1
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Dalal A, Bodak S, Babu SA. Picolinamide-assisted ortho-C-H functionalization of pyrenylglycine derivatives using aryl iodides. Org Biomol Chem 2024; 22:1279-1298. [PMID: 38258893 DOI: 10.1039/d3ob01731a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Chemical transformations involving the pyrenylglycine motif (an unnatural amino acid) and practical methods toward it are seldom known. This work aimed at developing a method for synthesizing novel pyrenylglycine (pyrene-based glycine) unnatural amino acid derivatives. To realize this, initially, a new pyrenylglycine substrate possessing the picolinamide moiety was assembled via the Ugi multicomponent reaction. The picolinamide moiety linked to amine substrates is a well-known bidentate directing group for accomplishing the site-selective γ-C-H functionalization of amines. Subsequently, it was aimed at using a Pd(II)-catalyzed bidentate directing group-aided γ-C-H arylation strategy for generating a wide range of unprecedented examples of C(2)-H arylated pyrenylglycines. Accordingly, pyrenylglycine possessing the picolinamide moiety was subjected to Pd(II)-catalyzed C(2)-H arylation in the non-K-region to afford a library of C(2)-arylated pyrenylglycines (π-extended pyrenes). Additionally, pyrenylglycine-based small peptides were assembled using C(2)-arylated pyrenylglycines. The X-ray structure of a representative compound was obtained, which corroborated the structure of pyrenylglycine and the regioselectivity of C(2)-H arylation of the pyrene in the non-K-region.
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Affiliation(s)
- Arup Dalal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Subhankar Bodak
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
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2
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Kaur R, Banga S, Babu SA. Construction of carbazole-based unnatural amino acid scaffolds via Pd(II)-catalyzed C(sp 3)-H functionalization. Org Biomol Chem 2022; 20:4391-4414. [PMID: 35583129 DOI: 10.1039/d2ob00658h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the synthesis of carbazole-based unnatural α-amino acid and non-α-amino acid derivatives via a Pd(II)-catalyzed bidentate directing group 8-aminoquinoline-aided β-C(sp3)-H activation/functionalization method. Various N-phthaloyl, DL-, L- and D-carboxamides derived from their corresponding α-amino acids, non-α-amino acids and aliphatic carboxamides were subjected to the β-C(sp3)-H functionalization with 3-iodocarbazoles in the presence of a Pd(II) catalyst to afford the corresponding carbazole moiety installed unnatural amino acid derivatives and aliphatic carboxamides. Carbazole motif-containing racemic (DL) and enantiopure (L and D) amino acid derivatives including phenylalanine, norvaline, leucine, norleucine and 2-aminooctanoic acid with anti-stereochemistry and various non-α-amino acid derivatives including GABA have been synthesized. Removal of the 8-aminoquinoline directing group, deprotection of the phthalimide moiety and the preparation of carbazole amino acid derivatives containing free amino- and carboxylate groups are shown. The carbazole motif is prevalent in alkaloids and biologically active molecules and functional materials. Thus, this work on the synthesis of carbazole-based unnatural amino acid derivatives would enrich the libraries of unnatural amino acid derivatives and carbazoles.
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Affiliation(s)
- Ramandeep Kaur
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Shefali Banga
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
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3
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Zeynaloo E, Zahran EM, Yang YP, Dikici E, Head T, Bachas LG, Daunert S. Reagentless electrochemical biosensors through incorporation of unnatural amino acids on the protein structure. Biosens Bioelectron 2022; 200:113861. [PMID: 34986438 PMCID: PMC9404255 DOI: 10.1016/j.bios.2021.113861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/19/2021] [Accepted: 12/01/2021] [Indexed: 11/19/2022]
Abstract
Typical protein biosensors employ chemical or genetic labeling of the protein, thus introducing an extraneous molecule to the wild-type parent protein, often changing the overall structure and properties of the protein. While these labeling methods have proven successful in many cases, they also have a series of disadvantages associated with their preparation and function. An alternative route for labeling proteins is the incorporation of unnatural amino acid (UAA) analogues, capable of acting as a label, into the structure of a protein. Such an approach, while changing the local microenvironment, poses less of a burden on the overall structure of the protein. L-DOPA is an analog of phenylalanine and contains a catechol moiety that participates in a quasi-reversible, two-electron redox process, thus making it suitable as an electrochemical label/reporter. The periplasmic glucose/galactose binding protein (GBP) was chosen to demonstrate this detection principle. Upon glucose binding, GBP undergoes a significant conformational change that is manifested as a change in the electrochemistry of L-DOPA. The electroactive GBP was immobilized onto gold nanoparticle-modified, polymerized caffeic acid, screen-printed carbon electrodes (GBP-LDOPA/AuNP/PCA/SPCE) for the purpose of direct measurement of glucose levels and serves as a proof-of-concept of the use of electrochemically-active unnatural amino acids as the label. The resulting reagentless GBP biosensors exhibited a highly selective and sensitive binding affinity for glucose in the micromolar range, laying the foundation for a new biosensing methodology based on global incorporation of an electroactive amino acid into the protein's primary sequence for highly selective electrochemical detection of compounds of interest.
