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Abdelkader EH, Qianzhu H, Huber T, Otting G. Genetic Encoding of 7-Aza-l-tryptophan: Isoelectronic Substitution of a Single CH-Group in a Protein for a Nitrogen Atom for Site-Selective Isotope Labeling. ACS Sens 2023; 8:4402-4406. [PMID: 37890165 DOI: 10.1021/acssensors.3c01904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Genetic encoding of a noncanonical amino acid (ncAA) in an in vivo expression system requires an aminoacyl-tRNA synthetase that specifically recognizes the ncAA, while the ncAA must not be recognized by the canonical protein expression machinery. We succeeded in genetically encoding 7-aza-tryptophan (7AW), which is isoelectronic with tryptophan. The system is fully orthogonal to protein expression in Escherichia coli, enabling high-yielding site-selective isotope labeling in vivo. 7AW is readily synthesized from serine and 7-aza-indole using a tryptophan synthetase β-subunit (TrpB) mutant, affording easy access to isotope-labeled 7AW. Using labeled 7AW produced from 15N/13C-labeled serine, we produced 7AW mutants of the 25 kDa Zika virus NS2B-NS3 protease. 15N-HSQC spectra display single cross-peaks at chemical shifts near those observed for the wild-type protein labeled with 15N/13C-tryptophan, confirming the structural integrity of the protein and yielding straightforward NMR resonance assignments for site-specific probing.
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Affiliation(s)
- Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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2
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My remembrances of H.G. Khorana: exploring the mechanism of bacteriorhodopsin with site-directed mutagenesis and FTIR difference spectroscopy. Biophys Rev 2023; 15:103-110. [PMID: 36909952 PMCID: PMC9995631 DOI: 10.1007/s12551-023-01046-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
H.G. Khorana's seminal contributions to molecular biology are well-known. He also had a lesser known but still major influence on current application of advanced vibrational spectroscopic techniques such as FTIR difference spectroscopy to explore the mechanism of bacteriorhodopsin and other integral membrane proteins. In this review, I provide a personal perspective of my collaborative research and interactions with Gobind, from 1982 to 1995 when our groups published over 25 papers together which resulted in an early picture of key features of the bacteriorhodopsin proton pump mechanism. Much of this early work served as a blueprint for subsequent advances based on combining protein bioengineering and vibrational spectroscopic techniques to study integral membrane proteins.
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3
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Interdisciplinary biophysical studies of membrane proteins bacteriorhodopsin and rhodopsin. Biophys Rev 2023; 15:111-125. [PMID: 36909961 PMCID: PMC9995646 DOI: 10.1007/s12551-022-01003-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/28/2022] [Indexed: 10/10/2022] Open
Abstract
The centenary of the birth of H. Gobind Khorana provides an auspicious opportunity to review the origins and evolution of parallel advances in biophysical methodology and molecular genetics technology used to study membrane proteins. Interdisciplinary work in the Khorana laboratory in the late 1970s and for the next three decades led to productive collaborations and fostered three subsequent scientific generations whose biophysical work on membrane proteins has led to detailed elucidation of the molecular mechanisms of energy transduction by the light-driven proton pump bacteriorhodopsin (bR) and signal transduction by the G protein-coupled receptor (GPCR) rhodopsin. This review will highlight the origins and advances of biophysical studies of membrane proteins made possible by the application of molecular genetics approaches to engineer site-specific alterations of membrane protein structures.
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4
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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5
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Mitri E, Barbieri L, Vaccari L, Luchinat E. 15N isotopic labelling for in-cell protein studies by NMR spectroscopy and single-cell IR synchrotron radiation FTIR microscopy: a correlative study. Analyst 2018; 143:1171-1181. [DOI: 10.1039/c7an01464c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The effect of 15N-enrichment on human cells analyzed by correlative in-cell NMR and single-cell SR-FTIR experiments.
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Affiliation(s)
- E. Mitri
- Elettra – Sincrotrone Trieste S.C.p.A
- SISSI Beamline – Chemical and Life Sciences Branch
- 34149, Basovizza
- Italy
| | - L. Barbieri
- Magnetic Resonance Centre (CERM)
- University of Florence
- 50019 Sesto Fiorentino
- Italy
- Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP)
| | - L. Vaccari
- Elettra – Sincrotrone Trieste S.C.p.A
- SISSI Beamline – Chemical and Life Sciences Branch
- 34149, Basovizza
- Italy
| | - E. Luchinat
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”
- University of Florence
- 50134 Florence
- Italy
- Magnetic Resonance Centre (CERM)
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6
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Priest M, Bezanilla F. Functional Site-Directed Fluorometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 869:55-76. [PMID: 26381940 DOI: 10.1007/978-1-4939-2845-3_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Initially developed in the mid-1990s to examine the conformational changes of the canonical Shaker voltage-gated potassium channel, functional site-directed fluorometry has since been expanded to numerous other voltage-gated and ligand-gated ion channels as well as transporters, pumps, and other integral membrane proteins. The power of functional site-directed fluorometry, also known as voltage-clamp fluorometry, lies in its ability to provide information on the conformational changes in a protein in response to changes in its environment with high temporal resolution while simultaneously monitoring the function of that protein. Over time, applications of site-directed fluorometry have expanded to examine the interactions of ion channels with modulators ranging from membrane potential to ligands to accessory protein subunits to lipids. In the future, the range of questions answerable by functional site-directed fluorometry and its interpretive power should continue to improve, making it an even more powerful technique for dissecting the conformational dynamics of ion channels and other membrane proteins.
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Affiliation(s)
- Michael Priest
- Department of Biochemistry and Molecular Biology and Committee on Neurobiology, University of Chicago, Gordon Center for Integrative Science W229M, 929 East 57th Street, 60637, Chicago, IL, USA.
