1
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Roux I, Fenollar-Ferrer C, Lee HJ, Chattaraj P, Lopez IA, Han K, Honda K, Brewer CC, Butman JA, Morell RJ, Martin DM, Griffith AJ. CHD7 variants associated with hearing loss and enlargement of the vestibular aqueduct. Hum Genet 2023; 142:1499-1517. [PMID: 37668839 PMCID: PMC10511616 DOI: 10.1007/s00439-023-02581-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 06/20/2023] [Indexed: 09/06/2023]
Abstract
Enlargement of the endolymphatic sac, duct, and vestibular aqueduct (EVA) is the most common inner ear malformation identified in patients with sensorineural hearing loss. EVA is associated with pathogenic variants in SLC26A4. However, in European-Caucasian populations, about 50% of patients with EVA carry no pathogenic alleles of SLC26A4. We tested for the presence of variants in CHD7, a gene known to be associated with CHARGE syndrome, Kallmann syndrome, and hypogonadotropic hypogonadism, in a cohort of 34 families with EVA subjects without pathogenic alleles of SLC26A4. In two families, NM_017780.4: c.3553A > G [p.(Met1185Val)] and c.5390G > C [p.(Gly1797Ala)] were detected as monoallelic CHD7 variants in patients with EVA. At least one subject from each family had additional signs or potential signs of CHARGE syndrome but did not meet diagnostic criteria for CHARGE. In silico modeling of these two missense substitutions predicted detrimental effects upon CHD7 protein structure. Consistent with a role of CHD7 in this tissue, Chd7 transcript and protein were detected in all epithelial cells of the endolymphatic duct and sac of the developing mouse inner ear. These results suggest that some CHD7 variants can cause nonsyndromic hearing loss and EVA. CHD7 should be included in DNA sequence analyses to detect pathogenic variants in EVA patients. Chd7 expression and mutant phenotype data in mice suggest that CHD7 contributes to the formation or function of the endolymphatic sac and duct.
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Affiliation(s)
- Isabelle Roux
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Cristina Fenollar-Ferrer
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
- Laboratory of Molecular Genetics, NIDCD, NIH, Bethesda, MD, 20892, USA
| | - Hyun Jae Lee
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Parna Chattaraj
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Ivan A Lopez
- The NIDCD National Temporal Laboratory at UCLA, Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Kyungreem Han
- Laboratory of Membrane Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Keiji Honda
- Department of Otorhinolaryngology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Carmen C Brewer
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - John A Butman
- Radiology and Imaging Sciences, Clinical Center, NIH, Bethesda, MD, 20892, USA
| | - Robert J Morell
- Genomics and Computational Biology Core, NIDCD, NIH, Bethesda, MD, 20892, USA
| | - Donna M Martin
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
- Department of Otolaryngology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
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2
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Leone V, Bradshaw RT, Koshy C, Lee PS, Fenollar-Ferrer C, Heinz V, Ziegler C, Forrest LR. Insights into autoregulation of a membrane protein complex by its cytoplasmic domains. Biophys J 2023; 122:577-594. [PMID: 36528790 PMCID: PMC9941749 DOI: 10.1016/j.bpj.2022.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Membrane transporters mediate the passage of molecules across membranes and are essential for cellular function. While the transmembrane region of these proteins is responsible for substrate transport, often the cytoplasmic regions are required for modulating their activity. However, it can be difficult to obtain atomic-resolution descriptions of these autoregulatory domains by classical structural biology techniques, especially if they lack a single, defined structure. The betaine permease, BetP, a homotrimer, is a prominent and well-studied example of a membrane protein whose autoregulation depends on cytoplasmic N- and C-terminal segments. These domains sense and transduce changes in K+ concentration and in lipid bilayer properties caused by osmotic stress. However, structural data for these terminal domains is incomplete, which hinders a clear description of the molecular mechanism of autoregulation. Here we used microsecond-scale molecular simulations of the BetP trimer to compare reported conformations of the 45-amino-acid long C-terminal tails. The simulations provide support for the idea that the conformation derived from electron microscopy (EM) data represents a more stable global orientation of the C-terminal segment under downregulating conditions while also providing a detailed molecular description of its dynamics and highlighting specific interactions with lipids, ions, and neighboring transporter subunits. A missing piece of the molecular puzzle is the N-terminal segment, whose dynamic nature has prevented structural characterization. Using Rosetta to generate ensembles of de novo conformations in the context of the EM-derived structure robustly identifies two features of the N-terminal tail, namely 1) short helical elements and 2) an orientation that would confine potential interactions to the protomer in the counterclockwise direction (viewed from the cytoplasm). Since each C-terminal tail only contacts the protomer in the clockwise direction, these results indicate an intricate interplay between the three protomers of BetP in the downregulated protein and a multidirectionality that may facilitate autoregulation of transport.
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Affiliation(s)
- Vanessa Leone
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
| | - Richard T Bradshaw
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Caroline Koshy
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Paul Suhwan Lee
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Veronika Heinz
- Department of Structural Biology/Biophysics II, University of Regensburg, Regensburg, Germany
| | - Christine Ziegler
- Department of Structural Biology/Biophysics II, University of Regensburg, Regensburg, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
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3
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Guida E, Bisso A, Fenollar-Ferrer C, Napoli M, Anselmi C, Girardini JE, Carloni P, Sal GD. Editor's Note: Peptide Aptamers Targeting Mutant p53 Induce Apoptosis in Tumor Cells. Cancer Res 2022; 82:1844. [PMID: 35502549 DOI: 10.1158/0008-5472.can-22-0459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Donovan E, Avila C, Klausner S, Parikh V, Fenollar-Ferrer C, Blakely RD, Sarter M. Disrupted Choline Clearance and Sustained Acetylcholine Release In Vivo by a Common Choline Transporter Coding Variant Associated with Poor Attentional Control in Humans. J Neurosci 2022; 42:3426-3444. [PMID: 35232764 PMCID: PMC9034784 DOI: 10.1523/jneurosci.1334-21.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 02/20/2022] [Accepted: 02/23/2022] [Indexed: 11/21/2022] Open
Abstract
Transport of choline via the neuronal high-affinity choline transporter (CHT; SLC5A7) is essential for cholinergic terminals to synthesize and release acetylcholine (ACh). In humans, we previously demonstrated an association between a common CHT coding substitution (rs1013940; Ile89Val) and reduced attentional control as well as attenuated frontal cortex activation. Here, we used a CRISPR/Cas9 approach to generate mice expressing the I89V substitution and assessed, in vivo, CHT-mediated choline transport, and ACh release. Relative to wild-type (WT) mice, CHT-mediated clearance of choline in male and female mice expressing one or two Val89 alleles was reduced by over 80% in cortex and over 50% in striatum. Choline clearance in CHT Val89 mice was further reduced by neuronal inactivation. Deficits in ACh release, 5 and 10 min after repeated depolarization at a low, behaviorally relevant frequency, support an attenuated reloading capacity of cholinergic neurons in mutant mice. The density of CHTs in total synaptosomal lysates and neuronal plasma-membrane-enriched fractions was not impacted by the Val89 variant, indicating a selective impact on CHT function. When challenged with a visual disruptor to reveal attentional control mechanisms, Val89 mice failed to adopt a more conservative response bias. Structural modeling revealed that Val89 may attenuate choline transport by altering conformational changes of CHT that support normal transport rates. Our findings support the view that diminished sustained cholinergic signaling capacity underlies perturbed attentional performance in individuals expressing CHT Val89. The CHT Val89 mouse serves as a valuable model to study heritable risk for cognitive disorders arising from cholinergic dysfunction.SIGNIFICANCE STATEMENT Acetylcholine (ACh) signaling depends on the functional capacity of the neuronal choline transporter (CHT). Previous research demonstrated that humans expressing the common CHT coding variant Val89 exhibit attentional vulnerabilities and attenuated fronto-cortical activation during attention. Here, we find that mice engineered to express the Val89 variant exhibit reduced CHT-mediated choline clearance and a diminished capacity to sustain ACh release. Additionally, Val89 mice lack cognitive flexibility in response to an attentional challenge. These findings provide a mechanistic and cognitive framework for interpreting the attentional phenotype associated with the human Val89 variant and establish a model that permits a more invasive interrogation of CNS effects as well as the development of therapeutic strategies for those, including Val89 carriers, with presynaptic cholinergic perturbations.
