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Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024. [PMID: 39008623 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
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Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical 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
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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2
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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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3
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Guo X, Yan T, Rao J, An Y, Yue X, Miao X, Wang R, Sun W, Cai J, Xie J. Novel Feleucin-K3-Derived Peptides Modified with Sulfono-γ-AA Building Blocks Targeting Pseudomonas aeruginosa and Methicillin-Resistant Staphylococcus aureus Infections. J Med Chem 2023; 66:1254-1272. [PMID: 36350686 DOI: 10.1021/acs.jmedchem.2c01396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The prevalence of multidrug-resistant bacterial infections has led to dramatically increased morbidity and mortality. Antimicrobial peptides (AMPs) have great potential as new therapeutic agents to reverse this dangerous trend. Herein, a series of novel AMP Feleucin-K3 analogues modified with unnatural peptidomimetic sulfono-γ-AA building blocks were designed and synthesized. The structure-activity, structure-toxicity, and structure-stability relationships were investigated to discover the optimal antimicrobial candidates. Among them, K122 exhibited potent and broad-spectrum antimicrobial activity and high selectivity. K122 had a rapid bactericidal effect and a low tendency to induce resistance. Surprisingly, K122 showed excellent effectiveness against bacterial pneumonia. For biofilm and local skin infections, K122 significantly decreased the bacterial load and improved tissue injury at a dose of only 0.25 mg/kg, which was 160 times lower than the concentration deemed to be safe for local dermal applications. In summary, K122 is an outstanding candidate for the treatment of multidrug-resistant bacteria and biofilm infections.
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Affiliation(s)
- Xiaomin Guo
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Tiantian Yan
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Jing Rao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Yingying An
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Xin Yue
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Xiaokang Miao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Rui Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100050, China
| | - Wangsheng Sun
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida33620, United States
| | - Junqiu Xie
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou730000, China
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4
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Sloand JN, Miller MA, Medina SH. Fluorinated peptide biomaterials. Pept Sci (Hoboken) 2021; 113:e24184. [PMID: 34541446 PMCID: PMC8448251 DOI: 10.1002/pep2.24184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano-, micro-, and macrosupramolecular states that potentiate high-ordered organization into material scaffolds. These fluorine-tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous-directed hierarchical structures as material platforms in diverse biomedical applications.
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Affiliation(s)
- Janna N Sloand
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Michael A Miller
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Scott H Medina
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
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5
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.,School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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6
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Awad LF, Ayoup MS. Fluorinated phenylalanines: synthesis and pharmaceutical applications. Beilstein J Org Chem 2020; 16:1022-1050. [PMID: 32509033 PMCID: PMC7237815 DOI: 10.3762/bjoc.16.91] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
Recent advances in the chemistry of peptides containing fluorinated phenylalanines (Phe) represents a hot topic in drug research over the last few decades. ᴅ- or ʟ-fluorinated phenylalanines have had considerable industrial and pharmaceutical applications and they have been expanded also to play an important role as potential enzyme inhibitors as well as therapeutic agents and topography imaging of tumor ecosystems using PET. Incorporation of fluorinated aromatic amino acids into proteins increases their catabolic stability especially in therapeutic proteins and peptide-based vaccines. This review seeks to summarize the different synthetic approaches in the literature to prepare ᴅ- or ʟ-fluorinated phenylalanines and their pharmaceutical applications with a focus on published synthetic methods that introduce fluorine into the phenyl, the β-carbon or the α-carbon of ᴅ-or ʟ-phenylalanines.
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Affiliation(s)
- Laila Fathy Awad
- Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Alexandria, 21321, Egypt
| | - Mohammed Salah Ayoup
- Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Alexandria, 21321, Egypt
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7
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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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8
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Nandy T, Mondal S, Singh PC. Solvent organization around the noncanonical part of tyrosine modulates its fluorescence properties. Phys Chem Chem Phys 2019; 21:6042-6050. [DOI: 10.1039/c8cp06410e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Solvent interactions with the fluorocarbon group of noncanonical amino acids are the cause of their diverse fluorescence behaviors, which implies their usefulness as solvent-sensitive environmental sensors in many biological processes.
