1
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Percec V, Sahoo D. From Frank-Kasper, Quasicrystals, and Biological Membrane Mimics to Reprogramming In Vivo the Living Factory to Target the Delivery of mRNA with One-Component Amphiphilic Janus Dendrimers. Biomacromolecules 2024; 25:1353-1370. [PMID: 38232372 DOI: 10.1021/acs.biomac.3c01390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
This Perspective is dedicated to the 25th Anniversary of Biomacromolecules. It provides a personal view on the developing field of the polymer and biology interface over the 25 years since the journal was launched by the American Chemical Society (ACS). This Perspective is meant to bridge an article published in the first issue of the journal and recent bioinspired developments in the laboratory of the corresponding author. The discovery of supramolecular spherical helices self-organizing into Frank-Kasper and quasicrystals as models of icosahedral viruses, as well as of columnar helical assemblies that mimic rodlike viruses by supramolecular dendrimers, is briefly presented. The transplant of these assemblies from supramolecular dendrimers to block copolymers, giant surfactants, and other self-organized soft matter follows. Amphiphilic self-assembling Janus dendrimers and glycodendrimers as mimics of biological membranes and their glycans are discussed. New concepts derived from them that evolved in the in vivo targeted delivery of mRNA with the simplest one-component synthetic vector systems are introduced. Some synthetic methodologies employed during the synthesis and self-assembly are explained. Unraveling bioinspired applications of novel materials concludes this brief 25th Anniversary Perspective of Biomacromolecules.
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Affiliation(s)
- Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Dipankar Sahoo
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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2
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Britton D, Legocki J, Aristizabal O, Mishkit O, Liu C, Jia S, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance. ACS APPLIED NANO MATERIALS 2023; 6:21245-21257. [PMID: 38037605 PMCID: PMC10682962 DOI: 10.1021/acsanm.3c04357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Theranostic materials research is experiencing rapid growth driven by the interest in integrating both therapeutic and diagnostic modalities. These materials offer the unique capability to not only provide treatment but also track the progression of a disease. However, to create an ideal theranostic biomaterial without compromising drug encapsulation, diagnostic imaging must be optimized for improved sensitivity and spatial localization. Herein, we create a protein-engineered fluorinated coiled-coil fiber, Q2TFL, capable of improved sensitivity to 19F magnetic resonance spectroscopy (MRS) detection. Leveraging residue-specific noncanonical amino acid incorporation of trifluoroleucine (TFL) into the coiled-coil, Q2, which self-assembles into nanofibers, we generate Q2TFL. We demonstrate that fluorination results in a greater increase in thermostability and 19F magnetic resonance detection compared to the nonfluorinated parent, Q2. Q2TFL also exhibits linear ratiometric 19F MRS thermoresponsiveness, allowing it to act as a temperature probe. Furthermore, we explore the ability of Q2TFL to encapsulate the anti-inflammatory small molecule, curcumin (CCM), and its impact on the coiled-coil structure. Q2TFL also provides hyposignal contrast in 1H MRI, echogenic signal with high-frequency ultrasound and sensitive detection by 19F MRS in vivo illustrating fluorination of coiled-coils for supramolecular assembly and their use with 1H MRI, 19F MRS and high frequency ultrasound as multimodal theranostic agents.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Orlando Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Orin Mishkit
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Paul Douglas Renfrew
- Center
for Computational Biology, Flatiron Institute,
Simons Foundation, New York, New York 10010, United States
| | - Richard Bonneau
- Center
for Computational Biology, Flatiron Institute,
Simons Foundation, New York, New York 10010, United States
- Center for
Genomics and Systems Biology, New York University, New York, New York 10003, United States
- Courant
Institute
of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Youssef Z. Wadghiri
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department
of Biomaterials, New York University College
of Dentistry, New York, New York 10010, United States
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3
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Gregorc J, Lensen N, Chaume G, Iskra J, Brigaud T. Trifluoromethylthiolation of Tryptophan and Tyrosine Derivatives: A Tool for Enhancing the Local Hydrophobicity of Peptides. J Org Chem 2023; 88:13169-13177. [PMID: 37672679 PMCID: PMC10507666 DOI: 10.1021/acs.joc.3c01373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 09/08/2023]
Abstract
The incorporation of fluorinated groups into peptides significantly affects their biophysical properties. We report herein the synthesis of Fmoc-protected trifluoromethylthiolated tyrosine (CF3S-Tyr) and tryptophan (CF3S-Trp) analogues on a gram scale (77-93% yield) and demonstrate their use as highly hydrophobic fluorinated building blocks for peptide chemistry. The developed methodology was successfully applied to the late-stage regioselective trifluoromethylthiolation of Trp residues in short peptides (66-80% yield) and the synthesis of various CF3S-analogues of biologically active monoamines. To prove the concept, Fmoc-(CF3S)Tyr and -Trp were incorporated into the endomorphin-1 chain (EM-1) and into model tripeptides by solid-phase peptide synthesis. A remarkable enhancement of the local hydrophobicity of the trifluoromethylthiolated peptides was quantified by the chromatographic hydrophobicity index determination method, demonstrating the high potential of CF3S-containing amino acids for the rational design of bioactive peptides.