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology and Committee on Neurobiology, University of Chicago, Gordon Center for Integrative Science W229M, 929 East 57th Street, 60637, Chicago, IL, USA.
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7
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Peuker S, Andersson H, Gustavsson E, Maiti KS, Kania R, Karim A, Niebling S, Pedersen A, Erdelyi M, Westenhoff S. Efficient Isotope Editing of Proteins for Site-Directed Vibrational Spectroscopy. J Am Chem Soc 2016; 138:2312-8. [DOI: 10.1021/jacs.5b12680] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sebastian Peuker
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Hanna Andersson
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Emil Gustavsson
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Kiran Sankar Maiti
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Rafal Kania
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Alavi Karim
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Stephan Niebling
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Anders Pedersen
- Swedish
NMR Centre at the University of Gothenburg, P.O. Box 465, SE-405 30 Gothenburg, Sweden
| | - Mate Erdelyi
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department
of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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8
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Quast RB, Mrusek D, Hoffmeister C, Sonnabend A, Kubick S. Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis. FEBS Lett 2015; 589:1703-12. [PMID: 25937125 DOI: 10.1016/j.febslet.2015.04.041] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Devid Mrusek
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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9
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Althaus T, Eisfeld W, Lohrmann R, Stockburger M. Application of Raman Spectroscopy to Retinal Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.199500029] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Maeda A. Application of FTIR Spectroscopy to the Structural Study on the Function of Bacteriorhodopsin. Isr J Chem 2013. [DOI: 10.1002/ijch.199500038] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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12
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Rathod R, Kang Z, Hartson SD, Kumauchi M, Xie A, Hoff WD. Side-chain specific isotopic labeling of proteins for infrared structural biology: The case of ring-D4-tyrosine isotope labeling of photoactive yellow protein. Protein Expr Purif 2012; 85:125-32. [DOI: 10.1016/j.pep.2012.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/18/2012] [Indexed: 10/28/2022]
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13
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Garand E, Kamrath MZ, Jordan PA, Wolk AB, Leavitt CM, McCoy AB, Miller SJ, Johnson MA. Determination of noncovalent docking by infrared spectroscopy of cold gas-phase complexes. Science 2012; 335:694-8. [PMID: 22267579 PMCID: PMC4038764 DOI: 10.1126/science.1214948] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Multidentate, noncovalent interactions between small molecules and biopolymer fragments are central to processes ranging from drug action to selective catalysis. We present a versatile and sensitive spectroscopic probe of functional groups engaged in hydrogen bonding in such contexts. This involves measurement of the frequency changes in specific covalent bonds upon complex formation, information drawn from otherwise transient complexes that have been extracted from solution and conformationally frozen near 10 kelvin in gas-phase clusters. Resonances closely associated with individual oscillators are easily identified through site-specific isotopic labeling, as demonstrated by application of the method to an archetypal system involving a synthetic tripeptide known to bind biaryl substrates through tailored hydrogen bonding to catalyze their asymmetric bromination. With such data, calculations readily converge on the plausible operative structures in otherwise computationally prohibitive, high-dimensionality landscapes.
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Affiliation(s)
- Etienne Garand
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Michael Z. Kamrath
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Peter A. Jordan
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Arron B. Wolk
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | | | - Anne B. McCoy
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
| | - Scott J. Miller
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520
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14
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Sudo Y, Tanaka R, Kobayashi T, Kamo N, Kohno T, Kojima C. Functional expression of a two-transmembrane HtrII protein using cell-free synthesis. Biophysics (Nagoya-shi) 2011; 7:51-58. [PMID: 27857592 PMCID: PMC5036783 DOI: 10.2142/biophysics.7.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 05/23/2011] [Indexed: 12/01/2022] Open
Abstract
An approach of cell-free synthesis is presented for the functional expression of transmembrane proteins without the need of refolding. The transmembrane region of the pharaonis halobacterial transducer protein, pHtrII, was translated with various large soluble tags added (thioredoxin, glutathione S-transferase, green fluorescent protein and maltose binding protein). In this system, all fusion pHtrII were translated in a soluble fraction, presumably, forming giant micelle-like structures. The detergent n-dodecyl-β-d-maltoside was added for enhancing the solubilization of the hydrophobic region of pHtrII. The activity of the expressed pHtrII, having various tags, was checked using a pull-down assay, using the fact that pHtrII forms a signaling complex with pharaonis phoborhodopsin (ppR) in the membrane, as also in the presence of a detergent. All tagged pHtrII showed a binding activity with ppR. Interestingly, the binding activity with ppR was positively correlated with the molecular weight of the soluble tags. Thus, larger soluble tags lead to higher binding activities. We could show, that our approach is beneficial for the preparation of active membrane proteins, and is also potentially applicable for larger membrane proteins, such as 7-transmembrane proteins.
