1
|
Feid C, Luma L, Fischer T, Löffler JG, Grebenovsky N, Wachtveitl J, Heckel A, Bredenbeck J. Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer. Angew Chem Int Ed Engl 2024; 63:e202317047. [PMID: 38103205 DOI: 10.1002/anie.202317047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/18/2023]
Abstract
Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient. Here, we introduce two novel donor ncAAs based on an iminothioindoxyl (ITI) chromophore. The dimethylamino-ITI (DMA-ITI) and julolidine-ITI (J-ITI) moieties overcome the limitation of AzAla with a 50 times higher Vis extinction coefficient. While ITI moieties are known for ultrafast photoswitching, DMA-ITI and J-ITI exclusively form a hot ground state on the sub-ps timescale instead, which is essential for their usage as vibrational energy donor. In VET measurements of donor-sensor dipeptides we investigate the performance of the new donors. We observe 20 times larger signals compared to the established AzAla donor, which opens unprecedented possibilities for the study of VET in proteins.
Collapse
Affiliation(s)
- Carolin Feid
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Larita Luma
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| | - Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt (Main), Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438, Frankfurt (Main), Germany
| |
Collapse
|
2
|
Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022; 61:e202200648. [PMID: 35226765 PMCID: PMC9401566 DOI: 10.1002/anie.202200648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 11/10/2022]
Abstract
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
Collapse
Affiliation(s)
- Jan G. Löffler
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Erhan Deniz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Carolin Feid
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Valentin G. Franz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Jens Bredenbeck
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| |
Collapse
|
3
|
Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan G. Löffler
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Erhan Deniz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Carolin Feid
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Valentin G. Franz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Jens Bredenbeck
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| |
Collapse
|
4
|
Mukherjee D, Ahmed IA, Gai F. Site-Specific Interrogation of Protein Structure and Stability. Methods Mol Biol 2022; 2376:65-87. [PMID: 34845603 DOI: 10.1007/978-1-0716-1716-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To execute their function or activity, proteins need to possess variability in local electrostatic environment, solvent accessibility, structure, and stability. However, assessing any protein property in a site-specific manner is not easy since native spectroscopic signals often lack the needed specificity. One strategy that overcomes this limitation is to use unnatural amino acids that exhibit distinct spectroscopic features. In this chapter, we describe several such unnatural amino acids (UAAs) and their respective applications in site-specific interrogation of protein structure and stability using standard biophysical methods, including circular dichroism (CD), infrared (IR), and fluorescence spectroscopies.
Collapse
Affiliation(s)
| | - Ismail A Ahmed
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
5
|
Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins. CRYSTALS 2021. [DOI: 10.3390/cryst11091032] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.
Collapse
|
6
|
Kubyshkin V. Experimental lipophilicity scale for coded and noncoded amino acid residues. Org Biomol Chem 2021; 19:7031-7040. [PMID: 34333582 DOI: 10.1039/d1ob01213d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Among other features, the polarity of amino acid residues is the key parameter for understanding their role in proteins. The wide occurrence of protein modifications in nature and the advent of genetic code engineering techniques created a need for an experimental polarity value integrating both coded (canonical) and noncoded (noncanonical) residues on one universal scale. To address this issue, this work reports on a polarity scale based on the experimental lipophilicity of methyl esters of N-acetylamino acids. The derivatization of amino acids was performed in two steps under mild conditions that allowed conversion of a wide array of amino acids into analytical derivatives. The partitioning/distribution between octan-1-ol and water/buffer was measured using the intensity of the NMR signal as a characteristic for the concentration. The reference set of twenty coded amino acids generated log P values spanning 5.1 units: from tryptophan being the most hydrophobic to aspartate being the most hydrophilic. Furthermore, lipophilicity was measured for a set of analogues of phenylalanine, tyrosine, tryptophan, methionine, proline, and lysine that are typical in nature and/or laboratory practice. The polarity scale reported here will aid the rationalization of amino acid replacements in proteins, and will guide further efforts in experimental genetic code engineering.