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Affiliation(s)
- Jure Gregorc
- Chair
of Organic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Nathalie Lensen
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Grégory Chaume
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Jernej Iskra
- Chair
of Organic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Thierry Brigaud
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
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4
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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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5
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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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6
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Fountain JN, Hawker MJ, Hartle L, Wu J, Montanari V, Sahoo JK, Davis LM, Kaplan DL, Kumar K. Towards Non-stick Silk: Tuning the Hydrophobicity of Silk Fibroin Protein. Chembiochem 2022; 23:e202200429. [PMID: 35998090 PMCID: PMC9830957 DOI: 10.1002/cbic.202200429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/22/2022] [Indexed: 02/03/2023]
Abstract
Silk fibroin protein is a biomaterial with excellent biocompatibility and low immunogenicity. These properties have catapulted the material as a leader for extensive use in stents, catheters, and wound dressings. Modulation of hydrophobicity of silk fibroin protein to further expand the scope and utility however has been elusive. We report that installing perfluorocarbon chains on the surface of silk fibroin transforms this water-soluble protein into a remarkably hydrophobic polymer that can be solvent-cast. A clear relationship emerged between fluorine content of the modified silk and film hydrophobicity. Water contact angles of the most decorated silk fibroin protein exceeded that of Teflon®. We further show that water uptake in prefabricated silk bars is dramatically reduced, extending their lifetimes, and maintaining mechanical integrity. These results highlight the power of chemistry under moderate conditions to install unnatural groups onto the silk fibroin surface and will enable further exploration into applications of this versatile biomaterial.
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Affiliation(s)
| | - Morgan J. Hawker
- Department of Chemistry and Biochemistry, California State University, Fresno, Fresno, CA 93740
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Lauren Hartle
- Department of Chemistry, Tufts University, Medford, MA 02155
- Present address: Prime Impact Fund, Cambridge, MA 02139
| | - Junqi Wu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | | | | | - Luke M. Davis
- Department of Chemistry, Tufts University, Medford, MA 02155
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
| | - Krishna Kumar
- Department of Chemistry, Tufts University, Medford, MA 02155
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155
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7
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Fluorinated Protein and Peptide Materials for Biomedical Applications. Pharmaceuticals (Basel) 2022; 15:ph15101201. [PMID: 36297312 PMCID: PMC9609677 DOI: 10.3390/ph15101201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Fluorination represents one of the most powerful modern design strategies to impart biomacromolecules with unique functionality, empowering them for widespread application in the biomedical realm. However, the properties of fluorinated protein materials remain unpredictable due to the heavy context-dependency of the surrounding atoms influenced by fluorine’s strong electron-withdrawing tendencies. This review aims to discern patterns and elucidate design principles governing the biochemical synthesis and rational installation of fluorine into protein and peptide sequences for diverse biomedical applications. Several case studies are presented to deconvolute the overgeneralized fluorous stabilization effect and critically examine the duplicitous nature of the resultant enhanced chemical and thermostability as it applies to use as biomimetic therapeutics, drug delivery vehicles, and bioimaging modalities.
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8
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Wolff M, Gast K, Evers A, Kurz M, Pfeiffer-Marek S, Schüler A, Seckler R, Thalhammer A. A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4. Biomolecules 2021; 11:biom11091305. [PMID: 34572518 PMCID: PMC8472270 DOI: 10.3390/biom11091305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022] Open
Abstract
Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.
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Affiliation(s)
- Martin Wolff
- Department of Physical Biochemistry, University of Potsdam, D-14476 Potsdam, Germany; (M.W.); (K.G.); (A.S.); (R.S.)
| | - Klaus Gast
- Department of Physical Biochemistry, University of Potsdam, D-14476 Potsdam, Germany; (M.W.); (K.G.); (A.S.); (R.S.)
| | - Andreas Evers
- Sanofi-Aventis Deutschland GmbH, D-65926 Frankfurt, Germany; (A.E.); (M.K.); (S.P.-M.)
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, D-65926 Frankfurt, Germany; (A.E.); (M.K.); (S.P.-M.)
| | | | - Anja Schüler
- Department of Physical Biochemistry, University of Potsdam, D-14476 Potsdam, Germany; (M.W.); (K.G.); (A.S.); (R.S.)
| | - Robert Seckler
- Department of Physical Biochemistry, University of Potsdam, D-14476 Potsdam, Germany; (M.W.); (K.G.); (A.S.); (R.S.)
| | - Anja Thalhammer
- Department of Physical Biochemistry, University of Potsdam, D-14476 Potsdam, Germany; (M.W.); (K.G.); (A.S.); (R.S.)
- Correspondence:
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9
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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10
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Roy G, Reier J, Garcia A, Martin T, Rice M, Wang J, Prophet M, Christie R, Dall'Acqua W, Ahuja S, Bowen MA, Marelli M. Development of a high yielding expression platform for the introduction of non-natural amino acids in protein sequences. MAbs 2021; 12:1684749. [PMID: 31775561 PMCID: PMC6927762 DOI: 10.1080/19420862.2019.1684749] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ability to genetically encode non-natural amino acids (nnAAs) into proteins offers an expanded tool set for protein engineering. nnAAs containing unique functional moieties have enabled the study of post-translational modifications, protein interactions, and protein folding. In addition, nnAAs have been developed that enable a variety of biorthogonal conjugation chemistries that allow precise and efficient protein conjugations. These are being studied to create the next generation of antibody-drug conjugates with improved efficacy, potency, and stability for the treatment of cancer. However, the efficiency of nnAA incorporation, and the productive yields of cell-based expression systems, have limited the utility and widespread use of this technology. We developed a process to isolate stable cell lines expressing a pyrrolysyl-tRNA synthetase/tRNApyl pair capable of efficient nnAA incorporation. Two different platform cell lines generated by these methods were used to produce IgG-expressing cell lines with normalized antibody titers of 3 g/L using continuous perfusion. We show that the antibodies produced by these platform cells contain the nnAA functionality that enables facile conjugations. Characterization of these highly active and robust platform hosts identified key parameters that affect nnAA incorporation efficiency. These highly efficient host platforms may help overcome the expression challenges that have impeded the developability of this technology for manufacturing proteins with nnAAs and represents an important step in expanding its utility.