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Affiliation(s)
- Elnaz Zeynaloo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Department of Chemistry, University of Miami, Miami, FL, 33134, United States
| | - Elsayed M Zahran
- Department of Chemistry, Ball State University, Muncie, IN, 47306, United States
| | - Yu-Ping Yang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States; Clinical and Translational Science Institute, University of Miami, Miami, FL, 33136, United States
| | - Trajen Head
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States
| | - Leonidas G Bachas
- Department of Chemistry, University of Miami, Miami, FL, 33134, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States; Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, United States; Clinical and Translational Science Institute, University of Miami, Miami, FL, 33136, United States.
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4
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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5
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Tomar R, Suwasia S, Choudhury AR, Venkataramani S, Babu SA. Azobenzene-based unnatural amino acid scaffolds via a Pd( ii)-catalyzed C(sp 3)–H arylation strategy. Chem Commun (Camb) 2022; 58:12967-12970. [DOI: 10.1039/d2cc04870a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Azobenzene-based unnatural amino acid motifs were constructed via the Pd(ii)-catalyzed diastereoselective β-C(sp3)–H arylation and Mills azo coupling tactics.
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Affiliation(s)
- Radha Tomar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Sonam Suwasia
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Sugumar Venkataramani
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
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6
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Deng J, Viel JH, Chen J, Kuipers OP. Synthesis and Characterization of Heterodimers and Fluorescent Nisin Species by Incorporation of Methionine Analogues and Subsequent Click Chemistry. ACS Synth Biol 2020; 9:2525-2536. [PMID: 32786360 PMCID: PMC7507115 DOI: 10.1021/acssynbio.0c00308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
![]()
Noncanonical
amino acids form a highly diverse pool of building
blocks that can render unique physicochemical properties to peptides
and proteins. Here, four methionine analogues with unsaturated and
varying side chain lengths were successfully incorporated at four
different positions in nisin in Lactococcus lactis through force feeding. This approach allows for residue-specific
incorporation of methionine analogues into nisin to expand their structural
diversity and alter their activity profiles. Moreover, the insertion
of methionine analogues with biorthogonal chemical reactivity, e.g.,
azidohomoalanine and homopropargylglycine, provides the opportunity
for chemical coupling to functional moieties and fluorescent probes
as well as for intermolecular coupling of nisin variants. All resulting
nisin conjugates retained antimicrobial activity, which substantiates
the potential of this method as a tool to further study its localization
and mode of action.
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Affiliation(s)
- Jingjing Deng
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jingqi Chen
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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7
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Smolskaya S, Andreev YA. Site-Specific Incorporation of Unnatural Amino Acids into Escherichia coli Recombinant Protein: Methodology Development and Recent Achievement. Biomolecules 2019; 9:biom9070255. [PMID: 31261745 PMCID: PMC6681230 DOI: 10.3390/biom9070255] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
More than two decades ago a general method to genetically encode noncanonical or unnatural amino acids (NAAs) with diverse physical, chemical, or biological properties in bacteria, yeast, animals and mammalian cells was developed. More than 200 NAAs have been incorporated into recombinant proteins by means of non-endogenous aminoacyl-tRNA synthetase (aa-RS)/tRNA pair, an orthogonal pair, that directs site-specific incorporation of NAA encoded by a unique codon. The most established method to genetically encode NAAs in Escherichia coli is based on the usage of the desired mutant of Methanocaldococcus janaschii tyrosyl-tRNA synthetase (MjTyrRS) and cognate suppressor tRNA. The amber codon, the least-used stop codon in E. coli, assigns NAA. Until very recently the genetic code expansion technology suffered from a low yield of targeted proteins due to both incompatibilities of orthogonal pair with host cell translational machinery and the competition of suppressor tRNA with release factor (RF) for binding to nonsense codons. Here we describe the latest progress made to enhance nonsense suppression in E. coli with the emphasis on the improved expression vectors encoding for an orthogonal aa-RA/tRNA pair, enhancement of aa-RS and suppressor tRNA efficiency, the evolution of orthogonal EF-Tu and attempts to reduce the effect of RF1.
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Affiliation(s)
- Sviatlana Smolskaya
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8, bld. 2, 119991 Moscow, Russia.
