1
|
Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
| |
Collapse
|
2
|
García-Montoya C, García-Linares S, Heras-Márquez D, Majnik M, Laxalde-Fernández D, Amigot-Sánchez R, Martínez-Del-Pozo Á, Palacios-Ortega J. The interaction of the ribotoxin α-sarcin with complex model lipid vesicles. Arch Biochem Biophys 2024; 751:109836. [PMID: 38000493 DOI: 10.1016/j.abb.2023.109836] [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] [Received: 10/10/2023] [Revised: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Fungal ribotoxins are extracellular RNases that inactivate ribosomes by cleaving a single phosphodiester bond at the universally conserved sarcin-ricin loop of the large rRNA. However, to reach the ribosomes, they need to cross the plasma membrane. It is there where these toxins show their cellular specificity, being especially active against tumoral or virus-infected cells. Previous studies have shown that fungal ribotoxins interact with negatively charged membranes, typically containing phosphatidylserine or phosphatidylglycerol. This ability is rooted on their long, non-structured, positively charged loops, and its N-terminal β-hairpin. However, its effect on complex lipid mixtures, including sphingophospholipids or cholesterol, remains poorly studied. Here, wild-type α-sarcin was used to evaluate its interaction with a variety of membranes not assayed before, which resemble much more closely mammalian cell membranes. The results confirm that α-sarcin is particularly sensitive to charge density on the vesicle surface. Its ability to induce vesicle aggregation is strongly influenced by both the lipid headgroup and the degree of saturation of the fatty acid chains. Acyl chain length is indeed particularly important for lipid mixing. Finally, cholesterol plays an important role in diluting the concentration of available negative charges and modulates the ability of α-sarcin to cross the membrane.
Collapse
Affiliation(s)
- Carmen García-Montoya
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | - Sara García-Linares
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | - Diego Heras-Márquez
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | - Manca Majnik
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | | | - Rafael Amigot-Sánchez
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain
| | | | - Juan Palacios-Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| |
Collapse
|
3
|
Wachira FW, Githirwa DC, McPartlon T, Nazarenko V, Gonzales JJC, Gazura MM, Leen C, Clary HR, Alston C, Klees LM, Yao L, An M. D-to-E and T19V Variants of the pH-Low Insertion Peptide and Their Doxorubicin Conjugates Interact with Membrane at Higher pH Ranges Than WT. Biochemistry 2023; 62:2997-3011. [PMID: 37793002 DOI: 10.1021/acs.biochem.3c00218] [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: 10/06/2023]
Abstract
To improve targeted cargo delivery to cancer cells, pH-Low Insertion Peptide (pHLIP) variants were developed to interact with the membrane at pH values higher than those of the WT. The Asp-to-Glu variants aim to increase side chain pKa without disturbing the sequence of protonations that underpin membrane insertion. The Thr19 variants represent efforts to perturb the critical Pro20 residue. To study the effect of cargo on pHLIP insertion, doxorubicin (Dox), a fluorescent antineoplastic drug, was conjugated to selected variants near the inserting C-terminus. Variants and conjugates were characterized on a POPC membrane using Trp and Dox fluorescence methods to define the entire pH range of insertion (pHinitial-pHfinal). Compared to WT with a pHi-pHf range of 6.7-5.6, D25E-D31E-D33E, D14E-D25E-D31E-D33E, and T19V-D25E variants demonstrated higher pHi-pHf ranges of 7.3-6.1, 7.3-6.3, and 8.2-5.4, respectively. The addition of Dox expanded the pHi-pHf range, mainly by shifting pHi to higher pH values (e.g., WT pHLIP-Dox has a pHi-pHf range of 7.7-5.2). Despite the low Hill coefficient observed for the conjugates, D14E-D25E-D31E-D33E pHLIP-Dox completed insertion by a pHf of 5.7. However, the Dox cargo remained in the hydrophobic membrane interior after pHLIP insertion, which may impede drug release. Finally, a logistic function can describe pHLIP insertion as a peripheral-to-TM (start-to-finish) two-state transition; wherever possible, we discuss data deviating from such sigmoidal fitting in support of the idea that pH-specific intermediate states distinct from the initial peripheral state and the final TM state exist at intervening pH values.