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Affiliation(s)
- Gargi Roy
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jason Reier
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Andrew Garcia
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Tom Martin
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Megan Rice
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jihong Wang
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Meagan Prophet
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Ronald Christie
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - William Dall'Acqua
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Sanjeev Ahuja
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
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11
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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: 30] [Impact Index Per Article: 7.5] [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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12
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Jiang L, Kirshenbaum K. A modular approach for organizing dimeric coiled coils on peptoid oligomer scaffolds. Org Biomol Chem 2020; 18:2312-2320. [PMID: 32159574 DOI: 10.1039/d0ob00453g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a general approach to promote the folding of synthetic oligopeptides capable of forming homodimeric coiled coil assemblies. By pre-organizing the peptides on macrocyclic oligomer scaffolds, the stability of the coiled coils is enhanced with an observed increase in the melting temperature of 30 °C to 40 °C. Molecular dynamics simulations substantiate the hypothesis that the enhanced stability is established by constraining motion at the peptide termini and by pre-organizing intramolecular helix-helix contacts. We demonstrate the modularity of this approach by using a family of peptoid scaffolds to promote the folding of a dimeric coiled coil. Importantly, this strategy for templating coiled coils allows preservation of native amino acid sequences. Comparing a macrocyclic peptoid scaffold to its linear counterparts indicates that both types of assemblies are effective for organizing stable coiled coils. These results will guide future designs of coiled coil peptides for biomedical applications and as building blocks for more complex supramolecular assemblies.
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Affiliation(s)
- Linhai Jiang
- Chemistry Department, New York University, New York, NY 10003, USA.
| | - Kent Kirshenbaum
- Chemistry Department, New York University, New York, NY 10003, USA.
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13
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Jia F, Zhang Y, Wang J, Peng J, Zhao P, Zhang L, Yao H, Ni J, Wang K. The effect of halogenation on the antimicrobial activity, antibiofilm activity, cytotoxicity and proteolytic stability of the antimicrobial peptide Jelleine-I. Peptides 2019; 112:56-66. [PMID: 30500360 DOI: 10.1016/j.peptides.2018.11.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022]
Abstract
Antimicrobial peptides (AMPs) are believed to be a promising class of antimicrobial agents against bacteria and fungi. To promote the clinical use of AMPs, their antimicrobial activity and susceptibility to protease degradation should be further improved. The antimicrobial peptide Jelleine-I was originally isolated from the royal jelly of honeybees (Apis mellifera) with a short sequence of PFKLSLHL-NH2 (953.24 Da). Here, a series of halogenated derivatives of the antimicrobial peptide Jelleine-I were designed and synthesized. The results showed that the in vitro antimicrobial activity, antibiofilm activity and in vivo antimicrobial efficacy were enhanced 1-8-fold after halogenation. Additionally, the proteolytic stability of Jelleine-I was improved 10-100-fold by halogenation. Meanwhile, the halogenated derivatives retained negligible hemolytic activity and cytotoxicity. Among these derivatives, the antimicrobial activity and antibiofilm activity of chlorine-Jelleine-I (Cl-J-I), bromine-Jelleine-I (Br-J-I), and iodine-Jelleine-I (I-J-I) were better than those of fluorine-Jelleine-I (F-J-I). The stabilities of Br-J-I and I-J-I against the degradation of enzymes and the serum were better than those of F-J-I and Cl-J-I. In conclusion, this study may offer a useful strategy to enhance antimicrobial efficacy and proteolytic stability by halogenation. The halogenated derivatives Cl-J-I, Br-J-I and I-J-I may be considered as potential antimicrobial agents against microbial infection.
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Affiliation(s)
- Fengjing Jia
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Yi Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Jiayi Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Jinxiu Peng
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Ping Zhao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Lishi Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Haiyan Yao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China
| | - Jingman Ni
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China.
| | - Kairong Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, School of Life Sciences, Lanzhou University, 222 Tian Shui South Road, Lanzhou, 730000, PR China.
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14
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Lee YJ, Schmidt MJ, Tharp JM, Weber A, Koenig AL, Zheng H, Gao J, Waters ML, Summerer D, Liu WR. Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader. Chem Commun (Camb) 2018; 52:12606-12609. [PMID: 27711380 DOI: 10.1039/c6cc05959g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorophenylalanines bearing 2-5 fluorine atoms at the phenyl ring have been genetically encoded by amber codon. Replacement of F59, a phenylalanine residue that is directly involved in interactions with trimethylated K9 of histone H3, in the Mpp8 chromodomain recombinantly with fluorophenylalanines significantly impairs the binding to a K9-trimethylated H3 peptide.
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Affiliation(s)
- Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, TX 7743, USA.
| | - M J Schmidt
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX 7743, USA.
| | - Annemarie Weber
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Amber L Koenig
- Department of Chemistry, Boston College, Boston, MA 02467, USA
| | - Hong Zheng
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jianmin Gao
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Marcey L Waters
- Department of Chemistry, Boston College, Boston, MA 02467, USA
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, 44227 Dortmund, Germany.
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 7743, USA.
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15
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Fang KY, Lieblich SA, Tirrell DA. Incorporation of Non-Canonical Amino Acids into Proteins by Global Reassignment of Sense Codons. Methods Mol Biol 2018; 1798:173-186. [PMID: 29868959 DOI: 10.1007/978-1-4939-7893-9_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Non-canonical amino acids are finding increasing use in basic and applied research. Proteins that evolved naturally for biological function did so by exploiting the chemistries of the canonical amino acids; however, when proteins are repurposed for biomedical and pharmacological applications, they are often subject to conditions different from those characteristic of their original biological environments. Non-canonical amino acids can impart properties that are inaccessible within canonical protein sequence space, and can thereby lead to improved or new functionality. We describe simple methods for global replacement of canonical amino acids by their non-canonical counterparts in recombinant proteins made in high yield in bacterial expression hosts. These methods can be used to engineer both chemical and physical properties of recombinant proteins.