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Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Rikou Tanaka
- Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-0031, Japan
| | - Toshitatsu Kobayashi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Toshiyuki Kohno
- Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-0031, Japan
| | - Chojiro Kojima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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15
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Zhu J, Lau JYC, Wu G. A solid-state (17)O NMR study of L-tyrosine in different ionization states: implications for probing tyrosine side chains in proteins. J Phys Chem B 2010; 114:11681-8. [PMID: 20712305 DOI: 10.1021/jp1055123] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report experimental characterization of (17)O quadrupole coupling (QC) and chemical shift (CS) tensors for the phenolic oxygen in three l-tyrosine (l-Tyr) compounds: l-Tyr, l-Tyr.HCl, and Na(2)(l-Tyr). This is the first time that these fundamental (17)O NMR tensors are completely determined for phenolic oxygens in different ionization states. We find that, while the (17)O QC tensor changes very little upon phenol ionization, the (17)O CS tensor displays a remarkable sensitivity. In particular, the isotropic (17)O chemical shift increases by approximately 60 ppm upon phenol ionization, which is 6 times larger than the corresponding change in the isotropic (13)C chemical shift for the C(zeta) nucleus of the same phenol group. By examining the CS tensor orientation in the molecular frame of reference, we discover a "cross-over" effect between delta(11) and delta(22) components for both (17)O and (13)C CS tensors. We demonstrate that the knowledge of such "cross-over" effects is crucial for understanding the relationship between the observed CS tensor components and chemical bonding. Our results suggest that solid-state (17)O NMR can potentially be used to probe the ionization state of tyrosine side chains in proteins.
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Affiliation(s)
- Jianfeng Zhu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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16
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Middleton CT, Woys AM, Mukherjee SS, Zanni MT. Residue-specific structural kinetics of proteins through the union of isotope labeling, mid-IR pulse shaping, and coherent 2D IR spectroscopy. Methods 2010; 52:12-22. [PMID: 20472067 DOI: 10.1016/j.ymeth.2010.05.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 05/08/2010] [Accepted: 05/11/2010] [Indexed: 12/12/2022] Open
Abstract
We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for (13)C(18)O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide implicated in type 2 diabetes.
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Affiliation(s)
- Chris T Middleton
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1396, United States
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17
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Sobhanifar S, Reckel S, Junge F, Schwarz D, Kai L, Karbyshev M, Löhr F, Bernhard F, Dötsch V. Cell-free expression and stable isotope labelling strategies for membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2010; 46:33-43. [PMID: 19680602 DOI: 10.1007/s10858-009-9364-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 07/16/2009] [Indexed: 05/17/2023]
Abstract
Membrane proteins are highly underrepresented in the structural data-base and remain one of the most challenging targets for functional and structural elucidation. Their roles in transport and cellular communication, furthermore, often make over-expression toxic to their host, and their hydrophobicity and structural complexity make isolation and reconstitution a complicated task, especially in cases where proteins are targeted to inclusion bodies. The development of cell-free expression systems provides a very interesting alternative to cell-based systems, since it circumvents many problems such as toxicity or necessity for the transportation of the synthesized protein to the membrane, and constitutes the only system that allows for direct production of membrane proteins in membrane-mimetic environments which may be suitable for liquid state NMR measurements. The unique advantages of the cell-free expression system, including strong expression yields as well as the direct incorporation of almost any combination of amino acids with very little metabolic scrambling, has allowed for the development of a wide-array of isotope labelling techniques which facilitate structural investigations of proteins whose spectral congestion and broad line-widths may have earlier rendered them beyond the scope of NMR. Here we explore various labelling strategies in conjunction with cell-free developments, with a particular focus on alpha-helical transmembrane proteins which benefit most from such methods.
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Affiliation(s)
- Solmaz Sobhanifar
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
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18
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Andresen ER, Hamm P. Site-specific difference 2D-IR spectroscopy of bacteriorhodopsin. J Phys Chem B 2009; 113:6520-7. [PMID: 19358550 DOI: 10.1021/jp810397u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We demonstrate the extension of the principle of difference Fourier transform infrared (FTIR) spectroscopy to difference 2D-IR spectroscopy. To this end, we measure difference 2D-IR spectra of the protein bacteriorhodopsin in its early J- and K-intermediates. By comparing with the static 2D-IR spectrum of the protonated Schiff base of all-trans retinal, we demonstrate that the 2D-IR spectrum of the all-trans retinal chromophore in bacteriorhodopsin can be measured with the background from the remainder of the protein completely suppressed. We discuss several models to interpret the detailed line shape of the difference 2D-IR spectrum.
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Affiliation(s)
- Esben Ravn Andresen
- Physikalisch-Chemisches Institut, Universitat Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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19
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20
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Lim M, Rothschild KJ. Photocleavage-based affinity purification and printing of cell-free expressed proteins: application to proteome microarrays. Anal Biochem 2008; 383:103-15. [PMID: 18762158 PMCID: PMC2784287 DOI: 10.1016/j.ab.2008.07.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/10/2008] [Accepted: 07/29/2008] [Indexed: 11/29/2022]
Abstract
Proteome microarrays hold great promise for various biotechnological and biomedical applications, including mapping protein-protein interactions, drug discovery, and biomarker discovery. However, the need to express, purify, and print thousands of functional proteins at high density on a microarray substrate presents challenges that limit their widespread availability and use. We report the development of new methods, based on photocleavage, for the purification and printing of nascent proteins. Photocleavable biotin (PC-biotin) is incorporated into nascent proteins by misaminoacylated transfer RNAs (tRNAs) used in a coupled transcription/translation rabbit reticulocyte cell-free expression system. Proteins were affinity isolated onto (strept)avidin-coated beads and then photoreleased (PC-SNAG). Compared with polyhistidine tag-based affinity purification, PC-SNAG provided a higher purity yet a comparable yield using a glutathione-S-transferase (GST) test protein. Antibody-mediated PC-SNAG is also demonstrated. PC-SNAG proteins were found to exhibit native enzymatic activity and were suitable for the printing of ordered protein microarrays used in protein-protein interaction assays. Alternatively, when beads carrying photocleavably tethered proteins were placed in close proximity to an activated planar surface and then illuminated, proteins were transferred directly to the surface (PC-PRINT) to form discrete spots whose dimensions match those of the beads. PC-PRINT can provide an inexpensive method to fabricate very large-scale, high-density proteome microarrays. Moreover, transferring the proteins off the beads significantly reduces background autofluorescence observed with common bead types. To decode nascent proteins that are deposited by PC-PRINT from individual beads, the feasibility of using photocleavable quantum dot codes is demonstrated.