Collapse
Affiliation(s)
- Vladimir Kubyshkin
- Chemistry Department, University of Manitoba, 144 Dysart road, Winnipeg, Manitoba R3T 2N2, Canada.
| |
Collapse
|
7
|
D’Souza AR, Necelis MR, Kulesha A, Caputo GA, Makhlynets OV. Beneficial Impacts of Incorporating the Non-Natural Amino Acid Azulenyl-Alanine into the Trp-Rich Antimicrobial Peptide buCATHL4B. Biomolecules 2021; 11:421. [PMID: 33809374 PMCID: PMC8001250 DOI: 10.3390/biom11030421] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial peptides (AMPs) present a promising scaffold for the development of potent antimicrobial agents. Substitution of tryptophan by non-natural amino acid Azulenyl-Alanine (AzAla) would allow studying the mechanism of action of AMPs by using unique properties of this amino acid, such as ability to be excited separately from tryptophan in a multi-Trp AMPs and environmental insensitivity. In this work, we investigate the effect of Trp→AzAla substitution in antimicrobial peptide buCATHL4B (contains three Trp side chains). We found that antimicrobial and bactericidal activity of the original peptide was preserved, while cytocompatibility with human cells and proteolytic stability was improved. We envision that AzAla will find applications as a tool for studies of the mechanism of action of AMPs. In addition, incorporation of this non-natural amino acid into AMP sequences could enhance their application properties.
Collapse
Affiliation(s)
- Areetha R. D’Souza
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA; (A.R.D.); (A.K.)
| | - Matthew R. Necelis
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (M.R.N.); (G.A.C.)
| | - Alona Kulesha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA; (A.R.D.); (A.K.)
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (M.R.N.); (G.A.C.)
- Department of Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Olga V. Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA; (A.R.D.); (A.K.)
| |
Collapse
|
8
|
Prakash V, Ranbhor R, Ramakrishnan V. De Novo Designed Heterochiral Blue Fluorescent Protein. ACS OMEGA 2020; 5:26382-26388. [PMID: 33110966 PMCID: PMC7581079 DOI: 10.1021/acsomega.0c02574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/24/2020] [Indexed: 05/08/2023]
Abstract
Diversification of chain stereochemistry offers a tremendous increase in protein design space. We have designed a minimal fluorescent protein, pregnant with β-(1-azulenyl)-l-alanine in the hydrophobic core of a heterotactic protein scaffold, employing automated design tools such as automated repetitive simulated annealing molecular dynamics and IDeAS. The de novo designed heterochiral protein can be selectively excited at 342 nm, quite distant from the intrinsic fluorophore, and emits in the blue region. The structure and stability of the designed proteins were evaluated by established spectroscopic and calorimetric methods.
Collapse
Affiliation(s)
- Vivek Prakash
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
| | - Ranjit Ranbhor
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
| | - Vibin Ramakrishnan
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
- . Phone: +91-361-258-2227
| |
Collapse
|
9
|
Expanding the Scope of Orthogonal Translation with Pyrrolysyl-tRNA Synthetases Dedicated to Aromatic Amino Acids. Molecules 2020; 25:molecules25194418. [PMID: 32992991 PMCID: PMC7582959 DOI: 10.3390/molecules25194418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
In protein engineering and synthetic biology, Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRS), with its cognate tRNAPyl, is one of the most popular tools for site-specific incorporation of non-canonical amino acids (ncAAs). Numerous orthogonal pairs based on engineered MmPylRS variants have been developed during the last decade, enabling a substantial genetic code expansion, mainly with aliphatic pyrrolysine analogs. However, comparatively less progress has been made to expand the substrate range of MmPylRS towards aromatic amino acid residues. Therefore, we set to further expand the substrate scope of orthogonal translation by a semi-rational approach; redesigning the MmPylRS efficiency. Based on the randomization of residues from the binding pocket and tRNA binding domain, we identify three positions (V401, W417 and S193) crucial for ncAA specificity and enzyme activity. Their systematic mutagenesis enabled us to generate MmPylRS variants dedicated to tryptophan (such as β-(1-Azulenyl)-l-alanine or 1-methyl-l-tryptophan) and tyrosine (mainly halogenated) analogs. Moreover, our strategy also significantly improves the orthogonal translation efficiency with the previously activated analog 3-benzothienyl-l-alanine. Our study revealed the engineering of both first shell and distant residues to modify substrate specificity as an important strategy to further expand our ability to discover and recruit new ncAAs for orthogonal translation.
