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Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [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] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
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Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
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2
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Nie B, Duan Y, Xie X, Qiu L, Shi S, Fan Z, Zheng X, Jiang L. Systematic analysis of cuproptosis-related genes in immunological characterization and predictive drugs in Alzheimer's disease. Front Aging Neurosci 2023; 15:1204530. [PMID: 37920383 PMCID: PMC10618683 DOI: 10.3389/fnagi.2023.1204530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023] Open
Abstract
Objectives This study aimed to make a systematic analysis of cuproptosis-related genes (CRGs) in immunological characterization and predictive drugs in Alzheimer's disease (AD) through bioinformatics and biological experiments. Methods The molecular clusters related to CRGs and associated immune cell infiltrations in AD were investigated. The diagnostic models were constructed for AD and different AD subtypes. Moreover, drug prediction and molecular docking were also performed. Subsequently, a molecular dynamics (MD) simulation was conducted to further verify the findings. Finally, RT-qPCR validation was performed. Results The characterization of 12 AD-related CRGs was evaluated in AD, and a diagnostic model for AD showed a satisfying discrimination power based on five CRGs by LASSO regression analysis. The dysregulated CRGs and activated immune responses partially differed between patients with AD and healthy subjects. Furthermore, two molecular subtypes (clusters A and B) with different immune infiltration characteristics in AD were identified. Similarly, a diagnostic model for different AD subtypes was built with nine CRGs, which achieved a good performance. Molecular docking revealed the optimum conformation of CHEMBL261454 and its target gene CSNK1D, which was further validated by MD simulation. The RT-qPCR results were consistent with those of the comprehensive analysis. Conclusion This study systematically elucidated the complex relationship between cuproptosis and AD, providing novel molecular targets for treatment and diagnosis biomarkers of AD.
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Affiliation(s)
- Bin Nie
- Department of Clinical Laboratory, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
- Clinical Research and Translational Center, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
| | - Yefen Duan
- Department of Clinical Laboratory, Yibin No. 4 People’s Hospital, Yibin, China
| | - Xuelong Xie
- Department of Clinical Laboratory, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
- Clinical Research and Translational Center, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
| | - Lihua Qiu
- Imaging Department, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
| | - Shaorui Shi
- Department of Clinical Laboratory, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
- Clinical Research and Translational Center, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
| | - Zhili Fan
- Department of Clinical Laboratory, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
- Clinical Research and Translational Center, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
| | - Xuxiang Zheng
- Department of Clinical Laboratory, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
- Clinical Research and Translational Center, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
| | - Ling Jiang
- Department of Neurology, The Second People’s Hospital of Yibin·West China Yibin Hospital, Sichuan University, Yibin, China
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Szabo E, Nemes-Nikodem E, Vass KR, Zambo Z, Zrupko E, Torocsik B, Ozohanics O, Nagy B, Ambrus A. Structural and Biochemical Investigation of Selected Pathogenic Mutants of the Human Dihydrolipoamide Dehydrogenase. Int J Mol Sci 2023; 24:10826. [PMID: 37446004 PMCID: PMC10341545 DOI: 10.3390/ijms241310826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Clinically relevant disease-causing variants of the human dihydrolipoamide dehydrogenase (hLADH, hE3), a common component of the mitochondrial α-keto acid dehydrogenase complexes, were characterized using a multipronged approach to unravel the molecular pathomechanisms that underlie hLADH deficiency. The G101del and M326V