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Affiliation(s)
- Mark Lim
- AmberGen, Watertown, MA 02472, USA.
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21
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Katzen F, Fletcher JE, Yang JP, Kang D, Peterson TC, Cappuccio JA, Blanchette CD, Sulchek T, Chromy BA, Hoeprich PD, Coleman MA, Kudlicki W. Insertion of Membrane Proteins into Discoidal Membranes Using a Cell-Free Protein Expression Approach. J Proteome Res 2008; 7:3535-42. [DOI: 10.1021/pr800265f] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Katzen
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Julia E. Fletcher
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Jian-Ping Yang
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Douglas Kang
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Todd C. Peterson
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Jenny A. Cappuccio
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Craig D. Blanchette
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Todd Sulchek
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Brett A. Chromy
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Paul D. Hoeprich
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Matthew A. Coleman
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
| | - Wieslaw Kudlicki
- Invitrogen Corporation, 5791 Van Allen Way, Carlsbad, California 92008, and Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551
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22
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Jagus R, Beckler GS. Overview of eukaryotic in vitro translation and expression systems. ACTA ACUST UNITED AC 2008; Chapter 11:Unit 11.1. [PMID: 18228417 DOI: 10.1002/0471143030.cb1101s00] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ability to investigate cellular processes in vitro permits detailed analysis of the process and its molecular components. Eukaryotic translation and expression is one system that has been well studied. This overview describes the development of in vitro systems, including such approaches as continuous-flow systems, coupled transcription/translation, and the incorporation of non-natural amino acids. It also discusses molecular and genetic studies to probe translation, including post-translational fate of the synthesized proteins.
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Affiliation(s)
- Rosemary Jagus
- Center of Marine and Biotechnology and Greenebaum Cancer Center, Baltimore, Maryland, USA
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23
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Barth A. Infrared spectroscopy of proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1073-101. [PMID: 17692815 DOI: 10.1016/j.bbabio.2007.06.004] [Citation(s) in RCA: 2768] [Impact Index Per Article: 162.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 12/12/2022]
Abstract
This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.
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Affiliation(s)
- Andreas Barth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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24
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Rich PR, Iwaki M. Methods to probe protein transitions with ATR infrared spectroscopy. MOLECULAR BIOSYSTEMS 2007; 3:398-407. [PMID: 17533453 DOI: 10.1039/b702328f] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe techniques that can be used in conjunction with modern attenuated total reflection (ATR) infrared micro-prisms to allow proteins to be manipulated cyclically between different states whilst simultaneously monitoring both mid-IR and UV/visible/near IR changes. These methods provide increased flexibility of the types of changes that can be induced in proteins in comparison to transmission methods. Quantitative measurements can be made of vibrational changes associated with conversion between stable catalytic reaction intermediates, ligand binding and oxidation-reduction. Both hydrophobic and soluble proteins can be analysed and the ability to induce transitions repetitively allows IR difference spectra to be acquired at a signal/noise sufficient to resolve changes due to specific cofactors or amino acids. Such spectra can often be interpreted at the atomic level by standard IR methods of comparisons with model compounds, by isotope and mutation effects and, increasingly, by ab initio simulations. Combination of such analyses with atomic 3D structural models derived from X-ray and NMR studies can lead to a deeper understanding of molecular mechanisms of enzymatic reactions.
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Affiliation(s)
- Peter R Rich
- Glynn Laboratory of Bioenergetics, Department of Biology, University College London, Gower Street, London, U.K.
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25
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Zehender F, Labahn A, Koslowski T. Detecting protein-protein interactions by isotope-edited infrared spectroscopy: a numerical approach. J Phys Chem B 2005; 109:23674-8. [PMID: 16375347 DOI: 10.1021/jp053487c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a theoretical and numerical analysis of the vibrational coupling between isotope-edited amino acids in protein dimers. Depending on the presence and magnitude of coupling between 13Calpha=O peptide bond oscillators, characteristic level splittings of vibrational eigenstates are predicted. For the example of the Gramicidin A ion channel polypeptide, we observe typical IR fingerprints for the head-to-head and the antiparallel double-helical conformation of the dimer. We suggest that these findings can be used to clearly identify the structure of polypeptide aggregates using a particularly simple isotope substitution pattern.
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Affiliation(s)
- Fabian Zehender
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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26
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Ham S, Cha S, Choi JH, Cho M. Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects. J Chem Phys 2003. [DOI: 10.1063/1.1581855] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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27
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Bergo V, Mamaev S, Olejnik J, Rothschild KJ. Methionine changes in bacteriorhodopsin detected by FTIR and cell-free selenomethionine substitution. Biophys J 2003; 84:960-6. [PMID: 12547777 PMCID: PMC1302673 DOI: 10.1016/s0006-3495(03)74912-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Bacteriorhodopsin (BR) is an integral membrane protein, which functions as a light-driven proton pump in Halobacterium salinarum. We report evidence that one or more methionine residues undergo a structural change during the BR-->M portion of the BR photocycle. Selenomethionine was incorporated into BR using a cell-free protein translation system containing an amino acid mixture with selenomethionine substituted for methionine. BR-->M FTIR difference spectra recorded for unlabeled and selenomethionine-labeled cell-free expressed BR closely resemble the spectra of in vivo expressed BR. However, reproducible changes occur in two regions near 1,284 and 900 cm(-1) due to selenomethionine incorporation. Isotope labeled tyrosine was also co-incorporated with selenomethionine in order to confirm these assignments. Based on recent x-ray crystallographic studies, likely methionines which give rise to the FTIR difference bands are Met-118 and Met-145, which are located inside the retinal binding pocket and in a position to constrain the motion of retinal during photoisomerization. The assignment of methionine bands in the FTIR difference spectrum of BR provides a means to study methionine-chromophore interaction under physiological conditions. More generally, combining cell-free incorporations of selenomethionine into proteins with FTIR difference spectroscopy provides a useful method for investigating the role of methionines in protein structure and function.
