1
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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2
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Wang Z, Matthews H, Deng G, Zhou X, Chen Y. Thermodynamic Analysis of Tyrosyl-tRNA Synthetases Revealed Bacterial-Selective Tyrosine Derivatives. Aust J Chem 2021. [DOI: 10.1071/ch21218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The non-proteinogenic amino acids m-fluorotyrosine and 2,4-dihydroxyphenylalanine demonstrated a respective 6- and 12-fold greater binding affinity to the purified tyrosyl-tRNA synthetase from Escherichia coli than that from human cytosol. The differential binding was identified by probing the substrate selectivity of the two enzymes with structural analogues of tyrosine using a thermodynamic technique.
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3
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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4
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Zou H, Li L, Zhang T, Shi M, Zhang N, Huang J, Xian M. Biosynthesis and biotechnological application of non-canonical amino acids: Complex and unclear. Biotechnol Adv 2018; 36:1917-1927. [PMID: 30063950 DOI: 10.1016/j.biotechadv.2018.07.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/22/2018] [Accepted: 07/27/2018] [Indexed: 01/05/2023]
Abstract
Compared with the better-studied canonical amino acids, the distribution, metabolism and functions of natural non-canonical amino acids remain relatively obscure. Natural non-canonical amino acids have been mainly discovered in plants as secondary metabolites that perform diversified physiological functions. Due to their specific characteristics, a broader range of natural and artificial non-canonical amino acids have recently been applied in the development of functional materials and pharmaceutical products. With the rapid development of advanced methods in biotechnology, non-canonical amino acids can be incorporated into peptides, proteins and enzymes to improve the function and performance relative to their natural counterparts. Therefore, biotechnological application of non-canonical amino acids in artificial bio-macromolecules follows the central goal of synthetic biology to: create novel life forms and functions. However, many of the non-canonical amino acids are synthesized via chemo- or semi-synthetic methods, and few non-canonical amino acids can be synthesized using natural in vivo pathways. Therefore, further research is needed to clarify the metabolic pathways and key enzymes of the non-canonical amino acids. This will lead to the discovery of more candidate non-canonical amino acids, especially for those that are derived from microorganisms and are naturally bio-compatible with chassis strains for in vivo biosynthesis. In this review, we summarize representative natural and artificial non-canonical amino acids, their known information regarding associated metabolic pathways, their characteristics and their practical applications. Moreover, this review summarizes current barriers in developing in vivo pathways for the synthesis of non-canonical amino acids, as well as other considerations, future trends and potential applications of non-canonical amino acids in advanced biotechnology.
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Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Lei Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Tongtong Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Nan Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jingling Huang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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5
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Oyala PH, Ravichandran KR, Funk MA, Stucky PA, Stich TA, Drennan CL, Britt RD, Stubbe J. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example. J Am Chem Soc 2016; 138:7951-64. [PMID: 27276098 PMCID: PMC4929525 DOI: 10.1021/jacs.6b03605] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Fluorinated tyrosines
(FnY’s, n = 2
and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the
recently evolved M. jannaschii Y-tRNA synthetase/tRNA
pair. Class Ia RNRs require four redox active Y’s, a stable
Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y’s (356
in β and 731 and 730 in α) to initiate the radical-dependent
nucleotide reduction process. FnY (3,5;
2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β
and the X-ray structures of each resulting β with a diferric
cluster are reported and compared with wt-β2 crystallized under
the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe2+, and O2 to produce ∼1
Y·/β2 and ∼3 Fe3+/β2. The FnY· are stable and active in nucleotide
reduction with activities that vary from 5% to 85% that of wt-β2.