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Affiliation(s)
- Tonima Nandy
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Saptarsi Mondal
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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9
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Huhmann S, Koksch B. Fine-Tuning the Proteolytic Stability of Peptides with Fluorinated Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800803] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Susanne Huhmann
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry; Freie Universität Berlin; Takustr. 3 14169 Berlin Germany
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10
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Mondal S, Biswas B, Nandy T, Singh PC. Understanding the Role of Hydrophobic Terminal in the Hydrogen Bond Network of the Aqueous Mixture of 2,2,2-Trifluoroethanol: IR, Molecular Dynamics, Quantum Chemical as Well as Atoms in Molecules Studies. J Phys Chem B 2018; 122:6616-6626. [DOI: 10.1021/acs.jpcb.8b04365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biswajit Biswas
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Tonima Nandy
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
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11
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12
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Mondal S, Chaterjee S, Halder R, Jana B, Singh PC. Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules. J Phys Chem B 2017; 121:7681-7688. [PMID: 28737391 DOI: 10.1021/acs.jpcb.7b03420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Soumit Chaterjee
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Ritaban Halder
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Biman Jana
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
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13
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Kohlmann J, Braun T, Laubenstein R, Herrmann R. Suzuki-Miyaura Cross-Coupling Reactions of Highly Fluorinated Arylboronic Esters: Catalytic Studies and Stoichiometric Model Reactions on the Transmetallation Step. Chemistry 2017; 23:12218-12232. [DOI: 10.1002/chem.201700549] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Johannes Kohlmann
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Thomas Braun
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Reik Laubenstein
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Roy Herrmann
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
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14
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Tressler CM, Zondlo NJ. Perfluoro-tert-butyl Homoserine Is a Helix-Promoting, Highly Fluorinated, NMR-Sensitive Aliphatic Amino Acid: Detection of the Estrogen Receptor·Coactivator Protein-Protein Interaction by 19F NMR. Biochemistry 2017; 56:1062-1074. [PMID: 28165218 PMCID: PMC5894335 DOI: 10.1021/acs.biochem.6b01020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Highly fluorinated amino acids can stabilize proteins and complexes with proteins, via enhanced hydrophobicity, and provide novel methods for identification of specific molecular events in complex solutions, via selective detection by 19F NMR and the absence of native 19F signals in biological contexts. However, the potential applications of 19F NMR in probing biological processes are limited both by the strong propensities of most highly fluorinated amino acids for the extended conformation and by the relatively modest sensitivity of NMR spectroscopy, which typically constrains measurements to mid-micromolar concentrations. Herein, we demonstrate that perfluoro-tert-butyl homoserine exhibits a propensity for compact conformations, including α-helix and polyproline helix (PPII), that is similar to that of methionine. Perfluoro-tert-butyl homoserine has nine equivalent fluorines that do not couple to any other nuclei, resulting in a sharp singlet that can be sensitively detected rapidly at low micromolar concentrations. Perfluoro-tert-butyl homoserine was incorporated at sites of leucine residues within the α-helical LXXLL short linear motif of estrogen receptor (ER) coactivator peptides. A peptide containing perfluoro-tert-butyl homoserine at position i + 3 of the ER coactivator LXXLL motif exhibited a Kd of 2.2 μM for the estradiol-bound estrogen receptor, similar to that of the native ligand. 19F NMR spectroscopy demonstrated the sensitive detection (5 μM concentration, 128 scans) of binding of the peptide to the ER and of inhibition of protein-protein interaction by the native ligand or by the ER antagonist tamoxifen. These results suggest diverse potential applications of perfluoro-tert-butyl homoserine in probing protein function and protein-protein interfaces in complex solutions.
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Affiliation(s)
- Caitlin M. Tressler
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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15
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Jeong WJ, Choi SH, Jin KS, Lim YB. Tuning Oligovalent Biomacromolecular Interfaces Using Double-Layered α-Helical Coiled-Coil Nanoassemblies from Lariat-Type Building Blocks. ACS Macro Lett 2016; 5:1406-1410. [PMID: 35651205 DOI: 10.1021/acsmacrolett.6b00746] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The target affinity and selectivity of many biomacromolecules depend on the three-dimensional (3D) distribution of multiple ligands on their surfaces. Here, we devised a self-assembly strategy to control the target-tailored 3D distribution of multiple α-helical ligands on a coiled-coil core scaffold using novel lariat-type supramolecular building blocks. Depending on the coiled-coil composition and ligand grafting sites in the lariat building blocks, the structural and functional features of the self-assembled peptide nanostructures (SPNs) could be variably fine-tuned. Using oligovalent protein-RNA (Rev-RRE) interactions as a model system, we demonstrate that longer grafting reinforces the helicity of the peptide ligands, whereas shorter grafting strengthens the target binding affinity of the SPNs in both monovalent and oligovalent interactions. This supramolecular approach should be useful in developing precisely controllable multivalent ligands for biomacromolecular interactions.
