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Szabo I, Szewczyk A. Mitochondrial Ion Channels. Annu Rev Biophys 2023; 52:229-254. [PMID: 37159294 DOI: 10.1146/annurev-biophys-092622-094853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mitochondria are involved in multiple cellular tasks, such as ATP synthesis, metabolism, metabolite and ion transport, regulation of apoptosis, inflammation, signaling, and inheritance of mitochondrial DNA. The majority of the correct functioning of mitochondria is based on the large electrochemical proton gradient, whose component, the inner mitochondrial membrane potential, is strictly controlled by ion transport through mitochondrial membranes. Consequently, mitochondrial function is critically dependent on ion homeostasis, the disturbance of which leads to abnormal cell functions. Therefore, the discovery of mitochondrial ion channels influencing ion permeability through the membrane has defined a new dimension of the function of ion channels in different cell types, mainly linked to the important tasks that mitochondrial ion channels perform in cell life and death. This review summarizes studies on animal mitochondrial ion channels with special focus on their biophysical properties, molecular identity, and regulation. Additionally, the potential of mitochondrial ion channels as therapeutic targets for several diseases is briefly discussed.
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Affiliation(s)
- Ildiko Szabo
- Department of Biology, University of Padova, Italy;
| | - Adam Szewczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland;
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2
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Janssen K, Claes F, Van de Velde D, Wehbi VL, Houben B, Lampi Y, Nys M, Khodaparast L, Khodaparast L, Louros N, van der Kant R, Verniers J, Garcia T, Ramakers M, Konstantoulea K, Maragkou K, Duran-Romaña R, Musteanu M, Barbacid M, Scorneaux B, Beirnaert E, Schymkowitz J, Rousseau F. Exploiting the intrinsic misfolding propensity of the KRAS oncoprotein. Proc Natl Acad Sci U S A 2023; 120:e2214921120. [PMID: 36812200 PMCID: PMC9992772 DOI: 10.1073/pnas.2214921120] [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: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Mutant KRAS is a major driver of oncogenesis in a multitude of cancers but remains a challenging target for classical small molecule drugs, motivating the exploration of alternative approaches. Here, we show that aggregation-prone regions (APRs) in the primary sequence of the oncoprotein constitute intrinsic vulnerabilities that can be exploited to misfold KRAS into protein aggregates. Conveniently, this propensity that is present in wild-type KRAS is increased in the common oncogenic mutations at positions 12 and 13. We show that synthetic peptides (Pept-ins™) derived from two distinct KRAS APRs could induce the misfolding and subsequent loss of function of oncogenic KRAS, both of recombinantly produced protein in solution, during cell-free translation and in cancer cells. The Pept-ins exerted antiproliferative activity against a range of mutant KRAS cell lines and abrogated tumor growth in a syngeneic lung adenocarcinoma mouse model driven by mutant KRAS G12V. These findings provide proof-of-concept that the intrinsic misfolding propensity of the KRAS oncoprotein can be exploited to cause its functional inactivation.
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Affiliation(s)
- Kobe Janssen
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | | | | | | | - Bert Houben
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Yulia Lampi
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Mieke Nys
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Laleh Khodaparast
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Rob van der Kant
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Joffre Verniers
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Teresa Garcia
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Katerina Konstantoulea
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Katerina Maragkou
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Ramon Duran-Romaña
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Mónica Musteanu
- Experimental Oncology Group, Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas, Madrid28029, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid28029, Spain
| | - Mariano Barbacid
- Experimental Oncology Group, Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas, Madrid28029, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid28029, Spain
| | | | | | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, 3000Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven3000, Leuven, Belgium
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Aregbesola OA, Kumar A, Mokoena MP, Olaniran AO. Classic Pentachlorophenol Hydroxylating Phenylalanine 4-Monooxygenase from Indigenous Bacillus tropicus Strain AOA-CPS1: Cloning, Overexpression, Purification, Characterization and Structural Homology Modelling. Appl Biochem Biotechnol 2022; 194:635-658. [PMID: 34417677 DOI: 10.1007/s12010-021-03645-2] [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: 02/01/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022]
Abstract
The metabolically promiscuous pentachlorophenol (PCP) hydroxylating Phe4MO (represented as CpsB) was detected, amplified (from the genome of Bacillus tropicus strain AOA-CPS1), cloned, overexpressed, purified and characterized here. The 1.755-kb gene cloned in the pET15b vector expressed a ≅ 64 kDa monomeric protein which was purified to homogeneity by single-step affinity chromatography, with a total yield of 82.1%. The optimum temperature and pH of the enzyme were found to be 30 °C and 7.0, respectively. CpsB showed functional stability between pH 6.0-7.5 and temperature 25-30 °C. The enzyme-substrate reaction kinetic studies showed the allosteric nature of the enzyme and followed pre-steady state using NADH as a co-substrate with apparent vmax, Km, kcat and kcat/Km values of 0.465 μM.s-1, 140 μM, 0.099 s-1 and 7.07 × 10-4 μM-1.s-1, respectively, for the substrate PCP. The in-gel trypsin digestion experiments and bioinformatic tools confirmed that the reported enzyme is a Phe4MO with multiple putative conserved domains and metal ion-binding site. Though Phe4MO has been reported to have a diverse catalytic function, here we report, for the first time, that it functions as a PCP dehalogenase or PCP-4-monooxygenase by hydroxylating PCP. Hence, the use of this enzyme may be further explored in the bioremediation of PCP and other related xenobiotics.