Collapse
|
10
|
Baumann T, Hauf M, Schildhauer F, Eberl KB, Durkin PM, Deniz E, Löffler JG, Acevedo‐Rocha CG, Jaric J, Martins BM, Dobbek H, Bredenbeck J, Budisa N. Ortsaufgelöste Beobachtung von Schwingungsenergietransfer durch ein genetisch codiertes ultraschnelles Heizelement. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tobias Baumann
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Matthias Hauf
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Fabian Schildhauer
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Katharina B. Eberl
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Patrick M. Durkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
| | - Erhan Deniz
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Jan G. Löffler
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | | | - Jelena Jaric
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
- Derzeitige Adresse: Hospira Zagreb d.o.o.a Pfizer company Prudnicka cesta 60 10291 Prigorje Brdovecko Kroatien
| | - Berta M. Martins
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Unter den Linden 6 10099 Berlin Deutschland
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Unter den Linden 6 10099 Berlin Deutschland
| | - Jens Bredenbeck
- Institut für BiophysikJohann Wolfgang von Goethe-Universität Max-von-Laue-Straße 1 60438 Frankfurt Deutschland
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Straße 10 10623 Berlin Deutschland
- Department of ChemistryUniversity of Manitoba 44 Dysart Rd R3T 2N2 Winnipeg MB Kanada
| |
Collapse
|
11
|
Baumann T, Hauf M, Schildhauer F, Eberl KB, Durkin PM, Deniz E, Löffler JG, Acevedo-Rocha CG, Jaric J, Martins BM, Dobbek H, Bredenbeck J, Budisa N. Site-Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater. Angew Chem Int Ed Engl 2019; 58:2899-2903. [PMID: 30589180 DOI: 10.1002/anie.201812995] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 12/22/2022]
Abstract
Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site-selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site-specific incorporation of the non-canonical amino acid β-(1-azulenyl)-l-alanine (AzAla) through genetic code expansion. As an exception to Kasha's rule, AzAla undergoes ultrafast internal conversion and heating after S1 excitation while upon S2 excitation, it serves as a fluorescent label. We equipped PDZ3, a protein interaction domain of postsynaptic density protein 95, with this ultrafast heater at two distinct positions. We indeed observed VET from the incorporation sites in the protein to a bound peptide ligand on the picosecond timescale by ultrafast IR spectroscopy. This approach based on genetically encoded AzAla paves the way for detailed studies of VET and its role in a wide range of proteins.
Collapse
Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Fabian Schildhauer
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Katharina B Eberl
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Patrick M Durkin
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany
| | - Erhan Deniz
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Jan G Löffler
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | | | - Jelena Jaric
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,Present address: Hospira Zagreb d.o.o., a Pfizer company, Prudnicka cesta 60, 10291, Prigorje Brdovecko, Croatia
| | - Berta M Martins
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,Department of Chemistry, University of Manitoba, 44 Dysart Rd, R3T 2N2, Winnipeg, MB, Canada
| |
Collapse
|
12
|
Oliveira-Souza WP, Bronze F, Broos J, Marcondes MF, Oliveira V. On the efficient bio-incorporation of 5-hydroxy-tryptophan in recombinant proteins expressed in Escherichia coli with T7 RNA polymerase-based vectors. Biochem Biophys Res Commun 2017; 492:343-348. [DOI: 10.1016/j.bbrc.2017.08.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/27/2017] [Indexed: 11/26/2022]
|
13
|
Schumacher D, Lemke O, Helma J, Gerszonowicz L, Waller V, Stoschek T, Durkin PM, Budisa N, Leonhardt H, Keller BG, Hackenberger CPR. Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling. Chem Sci 2017; 8:3471-3478. [PMID: 28507719 PMCID: PMC5418632 DOI: 10.1039/c7sc00574a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/18/2017] [Indexed: 12/31/2022] Open
Abstract
The broad substrate tolerance of tubulin tyrosine ligase enables its wide applicability for protein functionalization.
The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations. This feature enabled one-step C-terminal biotinylation and fluorescent coumarin labeling of various functional proteins as demonstrated with ubiquitin, an antigen binding nanobody, and the apoptosis marker Annexin V. Its broad substrate tolerance establishes tubulin tyrosine ligase as a powerful tool for in vitro enzyme-mediated protein modification with single functional amino acids in a specific structural context.
Collapse
Affiliation(s)
- Dominik Schumacher
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Jonas Helma
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Lena Gerszonowicz
- Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Verena Waller
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Tina Stoschek
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Patrick M Durkin
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Nediljko Budisa
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Heinrich Leonhardt
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Christian P R Hackenberger
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| |
Collapse
|
14
|
Gosavi PM, Korendovych IV. Minimalist IR and fluorescence probes of protein function. Curr Opin Chem Biol 2016; 34:103-109. [PMID: 27599185 DOI: 10.1016/j.cbpa.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
Abstract
Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.