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Affiliation(s)
- Woo-jin Jeong
- Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Se-Hwan Choi
- Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Kyeong Sik Jin
- Pohang
Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yong-beom Lim
- Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
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16
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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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17
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Wang PSP, Schepartz A. β-Peptide bundles: Design. Build. Analyze. Biosynthesize. Chem Commun (Camb) 2016; 52:7420-32. [PMID: 27146019 DOI: 10.1039/c6cc01546h] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptides containing β-amino acids are unique non-natural polymers known to assemble into protein-like tertiary and quaternary structures. When composed solely of β-amino acids, the structures formed, defined assemblies of 14-helices called β-peptide bundles, fold cooperatively in water solvent into unique and discrete quaternary assemblies that are highly thermostable, bind complex substrates and metal ion cofactors, and, in certain cases, catalyze chemical reactions. In this Perspective, we recount the design and elaboration of β-peptide bundles and provide an outlook on recent, unexpected discoveries that could influence research on β-peptides and β-peptide bundles (and β-amino acid-containing proteins) for decades to come.
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Affiliation(s)
- Pam S P Wang
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06511, USA.
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18
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Ebrahimi KH, Hagedoorn PL, Hagen WR. Self-assembly is prerequisite for catalysis of Fe(II) oxidation by catalytically active subunits of ferritin. J Biol Chem 2015; 290:26801-10. [PMID: 26370076 PMCID: PMC4646333 DOI: 10.1074/jbc.m115.678375] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Indexed: 12/16/2022] Open
Abstract
Fe(III) storage by ferritin is an essential process of the iron homeostasis machinery. It begins by translocation of Fe(II) from outside the hollow spherical shape structure of the protein, which is formed as the result of self-assembly of 24 subunits, to a di-iron binding site, the ferroxidase center, buried in the middle of each active subunit. The pathway of Fe(II) to the ferroxidase center has remained elusive, and the importance of self-assembly for the functioning of the ferroxidase center has not been investigated. Here we report spectroscopic and metal ion binding studies with a mutant of ferritin from Pyrococcus furiosus (PfFtn) in which self-assembly was abolished by a single amino acid substitution. We show that in this mutant metal ion binding to the ferroxidase center and Fe(II) oxidation at this site was obliterated. However, metal ion binding to a conserved third site (site C), which is located in the inner surface of each subunit in the vicinity of the ferroxidase center and is believed to be the path for Fe(II) to the ferroxidase center, was not disrupted. These results are the basis of a new model for Fe(II) translocation to the ferroxidase center: self-assembly creates channels that guide the Fe(II) ions toward the ferroxidase center directly through the protein shell and not via the internal cavity and site C. The results may be of significance for understanding the molecular basis of ferritin-related disorders such as neuroferritinopathy in which the 24-meric structure with 432 symmetry is distorted.
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Affiliation(s)
| | - Peter-Leon Hagedoorn
- From the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Wilfred R Hagen
- From the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
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19
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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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20
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Marcsisin SR, Liptak C, Marineau J, Bradner JE, Engen JR. Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe. Anal Chem 2015; 87:6349-56. [PMID: 26023704 PMCID: PMC4470753 DOI: 10.1021/acs.analchem.5b01220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analysis of complex mixtures of proteins by hydrogen exchange (HX) mass spectrometry (MS) is limited by one's ability to resolve the protein(s) of interest from the proteins that are not of interest. One strategy for overcoming this problem is to tag the target protein(s) to allow for rapid removal from the mixture for subsequent analysis. Here we illustrate a new solution involving fluorous conjugation of a retrievable probe. The appended fluorous tag allows for facile immobilization on a fluorous surface. When a target protein is passed over the immobilized probe molecule, it can be efficiently captured and then exposed to a flowing stream of deuterated buffer for hydrogen exchange. The utility of this method is illustrated for a model system of the Elongin BC protein complex bound to a peptide from HIV Vif. Efficient capture is demonstrated, and deuteration when immobilized was identical to deuteration in conventional solution-phase hydrogen exchange MS. Protein captured from a crude bacterial cell lysate could also be deuterated without the need for separate purification steps before HX MS. The advantages and disadvantages of the method are discussed in light of miniaturization and automation.