Each FnY·-β2 has been characterized
by 9 and 130 GHz electron paramagnetic resonance and high-field electron
nuclear double resonance spectroscopies. The hyperfine interactions
associated with the 19F nucleus provide unique signatures
of each FnY· that are readily distinguishable
from unlabeled Y·’s. The variability of the abiotic FnY pKa’s
(6.4 to 7.8) and reduction potentials (−30 to +130 mV relative
to Y at pH 7.5) provide probes of enzymatic reactions proposed to
involve Y·’s in catalysis and to investigate the importance
and identity of hopping Y·’s within redox active proteins
proposed to protect them from uncoupled radical chemistry.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | | | | | - Paul A Stucky
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Troy A Stich
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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6
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Fraser SA, Easton CJ. Biosynthetic Incorporation of Fluorinated Amino Acids into Peptides and Proteins. Aust J Chem 2015. [DOI: 10.1071/ch14356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Native and engineered protein biosynthetic machinery processes a wide range of fluorinated α-amino acids for incorporation into peptides and proteins, either as substitutes for structurally similar amino acids normally found in proteins, or as additional ones. In the former case, replacement occurs wherever the normal amino acid is encoded, while the latter method is site-specific. The fluorinated peptides have a diverse variety of interesting properties. The biochemical synthetic methods are straightforward, to the point that they should routinely be assessed as alternatives to traditional solid- and solution-phase peptide synthesis.
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7
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Natarajan A, Schwans JP, Herschlag D. Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site. J Am Chem Soc 2014; 136:7643-54. [PMID: 24787954 PMCID: PMC4046884 DOI: 10.1021/ja413174b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 02/04/2023]
Abstract
Hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. But understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. It has been proposed for ketosteroid isomerase and other enzymes that active site hydrogen bonding groups provide energetic stabilization via "short, strong" or "low-barrier" hydrogen bonds that are formed due to matching of their pKa or proton affinity to that of the transition state. It has also been proposed that the ketosteroid isomerase and other enzyme active sites provide electrostatic environments that result in larger energetic responses (i.e., greater "sensitivity") to ground-state to transition-state charge rearrangement, relative to aqueous solution, thereby providing catalysis relative to the corresponding reaction in water. To test these models, we substituted tyrosine with fluorotyrosines (F-Tyr's) in the ketosteroid isomerase (KSI) oxyanion hole to systematically vary the proton affinity of an active site hydrogen bond donor while minimizing steric or structural effects. We found that a 40-fold increase in intrinsic F-Tyr acidity caused no significant change in activity for reactions with three different substrates. F-Tyr substitution did not change the solvent or primary kinetic isotope effect for proton abstraction, consistent with no change in mechanism arising from these substitutions. The observed shallow dependence of activity on the pKa of the substituted Tyr residues suggests that the KSI oxyanion hole does not provide catalysis by forming an energetically exceptional pKa-matched hydrogen bond. In addition, the shallow dependence provides no indication of an active site electrostatic environment that greatly enhances the energetic response to charge accumulation, consistent with prior experimental results.
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Affiliation(s)
- Aditya Natarajan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
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8
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Blatter N, Prokup A, Deiters A, Marx A. Modulating the pKaof a Tyrosine inKlenTaqDNA Polymerase that Is Crucial for Abasic Site Bypass by in Vivo Incorporation of a Non-canonical Amino Acid. Chembiochem 2014; 15:1735-7. [DOI: 10.1002/cbic.201400051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Indexed: 11/11/2022]
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9
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Deepankumar K, Shon M, Nadarajan SP, Shin G, Mathew S, Ayyadurai N, Kim BG, Choi SH, Lee SH, Yun H. Enhancing Thermostability and Organic Solvent Tolerance of ω-Transaminase through Global Incorporation of Fluorotyrosine. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300706] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Pond MP, Wenke BB, Preimesberger MR, Rice SL, Lecomte JTJ. 3-Fluorotyrosine as a complementary probe of hemoglobin structure and dynamics: a (19)F-NMR study of Synechococcus sp. PCC 7002 GlbN. Chem Biodivers 2013; 9:1703-17. [PMID: 22976963 DOI: 10.1002/cbdv.201100448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 (GlbN) contains three tyrosines (Tyr5, Tyr22, and Tyr53), each of which undergoes a structural rearrangement when the protein binds an exogenous ligand such as cyanide. We explored the use of 3-fluorotyrosine and (19)F-NMR spectroscopy for the characterization of GlbN. Assignment of (19)F resonances in fluorinated GlbN (GlbN*) was achieved with individual Tyr5Phe and Tyr53Phe replacements. We observed marked variations in chemical shift and linewidth reflecting the dependence of structural and dynamic properties on oxidation state, ligation state, and covalent attachment of the heme group. The isoelectronic complexes of ferric GlbN* with cyanide and ferrous GlbN* with carbon monoxide gave contrasting spectra, the latter exhibiting heterogeneity and enhanced internal motions on a microsecond-to-millisecond time scale. The strength of the H-bond network involving Tyr22 (B10) and bound cyanide was tested at high pH. 3-Fluorotyrosine at position 22 had a pK(a) value at least 3 units higher than its intrinsic value, 8.5. In addition, evidence was found for long-range communication among the tyrosine sites. These observations demonstrated the utility of the 3-fluorotyrosine approach to gain insight in hemoglobin properties.