substitutions both reduced the protein stability and triggered the disassembly of the functional/obligate hLADH homodimer and significant FAD losses, which altogether eventually manifested in a virtually undetectable catalytic activity in both cases. The I12T-hLADH variant proved also to be quite unstable, but managed to retain the dimeric enzyme form; the LADH activity, both in the forward and reverse catalytic directions and the affinity for the prosthetic group FAD were both significantly compromised. None of the above three variants lent themselves to an in-depth structural analysis via X-ray crystallography due to inherent protein instability. Crystal structures at 2.89 and 2.44 Å resolutions were determined for the I318T- and I358T-hLADH variants, respectively; structure analysis revealed minor conformational perturbations, which correlated well with the residual LADH activities, in both cases. For the dimer interface variants G426E-, I445M-, and R447G-hLADH, enzyme activities and FAD loss were determined and compared against the previously published structural data.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37-47 Tuzolto St., 1094 Budapest, Hungary
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Lipoamide dehydrogenase (LADH) deficiency: medical perspectives of the structural and functional characterization of LADH and its pathogenic variants. Biol Futur 2023:10.1007/s42977-023-00155-6. [PMID: 36842090 DOI: 10.1007/s42977-023-00155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
(Dihydro)lipoamide dehydrogenase (LADH) deficiency is an autosomal recessive genetic metabolic disorder. It generally presents with an onset in the neonatal age and premature death. The clinical picture usually involves metabolic decompensation and lactic acidosis that lead to neurological, cardiological, and/or hepatological outcomes. Severity of the disease is due to the fact that LADH is a common E3 subunit to the pyruvate, alpha-ketoglutarate, alpha-ketoadipate, and branched-chain alpha-keto acid dehydrogenase complexes and is also part of the glycine cleavage system; hence, a loss in LADH activity adversely affects several central metabolic pathways simultaneously. The severe clinical manifestations, however, often do not parallel the LADH activity loss, which implies the existence of auxiliary pathological pathways; stimulated reactive oxygen species (ROS) production as well as dissociation from the relevant multienzyme complexes proved to be auxiliary exacerbating pathomechanisms for selected disease-causing LADH mutations. This review provides an overview on the therapeutic challenges of inherited metabolic diseases, structural and functional characteristics of the mitochondrial alpha-keto acid dehydrogenase complexes, molecular pathogenesis and structural basis of LADH deficiency, and relevant potential future medical perspectives.
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Alfarsi A, Alfadhel M, Alameer S, Alhashem A, Tabarki B, Ababneh F, Al Fares A, Al Mutairi F. The phenotypic spectrum of dihydrolipoamide dehydrogenase deficiency in Saudi Arabia. Mol Genet Metab Rep 2021; 29:100817. [PMID: 34745891 PMCID: PMC8554626 DOI: 10.1016/j.ymgmr.2021.100817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 11/28/2022] Open
Abstract
Background Dihydrolipoamide dehydrogenase deficiency (DLDD) is a rare metabolic disorder inherited in an autosomal recessive manner. This heterogeneous disease has a variable clinical presentation, onset, and biochemical markers. Materials and methods We retrospectively reviewed the clinical and molecular diagnosis of eight cases with DLDD from four referral centers in Saudi Arabia. Results Remarkably, we found hepatic involvement ranging from acute hepatic failure to chronic hepatitis in five patients. In addition, neurological disorders in the form of seizures, developmental delay, ataxia, hypotonia and psychomotor symptoms were found in five patients, two of them with a combination of hepatic and neurological symptoms. In addition, only one patient had recurrent episodes of hypoglycemia. While most patients had the hepatic form of homozygous variant c.685G > T in the DLD gene, one patient was found to have a novel variant c.623C > T that had neurological and hepatic symptoms. Conclusions We describe the largest reported DLDD cohort in the Saudi population. Clinical, biochemical, radiological, and molecular characterization was reviewed and no clear genotype-phenotype correlation was found in this cohort.