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Affiliation(s)
- Eryn Donovan
- Department of Psychology, University of Michigan, Ann Arbor, Michigan 48109
| | - Cassandra Avila
- Department of Psychology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sarah Klausner
- Department of Psychology, University of Michigan, Ann Arbor, Michigan 48109
| | - Vinay Parikh
- Department of Psychology & Neuroscience Program, Temple University, Philadelphia, Pennsylvania 19122
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, Section of Human Genetics, National Institute on Deafness and Other Communication Disorders, Bethesda, Maryland 20892
| | - Randy D Blakely
- Stiles-Nicholson Brain Institute and Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458
| | - Martin Sarter
- Department of Psychology, Neuroscience Program and Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
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5
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Faridi R, Rea A, Fenollar-Ferrer C, O'Keefe RT, Gu S, Munir Z, Khan AA, Riazuddin S, Hoa M, Naz S, Newman WG, Friedman TB. New insights into Perrault syndrome, a clinically and genetically heterogeneous disorder. Hum Genet 2021; 141:805-819. [PMID: 34338890 DOI: 10.1007/s00439-021-02319-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/14/2021] [Indexed: 01/07/2023]
Abstract
Hearing loss and impaired fertility are common human disorders each with multiple genetic causes. Sometimes deafness and impaired fertility, which are the hallmarks of Perrault syndrome, co-occur in a person. Perrault syndrome is inherited as an autosomal recessive disorder characterized by bilateral mild to severe childhood sensorineural hearing loss with variable age of onset in both sexes and ovarian dysfunction in females who have a 46, XX karyotype. Since the initial clinical description of Perrault syndrome 70 years ago, the phenotype of some subjects may additionally involve developmental delay, intellectual deficit and other neurological disabilities, which can vary in severity in part dependent upon the genetic variants and the gene involved. Here, we review the molecular genetics and clinical phenotype of Perrault syndrome and focus on supporting evidence for the eight genes (CLPP, ERAL1, GGPS1, HARS2, HSD17B4, LARS2, RMND1, TWNK) associated with Perrault syndrome. Variants of these eight genes only account for approximately half of the individuals with clinical features of Perrault syndrome where the molecular genetic base remains under investigation. Additional environmental etiologies and novel Perrault disease-associated genes remain to be identified to account for unresolved cases. We also report a new genetic variant of CLPP, computational structural insight about CLPP and single cell RNAseq data for eight reported Perrault syndrome genes suggesting a common cellular pathophysiology for this disorder. Some unanswered questions are raised to kindle future research about Perrault syndrome.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alessandro Rea
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.,Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Raymond T O'Keefe
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.,Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Shoujun Gu
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zunaira Munir
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.,present address: Department of Neurosciences, University of Turin, 10124, Turin, Italy
| | - Asma Ali Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 54000, Pakistan
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Center, Jinnah Burn and Reconstructive Surgery Center, University of Health Sciences, Lahore, 54550, Pakistan
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan
| | - William G Newman
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK. .,Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.
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6
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Ramzan M, Philippe C, Belyantseva IA, Nakano Y, Fenollar-Ferrer C, Tona R, Yousaf R, Basheer R, Imtiaz A, Faridi R, Munir Z, Idrees H, Salman M, Nambot S, Vitobello A, Kartti S, Zarrik O, Witmer PD, Sobreria N, Ibrahimi A, Banfi B, Moutton S, Friedman TB, Naz S. Variants of human CLDN9 cause mild to profound hearing loss. Hum Mutat 2021; 42:1321-1335. [PMID: 34265170 DOI: 10.1002/humu.24260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 05/18/2021] [Accepted: 07/13/2021] [Indexed: 02/05/2023]
Abstract
Hereditary deafness is clinically and genetically heterogeneous. We investigated deafness segregating as a recessive trait in two families. Audiological examinations revealed an asymmetric mild to profound hearing loss with childhood or adolescent onset. Exome sequencing of probands identified a homozygous c.475G>A;p.(Glu159Lys) variant of CLDN9 (NM_020982.4) in one family and a homozygous c.370_372dupATC;p.(Ile124dup) CLDN9 variant in an affected individual of a second family. Claudin 9 (CLDN9) is an integral membrane protein and constituent of epithelial bicellular tight junctions (TJs) that form semipermeable, paracellular barriers between inner ear perilymphatic and endolymphatic compartments. Computational structural modeling predicts that substitution of a lysine for glutamic acid p.(Glu159Lys) alters one of two cis-interactions between CLDN9 protomers. The p.(Ile124dup) variant is predicted to locally misfold CLDN9 and mCherry tagged p.(Ile124dup) CLDN9 is not targeted to the HeLa cell membrane. In situ hybridization shows that mouse Cldn9 expression increases from embryonic to postnatal development and persists in adult inner ears coinciding with prominent CLDN9 immunoreactivity in TJs of epithelia outlining the scala media. Together with the Cldn9 deaf mouse and a homozygous frameshift of CLDN9 previously associated with deafness, the two bi-allelic variants of CLDN9 described here point to CLDN9 as a bona fide human deafness gene.
