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Khan S, Upadhyay S, Dave U, Kumar A, Gomes J. Structural and mechanistic insights into ALS patient derived mutations in D-amino acid oxidase. Int J Biol Macromol 2024; 256:128403. [PMID: 38035964 DOI: 10.1016/j.ijbiomac.2023.128403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
The D-amino acid oxidase protein modulates neurotransmission by controlling the levels of D-serine, a co-agonist of N-methyl-D-aspartate receptors. Mutations in the DAO gene have been associated with ALS, with some studies reporting pathogenic mechanisms of the R199W mutation. We have characterized two novel mutations R38H and Q201R found in ALS patients and report certain novel findings related to the R199W mutation. We report the first instance of crystal structure analysis of a patient-derived mutant of DAO, R38H, solved at 2.10 Å. The structure revealed significant perturbations and altered binding with the cofactor (FAD) and the inhibitor benzoate, supported by biochemical assays. Q201R-DAO also exhibited significantly lower ligand binding efficiency. Furthermore, kinetic analysis across all variants revealed reduced oxidase activity and substrate binding. Notably, R38H-DAO exhibited near-WT activity only at high substrate concentrations, while R199W-DAO and Q201R-DAO displayed drastic activity reduction. Additionally, structural perturbations were inferred for R199W-DAO and Q201R-DAO, evident by the higher oligomeric state in the holoenzyme form. We also observed thermal instability in case of R199W-DAO mutant. We hypothesize that the mutant enzymes may be rendered non-functional in a cellular context, potentially leading to NMDAR-associated excitotoxicity. The study provides novel insights into structural and functional aspects of DAO mutations in ALS.
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Affiliation(s)
- Shumayila Khan
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India; Indian Council of Medical Research, New Delhi 110029, India
| | - Saurabh Upadhyay
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Upma Dave
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Ashwani Kumar
- Macromolecular Crystallography Section, Beamline Development & Application Section, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India.
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2
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Souza INDO, Roychaudhuri R, de Belleroche J, Mothet JP. d-Amino acids: new clinical pathways for brain diseases. Trends Mol Med 2023; 29:1014-1028. [PMID: 37770379 DOI: 10.1016/j.molmed.2023.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
Free d-amino acids (d-AAs) are emerging as a novel and important class of signaling molecules in many organs, including the brain and endocrine systems. There has been considerable progress in our understanding of the fundamental roles of these atypical messengers, with increasingly recognized implications in a wide range of neuropathologies, including schizophrenia (SCZ), epilepsy, Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), substance abuse, and chronic pain, among others. Research has enabled the discovery that d-serine, d-aspartate and more recently d-cysteine are essential for the healthy development and function of the central nervous system (CNS). We discuss recent progress that has profoundly transformed our vision of numerous physiological processes but has also shown how d-AAs are now offering therapeutic promise in clinical settings for several human diseases.
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Affiliation(s)
- Isis Nem de Oliveira Souza
- Biophotonics and Synapse Physiopathology Team, Laboratoire LuMIn UMR9024 Université Paris-Saclay, ENS Paris-Saclay, CNRS, CentraleSupelec, 91190 Gif-sur-Yvette, France; Molecular Pharmacology Laboratory, Biomedical Sciences Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robin Roychaudhuri
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Birth Defects, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jacqueline de Belleroche
- Neurogenetics Group, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Jean-Pierre Mothet
- Biophotonics and Synapse Physiopathology Team, Laboratoire LuMIn UMR9024 Université Paris-Saclay, ENS Paris-Saclay, CNRS, CentraleSupelec, 91190 Gif-sur-Yvette, France.
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3
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Todd TW, Petrucelli L. Modelling amyotrophic lateral sclerosis in rodents. Nat Rev Neurosci 2022; 23:231-251. [PMID: 35260846 DOI: 10.1038/s41583-022-00564-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
The efficient study of human disease requires the proper tools, one of the most crucial of which is an accurate animal model that faithfully recapitulates the human condition. The study of amyotrophic lateral sclerosis (ALS) is no exception. Although the majority of ALS cases are considered sporadic, most animal models of this disease rely on genetic mutations identified in familial cases. Over the past decade, the number of genes associated with ALS has risen dramatically and, with each new genetic variant, there is a drive to develop associated animal models. Rodent models are of particular importance as they allow for the study of ALS in the context of a living mammal with a comparable CNS. Such models not only help to verify the pathogenicity of novel mutations but also provide critical insight into disease mechanisms and are crucial for the testing of new therapeutics. In this Review, we aim to summarize the full spectrum of ALS rodent models developed to date.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA.
