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Trofimenko E, Grasso G, Heulot M, Chevalier N, Deriu MA, Dubuis G, Arribat Y, Serulla M, Michel S, Vantomme G, Ory F, Dam LC, Puyal J, Amati F, Lüthi A, Danani A, Widmann C. Genetic, cellular, and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore. eLife 2021; 10:69832. [PMID: 34713805 PMCID: PMC8639150 DOI: 10.7554/elife.69832] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cell-penetrating peptides (CPPs) allow intracellular delivery of bioactive cargo molecules. The mechanisms allowing CPPs to enter cells are ill-defined. Using a CRISPR/Cas9-based screening, we discovered that KCNQ5, KCNN4, and KCNK5 potassium channels positively modulate cationic CPP direct translocation into cells by decreasing the transmembrane potential (Vm). These findings provide the first unbiased genetic validation of the role of Vm in CPP translocation in cells. In silico modeling and live cell experiments indicate that CPPs, by bringing positive charges on the outer surface of the plasma membrane, decrease the Vm to very low values (–150 mV or less), a situation we have coined megapolarization that then triggers formation of water pores used by CPPs to enter cells. Megapolarization lowers the free energy barrier associated with CPP membrane translocation. Using dyes of varying dimensions in CPP co-entry experiments, the diameter of the water pores in living cells was estimated to be 2 (–5) nm, in accordance with the structural characteristics of the pores predicted by in silico modeling. Pharmacological manipulation to lower transmembrane potential boosted CPP cellular internalization in zebrafish and mouse models. Besides identifying the first proteins that regulate CPP translocation, this work characterized key mechanistic steps used by CPPs to cross cellular membranes. This opens the ground for strategies aimed at improving the ability of cells to capture CPP-linked cargos in vitro and in vivo. Before a drug can have its desired effect, it must reach its target tissue or organ, and enter its cells. This is not easy because cells are surrounded by the plasma membrane, a fat-based barrier that separates the cell from its external environment. The plasma membrane contains proteins that act as channels, shuttling specific molecules in and out of the cell, and it also holds charge, with its inside surface being more negatively charged than its outside surface. Cell-penetrating peptides are short sequences of amino acids (the building blocks that form proteins) that carry positive charges. These positive charges allow them to cross the membrane easily, but it is not well understood how. To find out how cell-penetrating peptides cross the membrane, Trofimenko et al. attached them to dyes of different sizes. This revealed that the cell-penetrating peptides enter the cell through temporary holes called water pores, which measure about two nanometres across. The water pores form when the membrane becomes ‘megapolarized’, this is, when the difference in charge between the inside and the outside of the membrane becomes greater than normal. This can happen when the negative charge on the inside surface or the positive charge on the outer surface of the membrane increase. Megapolarization depends on potassium channels, which transport positive potassium ions outside the cell, making the outside of the membrane positive. When cell-penetrating peptides arrive at the outer surface of the cell near potassium channels, they make it even more positive. This increases the charge difference between the inside and the outside of the cell, allowing water pores to form. Once the peptides pass through the pores, the charge difference between the inside and the outside of the cell membrane dissipates, and the pores collapse. Drug developers are experimenting with attaching cell-penetrating peptides to drugs to help them get inside their target cells. Currently there are several experimental medications of this kind in clinical trials. Understanding how these peptides gain entry, and what size of molecule they could carry with them, provides solid ground for further drug development.