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Affiliation(s)
- Memoona Ramzan
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan.,Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Christophe Philippe
- UF Innovation en Diagnostic Genomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Yoko Nakano
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA.,Inflammation Program, University of Iowa, Iowa City, Iowa, USA
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA.,Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Rasheeda Basheer
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Ayesha Imtiaz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Zunaira Munir
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Hafiza Idrees
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Midhat Salman
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
| | - Sophie Nambot
- INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France.,Department of Medical Genetics, Reference Center for Developmental Anomalies, Dijon University Hospital, Dijon, France
| | - Antonio Vitobello
- UF Innovation en Diagnostic Genomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Oumaima Zarrik
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Johns Hopkins Genomics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nara Sobreria
- Johns Hopkins Genomics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Botond Banfi
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA.,Inflammation Program, University of Iowa, Iowa City, Iowa, USA.,Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Sebastien Moutton
- INSERM UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, Dijon, France.,Department of Medical Genetics, Reference Center for Developmental Anomalies, Dijon University Hospital, Dijon, France
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam campus, Lahore, Pakistan
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7
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Aguilar JI, Cheng MH, Font J, Schwartz AC, Ledwitch K, Duran A, Mabry SJ, Belovich AN, Zhu Y, Carter AM, Shi L, Kurian MA, Fenollar-Ferrer C, Meiler J, Ryan RM, Mchaourab HS, Bahar I, Matthies HJ, Galli A. Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia. eLife 2021; 10:68039. [PMID: 34002696 PMCID: PMC8131106 DOI: 10.7554/elife.68039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/02/2021] [Indexed: 12/30/2022] Open
Abstract
Parkinson disease (PD) is a progressive, neurodegenerative disorder affecting over 6.1 million people worldwide. Although the cause of PD remains unclear, studies of highly penetrant mutations identified in early-onset familial parkinsonism have contributed to our understanding of the molecular mechanisms underlying disease pathology. Dopamine (DA) transporter (DAT) deficiency syndrome (DTDS) is a distinct type of infantile parkinsonism-dystonia that shares key clinical features with PD, including motor deficits (progressive bradykinesia, tremor, hypomimia) and altered DA neurotransmission. Here, we define structural, functional, and behavioral consequences of a Cys substitution at R445 in human DAT (hDAT R445C), identified in a patient with DTDS. We found that this R445 substitution disrupts a phylogenetically conserved intracellular (IC) network of interactions that compromise the hDAT IC gate. This is demonstrated by both Rosetta molecular modeling and fine-grained simulations using hDAT R445C, as well as EPR analysis and X-ray crystallography of the bacterial homolog leucine transporter. Notably, the disruption of this IC network of interactions supported a channel-like intermediate of hDAT and compromised hDAT function. We demonstrate that Drosophila melanogaster expressing hDAT R445C show impaired hDAT activity, which is associated with DA dysfunction in isolated brains and with abnormal behaviors monitored at high-speed time resolution. We show that hDAT R445C Drosophila exhibit motor deficits, lack of motor coordination (i.e. flight coordination) and phenotypic heterogeneity in these behaviors that is typically associated with DTDS and PD. These behaviors are linked with altered dopaminergic signaling stemming from loss of DA neurons and decreased DA availability. We rescued flight coordination with chloroquine, a lysosomal inhibitor that enhanced DAT expression in a heterologous expression system. Together, these studies shed some light on how a DTDS-linked DAT mutation underlies DA dysfunction and, possibly, clinical phenotypes shared by DTDS and PD.
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Affiliation(s)
- Jenny I Aguilar
- Department of Pharmacology, Vanderbilt University, Nashville, United States.,Department of Surgery, University of Alabama at Birmingham, Birmingham, United States
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Josep Font
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Alexandra C Schwartz
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, United States
| | - Kaitlyn Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, United States.,Department of Chemistry, Vanderbilt University, Nashville, United States
| | - Amanda Duran
- Center for Structural Biology, Vanderbilt University, Nashville, United States.,Department of Chemistry, Vanderbilt University, Nashville, United States
| | - Samuel J Mabry
- Department of Surgery, University of Alabama at Birmingham, Birmingham, United States
| | - Andrea N Belovich
- Department of Biomedical Sciences, Idaho College of Osteopathic Medicine, Meridian, United States
| | - Yanqi Zhu
- Department of Surgery, University of Alabama at Birmingham, Birmingham, United States
| | - Angela M Carter
- Department of Surgery, University of Alabama at Birmingham, Birmingham, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, NIDA, NIH, Baltimore, United States
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences, University College London (UCL), London, United Kingdom
| | | | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, United States.,Department of Chemistry, Vanderbilt University, Nashville, United States.,Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Renae Monique Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Hassane S Mchaourab
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, United States
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Heinrich Jg Matthies
- Department of Surgery, University of Alabama at Birmingham, Birmingham, United States
| | - Aurelio Galli
- Department of Surgery, University of Alabama at Birmingham, Birmingham, United States.,Center for Inter-systemic Networks and Enteric Medical Advances, University of Alabama at Birmingham, Birmingham, United States
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8
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Meinke C, Quinlan MA, Paffenroth KC, Harrison FE, Fenollar-Ferrer C, Katamish RM, Stillman I, Ramamoorthy S, Blakely RD. Serotonin Transporter Ala276 Mouse: Novel Model to Assess the Neurochemical and Behavioral Impact of Thr276 Phosphorylation In Vivo. Neurochem Res 2021; 47:37-60. [PMID: 33830406 DOI: 10.1007/s11064-021-03299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/21/2021] [Accepted: 03/17/2021] [Indexed: 11/30/2022]
Abstract
The serotonin (5-HT) transporter (SERT) is a key regulator of 5-HT signaling and is a major target for antidepressants and psychostimulants. Human SERT coding variants have been identified in subjects with obsessive-compulsive disorder (OCD) and autism spectrum disorder (ASD) that impact transporter phosphorylation, cell surface trafficking and/or conformational dynamics. Prior to an initial description of a novel mouse line expressing the non-phosphorylatable SERT substitution Thr276Ala, we review efforts made to elucidate the structure and conformational dynamics of SERT with a focus on research implicating phosphorylation at Thr276 as a determinant of SERT conformational dynamics. Using the high-resolution structure of human SERT in inward- and outward-open conformations, we explore the conformation dependence of SERT Thr276 exposure, with results suggesting that phosphorylation is likely restricted to an inward-open conformation, consistent with prior biochemical studies. Assessment of genotypes from SERT/Ala276 heterozygous matings revealed a deviation from Mendelian expectations, with reduced numbers of Ala276 offspring, though no genotype differences were seen in growth or physical appearance. Similarly, no genotype differences were evident in midbrain or hippocampal 5-HT levels, midbrain and hippocampal SERT mRNA or midbrain protein levels, nor in midbrain synaptosomal 5-HT uptake kinetics. Behaviorally, SERT Ala276 homozygotes appeared normal in measures of anxiety and antidepressant-sensitive stress coping behavior. However, these mice displayed sex-dependent alterations in repetitive and social interactions, consistent with circuit-dependent requirements for Thr276 phosphorylation underlying these behaviors. Our findings indicate the utility of SERT Ala276 mice in evaluation of developmental, functional and behavioral consequences of regulatory SERT phosphorylation in vivo.
