1
|
Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
Collapse
Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
2
|
Dadová J, Wu KJ, Isenegger PG, Errey JC, Bernardes GL, Chalker JM, Raich L, Rovira C, Davis BG. Precise Probing of Residue Roles by Post-Translational β,γ-C,N Aza-Michael Mutagenesis in Enzyme Active Sites. ACS CENTRAL SCIENCE 2017; 3:1168-1173. [PMID: 29202018 PMCID: PMC5704290 DOI: 10.1021/acscentsci.7b00341] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Biomimicry valuably allows the understanding of the essential chemical components required to recapitulate biological function, yet direct strategies for evaluating the roles of amino acids in proteins can be limited by access to suitable, subtly-altered unnatural variants. Here we describe a strategy for dissecting the role of histidine residues in enzyme active sites using unprecedented, chemical, post-translational side-chain-β,γ C-N bond formation. Installation of dehydroalanine (as a "tag") allowed the testing of nitrogen conjugate nucleophiles in "aza-Michael"-1,4-additions (to "modify"). This allowed the creation of a regioisomer of His (iso-His, Hisiso) linked instead through its pros-Nπ atom rather than naturally linked via C4, as well as an aza-altered variant aza-Hisiso. The site-selective generation of these unnatural amino acids was successfully applied to probe the contributing roles (e.g., size, H-bonding) of His residues toward activity in the model enzymes subtilisin protease from Bacillus lentus and Mycobacterium tuberculosis pantothenate synthetase.
Collapse
Affiliation(s)
- Jitka Dadová
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kuan-Jung Wu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Patrick G. Isenegger
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - James C. Errey
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Gonçalo
J. L. Bernardes
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Justin M. Chalker
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (secció
de Química Orgànica) & Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| | - Benjamin G. Davis
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| |
Collapse
|
3
|
Le Bon C, Popot JL, Giusti F. Labeling and functionalizing amphipols for biological applications. J Membr Biol 2014; 247:797-814. [PMID: 24696186 PMCID: PMC4185061 DOI: 10.1007/s00232-014-9655-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/07/2014] [Indexed: 12/19/2022]
Abstract
Amphipols (APols) are short amphipathic polymers developed as an alternative to detergents for handling membrane proteins (MPs) in aqueous solution. MPs are, as a rule, much more stable following trapping with APols than they are in detergent solutions. The best-characterized APol to date, called A8-35, is a mixture of short-chain sodium polyacrylates randomly derivatized with octylamine and isopropylamine. Its solution properties have been studied in detail, and it has been used extensively for biochemical and biophysical studies of MPs. One of the attractive characteristics of APols is that it is relatively easy to label them, isotopically or otherwise, without affecting their physical-chemical properties. Furthermore, several variously modified APols can be mixed, achieving multiple functionalization of MP/APol complexes in the easiest possible manner. Labeled or tagged APols are being used to study the solution properties of APols, their miscibility, their biodistribution upon injection into living organisms, their association with MPs and the composition, structure and dynamics of MP/APol complexes, examining the exchange of surfactants at the surface of MPs, labeling MPs to follow their distribution in fractionation experiments or to immobilize them, increasing the contrast between APols and solvent or MPs in biophysical experiments, improving NMR spectra, etc. Labeling or functionalization of APols can take various courses, each of which has its specific constraints and advantages regarding both synthesis and purification. The present review offers an overview of the various derivatives of A8-35 and its congeners that have been developed in our laboratory and discusses the pros and cons of various synthetic routes.
Collapse
Affiliation(s)
- Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), CNRS/Université Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | | | | |
Collapse
|
4
|
Gan Q, Lu X, Dong W, Yuan Y, Qian J, Li Y, Shi J, Liu C. Endosomal pH-activatable magnetic nanoparticle-capped mesoporous silica for intracellular controlled release. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm32020g] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
5
|
Balija AM, Kohman RE, Zimmerman SC. Substituted 1,3,5-triazaadamantanes: biocompatible and degradable building blocks. Angew Chem Int Ed Engl 2008; 47:8072-4. [PMID: 18803197 DOI: 10.1002/anie.200802222] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy M Balija
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | |
Collapse
|
6
|
Balija A, Kohman R, Zimmerman S. Substituted 1,3,5-Triazaadamantanes: Biocompatible and Degradable Building Blocks. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
7
|
AL-Badri ZM, Som A, Lyon S, Nelson CF, Nüsslein K, Tew GN. Investigating the Effect of Increasing Charge Density on the Hemolytic Activity of Synthetic Antimicrobial Polymers. Biomacromolecules 2008; 9:2805-10. [DOI: 10.1021/bm800569x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zoha M. AL-Badri
- Departments of Polymer Science and Engineering, Biochemistry and Molecular Biology, and Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Abhigyan Som
- Departments of Polymer Science and Engineering, Biochemistry and Molecular Biology, and Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Sarah Lyon
- Departments of Polymer Science and Engineering, Biochemistry and Molecular Biology, and Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Christopher F. Nelson
- Departments of Polymer Science and Engineering, Biochemistry and Molecular Biology, and Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Klaus Nüsslein
- Departments of Polymer Science and Engineering, Biochemistry and Molecular Biology, and Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| | - Gregory N. Tew
- Departments of Polymer Science and Engineering, Biochemistry and Molecular Biology, and Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003
| |
Collapse
|
8
|
Gamblin DP, van Kasteren SI, Chalker JM, Davis BG. Chemical approaches to mapping the function of post-translational modifications. FEBS J 2008; 275:1949-59. [DOI: 10.1111/j.1742-4658.2008.06347.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
9
|
Abstract
Covalent modification methods allow an almost unlimited range of functionality to be introduced into proteins. In concert with genetic techniques, chemical strategies have had significant impact in the field of enzyme design. Major recent developments include introducing catalytic activity into inactive proteins, modifying the selectivity and/or reactivity of existing enzymes and designing novel enzyme-based biosensors. New chemical methods promise to further increase the range of functionality that can be incorporated into proteins. These results suggest that semi-synthetic methods will play a key role in the development of future biocatalysts.
Collapse
Affiliation(s)
- C M Tann
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | |
Collapse
|
10
|
Qi D, Tann CM, Haring D, Distefano MD. Generation of new enzymes via covalent modification of existing proteins. Chem Rev 2001; 101:3081-111. [PMID: 11710063 DOI: 10.1021/cr000059o] [Citation(s) in RCA: 232] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D Qi
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | | | | |
Collapse
|
11
|
Khumtaveeporn K, Ullmann A, Matsumoto K, Davis BG, Jones J. Expanding the utility of proteases in synthesis: broadening the substrate acceptance in non-coded amide bond formation using chemically modified mutants of subtilisin. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0957-4166(01)00024-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|