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Affiliation(s)
- Evgeniya Trofimenko
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence Research, Università della Svizzera italiana, Scuola Universitaria Professionale della Svizzera Italiana, Lugano, Switzerland
| | - Mathieu Heulot
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Nadja Chevalier
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Marco A Deriu
- PolitoBIOMed Lab Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Gilles Dubuis
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Yoan Arribat
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Marc Serulla
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Sebastien Michel
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gil Vantomme
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Florine Ory
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Linh Chi Dam
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Julien Puyal
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,CURML (University Center of Legal Medicine), Lausanne University Hospital, Lausanne, Switzerland
| | - Francesca Amati
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Anita Lüthi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence Research, Università della Svizzera italiana, Scuola Universitaria Professionale della Svizzera Italiana, Lugano, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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Sperti M, Malavolta M, Ciniero G, Borrelli S, Cavaglià M, Muscat S, Tuszynski JA, Afeltra A, Margiotta DPE, Navarini L. JAK inhibitors in immune-mediated rheumatic diseases: From a molecular perspective to clinical studies. J Mol Graph Model 2021; 104:107789. [DOI: 10.1016/j.jmgm.2020.107789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
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Highlighting the effect of amyloid beta assemblies on the mechanical properties and conformational stability of cell membrane. J Mol Graph Model 2020; 100:107670. [PMID: 32711259 DOI: 10.1016/j.jmgm.2020.107670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/05/2023]
Abstract
Alzheimer disease (AD) is the most common cause of dementia, characterized by a progressive decline in cognitive function due to the abnormal aggregation and deposition of Amyloid beta (Aβ) fibrils in the brain of patients. In this context, the molecular mechanisms of protein misfolding and aggregation that are known to induce significant biophysical alterations in cells, including destabilization of plasma membranes, remain partially unclear. Physical interaction between the Aβ assemblies and the membrane leads to the disruption of the cell membrane in multiple ways including, surface carpeting, generation of transmembrane channels and detergent-like membrane dissolution. Understanding the impact of amyloidogenic protein in different stages of aggregation with the plasma membrane, plays a crucial role to fully elucidate the pathological mechanisms of AD. Within this framework, computer simulations represent a powerful tool able to shed lights on the interactions governing the structural influence of Aβ proteins on biological membrane. In this study, molecular dynamics (MD) simulations have been performed in order to characterize how POPC bilayer conformational and mechanical properties are affected by the interaction with Aβ11-42 peptide, oligomer and fibril.
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Miceli M, Muscat S, Morbiducci U, Cavaglià M, Deriu MA. Ultrasonic waves effect on S-shaped β-amyloids conformational dynamics by non-equilibrium molecular dynamics. J Mol Graph Model 2020; 96:107518. [DOI: 10.1016/j.jmgm.2019.107518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
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5
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Horx P, Geyer A. Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics. PLoS One 2020; 15:e0230962. [PMID: 32282813 PMCID: PMC7153902 DOI: 10.1371/journal.pone.0230962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/12/2020] [Indexed: 01/29/2023] Open
Abstract
A designed disulfide-rich β-hairpin peptide that dimerizes spontaneously served as a hinge-type connection between proteins. Here, we analyze the range of dynamics of this hinge dimer with the aim of proposing new applications for the DNA-encodable peptide and establishing guidelines for the computational analysis of other disulfide hinges. A recent structural analysis based on nuclear magnetic resonance spectroscopy and ion mobility spectrometry revealed an averaged conformation in the hinge region which motivated us to investigate the dynamic behavior using a combination of molecular dynamics simulation, metadynamics and free energy surface analysis to characterize the conformational space available to the hinge. Principal component analysis uncovered two slow modes of the peptide, namely, the opening and closing motion and twisting of the two β-hairpins assembling the hinge. Applying a collective variable (CV) that mimics the first dominating mode, led to a major expansion of the conformational space. The description of the dynamics could be achieved by analysis of the opening angle and the twisting of the β-hairpins and, thus, offers a methodology that can also be transferred to other derivatives. It has been demonstrated that the hinge peptide’s lowest energy conformation consists of a large opening angle and strong twist but is separated by small energy barriers and can, thus, adopt a closed and untwisted structure. With the aim of proposing further applications for the hinge peptide, we simulated its behavior in the sterically congested environment of a four-helix bundle. Preliminary investigations show that one helix is pushed out and a three-helix bundle forms. The insights gained into the dynamics of the tetra-disulfide peptide and analytical guidelines developed in this study may contribute to the understanding of the structure and function of more complex hinge-type proteins, such as the IgG antibody family.
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Affiliation(s)
- Philip Horx
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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Pracht P, Bohle F, Grimme S. Automated exploration of the low-energy chemical space with fast quantum chemical methods. Phys Chem Chem Phys 2020; 22:7169-7192. [PMID: 32073075 DOI: 10.1039/c9cp06869d] [Citation(s) in RCA: 802] [Impact Index Per Article: 200.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
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7
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Metadynamics to Enhance Sampling in Biomolecular Simulations. Methods Mol Biol 2019. [PMID: 31396904 DOI: 10.1007/978-1-4939-9608-7_8] [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: 11/12/2023]
Abstract
Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.