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Affiliation(s)
- Katharine Y Fang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Seth A Lieblich
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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16
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Huhmann S, Stegemann AK, Folmert K, Klemczak D, Moschner J, Kube M, Koksch B. Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion. Beilstein J Org Chem 2017; 13:2869-2882. [PMID: 29564015 PMCID: PMC5753150 DOI: 10.3762/bjoc.13.279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/13/2017] [Indexed: 12/22/2022] Open
Abstract
Rapid digestion by proteases limits the application of peptides as therapeutics. One strategy to increase the proteolytic stability of peptides is the modification with fluorinated amino acids. This study presents a systematic investigation of the effects of fluorinated leucine and isoleucine derivatives on the proteolytic stability of a peptide that was designed to comprise substrate specificities of different proteases. Therefore, leucine, isoleucine, and their side-chain fluorinated variants were site-specifically incorporated at different positions of this peptide resulting in a library of 13 distinct peptides. The stability of these peptides towards proteolysis by α-chymotrypsin, pepsin, proteinase K, and elastase was studied, and this process was followed by an FL-RP-HPLC assay in combination with mass spectrometry. In a few cases, we observed an exceptional increase in proteolytic stability upon introduction of the fluorine substituents. The opposite phenomenon was observed in other cases, and this may be explained by specific interactions of fluorinated residues with the respective enzyme binding sites. Noteworthy is that 5,5,5-trifluoroisoleucine is able to significantly protect peptides from proteolysis by all enzymes included in this study when positioned N-terminal to the cleavage site. These results provide valuable information for the application of fluorinated amino acids in the design of proteolytically stable peptide-based pharmaceuticals.
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Affiliation(s)
- Susanne Huhmann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Anne-Katrin Stegemann
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Kristin Folmert
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Damian Klemczak
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Johann Moschner
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Michelle Kube
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Beate Koksch
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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17
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Baril SA, Koenig AL, Krone MW, Albanese KI, Qixin He C, Lee GY, Houk KN, Waters ML, Brustad EM. Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis. J Am Chem Soc 2017; 139:17253-17256. [PMID: 29111699 PMCID: PMC6040664 DOI: 10.1021/jacs.7b09223] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.
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Affiliation(s)
- Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amber L. Koenig
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mackenzie W. Krone
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cyndi Qixin He
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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18
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19
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Zarandi M, Cai R, Kovacs M, Popovics P, Szalontay L, Cui T, Sha W, Jaszberenyi M, Varga J, Zhang X, Block NL, Rick FG, Halmos G, Schally AV. Synthesis and structure-activity studies on novel analogs of human growth hormone releasing hormone (GHRH) with enhanced inhibitory activities on tumor growth. Peptides 2017; 89:60-70. [PMID: 28130121 DOI: 10.1016/j.peptides.2017.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 12/21/2022]
Abstract
The syntheses and biological evaluations of new GHRH analogs of Miami (MIA) series with greatly increased anticancer activity are described. In the design and synthesis of these analogs, the following previous substitutions were conserved: D-Arg2, Har9, Abu15, and Nle27. Most new analogs had Ala at position 8. Since replacements of both Lys12 and Lys21 with Orn increased resistance against enzymatic degradation, these modifications were kept. The substitutions of Arg at both positions 11 and 20 by His were also conserved. We kept D-Arg28, Har29 -NH2 at the C-terminus or inserted Agm or 12-amino dodecanoic acid amide at position 30. We incorporated pentafluoro-Phe (Fpa5), instead of Cpa, at position 6 and Tyr(Me) at position 10 and ω-amino acids at N-terminus of some analogs. These GHRH analogs were prepared by solid-phase methodology and purified by HPLC. The evaluation of the activity of the analogs on GH release was carried out in vitro on rat pituitaries and in vivo in male rats. Receptor binding affinities were measured in vitro by the competitive binding analysis. The inhibitory activity of the analogs on tumor proliferation in vitro was tested in several human cancer cell lines such as HEC-1A endometrial adenocarcinoma, HCT-15 colorectal adenocarcinoma, and LNCaP prostatic carcinoma. For in vivo tests, various cell lines including PC-3 prostate cancer, HEC-1A endometrial adenocarcinoma, HT diffuse mixed β cell lymphoma, and ACHN renal cell carcinoma cell lines were xenografted into nude mice and treated subcutaneously with GHRH antagonists at doses of 1-5μg/day. Analogs MIA-602, MIA-604, MIA-610, and MIA-640 showed the highest binding affinities, 30, 58, 48, and 73 times higher respectively, than GHRH (1-29) NH2. Treatment of LNCaP and HCT-15 cells with 5μM MIA-602 or MIA-690 decreased proliferation by 40%-80%. In accord with previous tests in various human cancer lines, analog MIA-602 showed high inhibitory activity in vivo on growth of PC-3 prostate cancer, HT-mixed β cell lymphoma, HEC-1A endometrial adenocarcinoma and ACHN renal cell carcinoma. Thus, GHRH analogs of the Miami series powerfully suppress tumor growth, but have only a weak endocrine GH inhibitory activity. The suppression of tumor growth could be induced in part by the downregulation of GHRH receptors levels.
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Affiliation(s)
- Marta Zarandi
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Renzhi Cai
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Magdolna Kovacs
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Petra Popovics
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Luca Szalontay
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Tengjiao Cui
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Wei Sha
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Hematology/Oncology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Sylvester Comprehensive Cancer Center, Miami, FL, United States
| | - Miklos Jaszberenyi
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Jozsef Varga
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States
| | - XianYang Zhang
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Norman L Block
- South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Sylvester Comprehensive Cancer Center, Miami, FL, United States; Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ferenc G Rick
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Urology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, United States
| | - Gabor Halmos
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States
| | - Andrew V Schally
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Hematology/Oncology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Sylvester Comprehensive Cancer Center, Miami, FL, United States.
