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Quiroz RCN, Philot EA, General IJ, Perahia D, Scott AL. Effect of phosphorylation on the structural dynamics, thermal stability of human dopamine transporter: A simulation study using normal modes, molecular dynamics and Markov State Model. J Mol Graph Model 2023; 118:108359. [PMID: 36279761 DOI: 10.1016/j.jmgm.2022.108359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The Human Dopamine Transporter (hDAT) plays an essential role in modulating the Influx/Efflux of dopamine, and it is involved in the mechanism of certain neurodegenerative diseases such as Parkinson's disease. Several studies have reported important states for Dopamine transport: outward-facing open state (OFo), the outward-facing closed state (OFc), the holo-occluded state closed (holo), and the inward-facing open state (IFo). Furthermore, experimental assays have shown that different phosphorylation conditions in hDAT can affect the rate of dopamine absorption. We present a protocol using hybrid simulation methods to study the conformational dynamics and stability of states of hDAT under different phosphorylation sites. With this protocol, we explored the conformational space of hDAT, identified the states, and evaluated the free energy differences and the transition probabilities between them in each of the phosphorylation cases. We also presented the conformational changes and correlated them with those described in the literature. There is a thesis/hypothesis that the phosphorylation condition corresponding to NP-333 system (where all sites Ser/Thr from residue 2 to 62 and 254 to 613 are phosphorylated, except residue 333) would decrease the rate of dopamine transport from the extracellular medium to the intracellular medium by hDAT as previously described in the literature by Lin et al., 2003. Our results corroborated this thesis/hypothesis and the data reported. It is probably due to the affectation/changes/alteration of the conformational dynamics of this system that makes the intermediate states more likely and makes it difficult to initial states associated with the uptake of dopamine in the extracellular medium, corroborating the experimental results. Furthermore, our results showed that just single phosphorylation/dephosphorylation could alter intrinsic protein motions affecting the sampling of one or more states necessary for dopamine transport. In this sense, the modification of phosphorylation influences protein movements and conformational preferences, affecting the stability of states and the transition between them and, therefore, the transport.
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Affiliation(s)
- R C N Quiroz
- Biossistemas, Universidade Federal do ABC, CCNH, Santo André, Brazil; Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - E A Philot
- Centro de Matemática, Computação e Cognição. Laboratório de Biofísica e Biologia Computacional. Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - I J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín, 1650, Buenos Aires, Argentina
| | - D Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, 4 avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - A L Scott
- UFABC - Universidade Federal Do ABC, Centro de Matemática, Computação e Cognição, Laboratório de Biofísica e Biologia Computacional, Brazil.
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2
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Laine E, Grudinin S. HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps. J Phys Chem B 2021; 125:2577-2588. [PMID: 33687221 DOI: 10.1021/acs.jpcb.0c11633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In light of the recent very rapid progress in protein structure prediction, accessing the multitude of functional protein states is becoming more central than ever before. Indeed, proteins are flexible macromolecules, and they often perform their function by switching between different conformations. However, high-resolution experimental techniques such as X-ray crystallography and cryogenic electron microscopy can catch relatively few protein functional states. Many others are only accessible under physiological conditions in solution. Therefore, there is a pressing need to fill this gap with computational approaches. We present HOPMA, a novel method to predict protein functional states and transitions by using a modified elastic network model. The method exploits patterns in a protein contact map, taking its 3D structure as input, and excludes some disconnected patches from the elastic network. Combined with nonlinear normal mode analysis, this strategy boosts the protein conformational space exploration, especially when the input structure is highly constrained, as we demonstrate on a set of more than 400 transitions. Our results let us envision the discovery of new functional conformations, which were unreachable previously, starting from the experimentally known protein structures. The method is computationally efficient and available at https://github.com/elolaine/HOPMA and https://team.inria.fr/nano-d/software/nolb-normal-modes.
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Affiliation(s)
- Elodie Laine
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005 Paris, France
| | - Sergei Grudinin
- CNRS, Inria, Grenoble INP, LJK, Univ. Grenoble Alpes, 38000 Grenoble, France
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3
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Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Curr Opin Struct Biol 2020; 64:34-41. [PMID: 32622329 DOI: 10.1016/j.sbi.2020.05.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022]
Abstract
With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangements of large structures and assemblies, albeit at low resolution. We present an overview of recent progress in the field with examples of successful applications highlighting the utility of such hybrid methods and pointing to emerging future directions guided by advances in experimental characterization of biomolecular systems structure and dynamics.