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Dal Magro R, Simonelli S, Cox A, Formicola B, Corti R, Cassina V, Nardo L, Mantegazza F, Salerno D, Grasso G, Deriu MA, Danani A, Calabresi L, Re F. The Extent of Human Apolipoprotein A-I Lipidation Strongly Affects the β-Amyloid Efflux Across the Blood-Brain Barrier in vitro. Front Neurosci 2019; 13:419. [PMID: 31156358 PMCID: PMC6532439 DOI: 10.3389/fnins.2019.00419] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/11/2019] [Indexed: 12/20/2022] Open
Abstract
Much evidence suggests a protective role of high-density lipoprotein (HDL) and its major apolipoprotein apoA-I, in Alzheimer’s disease (AD). The biogenesis of nascent HDL derived from a first lipidation of apoA-I, which is synthesized by the liver and intestine but not in the brain, in a process mediated by ABCA1. The maturation of nascent HDL in mature spherical HDL is due to a subsequent lipidation step, LCAT-mediated cholesterol esterification, and the change of apoA-I conformation. Therefore, different subclasses of apoA-I-HDL simultaneously exist in the blood circulation. Here, we investigated if and how the lipidation state affects the ability of apoA-I-HDL to target and modulate the cerebral β-amyloid (Aβ) content from the periphery, that is thus far unclear. In particular, different subclasses of HDL, each with different apoA-I lipidation state, were purified from human plasma and their ability to cross the blood-brain barrier (BBB), to interact with Aβ aggregates, and to affect Aβ efflux across the BBB was assessed in vitro using a transwell system. The results showed that discoidal HDL displayed a superior capability to promote Aβ efflux in vitro (9 × 10-5 cm/min), when compared to apoA-I in other lipidation states. In particular, no effect on Aβ efflux was detected when apoA-I was in mature spherical HDL, suggesting that apoA-I conformation, and lipidation could play a role in Aβ clearance from the brain. Finally, when apoA-I folded its structure in discoidal HDL, rather than in spherical ones, it was able to cross the BBB in vitro and strongly destabilize the conformation of Aβ fibrils by decreasing the order of the fibril structure (-24%) and the β-sheet content (-14%). These data suggest that the extent of apoA-I lipidation, and consequently its conformation, may represent crucial features that could exert their protective role in AD pathogenesis.
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Affiliation(s)
- Roberta Dal Magro
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Sara Simonelli
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Centro Grossi Paoletti, Università degli Studi di Milano, Milan, Italy
| | - Alysia Cox
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Beatrice Formicola
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Roberta Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Valeria Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Luca Nardo
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Domenico Salerno
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Laura Calabresi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Centro Grossi Paoletti, Università degli Studi di Milano, Milan, Italy
| | - Francesca Re
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
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Munsamy G, Agoni C, Soliman MES. A dual target of Plasmepsin IX and X: Unveiling the atomistic superiority of a core chemical scaffold in malaria therapy. J Cell Biochem 2019; 120:7876-7887. [PMID: 30430636 DOI: 10.1002/jcb.28062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023]
Abstract
Plasmepsin IX and X, members of the prominent aspartic family of proteases whose function were hitherto unknown have only recently been established as key mediators of erythrocyte invasion and egress of the virulent malarial parasite. Inhibitor 49c, a potent antimalarial peptidomimetic inhibitor initially developed to target Plasmepsin II has lately been proven to exhibit potent inhibitory activity against Plasmepsin IX and X. However, the molecular and structural dynamics supporting its inhibitory activity remain inconclusive. Hindering the motion of the flap and hinge region of an aspartic protease remains essential for disabling the catalytic activity of the enzyme. Integrating molecular dynamic simulations coupled with other advanced biocomputational tools, we reveal the enhanced structural mechanistic competence of 49c in complex with Plasmepsin IX and X relative to Pepstatin. Pepstatin, a known aspartic protease inhibitor which actively hinders the opening and closing of the flap tip and flexible loop and consequently limits access to the catalytic aspartic residues, however, its administration has been related to elevated levels of toxicity. Thermodynamic calculations reveal a higher relative binding free energy associated with Plasmepsin IX and X in complex with 49c as opposed to Pepstatin. A relatively compact and structurally rigid 49c bound complexes sequel into the restriction of the flap and hinge residues by restraining cohesive movement, consequently hindering their "twisting motion" from transpiring. Findings unveil an atomistic perspective into the structural superiority of 49c in complex with Plasmepsin IX and X.