| | - Yaroslav A Andreev
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8, bld. 2, 119991 Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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8
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Abstract
Fourier transform infrared (FTIR) spectroscopy has become one of the major techniques of structural characterization of proteins, peptides, and protein-membrane interactions. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or intermolecular interactions. The sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as 13C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, the structural features of membrane pore forming proteins and peptides, and much more. The purpose of this chapter was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, is also presented.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
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9
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Navo CD, Asín A, Gómez-Orte E, Gutiérrez-Jiménez MI, Compañón I, Ezcurra B, Avenoza A, Busto JH, Corzana F, Zurbano MM, Jiménez-Osés G, Cabello J, Peregrina JM. Cell-Penetrating Peptides Containing Fluorescent d
-Cysteines. Chemistry 2018; 24:7991-8000. [DOI: 10.1002/chem.201800603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Claudio D. Navo
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Alicia Asín
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Eva Gómez-Orte
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Marta I. Gutiérrez-Jiménez
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Ismael Compañón
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Begoña Ezcurra
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Alberto Avenoza
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Jesús H. Busto
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Francisco Corzana
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - María M. Zurbano
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Gonzalo Jiménez-Osés
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Juan Cabello
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Jesús M. Peregrina
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
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Bartoschik T, Galinec S, Kleusch C, Walkiewicz K, Breitsprecher D, Weigert S, Muller YA, You C, Piehler J, Vercruysse T, Daelemans D, Tschammer N. Near-native, site-specific and purification-free protein labeling for quantitative protein interaction analysis by MicroScale Thermophoresis. Sci Rep 2018; 8:4977. [PMID: 29563556 PMCID: PMC5862892 DOI: 10.1038/s41598-018-23154-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/05/2018] [Indexed: 12/21/2022] Open
Abstract
MicroScale Thermophoresis (MST) is a frequently used method for the quantitative characterization of intermolecular interactions with several advantages over other technologies. One of these is its capability to determine equilibrium constants in solution including complex biological matrices such as cell lysates. MST requires one binding partner to be fluorescent, which is typically achieved by labeling target proteins with a suitable fluorophore. Here, we present a near-native, site-specific in situ labeling strategy for MST experiments that enables reliable measurements in cell lysates and that has distinct advantages over routine covalent labeling techniques. To this end, we exploited the high-affinity interaction of tris-NTA with oligohistidine-tags, which are popular for purification, immobilization or detection of recombinant proteins. We used various DYE-tris-NTA conjugates to successfully label His-tagged proteins that were either purified or a component of cell lysate. The RED-tris-NTA was identified as the optimal dye conjugate with a high affinity towards oligohistidine-tags, a high fluorescence signal and an optimal signal-to-noise ratio in MST binding experiments. Owing to its emission in the red region of the spectrum, it also enables reliable measurements in complex biological matrices such as cell lysates allowing a more physiologically realistic assessment and eliminating the need for protein purification.
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Affiliation(s)
- Tanja Bartoschik
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | - Stefanie Galinec
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | - Christian Kleusch
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | | | | | - Sebastian Weigert
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen, Nuremberg Henkestr 91, 91052, Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen, Nuremberg Henkestr 91, 91052, Erlangen, Germany
| | - Changjiang You
- Division of Biophysics, Department of Biology, University Osnabrück, Barbarastr 11, 49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University Osnabrück, Barbarastr 11, 49076, Osnabrück, Germany
| | - Thomas Vercruysse
- KU Leuven Department of Immunology and Microbiology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Immunology and Microbiology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium
| | - Nuska Tschammer
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany.
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11
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Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics. J Mol Graph Model 2016; 71:192-199. [PMID: 27939931 DOI: 10.1016/j.jmgm.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/28/2022]
Abstract
The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.
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12
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Zhang H, Weingart J, Gruzdys V, Sun XL. Synthesis of an End-to-End Protein-Glycopolymer Conjugate via Bio-Orthogonal Chemistry. ACS Macro Lett 2016; 5:73-77. [PMID: 35668582 DOI: 10.1021/acsmacrolett.5b00805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report the synthesis of an end-to-end protein-glycopolymer conjugate, namely, site-specific modification of recombinant thrombomodulin at the C-terminus with a chain-end-functionalized glycopolymer. Thrombomodulin (TM) is an endothelial membrane glycoprotein that acts as a major cofactor in the protein C anticoagulant pathway. To closely mimic the glycoprotein structural feature of native TM, we proposed a site-specific glyco-engineering of recombinant TM with a glycopolymer. Briefly, recombinant TM containing the epidermal growth factor (EGF)-like domains 4, 5, and 6 (rTM456) and a C-terminal azidohomoalanine was modified with a dibenzylcyclooctyne (DBCO) chain-end-functionalized glycopolymer via copper-free click chemistry to afford the end-to-end TM-glycopolymer conjugate. The TM glycoconjugation was confirmed with SDS-PAGE, Western blot, and protein C activation assay, respectively. The reported site-specific end-to-end protein glycopolymer conjugation approach facilitates uniform glycoconjugate formation via biocompatible chemistry and in high efficiency providing a rational strategy for generating an rTM-based anticoagulant agent.
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Affiliation(s)
- Hailong Zhang
- Department of Chemistry,
Chemical and Biomedical Engineering and Center for Gene Regulation
in Health and Disease, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Jacob Weingart
- Department of Chemistry,
Chemical and Biomedical Engineering and Center for Gene Regulation
in Health and Disease, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Valentinas Gruzdys
- Department of Chemistry,
Chemical and Biomedical Engineering and Center for Gene Regulation
in Health and Disease, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Xue-Long Sun
- Department of Chemistry,
Chemical and Biomedical Engineering and Center for Gene Regulation
in Health and Disease, Cleveland State University, Cleveland, Ohio 44115, United States
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13
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Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C, Plateau P. Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Proteins 2016; 84:240-53. [PMID: 26676967 DOI: 10.1002/prot.24972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/30/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022]
Abstract
D-Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl-tRNA synthetases (aaRSs), and this strategy might be applicable to D-amino acids. Several aaRSs can aminoacylate their tRNA with a D-amino acid; of these, tyrosyl-tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its D-Tyr binding further, relative to L-Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain L-Tyr/D-Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge-altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards D-Tyr; one of these has an inverted stereospecificity, with a large preference for D-Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled.