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Affiliation(s)
- Oladipupo A Aregbesola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000, South Africa
| | - Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000, South Africa
| | - Mduduzi P Mokoena
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000, South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000, South Africa.
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George A, Ravi R, Tiwari PB, Srivastava SR, Jain V, Mahalakshmi R. Engineering a Hyperstable Yersinia pestis Outer Membrane Protein Ail Using Thermodynamic Design. J Am Chem Soc 2022; 144:1545-1555. [DOI: 10.1021/jacs.1c05964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjana George
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Roshika Ravi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Pankaj Bharat Tiwari
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Shashank Ranjan Srivastava
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal - 462066, India
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Khan A, Kuriachan G, Mahalakshmi R. Cellular Interactome of Mitochondrial Voltage-Dependent Anion Channels: Oligomerization and Channel (Mis)Regulation. ACS Chem Neurosci 2021; 12:3497-3515. [PMID: 34503333 DOI: 10.1021/acschemneuro.1c00429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Voltage-dependent anion channels (VDACs) of the outer mitochondrial membrane are known conventionally as metabolite flux proteins. However, research findings in the past decade have revealed the multifaceted regulatory roles of VDACs, from governing cellular physiology and mitochondria-mediated apoptosis to directly regulating debilitating cancers and neurodegenerative diseases. VDACs achieve these diverse functions by establishing isoform-dependent stereospecific interactomes in the cell with the cytosolic constituents and endoplasmic reticulum complexes, and the machinery of the mitochondrial compartments. VDACs are now increasingly recognized as regulatory hubs of the cell. Not surprisingly, even the transient misregulation of VDACs results directly in mitochondrial dysfunction. Additionally, human VDACs are now implicated in interaction with aggregation-prone cytosolic proteins, including Aβ, tau, and α-synuclein, contributing directly to the onset of Alzheimer's and Parkinson's diseases. Deducing the interaction dynamics and mechanisms can lead to VDAC-targeted peptide-based therapeutics that can alleviate neurodegenerative states. This review succinctly presents the latest findings of the VDAC interactome, and the mode(s) of VDAC-dependent regulation of biochemical physiology. We also discuss the relevance of VDACs in pathophysiological states and aggregation-associated diseases and address how VDACs will facilitate the development of next-generation precision medicines.
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Affiliation(s)
- Altmash Khan
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Gifty Kuriachan
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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Srivastava SR, Mahalakshmi R. Evolutionary selection of a 19-stranded mitochondrial β-barrel scaffold bears structural and functional significance. J Biol Chem 2020; 295:14653-14665. [PMID: 32817169 PMCID: PMC7586230 DOI: 10.1074/jbc.ra120.014366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
Transmembrane β-barrels of eukaryotic outer mitochondrial membranes (OMMs) are major channels of communication between the cytosol and mitochondria and are indispensable for cellular homeostasis. A structurally intriguing exception to all known transmembrane β-barrels is the unique odd-stranded, i.e. 19-stranded, structures found solely in the OMM. The molecular origins of this 19-stranded structure and its associated functional significance are unclear. In humans, the most abundant OMM transporter is the voltage-dependent anion channel. Here, using the human voltage-dependent anion channel as our template scaffold, we designed and engineered odd- and even-stranded structures of smaller (V216, V217, V218) and larger (V220, V221) barrel diameters. Determination of the structure, dynamics, and energetics of these engineered structures in bilayer membranes reveals that the 19-stranded barrel surprisingly holds modest to low stability in a lipid-dependent manner. However, we demonstrate that this structurally metastable protein possesses superior voltage-gated channel regulation, efficient mitochondrial targeting, and in vivo cell survival, with lipid-modulated stability, all of which supersede the occurrence of a metastable 19-stranded scaffold. We propose that the unique structural adaptation of these transmembrane transporters exclusively in mitochondria bears strong evolutionary basis and is functionally significant for homeostasis.