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Affiliation(s)
- Sean R. Marcsisin
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Cary Liptak
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Jason Marineau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
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21
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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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22
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Budisa N, Kubyshkin V, Schulze-Makuch D. Fluorine-rich planetary environments as possible habitats for life. Life (Basel) 2014; 4:374-85. [PMID: 25370378 PMCID: PMC4206852 DOI: 10.3390/life4030374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 11/16/2022] Open
Abstract
In polar aprotic organic solvents, fluorine might be an element of choice for life that uses selected fluorinated building blocks as monomers of choice for self-assembling of its catalytic polymers. Organofluorine compounds are extremely rare in the chemistry of life as we know it. Biomolecules, when fluorinated such as peptides or proteins, exhibit a "fluorous effect", i.e., they are fluorophilic (neither hydrophilic nor lipophilic). Such polymers, capable of creating self-sorting assemblies, resist denaturation by organic solvents by exclusion of fluorocarbon side chains from the organic phase. Fluorous cores consist of a compact interior, which is shielded from the surrounding solvent. Thus, we can anticipate that fluorine-containing "teflon"-like or "non-sticking" building blocks might be monomers of choice for the synthesis of organized polymeric structures in fluorine-rich planetary environments. Although no fluorine-rich planetary environment is known, theoretical considerations might help us to define chemistries that might support life in such environments. For example, one scenario is that all molecular oxygen may be used up by oxidation reactions on a planetary surface and fluorine gas could be released from F-rich magma later in the history of a planetary body to result in a fluorine-rich planetary environment.
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Affiliation(s)
- Nediljko Budisa
- Department of Chemistry, Technical University of Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Vladimir Kubyshkin
- Department of Chemistry, Technical University of Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Dirk Schulze-Makuch
- School of the Environment, Washington State University, Webster Hall 1148, Pullman, WA 99164, USA.
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23
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Wood SJ, Park YA, Kanneganti NP, Mukkisa HR, Crisman LL, Davis SE, Vandenbosch JL, Scaglione JB, Heyl DL. Modified Cysteine-Deleted Tachyplesin (CDT) Analogs as Linear Antimicrobial Peptides: Influence of Chain Length, Positive Charge, and Hydrophobicity on Antimicrobial and Hemolytic Activity. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9419-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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24
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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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25
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Tressler C, Zondlo NJ. (2S,4R)- and (2S,4S)-perfluoro-tert-butyl 4-hydroxyproline: two conformationally distinct proline amino acids for sensitive application in 19F NMR. J Org Chem 2014; 79:5880-6. [PMID: 24870929 PMCID: PMC4076032 DOI: 10.1021/jo5008674] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Indexed: 01/19/2023]
Abstract
(2S,4R)- and (2S,4S)-perfluoro-tert-butyl 4-hydroxyproline were synthesized (as Fmoc-, Boc-, and free amino acids) in 2-5 steps. The key step of each synthesis was a Mitsunobu reaction with perfluoro-tert-butanol, which incorporated a perfluoro-tert-butyl group, with nine chemically equivalent fluorines. Both amino acids were incorporated in model α-helical and polyproline helix peptides. Each amino acid exhibited distinct conformational preferences, with (2S,4R)-perfluoro-tert-butyl 4-hydroxyproline promoting polyproline helix. Peptides containing these amino acids were sensitively detected by (19)F NMR, suggesting their use in probes and medicinal chemistry.