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Affiliation(s)
- Geraldene Munsamy
- Department of Pharmaceutical Chemistry, Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Clement Agoni
- Department of Pharmaceutical Chemistry, Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Department of Pharmaceutical Chemistry, Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
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Grasso G, Morbiducci U, Massai D, Tuszynski JA, Danani A, Deriu MA. Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies. Biophys J 2019; 114:323-330. [PMID: 29401430 DOI: 10.1016/j.bpj.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 01/12/2023] Open
Abstract
The AXH domain of protein Ataxin 1 is thought to play a key role in the misfolding and aggregation pathway responsible for Spinocerebellar ataxia 1. For this reason, a molecular level understanding of AXH oligomerization pathway is crucial to elucidate the aggregation mechanism, which is thought to trigger the disease. This study employs classical and enhanced molecular dynamics to identify the structural and energetic basis of AXH tetramer stability. Results of this work elucidate molecular mechanisms behind the destabilizing effect of protein mutations, which consequently affect the AXH tetramer assembly. Moreover, results of the study draw attention for the first time, to our knowledge, to the R638 protein residue, which is shown to play a key role in AXH tetramer stability. Therefore, R638 might be also implicated in the AXH oligomerization pathway and stands out as a target for future experimental studies focused on self-association mechanisms and fibril formation of full-length ATX1.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland.
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11
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Visentin C, Navarro S, Grasso G, Regonesi ME, Deriu MA, Tortora P, Ventura S. Protein Environment: A Crucial Triggering Factor in Josephin Domain Aggregation: The Role of 2,2,2-Trifluoroethanol. Int J Mol Sci 2018; 19:ijms19082151. [PMID: 30042316 PMCID: PMC6121581 DOI: 10.3390/ijms19082151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022] Open
Abstract
The protein ataxin-3 contains a polyglutamine stretch that triggers amyloid aggregation when it is expanded beyond a critical threshold. This results in the onset of the spinocerebellar ataxia type 3. The protein consists of the globular N-terminal Josephin domain and a disordered C-terminal tail where the polyglutamine stretch is located. Expanded ataxin-3 aggregates via a two-stage mechanism: first, Josephin domain self-association, then polyQ fibrillation. This highlights the intrinsic amyloidogenic potential of Josephin domain. Therefore, much effort has been put into investigating its aggregation mechanism(s). A key issue regards the conformational requirements for triggering amyloid aggregation, as it is believed that, generally, misfolding should precede aggregation. Here, we have assayed the effect of 2,2,2-trifluoroethanol, a co-solvent capable of stabilizing secondary structures, especially α-helices. By combining biophysical methods and molecular dynamics, we demonstrated that both secondary and tertiary JD structures are virtually unchanged in the presence of up to 5% 2,2,2-trifluoroethanol. Despite the preservation of JD structure, 1% of 2,2,2-trifluoroethanol suffices to exacerbate the intrinsic aggregation propensity of this domain, by slightly decreasing its conformational stability. These results indicate that in the case of JD, conformational fluctuations might suffice to promote a transition towards an aggregated state without the need for extensive unfolding, and highlights the important role played by the environment on the aggregation of this globular domain.