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20
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Ravichandran KR, Zong AB, Taguchi AT, Nocera DG, Stubbe J, Tommos C. Formal Reduction Potentials of Difluorotyrosine and Trifluorotyrosine Protein Residues: Defining the Thermodynamics of Multistep Radical Transfer. J Am Chem Soc 2017; 139:2994-3004. [PMID: 28171730 DOI: 10.1021/jacs.6b11011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox-active tyrosines (Ys) play essential roles in enzymes involved in primary metabolism including energy transduction and deoxynucleotide production catalyzed by ribonucleotide reductases (RNRs). Thermodynamic characterization of Ys in solution and in proteins remains a challenge due to the high reduction potentials involved and the reactive nature of the radical state. The structurally characterized α3Y model protein has allowed the first determination of formal reduction potentials (E°') for a Y residing within a protein (Berry, B. W.; Martı́nez-Rivera, M. C.; Tommos, C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9739-9743). Using Schultz's technology, a series of fluorotyrosines (FnY, n = 2 or 3) was site-specifically incorporated into α3Y. The global protein properties of the resulting α3(3,5)F2Y, α3(2,3,5)F3Y, α3(2,3)F2Y and α3(2,3,6)F3Y variants are essentially identical to those of α3Y. A protein film square-wave voltammetry approach was developed to successfully obtain reversible voltammograms and E°'s of the very high-potential α3FnY proteins. E°'(pH 5.5; α3FnY(O•/OH)) spans a range of 1040 ± 3 mV to 1200 ± 3 mV versus the normal hydrogen electrode. This is comparable to the potentials of the most oxidizing redox cofactors in nature. The FnY analogues, and the ability to site-specifically incorporate them into any protein of interest, provide new tools for mechanistic studies on redox-active Ys in proteins and on functional and aberrant hole-transfer reactions in metallo-enzymes. The former application is illustrated here by using the determined α3FnY ΔE°'s to model the thermodynamics of radical-transfer reactions in FnY-RNRs and to experimentally test and support the key prediction made.
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Affiliation(s)
| | - Allan B Zong
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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21
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Extending enzyme molecular recognition with an expanded amino acid alphabet. Proc Natl Acad Sci U S A 2017; 114:2610-2615. [PMID: 28196894 DOI: 10.1073/pnas.1616816114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural enzymes are constructed from the 20 proteogenic amino acids, which may then require posttranslational modification or the recruitment of coenzymes or metal ions to achieve catalytic function. Here, we demonstrate that expansion of the alphabet of amino acids can also enable the properties of enzymes to be extended. A chemical mutagenesis strategy allowed a wide range of noncanonical amino acids to be systematically incorporated throughout an active site to alter enzymic substrate specificity. Specifically, 13 different noncanonical side chains were incorporated at 12 different positions within the active site of N-acetylneuraminic acid lyase (NAL), and the resulting chemically modified enzymes were screened for activity with a range of aldehyde substrates. A modified enzyme containing a 2,3-dihydroxypropyl cysteine at position 190 was identified that had significantly increased activity for the aldol reaction of erythrose with pyruvate compared with the wild-type enzyme. Kinetic investigation of a saturation library of the canonical amino acids at the same position showed that this increased activity was not achievable with any of the 20 proteogenic amino acids. Structural and modeling studies revealed that the unique shape and functionality of the noncanonical side chain enabled the active site to be remodeled to enable more efficient stabilization of the transition state of the reaction. The ability to exploit an expanded amino acid alphabet can thus heighten the ambitions of protein engineers wishing to develop enzymes with new catalytic properties.
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22
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Gee CT, Arntson KE, Urick AK, Mishra NK, Hawk LML, Wisniewski AJ, Pomerantz WCK. Protein-observed (19)F-NMR for fragment screening, affinity quantification and druggability assessment. Nat Protoc 2016; 11:1414-27. [PMID: 27414758 DOI: 10.1038/nprot.2016.079] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy can be used to quantify the binding affinity between proteins and low-complexity molecules, termed 'fragments'; this versatile screening approach allows researchers to assess the druggability of new protein targets. Protein-observed (19)F-NMR (PrOF NMR) using (19)F-labeled amino acids generates relatively simple spectra that are able to provide dynamic structural information toward understanding protein folding and function. Changes in these spectra upon the addition of fragment molecules can be observed and quantified. This protocol describes the sequence-selective labeling of three proteins (the first bromodomains of Brd4 and BrdT, and the KIX domain of the CREB-binding protein) using commercially available fluorinated aromatic amino acids and fluorinated precursors as example applications of the method developed by our research group. Fragment-screening approaches are discussed, as well as Kd determination, ligand-efficiency calculations and druggability assessment, i.e., the ability to target these proteins using small-molecule ligands. Experiment times on the order of a few minutes and the simplicity of the NMR spectra obtained make this approach well-suited to the investigation of small- to medium-sized proteins, as well as the screening of multiple proteins in the same experiment.
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Affiliation(s)
- Clifford T Gee
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Keith E Arntson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Neeraj K Mishra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura M L Hawk
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrea J Wisniewski
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
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23
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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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24
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Synthesis of protected enantiopure (R) and (S)-α-trifluoromethylalanine containing dipeptide building blocks ready to use for solid phase peptide synthesis. Amino Acids 2016; 48:1457-68. [PMID: 26920748 DOI: 10.1007/s00726-016-2200-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
Considering the increasing importance of fluorinated peptides, the development of efficient and reliable synthetic methods for the incorporation of unnatural fluorinated amino acids into peptides is a current matter of interest. In this study, we report the convenient Boc/benzyl and Cbz/tert-butyl protection of both enantiomers of the quaternarized amino acid α-trifluoromethylalanine [(R)- and (S)-α-Tfm-Ala]. Because of the deactivation of the nitrogen atom of this synthetic amino acid by the strong electron withdrawing trifluoromethyl group, the peptide coupling on this position is a challenge. In order to provide a robust synthetic methodology for the incorporation of enantiopure (R)- and (S)-α-trifluoromethylalanines into peptides, we report herein the preparation of dipeptides ready to use for solid phase peptide synthesis. The difficult peptide coupling on the nitrogen atom of the α-trifluoromethylalanines was performed in solution phase by means of highly electrophilic amino acid chlorides or mixed anhydrides. The synthetic effectiveness of this fluorinated dipeptide building block strategy is illustrated by the solid phase peptide synthesis (SPPS) of the Ac-Ala-Phe-(R)-α-Tfm-Ala-Ala-NH2 tetrapeptide.