Collapse
Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States.
| |
Collapse
|
15
|
Ridgway Z, Picciano AL, Gosavi PM, Moroz YS, Angevine CE, Chavis AE, Reiner JE, Korendovych IV, Caputo GA. Functional characterization of a melittin analog containing a non-natural tryptophan analog. Biopolymers 2016; 104:384-394. [PMID: 25670241 DOI: 10.1002/bip.22624] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/13/2015] [Accepted: 01/18/2015] [Indexed: 02/06/2023]
Abstract
Tryptophan (Trp) is a naturally occurring amino acid, which exhibits fluorescence emission properties that are dependent on the polarity of the local environment around the Trp side chain. However, this sensitivity also complicates interpretation of fluorescence emission data. A non-natural analogue of tryptophan, β-(1-azulenyl)-L-alanine, exhibits fluorescence insensitive to local solvent polarity and does not impact the structure or characteristics of several peptides examined. In this study, we investigated the effect of replacing Trp with β-(1-azulenyl)-L-alanine in the well-known bee-venom peptide melittin. This peptide provides a model framework for investigating the impact of replacing Trp with β-(1-azulenyl)-L-alanine in a functional peptide system that undergoes significant shifts in Trp fluorescence emission upon binding to lipid bilayers. Microbiological methods including assessment of the antimicrobial activity by minimal inhibitory concentration (MIC) assays and bacterial membrane permeability assays indicated little difference between the Trp and the β-(1-azulenyl)-L-alanine-substituted versions of melittin. Circular dichroism spectroscopy showed both that peptides adopted the expected α-helical structures when bound to phospholipid bilayers and electrophysiological analysis indicated that both created membrane disruptions leading to significant conductance increases across model membranes. Both peptides exhibited a marked protection of the respective fluorophores when bound to bilayers indicating a similar membrane-bound topology. As expected, while fluorescence quenching and CD indicate the peptides are stably bound to lipid vesicles, the peptide containing β-(1-azulenyl)-L-alanine exhibited no fluorescence emission shift upon binding while the natural Trp exhibited >10 nm shift in emission spectrum barycenter. Taken together, the β-(1-azulenyl)-L-alanine can serve as a solvent insensitive alternative to Trp that does not have significant impacts on structure or function of membrane interacting peptides.
Collapse
Affiliation(s)
- Zachary Ridgway
- Department of Chemistry and Biochemistry, Rowan University, Glassboro NJ 08028
| | - Angela L Picciano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro NJ 08028
| | | | - Yurii S Moroz
- Department of Chemistry, Syracuse University, Syracuse NY 13244.,Present affiliation: ChemBioCenter, Kyiv National Taras Shevchenko University, 61 Chervonotkatska Street, Kyiv 02094, Ukraine
| | | | - Amy E Chavis
- Department of Physics, Virginia Commonwealth University, Richmond VA 23284
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond VA 23284
| | | | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro NJ 08028.,School of Biomedical Sciences, Rowan University, Glassboro NJ, 08028
| |
Collapse
|
16
|
Shao J, Marcondes MFM, Oliveira V, Broos J. Development of Chemically Defined Media to Express Trp-Analog-Labeled Proteins in a Lactococcus lactis Trp Auxotroph. J Mol Microbiol Biotechnol 2016; 26:269-76. [PMID: 27172771 DOI: 10.1159/000445687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/20/2016] [Indexed: 11/19/2022] Open
Abstract
Chemically defined media for growth of Lactococcus lactis strains contain about 50 components, making them laborious and expensive growth media. However, they are crucial for metabolism studies as well as for expression of heterologous proteins labeled with unnatural amino acids. In particular, the L. lactis Trp auxotroph PA1002, overexpressing the tryptophanyl tRNA synthetase enzyme of L. lactis, is very suitable for the biosynthetic incorporation of Trp analogs in proteins because of its most relaxed substrate specificity reported towards Trp analogs. Here we present two much simpler defined media for L. lactis, which consist of only 24 or 31 components, respectively, and with which the L. lactis Trp auxotroph shows similar growth characteristics as with a 50-component chemically defined medium. Importantly, the expression levels of two recombinant proteins used for evaluation were up to 2-3 times higher in these new media than in the 50-component medium, without affecting the Trp analog incorporation efficiency. Taken together, the simplest chemically defined media reported so far for L. lactis are presented. Since L. lactis also shows auxotrophy for Arg, His, Ile, Leu Val, and Met, our simplified media may also be useful for the biosynthetic incorporation of analogs of these five amino acids.
Collapse
Affiliation(s)
- Jinfeng Shao
- Laboratory of Biophysical Chemistry and Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | | | | | | |
Collapse
|
17
|
Gosavi PM, Moroz YS, Korendovych IV. β-(1-Azulenyl)-L-alanine--a functional probe for determination of pKa of histidine residues. Chem Commun (Camb) 2016; 51:5347-50. [PMID: 25645241 DOI: 10.1039/c4cc08720h] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
β-(1-Azulenyl)-L-alanine (AzAla) can be incorporated into the influenza A virus M2 proton channel. AzAla's sensitivity to the protonation state of the nearby histidines and the lack of environmental fluorescence dependence allow for direct and straightforward determination of histidine pKa values in ion channels.
Collapse
Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA.
| | | | | |
Collapse
|