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Affiliation(s)
- Caitlin
M. Tressler
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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26
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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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27
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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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28
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Gerling UIM, Salwiczek M, Cadicamo CD, Erdbrink H, Czekelius C, Grage SL, Wadhwani P, Ulrich AS, Behrends M, Haufe G, Koksch B. Fluorinated amino acids in amyloid formation: a symphony of size, hydrophobicity and α-helix propensity. Chem Sci 2014. [DOI: 10.1039/c3sc52932k] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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29
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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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30
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Pace CJ, Gao J. Exploring and exploiting polar-π interactions with fluorinated aromatic amino acids. Acc Chem Res 2013; 46:907-15. [PMID: 23095018 DOI: 10.1021/ar300086n] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorination has become an increasingly attractive strategy in protein engineering for both basic research and biomedical applications. Thus researchers would like to understand the consequences of fluorination to the structure, stability, and function of target proteins. Although a substantial amount of work has focused on understanding the properties of fluorinated aliphatic amino acids, much less is known about fluorinated aromatic residues. In addition, polar-π interactions, often referred to as aromatic interactions, may play a significant role in protein folding and protein-protein interactions. Fluorination of aromatic residues presents an ideal strategy for probing polar-π interactions in proteins. This Account summarizes the recent studies of the incorporation of fluorinated aromatic amino acids into proteins. Herein we discuss the effects of fluorinating aromatic residues and rationalize them in the context of polar-π interactions. The results strongly support the proposal that polar-π interactions are energetically significant to protein folding and function. For example, an edge-face interaction of a pair of phenylalanines contributes as much as -1 kcal/mol to protein stability, while cation-π interactions can be much stronger. Furthermore, this new knowledge provides guidelines for protein engineering with fluorination. Importantly, incorporating perfluorinated aromatic residues into proteins enables novel mechanisms of molecular recognition that do not exist in native proteins, such as arene-perfluoroarene stacking. Such novel mechanisms can be used for programming protein folding specificity and engineering peptide-based materials.
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Affiliation(s)
- Christopher J. Pace
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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31
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Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle. Chem Sci 2013. [DOI: 10.1039/c2sc21117c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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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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33
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Buer BC, Meagher JL, Stuckey JA, Marsh ENG. Comparison of the structures and stabilities of coiled-coil proteins containing hexafluoroleucine and t-butylalanine provides insight into the stabilizing effects of highly fluorinated amino acid side-chains. Protein Sci 2012; 21:1705-15. [PMID: 22930450 PMCID: PMC3527707 DOI: 10.1002/pro.2150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/08/2022]
Abstract
Highly fluorinated analogs of hydrophobic amino acids are well known to increase the stability of proteins toward thermal unfolding and chemical denaturation, but there is very little data on the structural consequences of fluorination. We have determined the structures and folding energies of three variants of a de novo designed 4-helix bundle protein whose hydrophobic cores contain either hexafluoroleucine (hFLeu) or t-butylalanine (tBAla). Although the buried hydrophobic surface area is the same for all three proteins, the incorporation of tBAla causes a rearrangement of the core packing, resulting in the formation of a destabilizing hydrophobic cavity at the center of the protein. In contrast, incorporation of hFLeu, causes no changes in core packing with respect to the structure of the nonfluorinated parent protein which contains only leucine in the core. These results support the idea that fluorinated residues are especially effective at stabilizing proteins because they closely mimic the shape of the natural residues they replace while increasing buried hydrophobic surface area.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - Jennifer L Meagher
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
| | - Jeanne A Stuckey
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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34
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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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35
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Yuvienco C, More HT, Haghpanah JS, Tu RS, Montclare JK. Modulating Supramolecular Assemblies and Mechanical Properties of Engineered Protein Materials by Fluorinated Amino Acids. Biomacromolecules 2012; 13:2273-8. [DOI: 10.1021/bm3005116] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Carlo Yuvienco
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
| | - Haresh T. More
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
| | - Jennifer S. Haghpanah
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
| | - Raymond S. Tu
- Department of Chemical
Engineering, City College of New York, New York, New York 10031, United States
| | - Jin Kim Montclare
- Department of Chemical
and Biological Sciences, Polytechnic Institute of NYU, Brooklyn, New York 11201, United States
- Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn,
New York 11203, United States
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36
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Lim DS, Lin JH, Welch JT. The Synthesis and Characterization of a Pentafluorosulfanylated Peptide. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200327] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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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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38
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Buer BC, Meagher JL, Stuckey JA, Marsh ENG. Structural basis for the enhanced stability of highly fluorinated proteins. Proc Natl Acad Sci U S A 2012; 109:4810-5. [PMID: 22411812 PMCID: PMC3324029 DOI: 10.1073/pnas.1120112109] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Noncanonical amino acids have proved extremely useful for modifying the properties of proteins. Among them, extensively fluorinated (fluorous) amino acids seem particularly effective in increasing protein stability; however, in the absence of structural data, the basis of this stabilizing effect remains poorly understood. To address this problem, we solved X-ray structures for three small proteins with hydrophobic cores that are packed with either fluorocarbon or hydrocarbon side chains and compared their stabilities. Although larger, the fluorinated residues are accommodated within the protein with minimal structural perturbation, because they closely match the shape of the hydrocarbon side chains that they replace. Thus, stability increases seem to be better explained by increases in buried hydrophobic surface area that accompany fluorination than by specific fluorous interactions between fluorinated side chains. This finding is illustrated by the design of a highly fluorinated protein that, by compensating for the larger volume and surface area of the fluorinated side chains, exhibits similar stability to its nonfluorinated counterpart. These structure-based observations should inform efforts to rationally modulate protein function using noncanonical amino acids.