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Affiliation(s)
- Carina Meinke
- International Max Planck Research School for Brain and Behavior, Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA.,Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | - Meagan A Quinlan
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | | | - Fiona E Harrison
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Cristina Fenollar-Ferrer
- Laboratories of Molecular Genetics and Molecular Biology, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Rania M Katamish
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | - Isabel Stillman
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | | | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA. .,Florida Atlantic University Brain Institute, Rm 109, MC-17, 5353 Parkside Dr, Jupiter, FL, 35348, USA.
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9
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Kim JH, Matsubara T, Lee J, Fenollar-Ferrer C, Han K, Kim D, Jia S, Chang CJ, Yang H, Nagano T, Krausz KW, Yim SH, Gonzalez FJ. Lysosomal SLC46A3 modulates hepatic cytosolic copper homeostasis. Nat Commun 2021; 12:290. [PMID: 33436590 PMCID: PMC7804329 DOI: 10.1038/s41467-020-20461-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023] Open
Abstract
The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) causes hepatic toxicity associated with prominent lipid accumulation in humans. Here, the authors report that the lysosomal copper transporter SLC46A3 is induced by TCDD and underlies the hepatic lipid accumulation in mice, potentially via effects on mitochondrial function. SLC46A3 was localized to the lysosome where it modulated intracellular copper levels. Forced expression of hepatic SLC46A3 resulted in decreased mitochondrial membrane potential and abnormal mitochondria morphology consistent with lower copper levels. SLC46A3 expression increased hepatic lipid accumulation similar to the known effects of TCDD exposure in mice and humans. The TCDD-induced hepatic triglyceride accumulation was significantly decreased in Slc46a3-/- mice and was more pronounced when these mice were fed a high-fat diet, as compared to wild-type mice. These data are consistent with a model where lysosomal SLC46A3 induction by TCDD leads to cytosolic copper deficiency resulting in mitochondrial dysfunction leading to lower lipid catabolism, thus linking copper status to mitochondrial function, lipid metabolism and TCDD-induced liver toxicity.
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Affiliation(s)
- Jung-Hwan Kim
- Department of Pharmacology, School of Medicine, Institute of Health Sciences, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Tsutomu Matsubara
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Anatomy and Regenerative Biology, Osaka City University Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Jaekwon Lee
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kyungreem Han
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Donghwan Kim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shang Jia
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Christopher J Chang
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Heejung Yang
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- College of Pharmacy, Kangwon National University, Chuncheon, Republic of Korea
| | - Tomokazu Nagano
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Sumitomo Dainippon Pharma Co. Ltd., Osaka, Japan
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sun-Hee Yim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, 41163, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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10
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Katsuno T, Belyantseva IA, Cartagena-Rivera AX, Ohta K, Crump SM, Petralia RS, Ono K, Tona R, Imtiaz A, Rehman A, Kiyonari H, Kaneko M, Wang YX, Abe T, Ikeya M, Fenollar-Ferrer C, Riordan GP, Wilson EA, Fitzgerald TS, Segawa K, Omori K, Ito J, Frolenkov GI, Friedman TB, Kitajiri SI. TRIOBP-5 sculpts stereocilia rootlets and stiffens supporting cells enabling hearing. JCI Insight 2019; 4:128561. [PMID: 31217345 DOI: 10.1172/jci.insight.128561] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/08/2019] [Indexed: 01/19/2023] Open
Abstract
TRIOBP remodels the cytoskeleton by forming unusually dense F-actin bundles and is implicated in human cancer, schizophrenia, and deafness. Mutations ablating human and mouse TRIOBP-4 and TRIOBP-5 isoforms are associated with profound deafness, as inner ear mechanosensory hair cells degenerate after stereocilia rootlets fail to develop. However, the mechanisms regulating formation of stereocilia rootlets by each TRIOBP isoform remain unknown. Using 3 new Triobp mouse models, we report that TRIOBP-5 is essential for thickening bundles of F-actin in rootlets, establishing their mature dimensions and for stiffening supporting cells of the auditory sensory epithelium. The coiled-coil domains of this isoform are required for reinforcement and maintenance of stereocilia rootlets. A loss of TRIOBP-5 in mouse results in dysmorphic rootlets that are abnormally thin in the cuticular plate but have increased widths and lengths within stereocilia cores, and causes progressive deafness recapitulating the human phenotype. Our study extends the current understanding of TRIOBP isoform-specific functions necessary for life-long hearing, with implications for insight into other TRIOBPopathies.
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Affiliation(s)
- Tatsuya Katsuno
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Alexander X Cartagena-Rivera
- Section on Auditory Mechanics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Keisuke Ohta
- Advanced Imaging Research Center, Kurume University School of Medicine, Kurume, Japan
| | - Shawn M Crump
- Department of Physiology, University of Kentucky, Lexington, Kentucky, USA
| | - Ronald S Petralia
- Advanced Imaging Core, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Kazuya Ono
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Risa Tona
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Ayesha Imtiaz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Atteeq Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, Riken Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, Riken Center for Biosystems Dynamics Research, Kobe, Japan
| | - Ya-Xian Wang
- Advanced Imaging Core, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, Riken Center for Biosystems Dynamics Research, Kobe, Japan
| | - Makoto Ikeya
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA.,Laboratory of Molecular and Cellular Neurobiology, National Institute of Mental Health, NIH, Bethesda, Maryland, USA
| | - Gavin P Riordan
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Elisabeth A Wilson
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Tracy S Fitzgerald
- Mouse Auditory Testing Core Facility, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Kohei Segawa
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichi Omori
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Juichi Ito
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Shin-Ichiro Kitajiri
- Department of Otolaryngology-Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
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11
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Imtiaz A, Belyantseva IA, Beirl AJ, Fenollar-Ferrer C, Bashir R, Bukhari I, Bouzid A, Shaukat U, Azaiez H, Booth KT, Kahrizi K, Najmabadi H, Maqsood A, Wilson EA, Fitzgerald TS, Tlili A, Olszewski R, Lund M, Chaudhry T, Rehman AU, Starost MF, Waryah AM, Hoa M, Dong L, Morell RJ, Smith RJH, Riazuddin S, Masmoudi S, Kindt KS, Naz S, Friedman TB. CDC14A phosphatase is essential for hearing and male fertility in mouse and human. Hum Mol Genet 2019; 27:780-798. [PMID: 29293958 DOI: 10.1093/hmg/ddx440] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022] Open
Abstract
The Cell Division-Cycle-14 gene encodes a dual-specificity phosphatase necessary in yeast for exit from mitosis. Numerous disparate roles of vertebrate Cell Division-Cycle-14 (CDC14A) have been proposed largely based on studies of cultured cancer cells in vitro. The in vivo functions of vertebrate CDC14A are largely unknown. We generated and analyzed mutations of zebrafish and mouse CDC14A, developed a computational structural model of human CDC14A protein and report four novel truncating and three missense alleles of CDC14A in human families segregating progressive, moderate-to-profound deafness. In five of these families segregating pathogenic variants of CDC14A, deaf males are infertile, while deaf females are fertile. Several recessive mutations of mouse Cdc14a, including a CRISPR/Cas9-edited phosphatase-dead p.C278S substitution, result in substantial perinatal lethality, but survivors recapitulate the human phenotype of deafness and male infertility. CDC14A protein localizes to inner ear hair cell kinocilia, basal bodies and sound-transducing stereocilia. Auditory hair cells of postnatal Cdc14a mutants develop normally, but subsequently degenerate causing deafness. Kinocilia of germ-line mutants of mouse and zebrafish have normal lengths, which does not recapitulate the published cdc14aa knockdown morphant phenotype of short kinocilia. In mutant male mice, degeneration of seminiferous tubules and spermiation defects result in low sperm count, and abnormal sperm motility and morphology. These findings for the first time define a new monogenic syndrome of deafness and male infertility revealing an absolute requirement in vivo of vertebrate CDC14A phosphatase activity for hearing and male fertility.