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Affiliation(s)
- Matthew P Pond
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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11
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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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12
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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: 331] [Impact Index Per Article: 25.5] [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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13
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Hoesl MG, Acevedo-Rocha CG, Nehring S, Royter M, Wolschner C, Wiltschi B, Budisa N, Antranikian G. Lipase Congeners Designed by Genetic Code Engineering. ChemCatChem 2010. [DOI: 10.1002/cctc.201000253] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Wilkins BJ, Marionni S, Young DD, Liu J, Wang Y, Di Salvo ML, Deiters A, Cropp TA. Site-Specific Incorporation of Fluorotyrosines into Proteins in Escherichia coli by Photochemical Disguise. Biochemistry 2010; 49:1557-9. [DOI: 10.1021/bi100013s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bryan J. Wilkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Samuel Marionni
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Douglas D. Young
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Jia Liu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Yan Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Martino L. Di Salvo
- Dipartimento di Scienze Biochimiche and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro, 5-00185 Roma, Italy
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - T. Ashton Cropp
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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15
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Incorporation of non-natural modules into proteins: structural features beyond the genetic code. Biotechnol Lett 2009; 31:1129-39. [DOI: 10.1007/s10529-009-0002-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 04/02/2009] [Accepted: 04/06/2009] [Indexed: 11/25/2022]
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16
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Gopishetty B, Ren L, Waller TM, Wavreille AS, Lopez M, Thakkar A, Zhu J, Pei D. Synthesis of 3,5-difluorotyrosine-containing peptides: application in substrate profiling of protein tyrosine phosphatases. Org Lett 2008; 10:4605-8. [PMID: 18798640 DOI: 10.1021/ol801868a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fully protected 3,5-difluorotyrosine (F2Y), Fmoc-F2Y(tBu)-OH, is efficiently prepared by a chemoenzymatic process and incorporated into individual peptides and combinatorial peptide libraries. The F2Y-containing peptides display kinetic properties toward protein tyrosine phosphatases (PTPs) similar to their corresponding tyrosine-containing counterparts but are resistant to tyrosinase action. These properties make F2Y a useful tyrosine surrogate during peptide library screening for optimal PTP substrates.
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Affiliation(s)
- Bhaskar Gopishetty
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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17
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Photostability of green and yellow fluorescent proteins with fluorinated chromophores, investigated by fluorescence correlation spectroscopy. Biophys Chem 2008; 136:38-43. [DOI: 10.1016/j.bpc.2008.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 04/10/2008] [Accepted: 04/10/2008] [Indexed: 11/17/2022]
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18
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Song L, Teng Q, Phillips RS, Brewer JM, Summers AO. 19F-NMR Reveals Metal and Operator-induced Allostery in MerR. J Mol Biol 2007; 371:79-92. [PMID: 17560604 DOI: 10.1016/j.jmb.2007.04.085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2007] [Revised: 04/15/2007] [Accepted: 04/17/2007] [Indexed: 11/18/2022]
Abstract
Metalloregulators of the MerR family activate transcription upon metal binding by underwinding the operator-promoter DNA to permit open complex formation by pre-bound RNA polymerase. Historically, MerR's allostery has been monitored only indirectly via nuclease sensitivity or by fluorescent nucleotide probes and was very specific for Hg(II), although purified MerR binds several thiophilic metals. To observe directly MerR's ligand-induced behavior we made 2-fluorotyrosine-substituted MerR and found similar, minor changes in (19)F chemical shifts of tyrosine residues in the free protein exposed to Hg(II), Cd(II) or Zn(II). However, DNA binding elicits large chemical shift changes in MerR's tyrosine residues and in DNA-bound MerR Hg(II) provokes changes very distinct from those of Cd(II) or Zn(II). These chemical shift changes and other biophysical and phenotypic properties of wild-type MerR and relevant mutants reveal elements of an allosteric network that enables the coordination state of the metal binding site to direct metal-specific movements in the distant DNA binding site and the DNA-bound state also to affect the metal binding domain.
