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Tortora F, Guerrera V, Lettieri G, Febbraio F, Piscopo M. Prediction of Pesticide Interactions with Proteins Involved in Human Reproduction by Using a Virtual Screening Approach: A Case Study of Famoxadone Binding CRBP-III and Izumo. Int J Mol Sci 2024; 25:5790. [PMID: 38891976 PMCID: PMC11171824 DOI: 10.3390/ijms25115790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
In recent years, the awareness that pesticides can have other effects apart from generic toxicity is growing. In particular, several pieces of evidence highlight their influence on human fertility. In this study, we investigated, by a virtual screening approach, the binding between pesticides and proteins present in human gametes or associated with reproduction, in order to identify new interactions that could affect human fertility. To this aim, we prepared ligand (pesticides) and receptor (proteins) 3D structure datasets from online structural databases (such as PubChem and RCSB), and performed a virtual screening analysis using Autodock Vina. In the comparison of the predicted interactions, we found that famoxadone was predicted to bind Cellular Retinol Binding Protein-III in the retinol-binding site with a better minimum energy value of -10.4 Kcal/mol and an RMSD of 3.77 with respect to retinol (-7.1 Kcal/mol). In addition to a similar network of interactions, famoxadone binding is more stabilized by additional hydrophobic patches including L20, V29, A33, F57, L117, and L118 amino acid residues and hydrogen bonds with Y19 and K40. These results support a possible competitive effect of famoxadone on retinol binding with impacts on the ability of developing the cardiac tissue, in accordance with the literature data on zebrafish embryos. Moreover, famoxadone binds, with a minimum energy value between -8.3 and -8.0 Kcal/mol, to the IZUMO Sperm-Egg Fusion Protein, interacting with a network of polar and hydrophobic amino acid residues in the cavity between the 4HB and Ig-like domains. This binding is more stabilized by a predicted hydrogen bond with the N185 residue of the protein. A hindrance in this position can probably affect the conformational change for JUNO binding, avoiding the gamete membrane fusion to form the zygote. This work opens new interesting perspectives of study on the effects of pesticides on fertility, extending the knowledge to other typologies of interaction which can affect different steps of the reproductive process.
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Affiliation(s)
- Fabiana Tortora
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy;
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
| | - Valentina Guerrera
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
| | - Gennaro Lettieri
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126 Naples, Italy (M.P.)
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Via Cinthia, 21, 80126 Naples, Italy (M.P.)
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Haji-Ghassemi O, Yuchi Z, Van Petegem F. The Cardiac Ryanodine Receptor Phosphorylation Hotspot Embraces PKA in a Phosphorylation-Dependent Manner. Mol Cell 2019; 75:39-52.e4. [PMID: 31078384 DOI: 10.1016/j.molcel.2019.04.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/05/2019] [Accepted: 04/11/2019] [Indexed: 12/22/2022]
Abstract
Ryanodine receptors (RyRs) are intracellular Ca2+ release channels controlling essential cellular functions. RyRs are targeted by cyclic AMP (cAMP)-dependent protein kinase A (PKA), a controversial regulation implicated in disorders ranging from heart failure to Alzheimer's. Using crystal structures, we show that the phosphorylation hotspot domain of RyR2 embraces the PKA catalytic subunit, with an extensive interface not seen in PKA complexes with peptides. We trapped an intermediary open-form PKA bound to the RyR2 domain and an ATP analog, showing that PKA can engage substrates in an open form. Phosphomimetics or prior phosphorylation at nearby sites in RyR2 either enhance or reduce the activity of PKA. Finally, we show that a phosphomimetic at S2813, a well-known target site for calmodulin-dependent kinase II, induces the formation of an alpha helix in the phosphorylation domain, resulting in increased interactions and PKA activity. This shows that the different phosphorylation sites in RyR2 are not independent.