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Affiliation(s)
- Ayesha Imtiaz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.,School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Alisha J Beirl
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular and Cellular Neurobiology, Section on Molecular and Cellular Signaling, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Rasheeda Bashir
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Ihtisham Bukhari
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Amal Bouzid
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax 3451, Tunisia
| | - Uzma Shaukat
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54590, Pakistan
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, 52242, IA, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, 52242, IA, USA.,The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, 52242, IA, USA
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran 1987513834, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran 1987513834, Iran
| | - Azra Maqsood
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.,School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Elizabeth A Wilson
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | | | - Abdelaziz Tlili
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax 3451, Tunisia
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Merete Lund
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Taimur Chaudhry
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Matthew F Starost
- Division of Veterinary Resources, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ali M Waryah
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54590, Pakistan
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Robert J Morell
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, 52242, IA, USA.,The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, 52242, IA, USA
| | - Sheikh Riazuddin
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore 54590, Pakistan.,Pakistan Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan.,Laboratory for Research in Genetic Diseases, Burn Centre, Allama Iqbal Medical College, University of Health Sciences, Lahore 54590, Pakistan
| | - Saber Masmoudi
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax 3451, Tunisia
| | - Katie S Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
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12
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Ballesteros A, Fenollar-Ferrer C, Swartz KJ. Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins. eLife 2018; 7:38433. [PMID: 30063209 PMCID: PMC6067890 DOI: 10.7554/elife.38433] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 02/03/2023] Open
Abstract
The hair cell mechanotransduction (MET) channel complex is essential for hearing, yet it's molecular identity and structure remain elusive. The transmembrane channel-like 1 (TMC1) protein localizes to the site of the MET channel, interacts with the tip-link responsible for mechanical gating, and genetic alterations in TMC1 alter MET channel properties and cause deafness, supporting the hypothesis that TMC1 forms the MET channel. We generated a model of TMC1 based on X-ray and cryo-EM structures of TMEM16 proteins, revealing the presence of a large cavity near the protein-lipid interface that also harbors the Beethoven mutation, suggesting that it could function as a permeation pathway. We also find that hair cells are permeable to 3 kDa dextrans, and that dextran permeation requires TMC1/2 proteins and functional MET channels, supporting the presence of a large permeation pathway and the hypothesis that TMC1 is a pore forming subunit of the MET channel complex.
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Affiliation(s)
- Angela Ballesteros
- Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, National Institutes of Health, Bethesda, United States.,Laboratory of Molecular Genetics, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States.,Molecular Biology and Genetics Section, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, United States
| | - Kenton Jon Swartz
- Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
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13
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Zhao J, Krystofiak ES, Ballesteros A, Cui R, Van Itallie CM, Anderson JM, Fenollar-Ferrer C, Kachar B. Multiple claudin-claudin cis interfaces are required for tight junction strand formation and inherent flexibility. Commun Biol 2018; 1:50. [PMID: 30271933 PMCID: PMC6123731 DOI: 10.1038/s42003-018-0051-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/03/2018] [Indexed: 02/07/2023] Open
Abstract
Tight junctions consist of a network of sealing strands that create selective ion permeability barriers between adjoining epithelial or endothelial cells. The current model for tight junction strands consists of paired rows of claudins (Cldn) coupled by a cis interface (X-1) derived from crystalline Cldn15. Here we show that tight junction strands exhibit a broad range of lateral bending, indicating diversity in cis interactions. By combining protein–protein docking, coevolutionary analysis, molecular dynamics, and a mutagenesis screen, we identify a new Cldn–Cldn cis interface (Cis-1) that shares interacting residues with X-1 but has an ~ 17° lateral rotation between monomers. In addition, we found that a missense mutation in a Cldn14 that causes deafness and contributes stronger to Cis-1 than to X-1 prevents strand formation in cultured cells. Our results suggest that Cis-1 contributes to the inherent structural flexibility of tight junction strands and is required for maintaining permeability barrier function and hearing. Jun Zhao, Evan S. Krystofiak, and colleagues identified a new cis interface (Cis-1) essential for the formation of normal tight junctions. This study suggests that Cis-1 contributes to maintaining structural flexibility of tight junction strands for proper ion balance and hearing.
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Affiliation(s)
- Jun Zhao
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA.,Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
| | - Evan S Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA
| | - Angela Ballesteros
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA.,Molecular Physiology and Biophysics Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - Runjia Cui
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA
| | - Christina M Van Itallie
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD, 20892, USA
| | - James M Anderson
- Laboratory of Tight Junction Structure and Function, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD, 20892, USA
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke, 35 Convent Drive, Bethesda, MD, 20892, USA. .,Laboratory of Molecular & Cellular Neurobiology, National Institute of Mental Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, 35A Convent Drive, Bethesda, MD, 20892, USA.
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14
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Vergara-Jaque A, Fenollar-Ferrer C, Mulligan C, Mindell JA, Forrest LR. Family resemblances: A common fold for some dimeric ion-coupled secondary transporters. ACTA ACUST UNITED AC 2016; 146:423-34. [PMID: 26503722 PMCID: PMC4621753 DOI: 10.1085/jgp.201511481] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The structures of two bacterial antiporters that act as multidrug resistance efflux pumps, MtrF and YdaH, resemble each other and that of the sodium-coupled succinate symporter VcINDY. Membrane transporter proteins catalyze the passage of a broad range of solutes across cell membranes, allowing the uptake and efflux of crucial compounds. Because of the difficulty of expressing, purifying, and crystallizing integral membrane proteins, relatively few transporter structures have been elucidated to date. Although every membrane transporter has unique characteristics, structural and mechanistic similarities between evolutionarily diverse transporters have been identified. Here, we compare two recently reported structures of membrane proteins that act as antimicrobial efflux pumps, namely MtrF from Neisseria gonorrhoeae and YdaH from Alcanivorax borkumensis, both with each other and with the previously published structure of a sodium-dependent dicarboxylate transporter from Vibrio cholerae, VcINDY. MtrF and YdaH belong to the p-aminobenzoyl-glutamate transporter (AbgT) family and have been reported as having architectures distinct from those of all other families of transporters. However, our comparative analysis reveals a similar structural arrangement in all three proteins, with highly conserved secondary structure elements. Despite their differences in biological function, the overall “design principle” of MtrF and YdaH appears to be almost identical to that of VcINDY, with a dimeric quaternary structure, helical hairpins, and clear boundaries between the transport and scaffold domains. This observation demonstrates once more that the same secondary transporter architecture can be exploited for multiple distinct transport modes, including cotransport and antiport. Based on our comparisons, we detected conserved motifs in the substrate-binding region and predict specific residues likely to be involved in cation or substrate binding. These findings should prove useful for the future characterization of the transport mechanisms of these families of secondary active transporters.