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Affiliation(s)
- Vladislav Bergo
- Physics Deptartment, Boston University, Boston, Massachusetts 02215, USA
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28
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Barth A. The infrared absorption of amino acid side chains. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 74:141-73. [PMID: 11226511 DOI: 10.1016/s0079-6107(00)00021-3] [Citation(s) in RCA: 877] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Amino acid side chains play fundamental roles in stabilising protein structures and in catalysing enzymatic reactions. These fields are increasingly investigated by infrared spectroscopy at the molecular level. To help the interpretation of the spectra, a review of the infrared absorption of amino acid side chains in H(2)O and 2H(2)O is given. The spectral region of 2600-900cm(-1) is covered.
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Affiliation(s)
- A Barth
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Theodor Stern-Kai 7, Haus 74, D-60590 Frankfurt am Main, Germany.
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29
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Kowal AK, Kohrer C, RajBhandary UL. Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria. Proc Natl Acad Sci U S A 2001; 98:2268-73. [PMID: 11226228 PMCID: PMC30127 DOI: 10.1073/pnas.031488298] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2000] [Indexed: 01/07/2023] Open
Abstract
Two critical requirements for developing methods for the site-specific incorporation of amino acid analogues into proteins in vivo are (i) a suppressor tRNA that is not aminoacylated by any of the endogenous aminoacyl-tRNA synthetases (aaRSs) and (ii) an aminoacyl-tRNA synthetase that aminoacylates the suppressor tRNA but no other tRNA in the cell. Here we describe two such aaRS-suppressor tRNA pairs, one for use in the yeast Saccharomyces cerevisiae and another for use in Escherichia coli. The "21st synthetase-tRNA pairs" include E. coli glutaminyl-tRNA synthetase (GlnRS) along with an amber suppressor derived from human initiator tRNA, for use in yeast, and mutants of the yeast tyrosyl-tRNA synthetase (TyrRS) along with an amber suppressor derived from E. coli initiator tRNA, for use in E. coli. The suppressor tRNAs are aminoacylated in vivo only in the presence of the heterologous aaRSs, and the aminoacylated tRNAs function efficiently in suppression of amber codons. Plasmids carrying the E. coli GlnRS gene can be stably maintained in yeast. However, plasmids carrying the yeast TyrRS gene could not be stably maintained in E. coli. This lack of stability is most likely due to the fact that the wild-type yeast TyrRS misaminoacylates the E. coli proline tRNA. By using error-prone PCR, we have isolated and characterized three mutants of yeast TyrRS, which can be stably expressed in E. coli. These mutants still aminoacylate the suppressor tRNA essentially quantitatively in vivo but show increased discrimination in vitro for the suppressor tRNA over the E. coli proline tRNA by factors of 2.2- to 6.8-fold.
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Affiliation(s)
- A K Kowal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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30
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Behrens C, Nielsen JN, Fan XJ, Doisy X, Kim KH, Praetorius-Ibba M, Nielsen PE, Ibba M. Development of Strategies for the Site-Specific In Vivo Incorporation of Photoreactive Amino Acids: p-Azidophenylalanine, p-Acetylphenylalanine and Benzofuranylalanine. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00828-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Fahmy K, Sakmar TP, Siebert F. Structural determinants of active state conformation of rhodopsin: molecular biophysics approaches. Methods Enzymol 2000; 315:178-96. [PMID: 10736702 DOI: 10.1016/s0076-6879(00)15843-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Affiliation(s)
- K Fahmy
- Institut für Biophysik und Strahlenbiologie, Albert-Ludwigs-Universität, Freiburg, Germany
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32
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Gite S, Mamaev S, Olejnik J, Rothschild K. Ultrasensitive fluorescence-based detection of nascent proteins in gels. Anal Biochem 2000; 279:218-25. [PMID: 10706791 DOI: 10.1006/abio.1999.4472] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The most common method of analysis of proteins synthesized in a cell-free translation system (e.g., nascent proteins) involves the use of radioactive amino acids such as [(35)S]methionine or [(14)C]leucine. We report a sensitive, nonisotopic, fluorescence-based method for the detection of nascent proteins directly in polyacrylamide gels. A fluorescent reporter group is incorporated at the N-terminus of nascent proteins using an Escherichia coli initiator tRNA(fmet) misaminoacylated with methionine modified at the alpha-amino group. In addition to the normal formyl group, we find that the protein translational machinery accepts BODIPY-FL, a relatively small fluorophore with a high fluorescent quantum yield, as an N-terminal modification. Under the optimal conditions, fluorescent bands from nanogram levels of in vitro-produced proteins could be detected directly in gels using a conventional UV-transilluminator. Higher sensitivity ( approximately 100-fold) could be obtained using a laser-based fluorescent gel scanner. The major advantages of this approach include elimination of radioactivity and the rapid detection of the protein bands immediately after electrophoresis without any downstream processing. The ability to rapidly synthesize nascent proteins containing an N-terminal tag facilitates many biotechnological applications including functional analysis of gene products, drug discovery, and mutation screening.