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Janežič M, Dileep KV, Zhang KYJ. A multidimensional computational exploration of congenital myasthenic syndrome causing mutations in human choline acetyltransferase. J Cell Biochem 2021; 122:787-800. [PMID: 33650116 DOI: 10.1002/jcb.29913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/09/2022]
Abstract
Missense mutations of human choline acetyltransferase (CHAT) are mainly associated with congenital myasthenic syndrome (CMS). To date, several pathogenic mutations have been reported, but due to the rarity and genetic complexity of CMS and difficult genotype-phenotype correlations, the CHAT mutations, and their consequences are underexplored. In this study, we systematically sift through the available genetic data in search of previously unreported pathogenic mutations and use a dynamic in silico model to provide structural explanations for the pathogenicity of the reported deleterious and undetermined variants. Through rigorous multiparameter analyses, we conclude that mutations can affect CHAT through a variety of different mechanisms: by disrupting the secondary structure, by perturbing the P-loop through long-range allosteric interactions, by disrupting the domain connecting loop, and by affecting the phosphorylation process. This study provides the first dynamic look at how mutations affect the structure and catalytic activity in CHAT and highlights the need for further genomic research to better understand the pathology of CHAT.
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Affiliation(s)
- Matej Janežič
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kalarickal V Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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Ahmad I, Shaikh M, Surana S, Ghosh A, Patel H. p38α MAP kinase inhibitors to overcome EGFR tertiary C797S point mutation associated with osimertinib in non-small cell lung cancer (NSCLC): emergence of fourth-generation EGFR inhibitor. J Biomol Struct Dyn 2020; 40:3046-3059. [DOI: 10.1080/07391102.2020.1844801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Matin Shaikh
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Sanjay Surana
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
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Mechanistic insights into the loss-of-function mechanisms of rare human D-amino acid oxidase variants implicated in amyotrophic lateral sclerosis. Sci Rep 2020; 10:17146. [PMID: 33051492 PMCID: PMC7555490 DOI: 10.1038/s41598-020-74048-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Impaired enzymatic activity in D-amino acid oxidase (DAAO) caused by missense mutations has been shown to trigger amyotrophic lateral sclerosis (ALS) through an abnormal accumulation of D-serine in the spinal cord. While loss of enzymatic functions of certain ALS-causing DAAO variants have been studied before, a detailed understanding of structure-dynamics-function relationship of the rare DAAO variants has not been investigated hitherto. To address this, we carried out a comprehensive study of all the reported rare DAAO variants. By employing a spectrum of bioinformatics analyses along with extensive structural dynamics simulations, we show that certain rare variants disrupted key interactions with the active site and decreased the conformational flexibility of active site loop comprising residues 216-228, which is essential for substrate binding and product release. Moreover, these variants lost crucial interactions with the cofactor flavin-adenine-dinucleotide, resulting in weaker binding affinity. A detailed inspection revealed that these variants exhibited such characteristics due to the abrogation of specific salt bridges. Taken together, our study provides a gateway into the structural-dynamic features of the rare DAAO variants and highlights the importance of informatics-based integrated analyses in the screening and prioritization of variants a priori to the clinical-functional characterization.
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Gu SX, Wang HF, Zhu YY, Chen FE. Natural Occurrence, Biological Functions, and Analysis of D-Amino Acids. PHARMACEUTICAL FRONTS 2020. [DOI: 10.1055/s-0040-1713820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractThis review covers the recent development on the natural occurrence, functional elucidations, and analysis of amino acids of the D (dextro) configuration. In the pharmaceutical field, amino acids are not only used directly as clinical drugs and nutriments, but also widely applied as starting materials, catalysts, or chiral ligands for the synthesis of active pharmaceutical ingredients. Earler belief hold that only L-amino acids exist in nature and D-amino acids were artificial products. However, increasing evidence indicates that D-amino acids are naturally occurring in living organisms including human beings, plants, and microorganisms, playing important roles in biological processes. While D-amino acids have similar physical and chemical characteristics with their respective L-enantiomers in an achiral measurement, the biological functions of D-amino acids are remarkably different from those of L-ones. With the rapid development of chiral analytical techniques for D-amino acids, studies on the existence, formation mechanisms, biological functions as well as relevant physiology and pathology of D-amino acids have achieved great progress; however, they are far from being sufficiently explored.