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25
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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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26
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Ohtake K, Yamaguchi A, Mukai T, Kashimura H, Hirano N, Haruki M, Kohashi S, Yamagishi K, Murayama K, Tomabechi Y, Itagaki T, Akasaka R, Kawazoe M, Takemoto C, Shirouzu M, Yokoyama S, Sakamoto K. Protein stabilization utilizing a redefined codon. Sci Rep 2015; 5:9762. [PMID: 25985257 PMCID: PMC4434908 DOI: 10.1038/srep09762] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/18/2015] [Indexed: 12/30/2022] Open
Abstract
Recent advances have fundamentally changed the ways in which synthetic amino acids are incorporated into proteins, enabling their efficient and multiple-site incorporation, in addition to the 20 canonical amino acids. This development provides opportunities for fresh approaches toward addressing fundamental problems in bioengineering. In the present study, we showed that the structural stability of proteins can be enhanced by integrating bulky halogenated amino acids at multiple selected sites. Glutathione S-transferase was thus stabilized significantly (by 5.2 and 5.6 kcal/mol) with 3-chloro- and 3-bromo-l-tyrosines, respectively, incorporated at seven selected sites. X-ray crystallographic analyses revealed that the bulky halogen moieties filled internal spaces within the molecules, and formed non-canonical stabilizing interactions with the neighboring residues. This new mechanism for protein stabilization is quite simple and applicable to a wide range of proteins, as demonstrated by the rapid stabilization of the industrially relevant azoreductase.
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Affiliation(s)
- Kazumasa Ohtake
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Atsushi Yamaguchi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takahito Mukai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroki Kashimura
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Nobutaka Hirano
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Mitsuru Haruki
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Sosuke Kohashi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Kenji Yamagishi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Kazutaka Murayama
- Biomedical Engineering Research Organization, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Yuri Tomabechi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Itagaki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ryogo Akasaka
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Masahito Kawazoe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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27
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More HT, Zhang KS, Srivastava N, Frezzo JA, Montclare JK. Influence of fluorination on protein-engineered coiled-coil fibers. Biomacromolecules 2015; 16:1210-7. [PMID: 25794312 DOI: 10.1021/bm5019062] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We describe the design and characterization of fluorinated coiled-coil proteins able to assemble into robust nano- and microfibers. Fluorination is achieved biosynthetically by residue-specific incorporation of 5,5,5-trifluoroleucine (TFL). The fluorinated proteins C+TFL and Q+TFL are highly α-helical as confirmed via circular dichroism (CD) and more resistant to thermal denaturation compared to their nonfluorinated counterparts, C and Q. The fluorinated proteins demonstrate enhanced fiber assembly at pH 8.0 with higher order structure in contrast to nonfluorinated proteins, which are unable to form fibers under the same conditions. Ionic strength dependent fiber assembly is observed for fluorinated as well as wild-type proteins in which the fluorinated proteins exhibited more stable, thicker fibers. The fluorinated and nonfluorinated proteins reveal metal ion-dependent small molecule recognition and supramolecular assemblies. In the presence of Zn (II), enhanced thermal stability and fiber assembly is observed for the fluorinated proteins and their nonfluorinated counterparts. Whereas Ni (II) promotes aggregation with no fiber assembly, the stabilization of α-helix by Zn (II) results in enhanced binding to curcumin by the fluorinated proteins. Surprisingly, the nonfluorinated proteins exhibit multiple-fold increase in curcumin binding in the presence of Zn (II). In the context of the growing number of protein-based fiber assemblies, these fluorinated coiled-coil proteins introduce a new paradigm in the development of highly stable, robust self-assembling fibers under more physiologically relevant pH conditions that promotes the binding and release of small molecules in response to external cues.
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Affiliation(s)
- Haresh T More
- †Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - Kevin S Zhang
- †Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - Nikita Srivastava
- †Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - Joseph A Frezzo
- †Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - Jin K Montclare
- †Department of Chemical and Biomolecular Engineering, New York University Polytechnic School of Engineering, Brooklyn, New York 11201, United States.,∫Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn, New York 11203, United States.,§Department of Chemistry, New York University, New York, New York 10003, United States
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28
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Synthesis of β-amino-α-trifluoromethyl-α-amino acids exhibiting intramolecular interaction of CF3 with NHβ. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.10.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Tuley A, Wang YS, Fang X, Kurra Y, Rezenom YH, Liu WR. The genetic incorporation of thirteen novel non-canonical amino acids. Chem Commun (Camb) 2014; 50:2673-5. [PMID: 24473369 DOI: 10.1039/c3cc49068h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Thirteen novel non-canonical amino acids were synthesized and tested for suppression of an amber codon using a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl)(CUA) pair. Suppression was observed with varied efficiencies. One non-canonical amino acid in particular contains an azide that can be applied for site-selective protein labeling.