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Affiliation(s)
- Shashank Ranjan Srivastava
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.
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Pittalà MGG, Saletti R, Reina S, Cunsolo V, De Pinto V, Foti S. A High Resolution Mass Spectrometry Study Reveals the Potential of Disulfide Formation in Human Mitochondrial Voltage-Dependent Anion Selective Channel Isoforms (hVDACs). Int J Mol Sci 2020; 21:E1468. [PMID: 32098132 PMCID: PMC7073118 DOI: 10.3390/ijms21041468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/13/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
The voltage-dependent anion-selective channels (VDACs), which are also known as eukaryotic porins, are pore-forming proteins, which allow for the passage of ions and small molecules across the outer mitochondrial membrane (OMM). They are involved in complex interactions that regulate organelle and cellular metabolism. We have recently reported the post-translational modifications (PTMs) of the three VDAC isoforms purified from rat liver mitochondria (rVDACs), showing, for the first time, the over-oxidation of the cysteine residues as an exclusive feature of VDACs. Noteworthy, this peculiar PTM is not detectable in other integral membrane mitochondrial proteins, as defined by their elution at low salt concentration by a hydroxyapatite column. In this study, the association of tryptic and chymotryptic proteolysis with UHPLC/High Resolution nESI-MS/MS, allowed for us to extend the investigation to the human VDACs. The over-oxidation of the cysteine residues, essentially irreversible in cell conditions, was as also certained in VDAC isoforms from human cells. In human VDAC2 and 3 isoforms the permanently reduced state of a cluster of close cysteines indicates the possibility that disulfide bridges are formed in the proteins. Importantly, the detailed oxidative PTMs that are found in human VDACs confirm and sustain our previous findings in rat tissues, claiming for a predictable characterization that has to be conveyed in the functional role of VDAC proteins within the cell. Data are available via ProteomeXchange with identifier PXD017482.
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Affiliation(s)
- Maria G. G. Pittalà
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy;
| | - Rosaria Saletti
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (V.C.); (S.F.)
| | - Simona Reina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
| | - Vincenzo Cunsolo
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (V.C.); (S.F.)
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 64, 95123 Catania, Italy;
| | - Salvatore Foti
- Department of Chemical Sciences, Organic Mass Spectrometry Laboratory, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (V.C.); (S.F.)
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Gupta A, Mahalakshmi R. Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49878-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Gupta A, Mahalakshmi R. Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation. J Biol Chem 2019; 295:1181-1194. [PMID: 31844019 PMCID: PMC6996891 DOI: 10.1074/jbc.ra119.011342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/11/2019] [Indexed: 11/06/2022] Open
Abstract
Ninety-five percent of all transmembrane proteins exist in kinetically trapped aggregation-prone states that have been directly linked to neurodegenerative diseases. Interestingly, the primary sequence almost invariably avoids off-pathway aggregate formation, by folding reliably into its native, thermodynamically stabilized structure. However, with the rising incidence of protein aggregation diseases, it is now important to understand the underlying mechanism(s) of membrane protein aggregation. Micromolecular physicochemical and biochemical alterations in the primary sequence that trigger the formation of macromolecular cross-β aggregates can be measured only through combinatorial spectroscopic experiments. Here, we developed spectroscopic thermal perturbation with 117 experimental variables to assess how subtle protein sequence variations drive the molecular transition of the folded protein to oligomeric aggregates. Using the Yersinia pestis outer transmembrane β-barrel Ail as a model, we delineated how a single-residue substitution that alters the membrane-anchoring ability of Ail significantly contributes to the kinetic component of Ail stability. We additionally observed a stabilizing role for interface aliphatics, and that interface aromatics physicochemically contribute to Ail self-assembly and aggregation. Moreover, our method identified the formation of structured oligomeric intermediates during Ail aggregation. We show that the self-aggregation tendency of Ail is offset by the evolution of a thermodynamically compromised primary sequence that balances folding, stability, and oligomerization. Our approach provides critical information on how subtle changes in protein primary sequence trigger cross-β fibril formation, with insights that have direct implications for deducing the molecular progression of neurodegeneration and amyloidogenesis in humans.
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Affiliation(s)
- Ankit Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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