1
|
Maity S, Bingham C, Sheng W, Ehyaei N, Chakraborty D, Tahmasebi-Nick S, Kimmel TE, Vasileiou C, Geiger JH, Borhan B. Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins. Analyst 2023; 148:1085-1092. [PMID: 36722993 PMCID: PMC9992065 DOI: 10.1039/d2an01395a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro-Michael process. This series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON-OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.
Collapse
Affiliation(s)
- Soham Maity
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Courtney Bingham
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Wei Sheng
- Roche Tissue Diagnostics, 1910 E Innovation Park Dr, Oro Valley, AZ, 85755, USA
| | - Nona Ehyaei
- Lycia Therapeutics, 400 East Jamie Court, S San Francisco, CA 94080, USA
| | - Debarshi Chakraborty
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | | | - Thomas E Kimmel
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| |
Collapse
|
2
|
Hassan SI, Haque A, Jeilani YA, Ilmi R, Faizi MSH, Khan I, Mushtaque M. Thioxanthone-based organic probe with aggregation enhanced emission and exceptional mineral acids sensing abilities. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
3
|
Ghanbarpour A, Santos EM, Pinger C, Assar Z, Hossaini Nasr S, Vasileiou C, Spence D, Borhan B, Geiger JH. Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Chembiochem 2020; 21:3192-3196. [PMID: 32608180 PMCID: PMC8220890 DOI: 10.1002/cbic.202000405] [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: 06/24/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.
Collapse
Affiliation(s)
- Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Yale University Medical School, Department of Cell Biology, 333 S. Cedar Street, New Haven, CT 06510, USA
| | - Elizabeth M Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Dow Performance Silicones, 2200W Salzburg Road, Midland, MI 48686, USA
| | - Cody Pinger
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Zahra Assar
- Cayman Chemical, 1180 East Ellsworth Road, Ann Arbor, MI 48108, USA
| | - Seyedmehdi Hossaini Nasr
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Dana Spence
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| |
Collapse
|
4
|
Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
| |
Collapse
|
5
|
Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
Collapse
Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
| |
Collapse
|
6
|
Péresse T, Gautier A. Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging. Int J Mol Sci 2019; 20:E6142. [PMID: 31817528 PMCID: PMC6940837 DOI: 10.3390/ijms20246142] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.
Collapse
Affiliation(s)
- Tiphaine Péresse
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
| |
Collapse
|
7
|
Ghanbarpour A, Pinger C, Esmatpour Salmani R, Assar Z, Santos EM, Nosrati M, Pawlowski K, Spence D, Vasileiou C, Jin X, Borhan B, Geiger JH. Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches. J Am Chem Soc 2019; 141:17125-17132. [PMID: 31557439 DOI: 10.1021/jacs.9b04664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.
Collapse
Affiliation(s)
- Alireza Ghanbarpour
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Cody Pinger
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Rahele Esmatpour Salmani
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Zahra Assar
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Elizabeth M Santos
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Meisam Nosrati
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Kathryn Pawlowski
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Dana Spence
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Chrysoula Vasileiou
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Xiangshu Jin
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Babak Borhan
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - James H Geiger
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| |
Collapse
|
8
|
Gautier A, Tebo AG. Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing. Bioessays 2018; 40:e1800118. [DOI: 10.1002/bies.201800118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
| |
Collapse
|