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Affiliation(s)
- Alfred Tuley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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30
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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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31
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Asano A, Yamada T, Doi M. Modulating the structure of phenylalanine-incorporated ascidiacyclamide through fluorination. J Pept Sci 2014; 20:794-802. [DOI: 10.1002/psc.2668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/14/2014] [Accepted: 06/03/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Akiko Asano
- Osaka University of Pharmaceutical Sciences; 4-20-1, Nasahara Takatsuki Osaka 569-1094 Japan
| | - Takeshi Yamada
- Osaka University of Pharmaceutical Sciences; 4-20-1, Nasahara Takatsuki Osaka 569-1094 Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences; 4-20-1, Nasahara Takatsuki Osaka 569-1094 Japan
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32
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An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J Biotechnol 2014; 178:12-22. [DOI: 10.1016/j.jbiotec.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/08/2014] [Accepted: 02/14/2014] [Indexed: 11/19/2022]
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33
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Biswas T, Pawale VS, Choudhury D, Roy RP. Sorting of LPXTG peptides by archetypal sortase A: role of invariant substrate residues in modulating the enzyme dynamics and conformational signature of a productive substrate. Biochemistry 2014; 53:2515-24. [PMID: 24693991 DOI: 10.1021/bi4016023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Transpeptidase sortase catalyzes the covalent anchoring of surface proteins to the cell wall in Gram-positive bacteria. Sortase A (SrtA) of Staphylococcus aureus is a prototype enzyme and considered a bona fide drug target because several substrate proteins are virulence-related and implicated in pathogenesis. Besides, SrtA also works as a versatile tool in protein engineering. Surface proteins destined for cell wall anchoring contain a LPXTG sequence located in their C-terminus which serves as a substrate recognition motif for SrtA. Recent studies have implicated substrate-induced conformational dynamics in SrtA. In the present work, we have explored the roles of invariant Leu and Pro residues of the substrate in modulating the enzyme dynamics with a view to understand the selection process of a catalytically competent substrate. Overall results of molecular dynamics simulations and experiments carried out with noncanonical substrates and site-directed mutagenesis reveal that the kinked conformation due to Pro in LPXTG is obligatory for productive binding but does not per se control the enzyme dynamics. The Leu residue of the substrate appears to play the crucial role of an anchor to the beta6-beta7 loop directing the conformational transition of the enzyme from an "open" to a "closed" state subsequent to which the Pro residue facilitates the consummation of binding through predominant engagement of the loop and catalytic motif residues in hydrophobic interactions. Collectively, our study provides insights about specificity, tolerance, and conformational sorting of substrate by SrtA. These results have important implications in designing newer substrates and inhibitors for this multifaceted enzyme.
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Affiliation(s)
- Tora Biswas
- National Institute of Immunology, New Delhi 110 067, India
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34
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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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35
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Cho J, Sawaki K, Hanashima S, Yamaguchi Y, Shiro M, Saigo K, Ishida Y. Stabilization of β-peptide helices by direct attachment of trifluoromethyl groups to peptide backbones. Chem Commun (Camb) 2014; 50:9855-8. [DOI: 10.1039/c4cc02136c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct attachment of trifluoromethyl groups to peptide backbones was found to be a novel strategy for peptide folding stabilization, where the intramolecular hydrogen-bonding ability of backbone amides is enhanced.
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Affiliation(s)
- Joonil Cho
- RIKEN Center for Emergent Matter Science
- Wako, Japan
| | - Kyohei Sawaki
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Bunkyo-ku, Japan
| | - Shinya Hanashima
- RIKEN Global Research Cluster
- Structural Glycobiology Team
- Wako, Japan
| | - Yoshiki Yamaguchi
- RIKEN Global Research Cluster
- Structural Glycobiology Team
- Wako, Japan
| | | | - Kazuhiko Saigo
- School of Environmental Science and Engineering
- Kochi University of Technology
- Kochi 782-8502, Japan
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36
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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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37
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Hamed E, Xu T, Keten S. Poly(ethylene glycol) Conjugation Stabilizes the Secondary Structure of α-Helices by Reducing Peptide Solvent Accessible Surface Area. Biomacromolecules 2013; 14:4053-60. [DOI: 10.1021/bm401164t] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elham Hamed
- Department of Civil
and Environmental Engineering and Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Ting Xu
- Department of Materials
Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Sinan Keten
- Department of Civil
and Environmental Engineering and Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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38
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Krishnamurthy VM, Kumar K. Fluorination in the design of membrane protein assemblies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1063:227-43. [PMID: 23975781 DOI: 10.1007/978-1-62703-583-5_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Protein design approaches based on the binary patterning of nonpolar and polar amino acids have been successful in generating native-like protein structures of amphiphilic α-helices or idealized amphiphilic β-strands in aqueous solution. Such patterning is not possible in the nonpolar environment of biological membranes, precluding the application of conventional approaches to the design of membrane proteins that assemble into discrete aggregates. This review surveys a promising, new strategy for membrane protein design that exploits the unique properties of fluorocarbons-in particular, their ability to phase separate from both water (due to their hydrophobicity) and hydrocarbons (due to their lipophobicity)-to generate membrane protein assemblies. The ability to design such discrete assemblies should enable the disruption of protein-protein interactions and provide templates for novel biomaterials and therapeutics.
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39
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Lozano MM, Liu Z, Sunnick E, Janshoff A, Kumar K, Boxer SG. Colocalization of the ganglioside G(M1) and cholesterol detected by secondary ion mass spectrometry. J Am Chem Soc 2013; 135:5620-30. [PMID: 23514537 PMCID: PMC3639293 DOI: 10.1021/ja310831m] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The characterization of the lateral organization of components in biological membranes and the evolution of this arrangement in response to external triggers remain a major challenge. The concept of lipid rafts is widely invoked; however, direct evidence of the existence of these ephemeral entities remains elusive. We report here the use of secondary ion mass spectrometry (SIMS) to image the cholesterol-dependent cohesive phase separation of the ganglioside GM1 into nano- and microscale assemblies in a canonical lipid raft composition of lipids. This assembly of domains was interrogated in a model membrane system composed of palmitoyl sphingomyelin (PSM), cholesterol, and an unsaturated lipid (dioleoylphosphatidylcholine, DOPC). Orthogonal isotopic labeling of every lipid bilayer component and monofluorination of GM1 allowed generation of molecule specific images using a NanoSIMS. Simultaneous detection of six different ion species in SIMS, including secondary electrons, was used to generate ion ratio images whose signal intensity values could be correlated to composition through the use of calibration curves from standard samples. Images of this system provide the first direct, molecule specific, visual evidence for the colocalization of cholesterol and GM1 in supported lipid bilayers and further indicate the presence of three compositionally distinct phases: (1) the interdomain region; (2) micrometer-scale domains (d > 3 μm); (3) nanometer-scale domains (d = 100 nm to 1 μm) localized within the micrometer-scale domains and the interdomain region. PSM-rich, nanometer-scale domains prefer to partition within the more ordered, cholesterol-rich/DOPC-poor/GM1-rich micrometer-scale phase, while GM1-rich, nanometer-scale domains prefer to partition within the surrounding, disordered, cholesterol-poor/PSM-rich/DOPC-rich interdomain phase.