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Affiliation(s)
- Lingyun Song
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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19
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20
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Votchitseva YA, Efremenko EN, Varfolomeyev SD. Insertion of an unnatural amino acid into the protein structure: preparation and properties of 3-fluorotyrosine-containing organophosphate hydrolase. Russ Chem Bull 2006. [DOI: 10.1007/s11172-006-0262-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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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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22
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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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23
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Bae JH, Paramita Pal P, Moroder L, Huber R, Budisa N. Crystallographic Evidence for Isomeric Chromophores in 3-Fluorotyrosyl-Green Fluorescent Protein. Chembiochem 2004; 5:720-2. [PMID: 15122645 DOI: 10.1002/cbic.200300818] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jae Hyun Bae
- Max-Planck-Institut für Biochemie, Abt. Strukturforschung, Am Klopferspitz 18a, 82152 Martinsried, Germany
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24
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Park H, Merz KM. Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta5-3-ketosteroid isomerase: the catalytic diad versus the cooperative hydrogen bond mechanism. J Am Chem Soc 2003; 125:901-11. [PMID: 12537487 DOI: 10.1021/ja0208097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To further understand Delta(5)-3-ketosteroid isomerase (KSI) catalysis, we carried out molecular dynamics (MD) simulations of the KSI dimer ligated with a substrate and reaction intermediate analogue and high level ab initio calculations on relevant enzymatic reaction models. Simulation of the enzyme-substrate complex dimer systems showed asymmetric dynamics between the two monomers, in which the hydrogen bond pattern between the substrate and active site residues in the first and the second subunits supported the cooperative hydrogen bond (CH) and the catalytic diad (CD) mechanisms, respectively. On the other hand, only the CH mechanism was supported in the MD simulation of the enzyme-intermediate complex dimer. From MP2/6-31+G**//RHF/6-31G** calculations, we found the kinetic barriers for the two reaction mechanisms were similar. The CH route afforded a greater stabilization to the enolate intermediate than did the CD counterpart. Thus, the present computational studies indicate that the CH mechanism would be favored over the CD one in the catalytic action of KSI. However, the latter could not be ruled out conclusively because of the explicit appearance of a CD configuration in the MD trajectories of the enzyme-substrate complex and because of the similar intrinsic activation barrier for the CH and CD mechanisms. The appearance of configurations that favor the CD pathway is rationalized in terms of a model in which the KSI-substrate complex does not have a strong preference for one hydrogen bonding pattern over another, while the KSI-intermediate complex favors a cooperative hydrogen bond pattern in order to stabilize the reaction intermediate. This hypothesis is supported by the ab initio calculations which indicate that the CH intermediate is more stable than the CD one by approximately 6.3 kcal/mol.
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Affiliation(s)
- Hwangseo Park
- 152 Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park, PA 16802-6300, USA
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Minks C, Alefelder S, Moroder L, Huber R, Budisa N. Towards New Protein Engineering: In Vivo Building and Folding of Protein Shuttles for Drug Delivery and Targeting by the Selective Pressure Incorporation (SPI) Method. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00827-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Abstract
[reaction: see text] Furanomycin is a Streptomyces metabolite that substitutes for isoleucine in protein translation. We report a concise and modular synthesis starting from the Garner aldehyde and proceeding in seven steps to furanomycin. The key steps include a stereoselective acetylide addition and the Ag+-mediated cyclization of an alpha-allenic alcohol to construct the trans-2,5-dihydrofuran. The efficiency (12% overall yield) and flexibility of the route will provide ample quantities of furanomycin and analogues for protein engineering.
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Affiliation(s)
- M P VanBrunt
- Texas A&M University, Department of Chemistry, College Station 77842-3012, USA
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