Collapse
Affiliation(s)
- Faith W Wachira
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Dancan C Githirwa
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Thomas McPartlon
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Vladyslav Nazarenko
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Jerel J C Gonzales
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Makenzie M Gazura
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Caitlin Leen
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Hannah R Clary
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Claire Alston
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Lukas M Klees
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| | - Lan Yao
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
- Department of Physics, SUNY, Binghamton University, Binghamton, New York 13902, United States
| | - Ming An
- Department of Chemistry, State University of New York (SUNY), Binghamton University, Binghamton, New York 13902, United States
| |
Collapse
|
4
|
Rizzo S, Sikorski E, Park S, Im W, Vasquez‐Montes V, Ladokhin AS, Thévenin D. Promoting the activity of a receptor tyrosine phosphatase with a novel pH-responsive transmembrane agonist inhibits cancer-associated phenotypes. Protein Sci 2023; 32:e4742. [PMID: 37515426 PMCID: PMC10461461 DOI: 10.1002/pro.4742] [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: 05/23/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 07/30/2023]
Abstract
Cell signaling by receptor protein tyrosine kinases (RTKs) is tightly controlled by the counterbalancing actions of receptor protein tyrosine phosphatases (RPTPs). Due to their role in attenuating the signal-initiating potency of RTKs, RPTPs have long been viewed as therapeutic targets. However, the development of activators of RPTPs has remained limited. We previously reported that the homodimerization of a representative member of the RPTP family (protein tyrosine phosphatase receptor J or PTPRJ) is regulated by specific transmembrane (TM) residues. Disrupting this interaction by single point mutations promotes PTPRJ access to its RTK substrates (e.g., EGFR and FLT3), reduces RTK's phosphorylation and downstream signaling, and ultimately antagonizes RTK-driven cell phenotypes. Here, we designed and tested a series of first-in-class pH-responsive TM peptide agonists of PTPRJ that are soluble in aqueous solution but insert as a helical TM domain in lipid membranes when the pH is lowered to match that of the acidic microenvironment of tumors. The most promising peptide reduced EGFR's phosphorylation and inhibited cancer cell EGFR-driven migration and proliferation, similar to the PTPRJ's TM point mutations. Developing tumor-selective and TM-targeting peptide binders of critical RPTPs could afford a potentially transformative approach to studying RPTP's selectivity mechanism without requiring less specific inhibitors and represent a novel class of therapeutics against RTK-driven cancers.
Collapse
Affiliation(s)
- Sophie Rizzo
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Eden Sikorski
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Soohyung Park
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Victor Vasquez‐Montes
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Damien Thévenin
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| |
Collapse
|
5
|
Membrane Interactions of Apoptotic Inhibitor Bcl-xL: What Can Be Learned using Fluorescence Spectroscopy. BBA ADVANCES 2023; 3:100076. [PMID: 37082264 PMCID: PMC10074936 DOI: 10.1016/j.bbadva.2023.100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Permeabilization of the mitochondrial outer membrane-a point of no return in apoptotic regulation-is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition.
Collapse
|
6
|
Vasquez-Montes V, Goldberg AFX, Thévenin D, Ladokhin AS. Ca 2+ and Mg 2+ Influence the Thermodynamics of Peptide-Membrane Interactions. J Mol Biol 2022; 434:167826. [PMID: 36115657 PMCID: PMC10029193 DOI: 10.1016/j.jmb.2022.167826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 02/08/2023]
Abstract
Accurate quantitative estimates of protein-membrane interactions are critical to studies of membrane proteins. Here, we demonstrate that thermodynamic analyses based on current hydropathy scales do not account for the significant and experimentally determined effects that Ca2+ or Mg2+ have on protein-membrane interactions. We examined distinct modes of interaction (interfacial partitioning and folding and transmembrane insertion) by studying three highly divergent peptides: Bid-BH3 (derived from apoptotic regulator Bid), peripherin-2-derived prph2-CTER, and the cancer-targeting pH-Low-Insertion-Peptide (pHLIP). Fluorescence experiments demonstrate that adding 1-2 mM of divalent cations led to a substantially more favorable bilayer partitioning and insertion, with free energy differences of 5-15 kcal/mol.
Collapse
Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Andrew F X Goldberg
- Eye Research Institute, Oakland University, Rochester, MI 48309, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, United States. https://twitter.com/TheveninLab
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, United States.
| |
Collapse
|