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Affiliation(s)
- James M Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Ana Ligia Scott
- Laboratory of Bioinformatics and Computational Biology, Federal University of ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Superieure Paris-Saclay, UMR 8113, CNRS, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA.
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4
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Aouad MR, Messali M, Rezki N, Said MA, Lentz D, Zubaydi L, Warad I. Hydrophobic pocket docking, double-proton prototropic tautomerism in contradiction to single-proton transfer in thione ⇔thiol Schiff base with triazole-thione moiety: Green synthesis, XRD and DFT-analysis. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Girola N, Resende-Lara PT, Figueiredo CR, Massaoka MH, Azevedo RA, Cunha RLOR, Polonelli L, Travassos LR. Molecular, Biological and Structural Features of V L CDR-1 Rb44 Peptide, Which Targets the Microtubule Network in Melanoma Cells. Front Oncol 2019; 9:25. [PMID: 30740361 PMCID: PMC6355703 DOI: 10.3389/fonc.2019.00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/08/2019] [Indexed: 12/21/2022] Open
Abstract
Microtubules are important drug targets in tumor cells, owing to their role in supporting and determining the cell shape, organelle movement and cell division. The complementarity-determining regions (CDRs) of immunoglobulins have been reported to be a source of anti-tumor peptide sequences, independently of the original antibody specificity for a given antigen. We found that, the anti-Lewis B mAb light-chain CDR1 synthetic peptide Rb44, interacted with microtubules and induced depolymerization, with subsequent degradation of actin filaments, leading to depolarization of mitochondrial membrane-potential, increase of ROS, cell cycle arrest at G2/M, cleavage of caspase-9, caspase-3 and PARP, upregulation of Bax and downregulation of Bcl-2, altogether resulting in intrinsic apoptosis of melanoma cells. The in vitro inhibition of angiogenesis was also an Rb44 effect. Peritumoral injection of Rb44L1 delayed growth of subcutaneously grafted melanoma cells in a syngeneic mouse model. L1-CDRs from immunoglobulins and their interactions with tubulin-dimers were explored to interpret effects on microtubule stability. The opening motion of tubulin monomers allowed for efficient L1-CDR docking, impairment of dimer formation and microtubule dissociation. We conclude that Rb44 VL-CDR1 is a novel peptide that acts on melanoma microtubule network causing cell apoptosis in vitro and melanoma growth inhibition in vivo.
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Affiliation(s)
- Natalia Girola
- Department of Microbiology, Immunology and Parasitology, Experimental Oncology Unit, Federal University of São Paulo, São Paulo, Brazil
| | - Pedro T Resende-Lara
- Computational Biology and Bioinformatics Laboratory, Federal University of ABC, Santo André, Brazil
| | - Carlos R Figueiredo
- Department of Microbiology, Immunology and Parasitology, Experimental Oncology Unit, Federal University of São Paulo, São Paulo, Brazil.,Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Ricardo A Azevedo
- Department of Microbiology, Immunology and Parasitology, Experimental Oncology Unit, Federal University of São Paulo, São Paulo, Brazil
| | - Rodrigo L O R Cunha
- Chemical Biology Laboratory, Natural and Human Sciences Center, Federal University of ABC, Santo André, Brazil
| | - Luciano Polonelli
- Unit of Biomedical, Biotechnological and Translational Sciences, Department of Medicine and Surgery, Universitá degli Studi di Parma, Parma, Italy
| | - Luiz R Travassos
- Department of Microbiology, Immunology and Parasitology, Experimental Oncology Unit, Federal University of São Paulo, São Paulo, Brazil.,Recepta Biopharma, São Paulo, Brazil
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Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands. Molecules 2018; 23:molecules23020490. [PMID: 29473857 PMCID: PMC6017819 DOI: 10.3390/molecules23020490] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
Dipeptidyl peptidase-4 (DPP-4) is a target to treat type II diabetes mellitus. Therefore, it is important to understand the structural aspects of this enzyme and its interaction with drug candidates. This study involved molecular dynamics simulations, normal mode analysis, binding site detection and analysis of molecular interactions to understand the protein dynamics. We identified some DPP-4 functional motions contributing to the exposure of the binding sites and twist movements revealing how the two enzyme chains are interconnected in their bioactive form, which are defined as chains A (residues 40-767) and B (residues 40-767). By understanding the enzyme structure, its motions and the regions of its binding sites, it will be possible to contribute to the design of new DPP-4 inhibitors as drug candidates to treat diabetes.