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Affiliation(s)
- Mónica M. Lozano
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
| | - Zhao Liu
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155-5813
| | - Eva Sunnick
- Institute of Physical Chemistry, University of Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Andreas Janshoff
- Institute of Physical Chemistry, University of Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Krishna Kumar
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155-5813
- Cancer Center, Tufts Medical Center, Boston, Massachusetts 02110
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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40
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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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41
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Engineering protein filaments with enhanced thermostability for nanomaterials. Biotechnol J 2012; 8:228-36. [DOI: 10.1002/biot.201200009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/07/2012] [Accepted: 08/30/2012] [Indexed: 11/07/2022]
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42
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Clark GA, Baleja JD, Kumar K. Cross-strand interactions of fluorinated amino acids in β-hairpin constructs. J Am Chem Soc 2012; 134:17912-21. [PMID: 23078597 DOI: 10.1021/ja212080f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We describe herein the design, synthesis, and thermodynamic characterization of fluorinated β-hairpin constructs. Introduction of hexafluoroleucine (Hfl) did not perturb β-hairpin formation, as judged by (1)H NMR structures of four peptides determined to <1 Å backbone RMSDs, allowing direct comparison of thermodynamic stabilities of fluorinated peptides to their hydrocarbon counterparts. Judicious fluorination of peptides often results in increased thermal and chemical stability of the resultant folded structures. However, we found that when cross-strand residue partners were varied, the side-chain interaction energies followed the order Leu-Leu > Hfl-Leu > Hfl-Hfl. All peptides were more structured in 90% MeOH than in aqueous buffers. The peptides with Hfl-Leu or Hfl-Hfl cross-strand partners showed increased interaction energies in this solvent compared to those in water, in contrast to the insignificant effect on Leu-Leu. Our results inform the binding and assembly of peptides containing Hfl in the context of β-sheet structures and may be useful in interpreting binding of fluorinated ligands and peptides to biological targets.
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Affiliation(s)
- Ginevra A Clark
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, USA
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43
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Buer BC, Levin BJ, Marsh ENG. Influence of Fluorination on the Thermodynamics of Protein Folding. J Am Chem Soc 2012; 134:13027-34. [DOI: 10.1021/ja303521h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin C. Buer
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
| | - Benjamin J. Levin
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
| | - E. Neil G. Marsh
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
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44
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Buer BC, Marsh ENG. Fluorine: a new element in protein design. Protein Sci 2012; 21:453-62. [PMID: 22274989 PMCID: PMC3375745 DOI: 10.1002/pro.2030] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 01/09/2012] [Indexed: 11/08/2022]
Abstract
Fluorocarbons are quintessentially man-made molecules, fluorine being all but absent from biology. Perfluorinated molecules exhibit novel physicochemical properties that include extreme chemical inertness, thermal stability, and an unusual propensity for phase segregation. The question we and others have sought to answer is to what extent can these properties be engineered into proteins? Here, we review recent studies in which proteins have been designed that incorporate highly fluorinated analogs of hydrophobic amino acids with the aim of creating proteins with novel chemical and biological properties. Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure and biological activity. Most studies have focused on small proteins that can be produced by peptide synthesis as synthesis of large proteins containing specifically fluorinated residues remains challenging. However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn 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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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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Merkel L, Budisa N. Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes. Org Biomol Chem 2012; 10:7241-61. [DOI: 10.1039/c2ob06922a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Frandsen JL, Ghandehari H. Recombinant protein-based polymers for advanced drug delivery. Chem Soc Rev 2012; 41:2696-706. [DOI: 10.1039/c2cs15303c] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Rodriguez-Granillo A, Annavarapu S, Zhang L, Koder RL, Nanda V. Computational design of thermostabilizing D-amino acid substitutions. J Am Chem Soc 2011; 133:18750-9. [PMID: 21978298 PMCID: PMC3443866 DOI: 10.1021/ja205609c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Judicious incorporation of D-amino acids in engineered proteins confers many advantages such as preventing degradation by endogenous proteases and promoting novel structures and functions not accessible to homochiral polypeptides. Glycine to D-alanine substitutions at the carboxy termini can stabilize α-helices by reducing conformational entropy. Beyond alanine, we propose additional side chain effects on the degree of stabilization conferred by D-amino acid substitutions. A detailed, molecular understanding of backbone and side chain interactions is important for developing rational, broadly applicable strategies in using D-amino acids to increase protein thermostability. Insight from structural bioinformatics combined with computational protein design can successfully guide the selection of stabilizing D-amino acid mutations. Substituting a key glycine in the Trp-cage miniprotein with D-Gln dramatically stabilizes the fold without altering the protein backbone. Stabilities of individual substitutions can be understood in terms of the balance of intramolecular forces both at the α-helix C-terminus and throughout the protein.
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Affiliation(s)
- Agustina Rodriguez-Granillo
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ and the Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854
| | - Srinivas Annavarapu
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ and the Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854
| | - Lei Zhang
- Department of Physics, The City College of New York, New York, New York 10031
| | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, New York 10031
| | - Vikas Nanda
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ and the Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854
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