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Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | | | - Zoltan Palmai
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Najette Amara
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Sandra Wydau-Dematteis
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Erwan Bigan
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Karen Druart
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Clara Moch
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Pierre Plateau
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
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14
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Druart K, Palmai Z, Omarjee E, Simonson T. Protein:Ligand binding free energies: A stringent test for computational protein design. J Comput Chem 2015; 37:404-15. [PMID: 26503829 DOI: 10.1002/jcc.24230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/29/2023]
Abstract
A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl-tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l-tyrosine (l-Tyr), compared to the analogs d-Tyr, p-acetyl-, and p-azido-phenylalanine (ac-Phe, az-Phe). We simulate l- and d-Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous "MD/GBSA" procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l-Tyr, ac- and az-Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l-Tyr or d-Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l-Tyr is the ligand and a d-Tyr specific mutant when d-Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln.
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Affiliation(s)
- Karen Druart
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Zoltan Palmai
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Eyaz Omarjee
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Thomas Simonson
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
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15
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Cheruku P, Huang JH, Yen HJ, Iyer RS, Rector KD, Martinez JS, Wang HL. Tyrosine-derived stimuli responsive, fluorescent amino acids. Chem Sci 2015; 6:1150-1158. [PMID: 29560202 PMCID: PMC5811119 DOI: 10.1039/c4sc02753a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/29/2014] [Indexed: 12/21/2022] Open
Abstract
A series of fluorescent unnatural amino acids (UAAs) bearing stilbene and meta-phenylenevinylene (m-PPV) backbone have been synthesized and their optical properties were studied. These novel UAAs were derived from protected diiodo-l-tyrosine using palladium-catalyzed Heck couplings with a series of styrene analogs. Unlike the other fluorescent UAAs, whose emissions are restricted to a narrow range of wavelengths, these new amino acids display the emission peaks at broad range wavelengths (from 400-800 nm); including NIR with QY of 4% in HEPES buffer. The incorporation of both pyridine and phenol functional groups leads to distinct red, green, and blue (RGB) emission, in its basic, acidic and neutral states, respectively. More importantly, these amino acids showed reversible pH and redox response showing their promise as stimuli responsive fluorescent probes. To further demonstrate the utility of these UAAs in peptide synthesis, one of the amino acids was incorporated into a cell penetrating peptide (CPP) sequence through standard solid phase peptide synthesis. Resultant CPP was treated with two different cell lines and the internalization was monitored by confocal fluorescence microscopy.
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Affiliation(s)
- Pradeep Cheruku
- C-PCS, Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - Jen-Huang Huang
- Defense System and Analysis Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA
| | - Hung-Ju Yen
- C-PCS, Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - Rashi S Iyer
- Defense System and Analysis Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA
| | - Kirk D Rector
- C-PCS, Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - Jennifer S Martinez
- Center of Integrated Nanotechnologies (CINT) , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA
| | - Hsing-Lin Wang
- C-PCS, Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
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16
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Steen Redeker E, Ta DT, Cortens D, Billen B, Guedens W, Adriaensens P. Protein Engineering For Directed Immobilization. Bioconjug Chem 2013; 24:1761-77. [DOI: 10.1021/bc4002823] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Erik Steen Redeker
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Duy Tien Ta
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - David Cortens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Brecht Billen
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Wanda Guedens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Peter Adriaensens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
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17
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Zhang H, Weingart J, Jiang R, Peng J, Wu Q, Sun XL. Bio-inspired liposomal thrombomodulin conjugate through bio-orthogonal chemistry. Bioconjug Chem 2013; 24:550-9. [PMID: 23458546 DOI: 10.1021/bc300399f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report the synthesis of bioinspired liposomal thrombomodulin (TM) conjugates by chemoselective and site-specific liposomal conjugation of recombinant TM at C-terminus. TM is an endothelial cell membrane protein that acts as a major cofactor in the protein C anticoagulant pathway. To closely mimic membrane protein structural features of TM, we proposed membrane-mimetic re-expression of recombinant TM onto liposome. A recombinant TM containing the EGF-like 456 domains and an azidohomoalanine at C-terminus was expressed in E. coli. Conjugation of the recombinant TM onto liposome via Staudinger ligation and copper-free click chemistry were investigated as an optimal platform for exploring membrane protein TM's activity, respectively. The bioinspired liposomal TM conjugates were confirmed with Western blotting and protein C activation activity. The recombinant TM-liposome conjugates showed a 2-fold higher k(cat)/K(m) value for protein C activation than that of the recombinant TM alone, which indicated that the lipid membrane has a beneficiary effect on the recombinant TM's activity. The reported liposomal protein conjugate approach provides a rational design strategy for both studying membrane protein TM's functions and generating a membrane protein TM-based anticoagulant agent.