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Affiliation(s)
- S Gite
- AmberGen, Inc., 1106, Commonwealth Avenue, Boston, Massachusetts, 02215, USA
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33
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34
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Sydor JR, Seidel RP, Goody RS, Engelhard M. Cell-free synthesis of the Ras-binding domain of c-Raf-1: binding studies to fluorescently labelled H-ras. FEBS Lett 1999; 452:375-8. [PMID: 10386625 DOI: 10.1016/s0014-5793(99)00633-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has previously been shown that the transient kinetics of the interaction between the Ras-binding domain of c-Raf-1 and the proto-oncoprotein Ras can be followed by stopped-flow measurements using the 2',3'-(N-methylanthraniloyl) fluorescence of 2',3'-(N-methylanthraniloyl) guanyl-5'-yl-imidodiphosphate-labelled Ras. In continuation of this work, we demonstrate that the His-tagged Ras-binding domain of c-Raf-1 can also be synthesized in a cell-free expression system. After purification by Ni2+ affinity chromatography, His-tagged Ras-binding domain of c-Raf-1 could be isolated in sufficient amounts for biochemical and biophysical investigations. The results obtained describe the first example of a cell-free synthesized protein which has been used for stopped-flow measurements to determine the transient kinetics of protein-protein interactions with an effector.
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Affiliation(s)
- J R Sydor
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, Dortmund, Germany
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35
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Chollet A, Turcatti G. Biophysical approaches to G protein-coupled receptors: structure, function and dynamics. J Comput Aided Mol Des 1999; 13:209-19. [PMID: 10216829 DOI: 10.1023/a:1008052002695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
G protein-coupled receptors (GPCR) represent a large family of drug targets for which there is no high resolution structural information. In order to understand the mechanisms of ligand recognition and receptor activation, there is a strong need for novel biophysical methods. In this Perspective we provide an overview of recent experimental approaches used to explore the molecular architecture and dynamics of GPCR and their interactions with ligands and G proteins using biophysical, non-crystallographic, methods.
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Affiliation(s)
- A Chollet
- Serono Pharmaceutical Research Institute, Geneva, Switzerland
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36
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Kigawa T, Yabuki T, Yoshida Y, Tsutsui M, Ito Y, Shibata T, Yokoyama S. Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Lett 1999; 442:15-9. [PMID: 9923595 DOI: 10.1016/s0014-5793(98)01620-2] [Citation(s) in RCA: 404] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have improved the productivity of an Escherichia coli cell-free protein synthesis system. First, creatine phosphate and creatine kinase were used as the energy source regeneration system, and the other components of the reaction mixture were optimized. Second, the E. coli S30 cell extract was condensed by dialysis against a polyethylene glycol solution to increase the rate of synthesis. Third, during the protein synthesis, the reaction mixture was dialyzed against a low-molecular-weight substrate solution to prolong the reaction. Thus, the yield of chloramphenicol acetyltransferase was raised to 6 mg/ml of reaction mixture. Stable-isotope labeling of a protein with 13C/15N-labeled amino acids for NMR spectroscopy was achieved by this method.
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Affiliation(s)
- T Kigawa
- Cellular Signaling Laboratory, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama, Japan
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37
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Liu X, Lee MJ, Coleman M, Rath P, Nilsson A, Fischer WB, Bizounok M, Herzfeld J, Karstens WF, Raap J, Lugtenburg J, Rothschild KJ. Detection of threonine structural changes upon formation of the M-intermediate of bacteriorhodopsin: evidence for assignment to Thr-89. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1365:363-72. [PMID: 9711293 DOI: 10.1016/s0005-2728(98)00088-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The behavior of threonine residues in the bacteriorhodopsin (bR) photocycle has been investigated by Fourier transform infrared difference spectroscopy. L-Threonine labeled at the hydroxyl group with 18O (L-[3-(18)O]threonine) was incorporated into bR and the bR-->M FTIR difference spectra measured. Bands are assigned to threonine vibrational modes on the basis of 18O induced isotope frequency shifts and normal mode calculations. In the 3500 cm-1 region, a negative band is assigned to the OH stretch of threonine. In the 1125 cm-1 region, a negative band is assigned to a mixed CH3 rock/CO stretch mode. The frequency of both these bands indicates the presence of at least one hydrogen bonded threonine hydroxyl group in light adapted bR which undergoes a change in structure by formation of the M intermediate. Spectral changes induced by the substitution Thr-89-->Asn but not Thr-46-->Asn or Asp-96-->Asn are consistent with the assignment of these bands to Thr-89. These results along with another related study on the mutant Thr-89-->Asn indicate that the active site of bR includes Thr-89 and that its interaction with the retinylidene Schiff base and Asp-85 may play an important role in regulating the color of bacteriorhodopsin and the transfer of a proton to the Schiff base.
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Affiliation(s)
- X Liu
- Physics Department, Boston University, MA 02215, USA
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38
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di Cera E. Site-specific analysis of mutational effects in proteins. ADVANCES IN PROTEIN CHEMISTRY 1998; 51:59-119. [PMID: 9615169 DOI: 10.1016/s0065-3233(08)60651-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- E di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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39
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Arkin IT, MacKenzie KR, Brünger AT. Site-Directed Dichroism As a Method for Obtaining Rotational and Orientational Constraints for Oriented Polymers. J Am Chem Soc 1997. [DOI: 10.1021/ja964253x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Abstract
The passage of molecules and information across cell membranes is mediated largely by membrane-spanning proteins acting as channels, pumps, receptors and enzymes. These proteins perform many tasks: they control electrochemical gradients across the membrane, receive signals from the environment or from other cells, convert light energy into chemical signals, transport small molecules into and out of cells, and harness proton gradients to generate the energy consumed in metabolism. Indeed, of the estimated 50000–100000 genes in the human genome, fully 20–40 % are thought to encode integral membrane proteins. If one also includes membrane-associated proteins, which are attached to the membrane surface through fatty acyl chains or electrostatic interactions, this percentage is likely to be much higher.