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Affiliation(s)
- Omid Haji-Ghassemi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhiguang Yuchi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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Stival C, Ritagliati C, Xu X, Gervasi MG, Luque GM, Baró Graf C, De la Vega-Beltrán JL, Torres N, Darszon A, Krapf D, Buffone MG, Visconti PE, Krapf D. Disruption of protein kinase A localization induces acrosomal exocytosis in capacitated mouse sperm. J Biol Chem 2018; 293:9435-9447. [PMID: 29700114 DOI: 10.1074/jbc.ra118.002286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/19/2018] [Indexed: 11/06/2022] Open
Abstract
Protein kinase A (PKA) is a broad-spectrum Ser/Thr kinase involved in the regulation of several cellular activities. Thus, its precise activation relies on being localized at specific subcellular places known as discrete PKA signalosomes. A-Kinase anchoring proteins (AKAPs) form scaffolding assemblies that play a pivotal role in PKA regulation by restricting its activity to specific microdomains. Because one of the first signaling events observed during mammalian sperm capacitation is PKA activation, understanding how PKA activity is restricted in space and time is crucial to decipher the critical steps of sperm capacitation. Here, we demonstrate that the anchoring of PKA to AKAP is not only necessary but also actively regulated during sperm capacitation. However, we find that once capacitated, the release of PKA from AKAP promotes a sudden Ca2+ influx through the sperm-specific Ca2+ channel CatSper, starting a tail-to-head Ca2+ propagation that triggers the acrosome reaction. Three-dimensional super-resolution imaging confirmed a redistribution of PKA within the flagellar structure throughout the capacitation process, which depends on anchoring to AKAP. These results represent a new signaling event that involves CatSper Ca2+ channels in the acrosome reaction, sensitive to PKA stimulation upon release from AKAP.
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Affiliation(s)
- Cintia Stival
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina
| | - Carla Ritagliati
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina
| | - Xinran Xu
- the Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523
| | - Maria G Gervasi
- the Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
| | - Guillermina M Luque
- the Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires C1428ADN, Argentina
| | - Carolina Baró Graf
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina
| | - José Luis De la Vega-Beltrán
- the Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, México, and
| | - Nicolas Torres
- the Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires C1428ADN, Argentina
| | - Alberto Darszon
- the Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, México, and
| | - Diego Krapf
- the Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523.,the School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523
| | - Mariano G Buffone
- the Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires C1428ADN, Argentina
| | - Pablo E Visconti
- the Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
| | - Dario Krapf
- From the Laboratoty of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario 2000, Argentina,
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Søberg K, Skålhegg BS. The Molecular Basis for Specificity at the Level of the Protein Kinase a Catalytic Subunit. Front Endocrinol (Lausanne) 2018; 9:538. [PMID: 30258407 PMCID: PMC6143667 DOI: 10.3389/fendo.2018.00538] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022] Open
Abstract
Assembly of multi enzyme complexes at subcellular localizations by anchoring- and scaffolding proteins represents a pivotal mechanism for achieving spatiotemporal regulation of cellular signaling after hormone receptor targeting [for review, see (1)]. In the 3' 5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase (PKA) signaling pathway it is generally accepted that specificity is secured at several levels. This includes at the first level stimulation of receptors coupled to heterotrimeric G proteins which through stimulation of adenylyl cyclase (AC) forms the second messenger cAMP. Cyclic AMP has several receptors including PKA. PKA is a tetrameric holoenzyme consisting of a regulatory (R) subunit dimer and two catalytic (C) subunits. The R subunit is the receptor for cAMP and compartmentalizes cAMP signals through binding to cell and tissue-specifically expressed A kinase anchoring proteins (AKAPs). The current dogma tells that in the presence of cAMP, PKA dissociates into an R subunit dimer and two C subunits which are free to phosphorylate relevant substrates in the cytosol and nucleus. The release of the C subunit has raised the question how specificity of the cAMP and PKA signaling pathway is maintained when the C subunit no longer is attached to the R subunit-AKAP complex. An increasing body of evidence points toward a regulatory role of the cAMP and PKA signaling pathway by targeting the C subunits to various C subunit binding proteins in the cytosol and nucleus. Moreover, recent identification of isoform specific amino acid sequences, motifs and three dimensional structures have together provided new insight into how PKA at the level of the C subunit may act in a highly isoform-specific fashion. Here we discuss recent understanding of specificity of the cAMP and PKA signaling pathway based on C subunit subcellular targeting as well as evolution of the C subunit structure that may contribute to the dynamic regulation of C subunit activity.
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Affiliation(s)
- Kristoffer Søberg
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Bjørn Steen Skålhegg
- Section for Molecular Nutrition, University of Oslo, Oslo, Norway
- *Correspondence: Bjørn Steen Skålhegg
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Evolution of the cAMP-dependent protein kinase (PKA) catalytic subunit isoforms. PLoS One 2017; 12:e0181091. [PMID: 28742821 PMCID: PMC5526564 DOI: 10.1371/journal.pone.0181091] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/25/2017] [Indexed: 01/16/2023] Open
Abstract
The 3’,5’-cyclic adenosine monophosphate (cAMP)-dependent protein kinase, or protein kinase A (PKA), pathway is one of the most versatile and best studied signaling pathways in eukaryotic cells. The two paralogous PKA catalytic subunits Cα and Cβ, encoded by the genes PRKACA and PRKACB, respectively, are among the best understood model kinases in signal transduction research. In this work, we explore and elucidate the evolution of the alternative 5’ exons and the splicing pattern giving rise to the numerous PKA catalytic subunit isoforms. In addition to the universally conserved Cα1/Cβ1 isoforms, we find kinase variants with short N-termini in all main vertebrate classes, including the sperm-specific Cα2 isoform found to be conserved in all mammals. We also describe, for the first time, a PKA Cα isoform with a long N-terminus, paralogous to the PKA Cβ2 N-terminus. An analysis of isoform-specific variation highlights residues and motifs that are likely to be of functional importance.