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Affiliation(s)
- Hailong Zhang
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA
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18
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Metz AE, Kozlowski MC. 2-Aryl-2-nitroacetates as central precursors to aryl nitromethanes, α-ketoesters, and α-amino acids. J Org Chem 2013; 78:717-22. [PMID: 23245626 PMCID: PMC3548967 DOI: 10.1021/jo302071s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitroarylacetates are useful small molecular building blocks that act as precursors to α-ketoesters and aryl nitromethanes as well as α-amino acids. Methods were developed that produce each of these compound types in good yields. Two different conditions for decarboxylation are discussed for substrates with neutral and electron-poor aryl groups versus electron-rich aryl groups. For formation of the α-ketoesters, new mild conditions for the Nef disproportionation were identified.
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Affiliation(s)
- Alison E. Metz
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 1910-6323 (USA)
| | - Marisa C. Kozlowski
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 1910-6323 (USA)
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19
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Tatulian SA. Structural characterization of membrane proteins and peptides by FTIR and ATR-FTIR spectroscopy. Methods Mol Biol 2013; 974:177-218. [PMID: 23404277 DOI: 10.1007/978-1-62703-275-9_9] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is widely used in structural characterization of proteins or peptides. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or upon intermolecular interactions. Sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as (13)C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, and molecular architecture of membrane pore or channel forming proteins and peptides. The purpose of this article was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, are also presented.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
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20
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Butterfield S, Hejjaoui M, Fauvet B, Awad L, Lashuel HA. Chemical strategies for controlling protein folding and elucidating the molecular mechanisms of amyloid formation and toxicity. J Mol Biol 2012; 421:204-36. [PMID: 22342932 DOI: 10.1016/j.jmb.2012.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 12/12/2022]
Abstract
It has been more than a century since the first evidence linking the process of amyloid formation to the pathogenesis of Alzheimer's disease. During the last three decades in particular, increasing evidence from various sources (pathology, genetics, cell culture studies, biochemistry, and biophysics) continues to point to a central role for the pathogenesis of several incurable neurodegenerative and systemic diseases. This is in part driven by our improved understanding of the molecular mechanisms of protein misfolding and aggregation and the structural properties of the different aggregates in the amyloid pathway and the emergence of new tools and experimental approaches that permit better characterization of amyloid formation in vivo. Despite these advances, detailed mechanistic understanding of protein aggregation and amyloid formation in vitro and in vivo presents several challenges that remain to be addressed and several fundamental questions about the molecular and structural determinants of amyloid formation and toxicity and the mechanisms of amyloid-induced toxicity remain unanswered. To address this knowledge gap and technical challenges, there is a critical need for developing novel tools and experimental approaches that will not only permit the detection and monitoring of molecular events that underlie this process but also allow for the manipulation of these events in a spatial and temporal fashion both in and out of the cell. This review is primarily dedicated in highlighting recent results that illustrate how advances in chemistry and chemical biology have been and can be used to address some of the questions and technical challenges mentioned above. We believe that combining recent advances in the development of new fluorescent probes, imaging tools that enabled the visualization and tracking of molecular events with advances in organic synthesis, and novel approaches for protein synthesis and engineering provide unique opportunities to gain a molecular-level understanding of the process of amyloid formation. We hope that this review will stimulate further research in this area and catalyze increased collaboration at the interface of chemistry and biology to decipher the mechanisms and roles of protein folding, misfolding, and aggregation in health and disease.
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Affiliation(s)
- Sara Butterfield
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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21
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Small photoactivatable molecules for controlled fluorescence activation in living cells. Bioorg Med Chem 2010; 19:1023-9. [PMID: 20675143 DOI: 10.1016/j.bmc.2010.07.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 07/01/2010] [Accepted: 07/07/2010] [Indexed: 11/23/2022]
Abstract
The search for chemical probes which allow a controlled fluorescence activation in living cells represent a major challenge in chemical biology. To be useful, such probes have to be specifically targeted to cellular proteins allowing thereof the analysis of dynamic aspects of this protein in its cellular environment. The present paper describes different methods which have been developed to control cellular fluorescence activation emphasizing the photochemical activation methods known to be orthogonal to most cellular components and, in addition, allowing a spatio-temporal controlled triggering of the fluorescent signal.
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22
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Lopes A, Schmidt Am Busch M, Simonson T. Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase. J Comput Chem 2010; 31:1273-86. [PMID: 19862811 DOI: 10.1002/jcc.21414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A method for computational design of protein-ligand interactions is implemented and tested on the asparaginyl- and aspartyl-tRNA synthetase enzymes (AsnRS, AspRS). The substrate specificity of these enzymes is crucial for the accurate translation of the genetic code. The method relies on a molecular mechanics energy function and a simple, continuum electrostatic, implicit solvent model. As test calculations, we first compute AspRS-substrate binding free energy changes due to nine point mutations, for which experimental data are available; we also perform large-scale redesign of the entire active site of each enzyme (40 amino acids) and compare to experimental sequences. We then apply the method to engineer an increased binding of aspartyl-adenylate (AspAMP) into AsnRS. Mutants are obtained using several directed evolution protocols, where four or five amino acid positions in the active site are randomized. Promising mutants are subjected to molecular dynamics simulations; Poisson-Boltzmann calculations provide an estimate of the corresponding, AspAMP, binding free energy changes, relative to the native AsnRS. Several of the mutants are predicted to have an inverted binding specificity, preferring to bind AspAMP rather than the natural substrate, AsnAMP. The computed binding affinities are significantly weaker than the native, AsnRS:AsnAMP affinity, and in most cases, the active site structure is significantly changed, compared to the native complex. This almost certainly precludes catalytic activity. One of the designed sequences has a higher affinity and more native-like structure and may represent a valid candidate for Asp activity.