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Key Words
- BCAAs, Branched Chain Amino Acids
- BCKDH, Branched-chain a-keto acid dehydrogenase
- DCA, Dichloroacetate
- DLDD, Dihydrolipoamide Dehydrogenase Deficiency
- Dihydrolipoamide dehydrogenase deficiency
- Flavoprotein and E3
- Hypoglycemia
- IRB, Institutional Review Board
- KAIMRC, King Abdullah International Medical Research Centre
- Lactic acidosis
- MRI, Magnetic resonance imaging
- PDH, Pyruvate dehydrogenase
- Pyruvate dehydrogenase complex
- WES, Whole Exome Sequencing
- αKGDH, alpha-ketoglutarate dehydrogenase
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Affiliation(s)
- Anar Alfarsi
- Genetics & Precision Medicine Department, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Genetics & Precision Medicine Department, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Seham Alameer
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Jeddah, Saudi Arabia
| | - Amal Alhashem
- Division of Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell biology, college of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Division of Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Faroug Ababneh
- Genetics & Precision Medicine Department, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Ahmed Al Fares
- King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,Division of Translational Pathology, Department of Pathology, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Fuad Al Mutairi
- Genetics & Precision Medicine Department, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
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The Effects of a Ketogenic Diet on Patients with Dihydrolipoamide Dehydrogenase Deficiency. Nutrients 2021; 13:nu13103523. [PMID: 34684524 PMCID: PMC8540285 DOI: 10.3390/nu13103523] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Dihydrolipoamide dehydrogenase (DLD lipoamide dehydrogenase, the E3 subunit of the pyruvate dehydrogenase complex (PDHC)) is the third catalytic enzyme of the PDHC, which converts pyruvate to acetyl-CoA catalyzed with the introduction of acetyl-CoA to the tricyclic acid (TCA) cycle. In humans, PDHC plays an important role in maintaining glycose homeostasis in an aerobic, energy-generating process. Inherited DLD-E3 deficiency, caused by the pathogenic variants in DLD, leads to variable presentations and courses of illness, ranging from myopathy, recurrent episodes of liver disease and vomiting, to Leigh disease and early death. Currently, there is no consensus on treatment guidelines, although one suggested solution is a ketogenic diet (KD). Objective: To describe the use and effects of KD in patients with DLD-E3 deficiency, compared to the standard treatment. Results: Sixteen patients were included. Of these, eight were from a historical cohort, and of the other eight, four were on a partial KD. All patients were homozygous for the D479V (or D444V, which corresponds to the mutated mature protein without the mitochondrial targeting sequence) pathogenic variant in DLD. The treatment with partial KD was found to improve patient survival. However, compared to a historical cohort, the patients’ quality of life (QOL) was not significantly improved. Conclusions: The use of KD offers an advantage regarding survival; however, there is no significant improvement in QOL.
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Szabo E, Wilk P, Nagy B, Zambo Z, Bui D, Weichsel A, Arjunan P, Torocsik B, Hubert A, Furey W, Montfort WR, Jordan F, Weiss MS, Adam-Vizi V, Ambrus A. Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants. Hum Mol Genet 2020; 28:3339-3354. [PMID: 31334547 DOI: 10.1093/hmg/ddz177] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/13/2022] Open
Abstract
Human dihydrolipoamide dehydrogenase (hLADH, hE3) deficiency (OMIM# 246900) is an often prematurely lethal genetic disease usually caused by inactive or partially inactive hE3 variants. Here we report the crystal structure of wild-type hE3 at an unprecedented high resolution of 1.75 Å and the structures of six disease-causing hE3 variants at resolutions ranging from 1.44 to 2.34 Å. P453L proved to be the most deleterious substitution in structure as aberrations extensively compromised the active site. The most prevalent G194C-hE3 variant primarily exhibited structural alterations close to the substitution site, whereas the nearby cofactor-binding residues were left unperturbed. The G426E substitution mainly interfered with the local charge distribution introducing dynamics to the substitution site in the dimer interface; G194C and G426E both led to minor structural changes. The R460G, R447G and I445M substitutions all perturbed a solvent accessible channel, the so-called H+/H2O channel, leading to the active site. Molecular pathomechanisms of enhanced reactive oxygen species (ROS) generation and impaired binding to multienzyme complexes were also addressed according to the structural data for the relevant mutations. In summary, we present here for the first time a comprehensive study that links three-dimensional structures of disease-causing hE3 variants to residual hLADH activities, altered capacities for ROS generation, compromised affinities for multienzyme complexes and eventually clinical symptoms. Our results may serve as useful starting points for future therapeutic intervention approaches.