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Rahman MS, Lee JS, Kwon WS, Pang MG. Sperm proteomics: road to male fertility and contraception. Int J Endocrinol 2013; 2013:360986. [PMID: 24363670 PMCID: PMC3864079 DOI: 10.1155/2013/360986] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 11/01/2013] [Accepted: 11/02/2013] [Indexed: 12/23/2022] Open
Abstract
Spermatozoa are highly specialized cells that can be easily obtained and purified. Mature spermatozoa are transcriptionally and translationally inactive and incapable of protein synthesis. In addition, spermatozoa contain relatively higher amounts of membrane proteins compared to other cells; therefore, they are very suitable for proteomic studies. Recently, the application of proteomic approaches such as the two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in-gel electrophoresis has identified several sperm-specific proteins. These findings have provided a further understanding of protein functions involved in different sperm processes as well as of the differentiation of normal state from an abnormal one. In addition, studies on the sperm proteome have demonstrated the importance of spermatozoal posttranslational modifications and their ability to induce physiological changes responsible for fertilization. Large-scale proteomic studies to identify hundreds to thousands of sperm proteins will ultimately result in the development of novel biomarkers that may help to detect fertility, the state of complete contraception, and beyond. Eventually, these protein biomarkers will allow for a better diagnosis of sperm dysfunctions and aid in drug development. This paper reviews the recent scientific publications available from the PubMed database to address sperm proteomics and its potential application to characterize male fertility and contraception.
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Affiliation(s)
- Md Saidur Rahman
- Department of Animal Science and Technology, School of Bioresource and Bioscience, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea
| | - June-Sub Lee
- Department of Animal Science and Technology, School of Bioresource and Bioscience, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea
| | - Woo-Sung Kwon
- Department of Animal Science and Technology, School of Bioresource and Bioscience, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea
| | - Myung-Geol Pang
- Department of Animal Science and Technology, School of Bioresource and Bioscience, Chung-Ang University, 4726 Seodong-daero, Anseong, Gyeonggi-Do 456-756, Republic of Korea
- *Myung-Geol Pang:
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Bastidas AC, Deal MS, Steichen JM, Keshwani MM, Guo Y, Taylor SS. Role of N-terminal myristylation in the structure and regulation of cAMP-dependent protein kinase. J Mol Biol 2012; 422:215-29. [PMID: 22617327 DOI: 10.1016/j.jmb.2012.05.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 05/03/2012] [Accepted: 05/15/2012] [Indexed: 01/13/2023]
Abstract
The catalytic (C) subunit of cAMP-dependent protein kinase [protein kinase A (PKA)] is a major target of cAMP signaling, and its regulation is of fundamental importance to biological processes. One mode of regulation is N-myristylation, which has eluded structural and functional characterization so far because most crystal structures are of the non-myristylated enzyme, are phosphorylated on Ser10, and generally lack electron density for the first 13 residues. We crystallized myristylated wild-type (WT) PKA and a K7C mutant as binary (bound to a substrate peptide) and ternary [bound to a substrate peptide and adenosine-5'-(β,γ-imido)triphosphate] complexes. There was clear electron density for the entire N-terminus in the binary complexes, both refined to 2.0 Å, and K7C ternary complex, refined to 1.35 Å. The N-termini in these three structures display a novel conformation with a previously unseen helix from residues 1 to 7. The K7C mutant appears to have a more stable N-terminus, and this correlated with a significant decrease in the B-factors for the N-terminus in the myr-K7C complexes compared to the WT binary complex. The N-terminus of the myristylated WT ternary complex, refined to 2.0 Å, was disordered as in previous structures. In addition to a more ordered N-terminus, the myristylated K7C mutant exhibited a 53% increase in k(cat). The effect of nucleotide binding on the structure of the N-terminus in the WT protein and the kinetic changes in the K7C protein suggest that myristylation or occupancy of the myristyl binding pocket may serve as a site for allosteric regulation in the C-subunit.
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Affiliation(s)
- Adam C Bastidas
- Department of Pharmacology, University of California San Diego, San Diego, CA 92093, USA
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