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Affiliation(s)
- Anne Lopes
- Laboratoire de Biochimie, Department of Biology, UMR CNRS 7654, Ecole Polytechnique, 91128 Palaiseau, France
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23
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Aleksandrov A, Thompson D, Simonson T. Alchemical free energy simulations for biological complexes: powerful but temperamental.... J Mol Recognit 2010; 23:117-27. [PMID: 19693787 DOI: 10.1002/jmr.980] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Free energy simulations compare multiple ligand:receptor complexes by "alchemically" transforming one into another, yielding binding free energy differences. Since their introduction in the 1980s, many technical and theoretical obstacles were surmounted, and the method ("MDFE," since molecular dynamics are often used) has matured into a powerful tool. We describe its current status, its effectiveness, and the challenges it faces. MDFE has provided chemical accuracy for many systems but remains expensive, with significant human overhead costs. The bottlenecks have shifted, partly due to increased computer power. To study diverse sets of ligands, force field availability and accuracy can be a major difficulty. Another difficulty is the frequent need to consider multiple states, related to sidechain protonation or buried waters, for example. Sophisticated, automated methods to sample these states are maturing, such as constant pH simulations. Meanwhile, combinations of MDFE and simpler approaches, like continuum dielectric models, can be very effective. As illustrations, we show how, with careful force field parameterization, MDFE accurately predicts binding specificities between complex tetracycline ligands and their targets. We describe substrate binding to the aspartyl-tRNA synthetase enzyme, where many distinct electrostatic states play a role, and a histidine and a Mg(2+) ion act as coupled switches that help enforce a strict preference for the aspartate substrate, relative to several analogs. Overall, MDFE has achieved a predictive status, where novel ligands can be studied and molecular recognition elucidated in depth. It should play an increasing role in the analysis of complex cellular processes and biomolecular engineering.
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Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
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24
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25
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Specht A, Bolze F, Omran Z, Nicoud JF, Goeldner M. Photochemical tools to study dynamic biological processes. HFSP JOURNAL 2009; 3:255-64. [PMID: 20119482 PMCID: PMC2799987 DOI: 10.2976/1.3132954] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 04/21/2009] [Indexed: 11/19/2022]
Abstract
Light-responsive biologically active compounds offer the possibility to study the dynamics of biological processes. Phototriggers and photoswitches have been designed, providing the capability to rapidly cause the initiation of wide range of dynamic biological phenomena. We will discuss, in this article, recent developments in the field of light-triggered chemical tools, specially how two-photon excitation, "caged" fluorophores, and the photoregulation of protein activities in combination with time-resolved x-ray techniques should break new grounds in the understanding of dynamic biological processes.
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Affiliation(s)
- Alexandre Specht
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR 7199, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Frédéric Bolze
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Ziad Omran
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR 7199, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Jean-François Nicoud
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
| | - Maurice Goeldner
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR 7199, Université de Strasbourg-CNRS, 74 route du Rhin, F-67401 Illkirch-Graffenstaden Cedex, France
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26
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Picataggio S. Potential impact of synthetic biology on the development of microbial systems for the production of renewable fuels and chemicals. Curr Opin Biotechnol 2009; 20:325-9. [DOI: 10.1016/j.copbio.2009.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 11/29/2022]
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27
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28
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Doi Y, Ohtsuki T, Shimizu Y, Ueda T, Sisido M. Elongation Factor Tu Mutants Expand Amino Acid Tolerance of Protein Biosynthesis System. J Am Chem Soc 2007; 129:14458-62. [DOI: 10.1021/ja075557u] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Bachl J, Caldwell RB, Buerstedde JM. Biotechnology and the chicken B cell line DT40. Cytogenet Genome Res 2007; 117:189-94. [PMID: 17675859 DOI: 10.1159/000103179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 12/07/2006] [Indexed: 12/22/2022] Open
Abstract
Protein optimization is a major focus of the biotech and pharmaceutical industry. Various in vitro technologies have been developed to accelerate protein evolution and to achieve protein optimization of functional characteristics such as substrate specificity, enzymatic activity and thermostability. The chicken B cell line DT40 diversifies its immunoglobulin (Ig) gene by gene conversion and somatic hypermutation. This machinery can be directed to almost any gene inserted into the Ig locus. Enormously diverse protein libraries of any gene of interest can be quickly generated in DT40 by utilizing random shuffling of complex genetic domains (gene conversion) and by the introduction of novel non-templated genetic information (random mutagenesis). The unique characteristics of the chicken cell line DT40 make it a powerful in-cell diversification system to improve proteins of interest within living cells. One essential advantage of the DT40 protein optimization approach is the fact that variants are generated within an in-cell system thus allowing the direct screening for desired features in the context of intracellular networks. Utilizing specially designed selection strategies, such as the powerful fluorescent protein technology, enables the reliable identification of protein variants exhibiting the most desirable traits. Thus, DT40 is well positioned as a biotechnological tool to generate optimized proteins by applying a powerful combination of gene specific hypermutation, gene conversion and mutant selection.