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Affiliation(s)
- Eszter Szabo
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Piotr Wilk
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, 12489, Berlin, Germany
| | - Balint Nagy
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Zsofia Zambo
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - David Bui
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Andrzej Weichsel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Palaniappa Arjunan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, 15261, USA.,Biocrystallography Laboratory, Veterans Affairs Medical Center, Pittsburgh, PA, 15240, USA
| | - Beata Torocsik
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Agnes Hubert
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - William Furey
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, 15261, USA.,Biocrystallography Laboratory, Veterans Affairs Medical Center, Pittsburgh, PA, 15240, USA
| | - William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, 07102, USA
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, 12489, Berlin, Germany
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
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Ambrus A. An Updated View on the Molecular Pathomechanisms of Human Dihydrolipoamide Dehydrogenase Deficiency in Light of Novel Crystallographic Evidence. Neurochem Res 2019; 44:2307-2313. [PMID: 30847858 PMCID: PMC6776566 DOI: 10.1007/s11064-019-02766-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/22/2022]
Abstract
Dihydrolipoamide dehydrogenase (LADH, E3) deficiency is a rare (autosomal, recessive) genetic disorder generally presenting with an onset in the neonatal age and early death; the highest carrier rate has been found among Ashkenazi Jews. Acute clinical episodes usually involve severe metabolic decompensation and lactate acidosis that result in neurological, cardiological, and/or hepatological manifestations. Clinical severity is due to the fact that LADH is a common E3 subunit to the alpha-ketoglutarate, pyruvate, alpha-ketoadipate, and branched-chain alpha-keto acid dehydrogenase complexes, and is also a constituent in the glycine cleavage system, thus a loss in LADH function adversely affects multiple key metabolic routes. However, the severe clinical pictures frequently still do not parallel the LADH activity loss, which implies the involvement of auxiliary biochemical mechanisms; enhanced reactive oxygen species generation as well as affinity loss for multienzyme complexes proved to be key auxiliary exacerbating pathomechanisms. This review provides an overview and an up-to-date molecular insight into the pathomechanisms of this disease in light of the structural conclusions drawn from the first crystal structure of a disease-causing hE3 variant determined recently in our laboratory.
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest, 1094, Hungary.
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Ambrus A, Adam-Vizi V. Human dihydrolipoamide dehydrogenase (E3) deficiency: Novel insights into the structural basis and molecular pathomechanism. Neurochem Int 2017; 117:5-14. [PMID: 28579060 DOI: 10.1016/j.neuint.2017.05.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022]
Abstract
This review summarizes our present view on the molecular pathogenesis of human (h) E3-deficiency caused by a variety of genetic alterations with a special emphasis on the moonlighting biochemical phenomena related to the affected (dihydro)lipoamide dehydrogenase (LADH, E3, gene: dld), in particular the generation of reactive oxygen species (ROS). E3-deficiency is a rare autosomal recessive genetic disorder frequently presenting with a neonatal onset and premature death; the highest carrier rate of a single pathogenic dld mutation (1:94-1:110) was found among Ashkenazi Jews. Patients usually die during acute episodes that generally involve severe metabolic decompensation and lactic acidosis leading to neurological, cardiological, and/or hepatological manifestations. The disease owes its severity to the fact that LADH is the common E3 subunit of the alpha-ketoglutarate (KGDHc), pyruvate (PDHc), and branched-chain α-keto acid dehydrogenase complexes and is also part of the glycine cleavage system, hence the malfunctioning of LADH simultaneously incapacitates several central metabolic pathways. Nevertheless, the clinical pictures are usually not unequivocally portrayed through the loss of LADH activities and imply auxiliary mechanisms that exacerbate the symptoms and outcomes of this disorder. Enhanced ROS generation by disease-causing hE3 variants as well as by the E1-E2 subcomplex of the hKGDHc likely contributes to selected pathogeneses of E3-deficiency, which could be targeted by specific drugs or antioxidants; lipoic acid was demonstrated to be a potent inhibitor of ROS generation by hE3 in vitro. Flavin supplementation might prove to be beneficial for those mutations triggering FAD loss in the hE3 component. Selected pathogenic hE3 variants lose their affinity for the E2 component of the hPDHc, a mechanism which warrants scrutiny also for other E3-haboring complexes.
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary.
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary.