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Affiliation(s)
- Cristina Visentin
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Maria Elena Regonesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Paolo Tortora
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
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Yang LQ, Chen GY, Li Y, Zhang RP, Liu SQ, Sang P. Insight derived from molecular dynamics simulation into dynamics and molecular motions of cuticle-degrading serine protease Ver112. J Biomol Struct Dyn 2018; 37:2004-2016. [DOI: 10.1080/07391102.2018.1471418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali, P.R. China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali University, Dali, P.R. China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, P.R. China
| | - Gui-Yuan Chen
- College of Basic Medicine, Dali University, Dali, P.R. China
| | - Yi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, P.R. China
| | - Ruo-Peng Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, P.R. China
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, P.R. China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, P.R. China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali University, Dali, P.R. China
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Grasso G, Rebella M, Muscat S, Morbiducci U, Tuszynski J, Danani A, Deriu MA. Conformational Dynamics and Stability of U-Shaped and S-Shaped Amyloid β Assemblies. Int J Mol Sci 2018; 19:ijms19020571. [PMID: 29443891 PMCID: PMC5855793 DOI: 10.3390/ijms19020571] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/04/2018] [Accepted: 02/10/2018] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease is the most fatal neurodegenerative disorder characterized by the aggregation and deposition of Amyloid β (Aβ) oligomers in the brain of patients. Two principal variants of Aβ exist in humans: Aβ1–40 and Aβ1–42. The former is the most abundant in the plaques, while the latter is the most toxic species and forms fibrils more rapidly. Interestingly, fibrils of Aβ1–40 peptides can only assume U-shaped conformations while Aβ1–42 can also arrange as S-shaped three-stranded chains, as recently discovered. As alterations in protein conformational arrangement correlate with cell toxicity and speed of disease progression, it is important to characterize, at molecular level, the conformational dynamics of amyloid fibrils. In this work, Replica Exchange Molecular Dynamics simulations were carried out to compare the conformational dynamics of U-shaped and S-shaped Aβ17–42 small fibrils. Our computational results provide support for the stability of the recently proposed S-shaped model due to the maximized interactions involving the C-terminal residues. On the other hand, the U-shaped motif is characterized by significant distortions resulting in a more disordered assembly. Outcomes of our work suggest that the molecular architecture of the protein aggregates might play a pivotal role in formation and conformational stability of the resulting fibrils.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Martina Rebella
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
| | - Stefano Muscat
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
| | - Jack Tuszynski
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Marco A Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
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Deriu MA, Cangiotti M, Grasso G, Licandro G, Lavasanifar A, Tuszynski JA, Ottaviani MF, Danani A. Self-Assembled Ligands Targeting TLR7: A Molecular Level Investigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14460-14471. [PMID: 29200306 DOI: 10.1021/acs.langmuir.7b03168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Toll-like receptors (TLRs) are pattern recognition transmembrane proteins that play an important role in innate immunity. In particular, TLR7 plays a role in detecting nucleic acids derived from viruses and bacteria. The huge number of pathologies in which TLR7 is involved has led to an increasing interest in developing new compounds targeting this protein. Several conjugation strategies were proposed for TLR7 agonists to increase the potency while maintaining a low toxicity. In this work, we focus the attention on two promising classes of TLR7 compounds derived from the same pharmacophore conjugated with phospholipid and polyethylene glycol (PEG). A multidisciplinary investigation has been carried out by molecular dynamics (MD), dynamic light scattering (DLS), electron paramagnetic resonance (EPR), and cytotoxicity assessment. DLS and MD indicated how only the phospholipid conjugation provides the compound abilities to self-assemble in an orderly fashion with a maximal pharmacophore exposition to the solvent. Further EPR and cytotoxicity experiments highlighted that phospholipid compounds organize in stable aggregates and well interact with TLR7, whereas PEG conjugation was characterized by poorly stable aggregates at the cells surface. The methodological framework proposed in this study may be used to investigate, at a molecular level, the interactions generally occurring between aggregated ligands, to be used as drugs, and protein receptors.