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Meissner GO, de Resende Lara PT, Scott LPB, Braz ASK, Chaves-Moreira D, Matsubara FH, Soares EM, Trevisan-Silva D, Gremski LH, Veiga SS, Chaim OM. Molecular cloning and in silico characterization of knottin peptide, U2-SCRTX-Lit2, from brown spider (Loxosceles intermedia) venom glands. J Mol Model 2016; 22:196. [PMID: 27488102 DOI: 10.1007/s00894-016-3067-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/10/2016] [Indexed: 01/16/2023]
Abstract
Inhibitor cystine knots (ICKs) are a family of structural peptides with a large number of cysteine residues that form intramolecular disulfide bonds, resulting in a knot. These peptides are involved in a variety of biological functions including predation and defense, and are found in various species, such as spiders, scorpions, sea anemones, and plants. The Loxosceles intermedia venom gland transcriptome identified five groups of ICK peptides that represent more than 50 % of toxin-coding transcripts. Here, we describe the molecular cloning of U2-Sicaritoxin-Lit2 (U2-SCRTX-Lit2), bioinformatic characterization, structure prediction, and molecular dynamic analysis. The sequence of U2-SCRTX-Lit2 obtained from the transcriptome is similar to that of μ-Hexatoxin-Mg2, a peptide that inhibits the insect Nav channel. Bioinformatic analysis of sequences classified as ICK family members also showed a conservation of cysteine residues among ICKs from different spiders, with the three dimensional molecular model of U2-SCRTX-Lit2 similar in structure to the hexatoxin from μ-hexatoxin-Mg2a. Molecular docking experiments showed the interaction of U2-SCRTX-Lit2 to its predictable target-the Spodoptera litura voltage-gated sodium channel (SlNaVSC). After 200 ns of molecular dynamic simulation, the final structure of the complex showed stability in agreement with the experimental data. The above analysis corroborates the existence of a peptide toxin with insecticidal activity from a novel ICK family in L. intermedia venom and demonstrates that this peptide targets Nav channels.
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Affiliation(s)
- Gabriel Otto Meissner
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Pedro Túlio de Resende Lara
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Luis Paulo Barbour Scott
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Antônio Sérgio Kimus Braz
- Laboratory of Computational Biology and Bioinformatics, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Daniele Chaves-Moreira
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Fernando Hitomi Matsubara
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Eduardo Mendonça Soares
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Dilza Trevisan-Silva
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Luiza Helena Gremski
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil.,Laboratory of Molecular Immunopathology, Department of Clinical Pathology, Clinical Hospital of Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Silvio Sanches Veiga
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil
| | - Olga Meiri Chaim
- Department of Cell Biology, Federal University of Paraná, Jardim das Américas, 81531-990, Curitiba, Paraná, Brazil.
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8
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Binding of phenothiazines into allosteric hydrophobic pocket of human thioredoxin 1. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:279-86. [PMID: 26820562 DOI: 10.1007/s00249-016-1113-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/25/2015] [Accepted: 01/10/2016] [Indexed: 10/22/2022]
Abstract
Thioredoxins are multifunctional oxidoreductase proteins implicated in the antioxidant cellular apparatus and oxidative stress. They are involved in several pathologies and are promising anticancer targets. Identification of noncatalytic binding sites is of great interest for designing new allosteric inhibitors of thioredoxin. In a recent work, we predicted normal mode motions of human thioredoxin 1 and identified two major putative hydrophobic binding sites. In this work we investigated noncovalent interactions of human thioredoxin 1 with three phenotiazinic drugs acting as prooxidant compounds by using molecular docking and circular dichroism spectrometry to probe ligand binding into the previously predicted allosteric hydrophobic pockets. Our in silico and CD spectrometry experiments suggested one preferred allosteric binding site involving helix 3 and adopting the best druggable conformation identified by NMA. The CD spectra showed binding of thioridazine into thioredoxin 1 and suggested partial helix unfolding, which most probably concerns helix 3. Taken together, these data support the strategy to design thioredoxin inhibitors targeting a druggable allosteric binding site.