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10
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Ambrus A, Wang J, Mizsei R, Zambo Z, Torocsik B, Jordan F, Adam-Vizi V. Structural alterations induced by ten disease-causing mutations of human dihydrolipoamide dehydrogenase analyzed by hydrogen/deuterium-exchange mass spectrometry: Implications for the structural basis of E3 deficiency. Biochim Biophys Acta Mol Basis Dis 2016; 1862:2098-2109. [PMID: 27544700 DOI: 10.1016/j.bbadis.2016.08.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/11/2016] [Accepted: 08/16/2016] [Indexed: 01/06/2023]
Abstract
Pathogenic amino acid substitutions of the common E3 component (hE3) of the human alpha-ketoglutarate dehydrogenase and the pyruvate dehydrogenase complexes lead to severe metabolic diseases (E3 deficiency), which usually manifest themselves in cardiological and/or neurological symptoms and often cause premature death. To date, 14 disease-causing amino acid substitutions of the hE3 component have been reported in the clinical literature. None of the pathogenic protein variants has lent itself to high-resolution structure elucidation by X-ray or NMR. Hence, the structural alterations of the hE3 protein caused by the disease-causing mutations and leading to dysfunction, including the enhanced generation of reactive oxygen species by selected disease-causing variants, could only be speculated. Here we report results of an examination of the effects on the protein structure of ten pathogenic mutations of hE3 using hydrogen/deuterium-exchange mass spectrometry (HDX-MS), a new and state-of-the-art approach of solution structure elucidation. On the basis of the results, putative structural and mechanistic conclusions were drawn regarding the molecular pathogenesis of each disease-causing hE3 mutation addressed in this study.
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary.
| | - Junjie Wang
- Department of Chemistry, Rutgers University, Newark, NJ, USA
| | - Reka Mizsei
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsofia Zambo
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary
| | - Beata Torocsik
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ, USA.
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary.
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Ambrus A, Mizsei R, Adam-Vizi V. Structural alterations by five disease-causing mutations in the low-pH conformation of human dihydrolipoamide dehydrogenase (hLADH) analyzed by molecular dynamics - Implications in functional loss and modulation of reactive oxygen species generation by pathogenic hLADH forms. Biochem Biophys Rep 2015; 2:50-56. [PMID: 29594200 PMCID: PMC5871931 DOI: 10.1016/j.bbrep.2015.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/25/2015] [Accepted: 04/27/2015] [Indexed: 01/12/2023] Open
Abstract
Human dihydrolipoamide dehydrogenase (hLADH) is a flavoenzyme component (E3) of the human alpha-ketoglutarate dehydrogenase complex (α-KGDHc) and few other dehydrogenase complexes. Pathogenic mutations of hLADH cause severe metabolic diseases (atypical forms of E3 deficiency) that often escalate to cardiological or neurological presentations and even premature death; the pathologies are generally accompanied by lactic acidosis. hLADH presents a distinct conformation under acidosis (pH 5.5–6.8) with lower physiological activity and the capacity of generating reactive oxygen species (ROS). It has been shown by our laboratory that selected pathogenic mutations, besides lowering the physiological activity of hLADH, significantly stimulate ROS generation by hLADH, especially at lower pH, which might play a role in the pathogenesis of E3-deficiency in respective cases. Previously, we generated by molecular dynamics (MD) simulation the low-pH hLADH structure and analyzed the structural changes induced in this structure by eight of the pathogenic mutations of hLADH. In the absence of high resolution mutant structures these pieces of information are crucial for the mechanistic investigation of the molecular pathogeneses of the hLADH protein. In the present work we analyzed by molecular dynamics simulation the structural changes induced in the low-pH conformation of hLADH by five pathogenic mutations of hLADH; the structures of these disease-causing mutants of hLADH have never been examined before. 5 disease-causing mutants of hLADH were subjected to MD to reveal structural changes. MD simulations were carried out both in vacuum and in water supplemented with ions. Functional regions significantly affected by mutation were identified. Implicated residues are to be targeted in mechanistic studies of hLADH dysfunction.