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Affiliation(s)
- J Bachl
- GSF-National Research Center for Environment and Health, Institute for Molecular Radiobiology, Neuherberg-Munich, Germany
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30
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Krishnan B, Szymanska A, Gierasch LM. Site-specific fluorescent labeling of poly-histidine sequences using a metal-chelating cysteine. Chem Biol Drug Des 2007; 69:31-40. [PMID: 17313455 PMCID: PMC2896745 DOI: 10.1111/j.1747-0285.2007.00463.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coupling genetically encoded target sequences with specific and selective labeling strategies has made it possible to utilize fluorescence spectroscopy in complex mixtures to investigate the structure, function, and dynamics of proteins. Thus, there is a growing need for a repertoire of such labeling approaches to deploy based on a given application and to utilize in combination with one another by orthogonal reactivity. We have developed a simple approach to synthesize a fluorescent probe that binds to a poly-histidine sequence. The amino group of cysteine was converted into nitrilotriacetate to create a metal-chelating cysteine molecule, Cys-nitrilotriacetate. Two Cys-nitrilotriacetate molecules were then cross-linked using dibromobimane to generate a fluorophore capable of binding a His-tag on a protein, NTA(2)-BM. NTA(2)-BM is a potential fluorophore for selective tagging of proteins in vivo.
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Affiliation(s)
- Beena Krishnan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9305, USA
| | - Aneta Szymanska
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9305, USA
- Department of Chemistry, University of Gdansk, Sobieskiego 18, 80–952 Gdansk, Poland
| | - Lila M. Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9305, USA
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9336, USA
- Corresponding author: Lila M. Gierasch,
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Sando S, Ogawa A, Nishi T, Hayami M, Aoyama Y. In vitro selection of RNA aptamer against Escherichia coli release factor 1. Bioorg Med Chem Lett 2006; 17:1216-20. [PMID: 17188871 DOI: 10.1016/j.bmcl.2006.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Revised: 12/04/2006] [Accepted: 12/06/2006] [Indexed: 11/19/2022]
Abstract
A pool of 84-nt RNAs containing a randomized sequence of 50 nt was selected against gel-immobilized Escherichia coli release factor 1 (RF-1) responsible for translation termination at amber (UAG) stop codon. The strongest aptamer (class II-1) obtained from 43 clones bound to RF-1, but not to UAA/UGA-targeting RF-2, with Kd = 30+/-6 nM (SPR). A couple of unpaired hairpin domains in the aptamer were suggested as the sites of attachment of RF-1. By binding to and hence inhibiting the action of RF-1 specifically or bio-orthogonally, aptamer class II-1 enhanced the amber suppression efficiency in the presence of an anticodon-adjusted (CUA) suppressor tRNA without practically damaging the protein translation machinery of the cell-free extract of E. coli, as confirmed by the translation of amber-mutated (gfp(amber141) or gfp(amber178)) and wild-type (gfp(wild)) genes of GFP.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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Abstract
DNA synthesis has become one of the technological bases of a new concept in biology: synthetic biology. The vision of synthetic biology is a systematic, hierarchical design of artificial, biology-inspired systems using robust, standardized, and well-characterized building blocks. The design concept and examples from four fields of application (genetic circuits, protein design, platform technologies, and pathway engineering) are discussed, which demonstrate the usefulness and the promises of synthetic biology. The vision of synthetic biology is to develop complex systems by simplified solutions using available material and knowledge. Synthetic biology also opens a door toward new biomaterials that do not occur in nature.
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Affiliation(s)
- Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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Nakata H, Ohtsuki T, Abe R, Hohsaka T, Sisido M. Binding efficiency of elongation factor Tu to tRNAs charged with nonnatural fluorescent amino acids. Anal Biochem 2006; 348:321-3. [PMID: 16307719 DOI: 10.1016/j.ab.2005.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 07/27/2005] [Accepted: 08/08/2005] [Indexed: 11/26/2022]
Affiliation(s)
- Hidetaka Nakata
- Department of Bioscience and Biotechnology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
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Röhrig CH, Retz OA, Hareng L, Hartung T, Schmidt RR. A new strategy for the synthesis of dinucleotides loaded with glycosylated amino acids--investigations on in vitro non-natural amino acid mutagenesis for glycoprotein synthesis. Chembiochem 2005; 6:1805-16. [PMID: 16142818 DOI: 10.1002/cbic.200500079] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The in vitro non-natural amino acid mutagenesis method provides the opportunity to introduce non-natural amino acids site-specifically into proteins. To this end, a chemically synthesised aminoacylated dinucleotide is enzymatically ligated to a truncated suppressor transfer RNA. The loaded suppressor tRNA is then used in translation reactions to read an internal stop codon. Here we report an advanced and general strategy for the synthesis of the aminoacyl dinucleotide. The protecting group pattern developed for the dinucleotide facilitates highly efficient aminoacylation, followed by one-step global deprotection. The strategy was applied to the synthesis of dinucleotides loaded with 2-acetamido-2-deoxy-glycosylated amino acids, including N- and O-beta-glycosides and O- and C-alpha-glycosides of amino acids, thus enabling the extension of in vitro non-natural amino acid mutagenesis towards the synthesis of natural glycoproteins of high biological interest. We demonstrate the incorporation of the glycosylamino acids--although with low suppression efficiency--into the human interleukin granulocyte-colony stimulating factor (hG-CSF), as verified by the ELISA technique.