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Affiliation(s)
- Shuang-Xi Gu
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Hai-Feng Wang
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Yuan-Yuan Zhu
- School of Chemistry & Environmental Engineering, Wuhan Institute of Technology, Wuhan, People's Republic of China
| | - Fen-Er Chen
- Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan, People's Republic of China
- Department of Chemistry, Fudan University, Shanghai, People's Republic of China
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Dash R, Choi HJ, Moon IS. Mechanistic insights into the deleterious roles of Nasu-Hakola disease associated TREM2 variants. Sci Rep 2020; 10:3663. [PMID: 32107424 PMCID: PMC7046722 DOI: 10.1038/s41598-020-60561-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Recently, the critical roles played by genetic variants of TREM2 (Triggering Receptor Expressed on Myeloid cells 2) in Alzheimer's disease have been aggressively highlighted. However, few studies have focused on the deleterious roles of Nasu-Hakola disease (NHD) associated TREM2 variants. In order to get insights into the contributions made by these variants to neurodegeneration, we investigated the influences of four NHD associated TREM2 mutations (Y38C, W50C, T66M, and V126G) on loss-of-function, and followed this with in silico prediction and conventional molecular dynamics simulation. NHD mutations were predicted to be highly deleterious by eight different in silico bioinformatics tools and found to induce conformational changes by molecular dynamics simulation. As compared with the wild-type, the four variants produced substantial differences in the collective motions of loop regions, which not only promoted structural remodeling in the CDR2 (complementarity-determining region 2) loop but also in the CDR1 loop, by changing inter- and intra-loop hydrogen bonding networks. In addition, structural studies in a free energy landscape analysis showed that Y38, T66, and V126 are crucial for maintaining the structural features of CDR1 and CDR2 loops, and that mutations in these positions produced steric clashes and loss of ligand binding. These results showed the presence of mutations in the TREM2 ectodomain induced flexibility and caused structural alterations. Dynamical scenarios, as provided by the present study, may be critical to our understanding of the roles of these TREM2 mutations in neurodegenerative diseases.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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Padhi AK, Narain P, Gomes J. Rare Angiogenin and Ribonuclease 4 variants associated with amyotrophic lateral sclerosis exhibit loss-of-function: a comprehensive in silico study. Metab Brain Dis 2019; 34:1661-1677. [PMID: 31368019 DOI: 10.1007/s11011-019-00473-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS), a debilitating neurodegenerative disorder is related to mutations in a number of genes, and certain genes of the Ribonuclease (RNASE) superfamily trigger ALS more frequently. Even though missense mutations in Angiogenin (ANG) and Ribonuclease 4 (RNASE4) have been previously shown to cause ALS through loss-of-function mechanisms, understanding the role of rare variants with a plausible explanation of their functional loss mechanisms is an important mission. The study aims to understand if any of the rare ANG and RNASE4 variants catalogued in Project MinE consortium caused ALS due to loss of ribonucleolytic or nuclear translocation or both these activities. Several in silico analyses in combination with extensive molecular dynamics (MD) simulations were performed on wild-type ANG and RNASE4, along with six rare variants (T11S-ANG, R122H-ANG, D2E-RNASE4, N26K-RNASE4, T79A-RNASE4 and G119S-RNASE4) to study the structural and dynamic changes in the catalytic triad and nuclear localization signal residues responsible for ribonucleolytic and nuclear translocation activities respectively. Our comprehensive analyses comprising 1.2 μs simulations with a focus on physicochemical, structural and dynamic properties reveal that T11S-ANG, N26K-RNASE4 and T79A-RNASE4 variants would result in loss of ribonucleolytic activity due to conformational switching of catalytic His114 and His116 respectively but none of the variants would lose their nuclear translocation activity. Our study not only highlights the importance of rare variants but also demonstrates that elucidating the structure-function relationship of mutant effectors is crucial to gain insights into ALS pathophysiology and in developing effective therapeutics.
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Affiliation(s)
- Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
- Laboratory for Structural Bioinformatics, Field for Structural Molecular Biology, Centre for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Priyam Narain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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Identification and characterization of novel and rare susceptible variants in Indian amyotrophic lateral sclerosis patients. Neurogenetics 2019; 20:197-208. [PMID: 31432357 DOI: 10.1007/s10048-019-00584-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
Abstract
Rare missense variants play a crucial role in amyotrophic lateral sclerosis (ALS) pathophysiology. We report rare/novel missense variants from 154 Indian ALS patients, identified through targeted sequencing of 25 ALS-associated genes. As pathogenic variants could explain only a small percentage of ALS pathophysiology in our cohort, we investigated the frequency of tolerated and benign novel/rare variants, which could be potentially ALS susceptible. These variants were identified in 5.36% (8/149) of sporadic ALS (sALS) cases; with one novel variant each in ERBB4, SETX, DCTN1, and MATR3; four rare variants, one each in PON2 and ANG and two different rare variants in SETX. Identified variants were either absent or present at extremely rare frequencies (MAF < 0.01) in large population databases and were absent in 50 healthy controls sequenced through Sanger method. Furthermore, an oligogenic basis of ALS was observed in three sALS, with co-occurrence of intermediate-length repeat expansions in ATXN2 and a rare/novel variant in DCTN1 and SETX genes. Additionally, molecular dynamics and biochemical functional analysis of an angiogenin variant (R21G) identified from our cohort demonstrated loss of ribonucleolytic and nuclear translocation activities. Our findings suggest that rare variants could be potentially pathogenic and functional studies are warranted to decisively establish the pathogenic mechanisms associated with them.
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