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Key Words
- FAD, flavin adenine dinucleotide
- LADH, (dihydro)lipoamide dehydrogenase
- Lipoamide dehydrogenase
- MD, molecular dynamics
- Molecular dynamics
- Mutation
- NAD+/NADH, nicotinamide adenine dinucleotide (oxidized/reduced)
- PDHc, pyruvate dehydrogenase complex
- RMSD, root mean square deviation
- ROS, reactive oxygen species
- Reactive oxygen species
- S.E.M., standard error of the mean
- WT, wild-type
- α-KGDHc, alpha-ketoglutarate dehydrogenase complex
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary
| | - Reka Mizsei
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary
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Conformational Change Near the Redox Center of Dihydrolipoamide Dehydrogenase Induced by NAD(+) to Regulate the Enzyme Activity. J Fluoresc 2015; 25:577-83. [PMID: 25757537 DOI: 10.1007/s10895-015-1537-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/20/2015] [Indexed: 10/23/2022]
Abstract
Dihydrolipoamide dehydrogenase (LipDH) transfers two electrons from dihydrolipoamide (DHL) to NAD(+) mediated by FAD. Since this reaction is the final step of a series of catalytic reaction of pyruvate dehydrogenase multi-enzyme complex (PDC), LipDH is a key enzyme to maintain the fluent metabolic flow. We reported here the conformational change near the redox center of LipDH induced by NAD(+) promoting the access of the DHL to FAD. The increase in the affinity of DHL to redox center was evidenced by the decrease in K M responding to the increase in the concentration of NAD(+) in Lineweaver-Burk plots. The fluorescence intensity of FAD transiently reduced by the addition of DHL was not recovered but rather reduced by the binding of NAD(+) with LipDH. The fluorescence decay lifetimes of FAD and Trp were prolonged in the presence of NAD(+) to show that FAD would be free from the electron transfer from the neighboring Tyrs and the resonance energy transfer efficiency between Trp and FAD lowered. These results consistently reveal that the conformation near the FAD and the surroundings would be so rearranged by NAD(+) to allow the easier access of DHL to the redox center of LipDH.
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Carrozzo R, Torraco A, Fiermonte G, Martinelli D, Di Nottia M, Rizza T, Vozza A, Verrigni D, Diodato D, Parisi G, Maiorana A, Rizzo C, Pierri CL, Zucano S, Piemonte F, Bertini E, Dionisi-Vici C. Riboflavin responsive mitochondrial myopathy is a new phenotype of dihydrolipoamide dehydrogenase deficiency. The chaperon-like effect of vitamin B2. Mitochondrion 2014; 18:49-57. [PMID: 25251739 DOI: 10.1016/j.mito.2014.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/15/2014] [Indexed: 11/18/2022]
Abstract
Dihydrolipoamide dehydrogenase (DLD, E3) is a flavoprotein common to pyruvate, α-ketoglutarate and branched-chain α-keto acid dehydrogenases. We found two novel DLD mutations (p.I40Lfs*4; p.G461E) in a 19 year-old patient with lactic acidosis and a complex amino- and organic aciduria consistent with DLD deficiency, manifesting progressive exertional fatigue. Muscle biopsy showed mitochondrial proliferation and lack of DLD cross-reacting material. Riboflavin supplementation determined the complete resolution of exercise intolerance with the partial restoration of the DLD protein and disappearance of mitochondrial proliferation in the muscle. Morphological and functional studies support the riboflavin chaperon-like role in stabilizing DLD protein with rescue of its expression in the muscle.