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Affiliation(s)
| | | | - Jeanne A. Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; and
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - E. Neil G. Marsh
- Department of Chemistry and
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
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39
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40
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Wang G. Post-translational Modifications of Natural Antimicrobial Peptides and Strategies for Peptide Engineering. ACTA ACUST UNITED AC 2012; 1:72-79. [PMID: 24511461 DOI: 10.2174/2211550111201010072] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Natural antimicrobial peptides (AMPs) are gene-coded defense molecules discovered in all the three life domains: Eubacteria, Archaea, and Eukarya. The latter covers protists, fungi, plants, and animals. It is now recognized that amino acid composition, peptide sequence, and post-translational modifications determine to a large extent the structure and function of AMPs. This article systematically describes post-translational modifications of natural AMPs annotated in the antimicrobial peptide database (http://aps.unmc.edu/AP). Currently, 1147 out of 1755 AMPs in the database are modified and classified into more than 17 types. Through chemical modifications, the peptides fold into a variety of structural scaffolds that target bacterial surfaces or molecules within cells. Chemical modifications also confer desired functions to a particular peptide. Meanwhile, these modifications modulate other peptide properties such as stability. Elucidation of the relationship between AMP property and chemical modification inspires peptide engineering. Depending on the objective of our design, peptides may be modified in various ways so that the desired features can be enhanced whereas unwanted properties can be minimized. Therefore, peptide design plays an essential role in developing natural AMPs into a new generation of therapeutic molecules.
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Affiliation(s)
- Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA,
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41
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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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42
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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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43
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Nomura T, Kamada R, Ito I, Sakamoto K, Chuman Y, Ishimori K, Shimohigashi Y, Sakaguchi K. Probing phenylalanine environments in oligomeric structures with pentafluorophenylalanine and cyclohexylalanine. Biopolymers 2011; 95:410-9. [PMID: 21280026 DOI: 10.1002/bip.21594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Stabilization of protein structures and protein-protein interactions are critical in the engineering of industrially useful enzymes and in the design of pharmaceutically valuable ligands. Hydrophobic interactions involving phenylalanine residues play crucial roles in protein stability and protein-protein/peptide interactions. To establish an effective method to explore the hydrophobic environments of phenylalanine residues, we present a strategy that uses pentafluorophenylalanine (F5Phe) and cyclohexylalanine (Cha). In this study, substitution of F5Phe or Cha for three Phe residues at positions 328, 338, and 341 in the tetramerization domain of the tumor suppressor protein p53 was performed. These residues are located at the interfaces of p53-p53 interactions and are important in the stabilization of the tetrameric structure. The stability of the p53 tetrameric structure did not change significantly when F5Phe-containing peptides at positions Phe328 or Phe338 were used. In contrast, the substitution of Cha for Phe341 in the hydrophobic core enhanced the stability of the tetrameric structure with a T(m) value of 100 degrees C. Phe328 and Phe338 interact with each other through pi-interactions, whereas Phe341 is buried in the surrounding alkyl side-chains of the hydrophobic core of the p53 tetramerization domain. Furthermore, high pressure-assisted denaturation analysis indicated improvement in the occupancy of the hydrophobic core. Considerable stabilization of the p53 tetramer was achieved by filling the identified cavity in the hydrophobic core of the p53 tetramer. The results indicate the status of the Phe residues, indicating that the "pair substitution" of Cha and F5Phe is highly suitable for probing the environments of Phe residues.