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Zhang X, Lu J, Ren X, Du Y, Zheng Y, Ioannou PV, Holmgren A. Oxidation of structural cysteine residues in thioredoxin 1 by aromatic arsenicals enhances cancer cell cytotoxicity caused by the inhibition of thioredoxin reductase 1. Free Radic Biol Med 2015; 89:192-200. [PMID: 26169724 DOI: 10.1016/j.freeradbiomed.2015.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/18/2015] [Accepted: 07/07/2015] [Indexed: 01/06/2023]
Abstract
Thioredoxin systems, composed of thioredoxin reductase (TrxR), thioredoxin (Trx) and NADPH, play important roles in maintaining cellular redox homeostasis and redox signaling. Recently the cytosolic Trx1 system has been shown to be a cellular target of arsenic containing compounds. To elucidate the relationship of the structure of arsenic compounds with their ability of inhibiting TrxR1 and Trx1, and cytotoxicity, we have investigated the reaction of Trx1 system with seven arsenic trithiolates: As(Cys)3, As(GS)3, As(Penicillamine)3, As(Mercaptoethanesulfonate)3, As(Mercaptopurine)3, As(2-mercaptopyridine)3 and As(2-mercaptopyridine N-oxide)3. The cytotoxicity of these arsenicals was consistent with their ability to inhibit TrxR1 in vitro and in cells. Unlike other arsenicals, As(Mercaptopurine)3 which did not show inhibitory effects on TrxR1 had very weak cytotoxicity, indicating that TrxR1 is a reliable drug target for arsenicals. Moreover, the two aromatic compounds As(2-mercaptopyridine)3 and As(2-mercaptopyridine N-oxide)3 showed stronger cytotoxicity than the others. As(2-mercaptopyridine)3 which selectively oxidized two structural cysteines (Cys62 and Cys69) in Trx1 showed mild improvement in cytotoxicity. As(2-mercaptopyridine N-oxide)3 oxidized all the Cys residues in Trx1, exhibiting the strongest cytotoxicity. Oxidation of Trx1 by As(2-mercaptopyridine)3 and As(2-mercaptopyridine N-oxide)3 affected electron transfer from NADPH and TrxR1 to peroxiredoxin 1 (Prx1), which could result in the reactive oxygen species elevation and trigger cell death process. These results suggest that oxidation of structural cysteine residues in Trx1 by aromatic group in TrxR1-targeting drugs may sensitize tumor cells to cell death, providing a novel approach to regulate cellular redox signaling and also a basis for rational design of new anticancer agents.
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Affiliation(s)
- Xu Zhang
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - Jun Lu
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - Xiaoyuan Ren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - Yatao Du
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | - Yujuan Zheng
- Department of Oncology and Pathology, Cancer Centrum Karolinska, Karolinska Institutet, SE 171 76 Stockholm, Sweden.
| | | | - Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
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Xu Z, Zhong L. New insights into the posttranslational regulation of human cytosolic thioredoxin by S-palmitoylation. Biochem Biophys Res Commun 2015; 460:949-56. [PMID: 25839660 DOI: 10.1016/j.bbrc.2015.03.132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 02/01/2023]
Abstract
High level of palmitate is associated with metabolic disorders. We recently showed that enhanced level of S-palmitoylated cytosolic thioredoxin (Trx1) in mouse liver was new characteristic feature of insulin resistance. However, our understanding of the effect of S-palmitoylation on Trx1 is limited, and the tissue specificity of Trx1 S-palmitoylation is unclear. Here we show that S-palmitoylation also occurs at Cys73 of Trx1 in living endothelial cells, and the level of S-palmitoylated Trx1 undergoes regulation by insulin signaling. Trx1 prefers thiol-thioester exchange with palmitoyl-CoA to acetyl-CoA. S-palmitoylation alters conformation or secondary structure of Trx1, as well as decreases the ability of Trx1 to transfer electrons from thioredoxin reductase to S-nitrosylated protein-tyrosine phosphatase 1B and S-nitroso-glutathione. Our results demonstrate that S-palmitoylation is an important post-translational modification of human Trx1.
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Affiliation(s)
- Zhiyu Xu
- College of Life Sciences, University of Chinese Academy of Sciences, YuQuan Road 19(A), 100049 Beijing, China
| | - Liangwei Zhong
- College of Life Sciences, University of Chinese Academy of Sciences, YuQuan Road 19(A), 100049 Beijing, China.
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