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Affiliation(s)
- Rosalba Carrozzo
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Alessandra Torraco
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giuseppe Fiermonte
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, Bari, Italy
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Di Nottia
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Rizza
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angelo Vozza
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, Bari, Italy
| | - Daniela Verrigni
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daria Diodato
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giovanni Parisi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, Bari, Italy
| | - Arianna Maiorana
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristiano Rizzo
- Department of Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, Bari, Italy
| | - Stefania Zucano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari, Via E. Orabona 4, Bari, Italy
| | - Fiorella Piemonte
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Molecular dynamics study of the structural basis of dysfunction and the modulation of reactive oxygen species generation by pathogenic mutants of human dihydrolipoamide dehydrogenase. Arch Biochem Biophys 2013; 538:145-55. [PMID: 24012808 DOI: 10.1016/j.abb.2013.08.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/09/2013] [Accepted: 08/26/2013] [Indexed: 12/15/2022]
Abstract
Human dihydrolipoamide dehydrogenase (LADH, E3) is a component in the pyruvate-, alpha-ketoglutarate- and branched-chain ketoacid dehydrogenase complexes and in the glycine cleavage system. The pathogenic mutations of LADH cause severe metabolic disturbances, called E3 deficiency that often involve cardiological and neurological symptoms and premature death. Our laboratory has recently shown that some of the known pathogenic mutations augment the reactive oxygen species (ROS) generation capacity of LADH, which may contribute to the clinical presentations. A recent report concluded that elevated oxidative stress generated by the above mutants turns the lipoic acid cofactor on the E2 subunits dysfunctional. In the present contribution we generated by molecular dynamics (MD) simulation the conformation of LADH that is proposed to be compatible with ROS generation. We propose here for the first time the structural changes, which are likely to turn the physiological LADH conformation to its ROS-generating conformation. We also created nine of the pathogenic mutants of the ROS-generating conformation and again used MD simulation to detect structural changes that the mutations induced in this LADH conformation. We propose the structural changes that may lead to the modulation in ROS generation of LADH by the pathogenic mutations.
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Quinonez SC, Leber SM, Martin DM, Thoene JG, Bedoyan JK. Leigh syndrome in a girl with a novel DLD mutation causing E3 deficiency. Pediatr Neurol 2013; 48:67-72. [PMID: 23290025 PMCID: PMC4535688 DOI: 10.1016/j.pediatrneurol.2012.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
Abstract
We present the biochemical and molecular diagnosis of dihydrolipoamide dehydrogenase deficiency (also known as E3 deficiency) and Leigh syndrome in a 14-year-old girl with learning disability and episodic encephalopathy and ketoacidosis. The diagnosis was based on values of plasma amino acids and urine organic acids, obtained during acute encephalopathy, lactic ketoacidosis, and liver failure, precipitated by infectious mononucleosis. Enzymatic and molecular analyses confirmed dihydrolipoamide dehydrogenase deficiency. E3 activity from cultured skin fibroblasts ranged from 9-29% of the mean. Molecular analysis revealed compound heterozygosity for novel and known pathogenic mutations (p.I353T and p.G136del, respectively). The patient received dietary augmentation and continuous renal replacement therapy, given her severe, persistent lactic acidosis. Acute decompensation resulted in magnetic resonance imaging changes involving the posterior aspect of the putamen, lateral, and medial thalami, substantia nigra, lateral geniculate bodies, and splenium of the corpus callosum. The cortex and subcortical white matter of the right and left occipital lobes and perirolandic region were also affected. In our review of molecularly confirmed patients with dihydrolipoamide dehydrogenase deficiency, Leigh syndrome was common. Our patient, whose most severe decompensation occurred at a more advanced age than previously reported, provides further evidence of the heterogeneous presentations of dihydrolipoamide dehydrogenase deficiency.
