USA)
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 (USA)
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
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13
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Salwiczek M, Nyakatura EK, Gerling UIM, Ye S, Koksch B. Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions. Chem Soc Rev 2011; 41:2135-71. [PMID: 22130572 DOI: 10.1039/c1cs15241f] [Citation(s) in RCA: 327] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).
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Affiliation(s)
- Mario Salwiczek
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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14
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Nomura T, Kamada R, Ito I, Sakamoto K, Chuman Y, Ishimori K, Shimohigashi Y, Sakaguchi K. Probing phenylalanine environments in oligomeric structures with pentafluorophenylalanine and cyclohexylalanine. Biopolymers 2011; 95:410-9. [PMID: 21280026 DOI: 10.1002/bip.21594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Stabilization of protein structures and protein-protein interactions are critical in the engineering of industrially useful enzymes and in the design of pharmaceutically valuable ligands. Hydrophobic interactions involving phenylalanine residues play crucial roles in protein stability and protein-protein/peptide interactions. To establish an effective method to explore the hydrophobic environments of phenylalanine residues, we present a strategy that uses pentafluorophenylalanine (F5Phe) and cyclohexylalanine (Cha). In this study, substitution of F5Phe or Cha for three Phe residues at positions 328, 338, and 341 in the tetramerization domain of the tumor suppressor protein p53 was performed. These residues are located at the interfaces of p53-p53 interactions and are important in the stabilization of the tetrameric structure. The stability of the p53 tetrameric structure did not change significantly when F5Phe-containing peptides at positions Phe328 or Phe338 were used. In contrast, the substitution of Cha for Phe341 in the hydrophobic core enhanced the stability of the tetrameric structure with a T(m) value of 100 degrees C. Phe328 and Phe338 interact with each other through pi-interactions, whereas Phe341 is buried in the surrounding alkyl side-chains of the hydrophobic core of the p53 tetramerization domain. Furthermore, high pressure-assisted denaturation analysis indicated improvement in the occupancy of the hydrophobic core. Considerable stabilization of the p53 tetramer was achieved by filling the identified cavity in the hydrophobic core of the p53 tetramer. The results indicate the status of the Phe residues, indicating that the "pair substitution" of Cha and F5Phe is highly suitable for probing the environments of Phe residues.
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Affiliation(s)
- Takao Nomura
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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15
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Petrov D, Zagrovic B. Microscopic analysis of protein oxidative damage: effect of carbonylation on structure, dynamics, and aggregability of villin headpiece. J Am Chem Soc 2011; 133:7016-24. [PMID: 21506564 PMCID: PMC3088313 DOI: 10.1021/ja110577e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the most important irreversible oxidative modifications of proteins is carbonylation, the process of introducing a carbonyl group in reaction with reactive oxygen species. Notably, carbonylation increases with the age of cells and is associated with the formation of intracellular protein aggregates and the pathogenesis of age-related disorders such as neurodegenerative diseases and cancer. However, it is still largely unclear how carbonylation affects protein structure, dynamics, and aggregability at the atomic level. Here, we use classical molecular dynamics simulations to study structure and dynamics of the carbonylated headpiece domain of villin, a key actin-organizing protein. We perform an exhaustive set of molecular dynamics simulations of a native villin headpiece together with every possible combination of carbonylated versions of its seven lysine, arginine, and proline residues, quantitatively the most important carbonylable amino acids. Surprisingly, our results suggest that high levels of carbonylation, far above those associated with cell death in vivo, may be required to destabilize and unfold protein structure through the disruption of specific stabilizing elements, such as salt bridges or proline kinks, or tampering with the hydrophobic effect. On the other hand, by using thermodynamic integration and molecular hydrophobicity potential approaches, we quantitatively show that carbonylation of hydrophilic lysine and arginine residues is equivalent to introducing hydrophobic, charge-neutral mutations in their place, and, by comparison with experimental results, we demonstrate that this by itself significantly increases the intrinsic aggregation propensity of both structured, native proteins and their unfolded states. Finally, our results provide a foundation for a novel experimental strategy to study the effects of carbonylation on protein structure, dynamics, and aggregability using site-directed mutagenesis.
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Affiliation(s)
- Drazen Petrov
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria
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16
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Senguen FT, Lee NR, Gu X, Ryan DM, Doran TM, Anderson EA, Nilsson BL. Probing aromatic, hydrophobic, and steric effects on the self-assembly of an amyloid-β fragment peptide. ACTA ACUST UNITED AC 2011; 7:486-96. [DOI: 10.1039/c0mb00080a] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Positional effects of monofluorinated phenylalanines on histone acetyltransferase stability and activity. Bioorg Med Chem Lett 2009; 19:5449-51. [DOI: 10.1016/j.bmcl.2009.07.093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/17/2009] [Accepted: 07/20/2009] [Indexed: 11/22/2022]
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18
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Periole X, Cavalli M, Marrink SJ, Ceruso MA. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. J Chem Theory Comput 2009; 5:2531-43. [PMID: 26616630 DOI: 10.1021/ct9002114] [Citation(s) in RCA: 447] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this representation an elastic network is used as a structural scaffold to describe and maintain the overall shape of a protein and a physics-based coarse-grained model (MARTINI-2.1) is used to describe both inter- and intramolecular interactions in the system. The results show that when used in molecular dynamics simulations ELNEDIN models can be built so that the resulting structural and dynamical properties of a protein, including its collective motions, are comparable to those obtained using atomistic protein models. We then evaluate the behavior of such models in (1) long, microsecond time-scale, simulations, (2) the modeling of very large macromolecular assemblies, a viral capsid, and (3) the study of a protein-protein association process, the reassembly of the ROP homodimer. The results for this series of tests indicate that ELNEDIN models allow microsecond time-scale molecular dynamics simulations to be carried out readily, that large biological entities such as the viral capsid of the cowpea mosaic virus can be stably modeled as assemblies of independent ELNEDIN models, and that ELNEDIN models show significant promise for modeling protein-protein association processes.
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Affiliation(s)
- Xavier Periole
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco Cavalli
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco A Ceruso
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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