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Affiliation(s)
- Christoph H Röhrig
- Department of Chemistry, University of Konstanz, Fach M 725, 78457 Konstanz, Germany
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Ohtsuki T, Manabe T, Sisido M. Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures. FEBS Lett 2005; 579:6769-74. [PMID: 16310775 DOI: 10.1016/j.febslet.2005.11.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 11/01/2005] [Indexed: 11/28/2022]
Abstract
The ability to introduce non-natural amino acids into proteins opens up new vistas for the study of protein structure and function. This approach requires suppressor tRNAs that deliver the non-natural amino acid to a ribosome associated with an mRNA containing an expanded codon. The suppressor tRNAs must be absolutely protected from aminoacylation by any of the aminoacyl-tRNA synthetases in the protein synthesizing system, or a natural amino acid will be incorporated instead of the non-natural amino acid. Here, we found that some tRNAs with non-standard structures could work as efficient four-base suppressors fulfilling the above orthogonal conditions. Using these tRNAs, we successfully demonstrated incorporation of three different non-natural amino acids into a single protein.
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Affiliation(s)
- Takashi Ohtsuki
- Department of Bioscience and Biotechnology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
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Lodder M, Wang B, Hecht SM. The N-pentenoyl protecting group for aminoacyl-tRNAs. Methods 2005; 36:245-51. [PMID: 16076450 DOI: 10.1016/j.ymeth.2005.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 04/28/2005] [Indexed: 11/30/2022] Open
Abstract
The elaboration of misacylated transfer RNAs by T4 RNA ligase-mediated condensation of an aminoacylated pdCpA derivative and a tRNA (transcript) missing the two 3'-terminal nucleotides requires that the aminoacyl moiety of the dinucleotide be stabilized during the ligation reaction. This can be done conveniently by the use of a simple 4-pentenoyl group attached to N(alpha) of the amino acid. The pentenoyl amide can be deblocked readily with aqueous iodine, presumably via an iodolactone intermediate. This protecting group can be used in conjunction with side chain protecting group for amino acids having side chain functionality, thus permitting the elaboration of proteins bearing side chain protecting groups that can be removed in a subsequent step (e.g., caged proteins). In addition, an aminated analogue of the pentenoyl protecting group, the unnatural amino acid allylglycine, can be employed as part of the peptide backbone to afford a protein cleavable by iodine.
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Affiliation(s)
- Michiel Lodder
- Department of Chemistry, University of Virginia, Charlottesville, VA 22901, USA
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Affiliation(s)
- Christian Jäckel
- Free University Berlin, Department of Chemistry – Organic Chemistry Takustrasse 3, 14195 Berlin, Germany, Fax: +49‐30‐838‐55644
| | - Beate Koksch
- Free University Berlin, Department of Chemistry – Organic Chemistry Takustrasse 3, 14195 Berlin, Germany, Fax: +49‐30‐838‐55644
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Ilegems E, Pick HM, Vogel H. Downregulation of eRF1 by RNA interference increases mis-acylated tRNA suppression efficiency in human cells. Protein Eng Des Sel 2005; 17:821-7. [PMID: 15716307 DOI: 10.1093/protein/gzh096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The site-specific incorporation of non-natural amino acids into proteins by nonsense suppression has been widely used to investigate protein structure and function. Usually this technique exhibits low incorporation efficiencies of non-natural amino acids into proteins. We describe for the first time an approach for achieving an increased level of nonsense codon suppression with synthetic suppressor tRNAs in cultured human cells. We find that the intracellular concentration of the eukaryotic release factor 1 (eRF1) is a critical parameter influencing the efficiency of amino acid incorporation by nonsense suppression. Using RNA interference we were able to lower eRF1 gene expression significantly. We achieved a five times higher level of amino acid incorporation as compared with non-treated control cells, as demonstrated by enhanced green fluorescent protein (EGFP) fluorescence recovery after importing a mutated reporter mRNA together with an artificial amber suppressor tRNA.
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Affiliation(s)
- Erwin Ilegems
- Institute of Biomolecular Sciences, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
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Budisa N. Prolegomena zum experimentellen Engineering des genetischen Codes durch Erweiterung seines Aminosäurerepertoires. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200300646] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Budisa N. Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire. Angew Chem Int Ed Engl 2004; 43:6426-63. [PMID: 15578784 DOI: 10.1002/anie.200300646] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institut für Biochemie, Junior Research Group "Moleculare Biotechnologie", Am Klopferspitz 18a, 82152 Martinsried bei München, Germany.
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