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Affiliation(s)
- S O Smith
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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41
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Ludlam CF, Arkin IT, Liu XM, Rothman MS, Rath P, Aimoto S, Smith SO, Engelman DM, Rothschild KJ. Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban. Biophys J 1996; 70:1728-36. [PMID: 8785331 PMCID: PMC1225141 DOI: 10.1016/s0006-3495(96)79735-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Phospholamban is a 52-amino acid residue membrane protein that regulates Ca(2+)-ATPase activity in the sarcoplasmic reticulum of cardiac muscle cells. The hydrophobic C-terminal 28 amino acid fragment of phospholamban (hPLB) anchors the protein in the membrane and may form part of a Ca(2+)-selective ion channel. We have used polarized attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy along with site-directed isotope labeling to probe the local structure of hPLB. The frequency and dichroism of the amide I and II bands appearing at 1658 cm-1 and 1544 cm-1, respectively, show that dehydrated and hydrated hPLB reconstituted into dimyristoylphosphatidycholine bilayer membranes is predominantly alpha-helical and has a net transmembrane orientation. Specific local secondary structure of hPLB was probed by incorporating 13C at two positions in the protein backbone. A small band seen near 1614 cm-1 is assigned to the amide I mode of the 13C-labeled amide carbonyl group(s). The frequency and dichroism of this band indicate that residues 39 and 46 are alpha-helical, with an axial orientation that is approximately 30 degrees relative to the membrane normal. Upon exposure to 2H2O (D2O), 30% of the peptide amide groups in hPLB undergo a slow deuterium/hydrogen exchange. The remainder of the protein, including the peptide groups of Leu-39 and Leu-42, appear inaccessible to exchange, indicating that most of the hPLB fragment is embedded in the lipid bilayer. By extending spectroscopic characterization of PLB to include hydrated, deuterated as well as site-directed isotope-labeled hPLB films, our results strongly support models of PLB that predict the existence of an alpha-helical hydrophobic region spanning the membrane domain.
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Affiliation(s)
- C F Ludlam
- Department of Physics, Boston University, Massachusetts 02215, USA
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42
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Nilsson A, Rath P, Olejnik J, Coleman M, Rothschild KJ. Protein conformational changes during the bacteriorhodopsin photocycle. A Fourier transform infrared/resonance Raman study of the alkaline form of the mutant Asp-85-->Asn. J Biol Chem 1995; 270:29746-51. [PMID: 8530365 DOI: 10.1074/jbc.270.50.29746] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Bacteriorhodopsin is a light-driven proton pump, which undergoes a photocycle consisting of several distinct intermediates. Previous studies have established that the M-->N step of this photocycle involves a major conformational change of membrane embedded alpha-helices. In order to further investigate this conformational change, we have studied the photocycle of the high pH form of the mutant Asp-85-->Asn (D85Nalk). In contrast to wild type bacteriorhodopsin, D85Nalk has a deprotonated Schiff base and a blue-shifted absorption near 410 nm, yet it still transports protons in the same direction as wild type bacteriorhodopsin (Tittor, J., Schweiger, U., Oesterhelt, D. and Bamberg, E. (1994) Biophys. J., 67, 1682-1690). Resonance Raman spectroscopy of D85Nalk and D85Nalk regenerated with retinal labeled at the C-15 position with deuterium reveals the existence of an all-trans configuration of the chromophore. Fourier transform infrared difference spectroscopy shows that the photocycle of this light-adapted form involves similar events as the wild type bacteriorhodopsin photocycle including the M-->N protein conformational change. These results help to explain the ability of D85Nalk to transport protons and demonstrate that the M-->N conformational change can occur even in the photocycle of an unprotonated Schiff base form of bacteriorhodopsin.
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Affiliation(s)
- A Nilsson
- Physics Department, Boston University, Massachusetts 02215, USA
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43
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Liu XM, Sonar S, Lee CP, Coleman M, RajBhandary UL, Rothschild KJ. Site-directed isotope labeling and FTIR spectroscopy: assignment of tyrosine bands in the bR-->M difference spectrum of bacteriorhodopsin. Biophys Chem 1995; 56:63-70. [PMID: 7662870 DOI: 10.1016/0301-4622(95)00016-q] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fourier transform infrared difference spectroscopy has been used extensively to probe structural changes in bacteriorthodopsin and other retinal proteins. However, the absence of a general method to assign bands to individual chemical groups in a protein has limited the application of this technique. While site-directed mutagenesis has been successful in special cases for such assignments, in general, this approach induces perturbations in the structure and function of the protein, thereby preventing unambiguous band assignments. A new approach has recently been reported (Sonar et al., Nature Struct. Biol. 1 (1994) 512-517) which involves cell-free expression of bacteriorhodopsin and site-directed isotope labeling (SDIL). We have now used this method to re-examine bands assigned in the bR-->M difference spectrum to tyrosine residues. Our results show that out of 11 tyrosines in bR, only Tyr 185 is structurally active. This work further demonstrates the power of SDIL and FTIR to probe conformational changes at the level of individual amino acid residues in proteins.