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Affiliation(s)
- Ariela Vergara-Jaque
- Computational Structural Biology Unit and Membrane Transport Biophysics Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Unit and Membrane Transport Biophysics Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824
| | - Christopher Mulligan
- Computational Structural Biology Unit and Membrane Transport Biophysics Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824
| | - Joseph A Mindell
- Computational Structural Biology Unit and Membrane Transport Biophysics Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824
| | - Lucy R Forrest
- Computational Structural Biology Unit and Membrane Transport Biophysics Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20824
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15
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Abraham SJ, Chavan T, Cheng RC, Fenollar-Ferrer C, Han W, Islam SM, Jiang T, Khantwal CM, Mathews II, Stein RA, Roux B, Forrest LR, Mchaourab HS, Tajkhorshid E, Maduke M. An Outward-Facing Open Conformational State in a CLC Transporter. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Fenollar-Ferrer C, Anselmi C, Vergara Jaque A, Ali Karimi-Verzaneh H, Poblete-Vilches H, Mulligan C, Forster IC, Mindell JA, Faraldo-Gómez JD, Forrest LR. Computational Studies of Elevator-Like Movements in Secondary Transport. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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17
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Vergara-Jaque A, Fenollar-Ferrer C, Kaufmann D, Forrest LR. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. Front Pharmacol 2015; 6:183. [PMID: 26388773 PMCID: PMC4560100 DOI: 10.3389/fphar.2015.00183] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/04/2022] Open
Abstract
Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called “repeat-swap modeling” to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also occurs via an elevator-like mechanism.
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Affiliation(s)
- Ariela Vergara-Jaque
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Desirée Kaufmann
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Lucy R Forrest
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
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18
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Quy VC, Carnevale V, Manganaro L, Lusic M, Rossetti G, Leone V, Fenollar-Ferrer C, Raugei S, Del Sal G, Giacca M, Carloni P. HIV-1 integrase binding to its cellular partners: a perspective from computational biology. Curr Pharm Des 2015; 20:3412-21. [PMID: 24001231 DOI: 10.2174/13816128113199990631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 08/27/2013] [Indexed: 11/22/2022]
Abstract
Viral DNA integration into the infected cell genome is an essential step in the HIV-1 life cycle. Hence, the viral integrase enzyme has become an important target for antiviral therapy. The integrase's activity action relies on the binding to its cellular partners, therefore the knowledge of the structural determinants is very important from a therapeutic perspective. Here we first review published computer-aided structural predictions of HIV-1 integrase in complex with its interactors. These include DNA and the human HAT protein. Next, we present a prediction of the complex between HIV-1 integrase with the human prolyl-isomerase-1 (hPin1) enzyme. Interaction with hPin1 is crucial for efficient HIV-1 infection and it increases integrase stability (Manganaro et. al 2010, Nat. Med. 16, 329). The modeling presented here, which is validated against experimental data, provides a rationale for a variety of viral protein's mutations which impair protein function and HIV-1 virus replication in vivo without significantly affecting enzymatic activity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
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19
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Fenollar-Ferrer C, Patti M, Werner A, Knoepfel T, Forster IC, Forrest LR. The Na1 Binding Site in the Human Sodium-Phosphate Cotransporter NaPi-IIa. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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20
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Fenollar-Ferrer C, Patti M, Knöpfel T, Werner A, Forster IC, Forrest LR. Structural fold and binding sites of the human Na⁺-phosphate cotransporter NaPi-II. Biophys J 2014; 106:1268-79. [PMID: 24655502 DOI: 10.1016/j.bpj.2014.01.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 12/17/2022] Open
Abstract
Phosphate plays essential biological roles and its plasma level in humans requires tight control to avoid bone loss (insufficiency) or vascular calcification (excess). Intestinal absorption and renal reabsorption of phosphate are mediated by members of the SLC34 family of sodium-coupled transporters (NaPi-IIa,b,c) whose membrane expression is regulated by various hormones, circulating proteins, and phosphate itself. Consequently, NaPi-II proteins are also potentially important pharmaceutical targets for controlling phosphate levels. Their crucial role in Pi homeostasis is underscored by pathologies resulting from naturally occurring SLC34 mutations and SLC34 knockout animals. SLC34 isoforms have been extensively studied with respect to transport mechanism and structure-function relationships; however, the three-dimensional structure is unknown. All SLC34 transporters share a duplicated motif comprising a glutamine followed by a stretch of threonine or serine residues, suggesting the presence of structural repeats as found in other transporter families. Nevertheless, standard bioinformatic approaches fail to clearly identify a suitable template for molecular modeling. Here, we used hydrophobicity profiles and hidden Markov models to define a structural repeat common to all SLC34 isoforms. Similar approaches identify a relationship with the core regions in a crystal structure of Vibrio cholerae Na(+)-dicarboxylate transporter VcINDY, from which we generated a homology model of human NaPi-IIa. The aforementioned SLC34 motifs in each repeat localize to the center of the model, and were predicted to form Na(+) and Pi coordination sites. Functional relevance of key amino acids was confirmed by biochemical and electrophysiological analysis of expressed, mutated transporters. Moreover, the validity of the predicted architecture is corroborated by extensive published structure-function studies. The model provides key information for elucidating the transport mechanism and predicts candidate substrate binding sites.
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Affiliation(s)
- Cristina Fenollar-Ferrer
- Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Monica Patti
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Thomas Knöpfel
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Andreas Werner
- Epithelial Research Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Ian C Forster
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland.
| | - Lucy R Forrest
- Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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21
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Fenollar-Ferrer C, Stockner T, Schwarz TC, Pal A, Gotovina J, Hofmaier T, Jayaraman K, Adhikary S, Kudlacek O, Mehdipour AR, Tavoulari S, Rudnick G, Singh SK, Konrat R, Sitte HH, Forrest LR. Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter. Biochemistry 2014; 53:5444-60. [PMID: 25093911 PMCID: PMC4147951 DOI: 10.1021/bi500637f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Uptake
of neurotransmitters by sodium-coupled monoamine transporters
of the NSS family is required for termination of synaptic transmission.