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Affiliation(s)
- Takao Nomura
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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44
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Cametti M, Crousse B, Metrangolo P, Milani R, Resnati G. The fluorous effect in biomolecular applications. Chem Soc Rev 2011; 41:31-42. [PMID: 21691620 DOI: 10.1039/c1cs15084g] [Citation(s) in RCA: 319] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
From being a niche area only a few decades ago, fluorous chemistry has gained momentum and is, nowadays, a fervent area of research. It has brought forth, in fact, numerous applicative innovations that stretch among different fields: from catalysis to separation science, from supramolecular to materials and analytical chemistry. Recently, the unique features of perfluorinated compounds have reached the attention of the biochemists' audience. This tutorial review introduces the basic concepts of fluorous chemistry and illustrates its main biomolecular applications. Special attention has been given to fluorous microarrays and their combination with Mass-Spectroscopy (MS) techniques, to protein properties modification by the introduction of local fluorous domains, and to the most recent applications of (19)F-Magnetic Resonance Imaging ((19)F-MRI).
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Affiliation(s)
- Massimo Cametti
- NFMLab-DCMIC Giulio Natta, Politecnico di Milano, via Mancinelli 7, I-20131 Milan, Italy
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45
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Van Deventer JA, Fisk JD, Tirrell DA. Homoisoleucine: a translationally active leucine surrogate of expanded hydrophobic surface area. Chembiochem 2011; 12:700-2. [PMID: 21404412 PMCID: PMC3149977 DOI: 10.1002/cbic.201000731] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Indexed: 11/07/2022]
Affiliation(s)
- James A. Van Deventer
- Division of Chemistry and Chemical Engineering, Joseph J. Jacobs Institute for Molecular Engineering for Medicine, California Institute of Technology, Pasadena, CA 91125 (USA)
| | - John D. Fisk
- Department of Chemical and Biological Engineering and Department of Chemistry, Colorado State University, Fort Collins, CO 80523
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, Joseph J. Jacobs Institute for Molecular Engineering for Medicine, California Institute of Technology, Pasadena, CA 91125 (USA)
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46
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Senguen FT, Doran TM, Anderson EA, Nilsson BL. Clarifying the influence of core amino acid hydrophobicity, secondary structure propensity, and molecular volume on amyloid-β 16–22 self-assembly. ACTA ACUST UNITED AC 2011; 7:497-510. [DOI: 10.1039/c0mb00210k] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Senguen FT, Lee NR, Gu X, Ryan DM, Doran TM, Anderson EA, Nilsson BL. Probing aromatic, hydrophobic, and steric effects on the self-assembly of an amyloid-β fragment peptide. ACTA ACUST UNITED AC 2011; 7:486-96. [DOI: 10.1039/c0mb00080a] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Top A, Kiick KL. Multivalent protein polymers with controlled chemical and physical properties. Adv Drug Deliv Rev 2010; 62:1530-40. [PMID: 20562016 PMCID: PMC3025749 DOI: 10.1016/j.addr.2010.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 05/04/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
Abstract
In this review, we describe our work on the design, characterization, and modification of a series of alanine-rich helical polypeptides with novel functions. Glycosylation of the polypeptides has permitted investigation of polymer architecture effects on multivalent interactions. One of the members of this polypeptide family exhibits polymorphological behavior that is easily manipulated via simple changes in solution pH and temperature. Polypeptide-based fibrils formed at acidic pH and high temperature were shown to direct the one-dimensional organization of gold nanoparticles via electrostatic interactions. As a precursor to fibrils, aggregates likely comprising alanine-rich cores form at low temperatures and acidic pH and reversibly dissociate into monomers upon deprotonation. PEGylation of these polypeptides does not alter the self-association or conformational behavior of the polypeptide, suggesting potential applications in the development of assembled delivery vehicles, as modification of the polypeptides should be a useful strategy for controlling assembly.
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Affiliation(s)
- Ayben Top
- Department of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark, Delaware 19716
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark, Delaware 19716
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49
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Kwon OH, Yoo TH, Othon CM, Van Deventer JA, Tirrell DA, Zewail AH. Hydration dynamics at fluorinated protein surfaces. Proc Natl Acad Sci U S A 2010; 107:17101-6. [PMID: 20855583 PMCID: PMC2951393 DOI: 10.1073/pnas.1011569107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface.
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Affiliation(s)
- Oh-Hoon Kwon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - Tae Hyeon Yoo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Christina M. Othon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - James A. Van Deventer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Ahmed H. Zewail
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
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50
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Wilson CJ, Wilson DA, Feiring AE, Percec V. Disassembly via an environmentally friendly and efficient fluorous phase constructed with dendritic architectures. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/pola.24046] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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