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Affiliation(s)
- Marco A Deriu
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
| | - Michela Cangiotti
- Department of Pure and Applied Sciences, University of Urbino , Via Ca' Le Suore 2/4, Urbino,Marche 61029, Italy
| | - Gianvito Grasso
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
| | - Ginevra Licandro
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
| | | | | | - Maria Francesca Ottaviani
- Department of Pure and Applied Sciences, University of Urbino , Via Ca' Le Suore 2/4, Urbino,Marche 61029, Italy
| | - Andrea Danani
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
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15
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Lepre MG, Omar SI, Grasso G, Morbiducci U, Deriu MA, Tuszynski JA. Insights into the Effect of the G245S Single Point Mutation on the Structure of p53 and the Binding of the Protein to DNA. Molecules 2017; 22:E1358. [PMID: 28813011 PMCID: PMC6152093 DOI: 10.3390/molecules22081358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/13/2017] [Accepted: 08/13/2017] [Indexed: 12/20/2022] Open
Abstract
The transcription factor p53 is a potent tumor suppressor dubbed as the "guardian of the genome" because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be a structural hotspot mutation. To understand the behaviors and differences between the wild-type and mutant, both a dimer of the wild type p53 (wt-p53) and its G245S mutant (G245S-mp53), complexed with DNA, were simulated using molecular dynamics for more than 1 μs. wt-p53 and G245S-mp53 apo monomers were simulated for 1 μs as well. Conformational analyses and binding energy evaluations performed underline important differences and therefore provide insights to understand the G245S-mp53 loss of function. Our results indicate that the G245S mutation destabilizes several structural regions in the protein that are crucial for DNA binding when found in its apo form and highlight differences in the mutant-DNA complex structure compared to the wt protein. These findings not only provide means that can be applied to other p53 mutants but also serve as structural basis for further studies aimed at the development of cancer therapies based on restoring the function of p53.
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Affiliation(s)
- Marco Gaetano Lepre
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
| | - Sara Ibrahim Omar
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | - Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
| | - Marco Agostino Deriu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Jack A Tuszynski
- Department of Oncology, Department of Physics, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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Grasso G, Tuszynski JA, Morbiducci U, Licandro G, Danani A, Deriu MA. Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics. Biol Direct 2017; 12:2. [PMID: 28103906 PMCID: PMC5244572 DOI: 10.1186/s13062-016-0173-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/21/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties of the AT-3 N-terminal region, also called Josephin Domain (JD), play a key role in the first step of aggregation, having the JD an amyloidogenic propensity itself. For this reason, unraveling the intimate relationship between JD structural features and aggregation tendency may lead to a step forward in understanding the pathology and rationally design a cure. In this connection, computational modeling has demonstrated to be helpful in exploring the protein molecular dynamics and mechanism of action. RESULTS Conformational dynamics of the JD is here finely investigated by replica exchange molecular dynamics simulations able to sample the microsecond time scale and to provide both a thermodynamic and kinetic description of the protein conformational changes. Accessible structural conformations of the JD have been identified in: open, intermediate and closed like arrangement. Data indicated the closed JD arrangement as the most likely protein arrangement. The protein transition from closed toward intermediate/open states was characterized by a rate constant higher than 700 ns. This result also explains the inability of classical molecular dynamics to explore transitions from closed to open JD configuration on a time scale of hundreds of nanoseconds. CONCLUSION This work provides the first kinetic estimation of the JD transition pathway from open-like to closed-like arrangement and vice-versa, indicating the closed-like arrangement as the most likely configuration for a JD in water environment. More widely, the importance of our results is also underscored considering that the ability to provide a kinetic description of the protein conformational changes is a scientific challenge for both experimental and theoretical approaches to date. REVIEWERS This article was reviewed by Oliviero Carugo, Bojan Zagrovic.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Jack A. Tuszynski
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | | | - Ginevra Licandro
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Marco A. Deriu
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
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17
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Deriu MA, Grasso G, Tuszynski JA, Massai D, Gallo D, Morbiducci U, Danani A. Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis. Proteins 2016; 84:666-73. [DOI: 10.1002/prot.25017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Marco A. Deriu
- Istituto Dalle Molle Di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI); Centro Galleria 2 Manno CH-6928 Switzerland
| | - Gianvito Grasso
- Istituto Dalle Molle Di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI); Centro Galleria 2 Manno CH-6928 Switzerland
| | - Jack A. Tuszynski
- Department of Physics; University of Alberta; Edmonton Alberta Canada
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
- Department of Cardiothoracic; Transplantation, and Vascular Surgery (HTTG), Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School; Carl-Neuberg-Strabe 1 Hannover 30625 Germany
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
| | - Andrea Danani
- Istituto Dalle Molle Di Studi Sull'intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale Della Svizzera Italiana (SUPSI), Università Della Svizzera Italiana (USI); Centro Galleria 2 Manno CH-6928 Switzerland
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