Transport is tightly regulated by protein–protein interactions
involving the small cytoplasmic segments at the amino-
and carboxy-terminal ends of the transporter. Although structures
of homologues provide information about the transmembrane regions
of these transporters,
the structural arrangement of the terminal domains remains largely
unknown. Here, we combined molecular modeling, biochemical, and biophysical
approaches in an iterative manner to
investigate the structure of the 82-residue N-terminal and 30-residue
C-terminal domains of human serotonin transporter (SERT). Several
secondary structures were predicted in these domains, and structural
models were built using the Rosetta fragment-based methodology. One-dimensional 1H nuclear magnetic resonance and circular dichroism spectroscopy
supported the presence of helical elements in the isolated SERT N-terminal
domain. Moreover, introducing helix-breaking residues within those
elements altered the fluorescence resonance energy transfer signal
between terminal cyan fluorescent protein and yellow fluorescent protein
tags attached to full-length SERT, consistent with the notion that
the fold of the terminal domains is relatively well-defined. Full-length
models of SERT that are consistent with these and published
experimental data were generated. The resultant models predict confined
loci for the terminal domains and predict that they move apart during
the transport-related conformational cycle, as predicted by structures
of homologues and by the “rocking
bundle” hypothesis, which is consistent with spectroscopic
measurements. The models also suggest the nature of binding to regulatory
interaction partners. This study provides a structural context for
functional and regulatory mechanisms involving SERT terminal domains.
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Affiliation(s)
- Cristina Fenollar-Ferrer
- Computational Structural Biology Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
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22
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Abstract
The kidney and inner ear CLC-K chloride channels, which are involved in salt absorption and endolymph production, are regulated by extracellular Ca2+ in the millimolar concentration range. Recently, Gradogna et al. (2010. J. Gen. Physiol.http://dx.doi.org/10.1085/jgp.201010455) identified a pair of acidic residues (E261 and D278) located in the loop between helices I and J as forming a putative intersubunit Ca2+-binding site in hClC-Ka. In this study, we sought to explore the properties of the binding site in more detail. First, we verified that the site is conserved in hClC-Kb and rClC-K1. In addition, we could confer Ca2+ sensitivity to the Torpedo marmorata ClC-0 channel by exchanging its I–J loop with that from ClC-Ka, demonstrating a direct role of the loop in Ca2+ binding. Based on a structure of a bacterial CLC and a new sequence alignment, we built homology models of ClC-Ka. The models suggested additional amino acids involved in Ca2+ binding. Testing mutants of these residues, we could restrict the range of plausible models and positively identify two more residues (E259 and E281) involved in Ca2+ coordination. To investigate cation specificity, we applied extracellular Zn2+, Mg2+, Ba2+, Sr2+, and Mn2+. Zn2+ blocks ClC-Ka as well as its Ca2+-insensitive mutant, suggesting that Zn2+ binds to a different site. Mg2+ does not activate CLC-Ks, but the channels are activated by Ba2+, Sr2+, and Mn2+ with a rank order of potency of Ca2+ > Ba2+ > Sr2+ = Mn2+ for the human CLC-Ks. Dose–response analysis indicates that the less potent Ba2+ has a lower affinity rather than a lower efficacy. Interestingly, rClC-K1 shows an altered rank order (Ca2+ > Sr2+ >> Ba2+), but homology models suggest that residues outside the I–J loop are responsible for this difference. Our detailed characterization of the regulatory Ca2+-binding site provides a solid basis for the understanding of the physiological modulation of CLC-K channel function in the kidney and inner ear.
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Affiliation(s)
- Antonella Gradogna
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genoa, Italy
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23
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Fenollar-Ferrer C, Anselmi C, Carnevale V, Raugei S, Carloni P. Insights on the acetylated NF-κB transcription factor complex with DNA from molecular dynamics simulations. Proteins 2012; 80:1560-8. [PMID: 22419549 DOI: 10.1002/prot.24047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 01/15/2012] [Accepted: 01/25/2012] [Indexed: 11/10/2022]
Abstract
The nuclear factor-κB (NF-κB) is a DNA sequence-specific regulator of many important biological processes, whose activity is modulated by enzymatic acetylation. In one of the best functionally characterized NF-κB complexes, the p50/p65 heterodimer, acetylation of K221 at p65 causes a decrease of DNA dissociation rate, whilst the acetylation of K122 and K123, also at p65, markedly decreases the binding affinity for DNA. By means of molecular dynamics simulations based on the X-ray structure of the p50/p65 complex with DNA, we provide insights on the structural determinants of the acetylated complexes in aqueous solution. Lysine acetylation involves the loss of favorable electrostatic interactions between DNA and NF-κB, which is partially compensated by the reduction of the desolvation free-energy of the two binding partners. Acetylation at both positions K122 and K123 is associated with a decrease of the electrostatic potential at the p65/DNA interface, which is only partially counterbalanced by an increase of the local Na(+) concentration. It induces the disruption of base-specific and nonspecific interactions between DNA and NF-κB and it is consistent with the observed decrease of binding affinity. In contrast, acetylation at position K221 results in the loss of nonspecific protein-DNA interactions, but the DNA recognition sites are not affected. In addition, the loss of protein-DNA interactions is likely to be counterbalanced by an increase of the configurational entropy of the complex, which provides, at a speculative level, a justification for the observed decrease of NF-κB/DNA dissociation rate.
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24
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Liu H, Fenollar-Ferrer C, Cao A, Anselmi C, Carloni P, Liu J. Molecular dissection of human oncostatin M-mediated signal transductions through site-directed mutagenesis. Int J Mol Med 2009; 23:161-172. [PMID: 19148539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The binding of oncostatin M (OM) to type I and type II receptor complexes elicits various biological responses by activating MEK/ERK and JAK/STAT signaling pathways. Some OM effects are clinically desirable such as reducing hyperlipidemia through the activation of hepatic LDL receptor transcription, a downstream event of ERK activation. The OM pro-inflammatory responses via induction of acute phase protein gene expression have been associated with STAT activation. In this study, by conducting site-directed mutagenesis, bioassays and molecular modeling we have defined 4 OM residues that are differently involved in the activation of ERK or STAT signaling pathway in HepG2 cells. We show that mutation of Lys163 to alanine totally abolished OM-mediated signaling, possibly because such mutation causes the disruption of a stabilizing H-bond pattern at the OM interface with receptors. G120A mutation equally impaired activations of ERK and STAT signaling pathways also by impairing the OM/cognate protein interactions. Interestingly, mutations of Gln20 and Asn123 differentially affected OM signaling through the two pathways. Q20A and N123A retained strong activity in inducing ERK phosphorylation but they showed diminished ability in activating STAT1 and STAT3. We further showed that mutations at Gln20 and Asn123 reduced OM induction of inflammatory gene fibrinogen-beta to a greater extent than that of LDL receptor gene. The mutation of Asn123 is directly related to local structural modification at site 3 of OM. Collectively these results provide a structural basis of OM-mediated signaling and suggest a potential to improve OM therapeutic properties via structural modification.