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Affiliation(s)
- X M Liu
- Physics Department and Molecular Biophysics Laboratory, Boston University, MA 02215, USA
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44
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Kigawa T, Muto Y, Yokoyama S. Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis. JOURNAL OF BIOMOLECULAR NMR 1995; 6:129-34. [PMID: 8589601 DOI: 10.1007/bf00211776] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
For the application of multidimensional NMR spectroscopy to larger proteins, it would be useful to perform selective labeling of one of the 20 amino acids. For some amino acids, however, amino acid metabolism drastically reduces the efficiency and selectivity of labeling in in vivo expression systems. In the present study, a cell-free protein synthesis system was optimized, so that highly efficient and selective stable isotope labeling of proteins can be achieved in the absence of amino acid metabolism. The productivity of the E. coli cell-free coupled transcription-translation system was first improved, by about fivefold, by using the T7 RNA polymerase for transcription and also by improving the translation conditions. Thus, about 0.1 mg protein per 1 ml reaction mixture was synthesized. Then, this improved cell-free system was used for Asp- or Ser-selective 15N-labeling of the human c-Ha-Ras protein. With a 15 ml cell-free reaction, using less than 1 mg of 15N-labeled amino acid, 1 mg of the Ras protein was obtained. 1H-15N HSQC experiments confirmed that the Ras protein was efficiently labeled with high selectivity. These results indicate that this cell-free protein synthesis system is useful for NMR studies.
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Affiliation(s)
- T Kigawa
- Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan
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Olejnik J, Sonar S, Krzymañska-Olejnik E, Rothschild KJ. Photocleavable biotin derivatives: a versatile approach for the isolation of biomolecules. Proc Natl Acad Sci U S A 1995; 92:7590-4. [PMID: 7638235 PMCID: PMC41385 DOI: 10.1073/pnas.92.16.7590] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
While the strong biotin-avidin interaction has been widely used for the detection of biomolecules, its irreversibility complicates their isolation. We report the synthesis of a photocleavable biotin derivative (PCB) which eliminates many limitations of existing methods. This reagent contains a biotin moiety linked through a spacer arm to a photocleavable moiety, which reacts selectively with primary amino groups on any substrate. In experiments using [leucine]-enkephalin as a model substrate, we show that PCB retains its high affinity toward avidin/streptavidin and allows rapid (< 5 min) and efficient (> 99%) photorelease of the substrate in a completely unaltered form. Photocleavable biotins should be useful in numerous applications involving the isolation of proteins, nucleic acids, lipids, and cells.
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Affiliation(s)
- J Olejnik
- Physics Department, Boston University, MA 02215, USA
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Watts A, Ulrich AS, Middleton DA. Membrane protein structure: the contribution and potential of novel solid state NMR approaches. Mol Membr Biol 1995; 12:233-46. [PMID: 8520624 DOI: 10.3109/09687689509072423] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding applications in biological systems, including integral membrane proteins. Wild-type and genetically engineered proteins can be investigated and detailed information about side chains, prosthetic groups, ligands (e.g. drugs) and binding sites can be deduced. The molecular structure and dynamics of selected parts of the proteins are accessible by a range of different solid state NMR approaches. Inter- and intra-atomic distances can be determined rather accurately (within ångströms) and the orientation of molecular bonds (within 2 degrees) can be measured in ideal cases. Here, a brief description of the methods is given and then some specific examples described with an indication of the future potential for the approaches in studying membrane proteins. It is anticipated that this emerging NMR methodology will be more widely used in the future, not only for resolving local structure, but also for more expansive descriptions of membrane protein structure at atomic resolution.
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Affiliation(s)
- A Watts
- Department of Biochemistry, University of Oxford, UK
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Ibba M, Hennecke H. Relaxing the substrate specificity of an aminoacyl-tRNA synthetase allows in vitro and in vivo synthesis of proteins containing unnatural amino acids. FEBS Lett 1995; 364:272-5. [PMID: 7758582 DOI: 10.1016/0014-5793(95)00408-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It has previously been demonstrated that the unnatural amino acid p-Cl-phenylalanine can be attached to tRNA(Phe) by a modified phenylalanyl-tRNA synthetase with relaxed amino acid substrate specificity. We show that this modification to the translational machinery of Escherichia coli is the only requirement for the incorporation of either p-Cl- or p-Br-phenylalanine into full-length luciferase in vitro. The incorporation of p-Cl-phenylalanine was also demonstrated in vivo using a suitably modified host strain. These results represent the first description of the incorporation into a protein in vivo of an unnatural amino acid which is normally rejected by the cellular translational machinery.
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Affiliation(s)
- M Ibba
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH Zentrum, Zürich, Switzerland
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Fischer WB, Sonar S, Marti T, Khorana HG, Rothschild KJ. Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction. Biochemistry 1994; 33:12757-62. [PMID: 7947680 DOI: 10.1021/bi00209a005] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
FTIR-difference spectroscopy in combination with site-directed mutagenesis has been used to investigate the role of water during the photocycle of bacteriorhodopsin. At least one water molecule is detected which undergoes an increase in H-bonding during the primary bR-->K phototransition. Bands due to water appear in the OH stretch region of the bR-->K FTIR-difference spectrum which downshift by approximately 12 cm-1 when the sample is hydrated with H2(18)O. In contrast to 2H2O, the H2(18)O-induced shift is not complete, even after 24 h of hydration. This indicates that even though water is still able to exchange protons with the outside medium, it is partially trapped in the interior of the protein. In the mutant Y57D, these bands are absent while a new set of bands appear at much lower frequencies which undergo H2(18)O-induced shifts. It is concluded that the water molecule we detect is located inside the bR active-site and may interact with Tyr-57. The change in its hydrogen-bonding strength is most likely due to the photoinduced all-trans-->13-cis isomerization of the retinal chromophore and the associated movement of the positively charged Schiff base during the bR-->K transition. In contrast, a second water molecule, whose infrared difference bands are not affected by the Y57D mutation, appears to undergo a decrease in hydrogen bonding during the K-->L and L-->M transitions.
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Affiliation(s)
- W B Fischer
- Physics Department, Boston University, Massachusetts 02215
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