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Affiliation(s)
- Haiyan Liu
- Department of Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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25
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Guida E, Bisso A, Fenollar-Ferrer C, Napoli M, Anselmi C, Girardini JE, Carloni P, Del Sal G. Peptide aptamers targeting mutant p53 induce apoptosis in tumor cells. Cancer Res 2008; 68:6550-8. [PMID: 18701478 DOI: 10.1158/0008-5472.can-08-0137] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutations in the p53 tumor suppressor gene frequently result in expression of p53 point mutants that accumulate in cancer cells and actively collaborate with tumor progression through the acquisition of novel properties. Interfering with mutant p53 functions may represent a valid alternative for blocking tumor growth and development of aggressive phenotypes. The interactions and activities of selected proteins can be specifically modulated by the binding of peptide aptamers (PA). In the present work, we isolated PAs able to interact more efficiently with p53 conformational mutants compared with wild-type p53. The interaction between mutant p53 and PAs was further characterized using molecular modeling. Transient expression of PAs was able to reduce the transactivation activity of mutant p53 and to induce apoptosis specifically in cells expressing mutant p53. These PAs could provide a potential strategy to inhibit the oncogenic functions of mutant p53 and improve mutant p53-targeted cancer therapies.
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Affiliation(s)
- Elisa Guida
- The National Laboratory CIB, and Dipartimento di Biochimica, Biofisica, e Chimica delle Macromolecole (BBCM), University of Trieste, Italy
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26
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Fenollar-Ferrer C, Frau J, Donoso J, Muñoz F. Evolution of class C β-lactamases: factors influencing their hydrolysis and recognition mechanisms. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0463-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Fenollar-Ferrer C, Carnevale V, Raugei S, Carloni P. HIV-1 Integrase–DNA Interactions Investigated by Molecular Modelling. Computational and Mathematical Methods in Medicine 2008. [DOI: 10.1080/17486700802167918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
HIV-1 integrase is the viral enzyme responsible for the insertion of the viral DNA into the host cell chromosome. This process occurs through two distinct biochemical reactions: the 3′-processing of the viral DNA and the transesterification reaction. Because experimental structural information on the reaction intermediate is not available, several molecular models have been developed. Unfortunately, none of the models of the enzyme–substrate complex is fully consistent with the available molecular biological data. We have constructed a new theoretical model based on mutagenesis experiments and cross-linking data, using a relatively accurate computational setup. The structural features of the model along with its limitations are discussed here.
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Affiliation(s)
- C. Fenollar-Ferrer
- International School for Advanced Studies and CNR-INFM Democritos, Trieste, Italy
| | - V. Carnevale
- International School for Advanced Studies and CNR-INFM Democritos, Trieste, Italy
| | - S. Raugei
- International School for Advanced Studies and CNR-INFM Democritos, Trieste, Italy
| | - P. Carloni
- International School for Advanced Studies and CNR-INFM Democritos, Trieste, Italy
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28
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Fenollar-Ferrer C, Donoso J, Frau J, Muñoz F. Molecular Modeling ofHenry-Michaelis and Acyl-Enzyme Complexes between Imipenem andEnterobacter cloacae P99β-Lactamase. Chem Biodivers 2005; 2:645-56. [PMID: 17192008 DOI: 10.1002/cbdv.200590041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report a molecular-mechanics (AMBER*) study on the Henry-Michaelis complex and the corresponding acyl-enzyme adduct formed between imipenem (1), a transient inhibitor of beta-lactamases, and Enterobacter cloacae P99, a class C-beta-lactamase. We have examined the influence of the structural configuration of the functional groups in the substrate on their three-dimensional (3D) arrangement at the active site, which was compared with those adopted by typical penicillins and cephalosporins. Our results confirm that the carboxy group of the antibiotic plays a prominent role in the binding of the substrate to the active site, and that it activates Ser64 through interaction with the phenolic OH group of Tyr150. The binding of imipenem to E. cloacae P99 increases the distance between Tyr150 and Ser64 due to the presence of a hydrophobic Me group in the (R)-1-hydroxyethyl substituent at C(6). This, together with the 3D arrangement of its carboxy group, leads to an interaction with the active site in a manner that hinders H+ exchange between the nucleophile in Ser64 and its basic activator, the phenolic group of Tyr150.
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Affiliation(s)
- Cristina Fenollar-Ferrer
- Instituto Universitario de Investigación en Ciencias de la Salud, Departamento de Química, Universidad de las Islas Baleares, Ctra. de Vallemossa km 7.5, 07122 Palma de Mallorca, Spain
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29
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Abstract
The indiscriminate use of beta-lactams has considerably diminished their efficiency as a result of bacteria developing effective defense mechanisms against them. Recent pharmaceutical research has led to the synthesis of tricyclic beta-lactam antibiotics known as "tricyclic carbapenems" or "trinems". In this work, we studied the chemical reactivity, an essential property for antibiotic action, of trinems and found it to be similar to that of cephalosporins. Also, we elucidated the interaction pattern for sanfetrinem and 4beta-methoxy trinem and compared it to that for classical beta-lactams. The behavior of both trinems was found to be similar to that of penicillin G toward Staphylococcus aureus PC1, and that of cephalothin and imipenem toward Enterobacter cloacae P99.
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Affiliation(s)
- Hector J Fasoli
- Facultad de Ciencias Fisicomatematicas e Ingeniería, Universidad Católica Argentina, Alicia M. de Justo 1500, C1107AAZ, Argentina
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30
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Fenollar-Ferrer C, Frau J, Donoso J, Muñoz F. Role of beta-lactam carboxyl group on binding of penicillins and cephalosporins to class C beta-lactamases. Proteins 2003; 51:442-52. [PMID: 12696055 DOI: 10.1002/prot.10358] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular models for the Henry Michaelis complexes of Enterobacter cloacae, a class C beta-lactamase, with penicillin G and cephalotin have been constructed by using molecular mechanic calculations, based on the AMBER force field, to examine the molecular differentiation mechanisms between cephalosporins and penicillins in beta-lactamases. Ser318Ala and Thr316Ala mutations in both complexes and Asn346Ala and Thr316Ala/Asn346Ala double mutation in penicillin G complex have also been studied. Results confirm that Thr316, Ser318, and Asn346 play a crucial role in the substrate recognition, via their interactions with one of the oxygens of the antibiotic carboxyl group. Both mutation Ser318Ala and Thr316Ala strongly affect the correct binding of cephalotin to P99, the first mainly by precluding the discriminating salt bridge between carboxyl and serine OH groups, and the second one by the Ser318, Lys315, and Tyr150 spatial rearrangements. On the other hand, Ser318Ala mutation has little effect on penicillin G binding, but the Thr316Ala/Asn346Ala double mutation causes the departure of the antibiotic from the oxyanion hole. Molecular dynamic simulations allow us to interpret the experimental results of some class C and A beta-lactamases.
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31
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Fenollar-Ferrer C, Frau J, Vilanova B, Donoso J, Muñoz F. Molecular modelling studies on Henry–Michaelis complexes of a class-C β-lactamase and β-lactam compounds. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(01)00675-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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