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Affiliation(s)
- Shane C. Quinonez
- Department of Pediatrics, Division of Genetics, The University of Michigan, Ann Arbor, Michigan
| | - Steven M. Leber
- Department of Pediatrics, Division of Neurology, The University of Michigan, Ann Arbor, Michigan
| | - Donna M. Martin
- Department of Pediatrics, Division of Genetics, The University of Michigan, Ann Arbor, Michigan,Department of Human Genetics, The University of Michigan, Ann Arbor, Michigan
| | - Jess G. Thoene
- Department of Pediatrics, Division of Genetics, The University of Michigan, Ann Arbor, Michigan
| | - Jirair K. Bedoyan
- Department of Pediatrics, Division of Genetics, The University of Michigan, Ann Arbor, Michigan,Address correspondence to and current address: Jirair K. Bedoyan, M.D., Ph.D., Center for Human Genetics, 1500 Lakeside, University Hospitals Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, or
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Kim HJ. Characterization of Two Naturally Occurring Mutations (Gly-101 Deletion and Glu-340 to Lys Substitution) in Human Dihydrolipoamide Dehydrogenase of a Patient with Metabolic Acidosis. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.8.2477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Patel KP, O’Brien TW, Subramony SH, Shuster J, Stacpoole PW. The spectrum of pyruvate dehydrogenase complex deficiency: clinical, biochemical and genetic features in 371 patients. Mol Genet Metab 2012; 106:385-94. [PMID: 22896851 PMCID: PMC4003492 DOI: 10.1016/j.ymgme.2012.03.017] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CONTEXT Pyruvate dehydrogenase complex (PDC) deficiency is a genetic mitochondrial disorder commonly associated with lactic acidosis, progressive neurological and neuromuscular degeneration and, usually, death during childhood. There has been no recent comprehensive analysis of the natural history and clinical course of this disease. OBJECTIVE We reviewed 371 cases of PDC deficiency, published between 1970 and 2010, that involved defects in subunits E1α and E1β and components E1, E2, E3 and the E3 binding protein of the complex. DATA SOURCES AND EXTRACTION English language peer-reviewed publications were identified, primarily by using PubMed and Google Scholar search engines. RESULTS Neurodevelopmental delay and hypotonia were the commonest clinical signs of PDC deficiency. Structural brain abnormalities frequently included ventriculomegaly, dysgenesis of the corpus callosum and neuroimaging findings typical of Leigh syndrome. Neither gender nor any clinical or neuroimaging feature differentiated the various biochemical etiologies of the disease. Patients who died were younger, presented clinically earlier and had higher blood lactate levels and lower residual enzyme activities than subjects who were still alive at the time of reporting. Survival bore no relationship to the underlying biochemical or genetic abnormality or to gender. CONCLUSIONS Although the clinical spectrum of PDC deficiency is broad, the dominant clinical phenotype includes presentation during the first year of life; neurological and neuromuscular degeneration; structural lesions revealed by neuroimaging; lactic acidosis and a blood lactate:pyruvate ratio ≤ 20.
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Affiliation(s)
- Kavi P. Patel
- Department of Medicine (Division of Endocrinology, Metabolism and
Diabetes), College of Medicine, University of Florida, Gainesville, FL 32611,
USA
| | - Thomas W. O’Brien
- Department of Biochemistry and Molecular Biology, College of
Medicine, University of Florida, Gainesville, FL 32611, USA
| | | | - Jonathan Shuster
- Department of Epidemiology and Health Policy Research, College of
Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Peter W. Stacpoole
- Department of Medicine (Division of Endocrinology, Metabolism and
Diabetes), College of Medicine, University of Florida, Gainesville, FL 32611,
USA
- Department of Biochemistry and Molecular Biology, College of
Medicine, University of Florida, Gainesville, FL 32611, USA
- Corresponding author at: UF College of Medicine, 1600 SW
Archer Road M2-238, P.O. Box 100226, Gainesville, FL 32610, USA. Fax: +1
352 273 9013. (P.W. Stacpoole)
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18
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Patel KP, O'Brien TW, Subramony SH, Shuster J, Stacpoole PW. The spectrum of pyruvate dehydrogenase complex deficiency: clinical, biochemical and genetic features in 371 patients. Mol Genet Metab 2012; 105:34-43. [PMID: 22079328 PMCID: PMC3754811 DOI: 10.1016/j.ymgme.2011.09.032] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 01/01/2023]
Abstract
CONTEXT Pyruvate dehydrogenase complex (PDC) deficiency is a genetic mitochondrial disorder commonly associated with lactic acidosis, progressive neurological and neuromuscular degeneration and, usually, death during childhood. There has been no recent comprehensive analysis of the natural history and clinical course of this disease. OBJECTIVE We reviewed 371 cases of PDC deficiency, published between 1970 and 2010, that involved defects in subunits E1α and E1β and components E1, E2, E3 and the E3 binding protein of the complex. DATA SOURCES AND EXTRACTION English language peer-reviewed publications were identified, primarily by using PubMed and Google Scholar search engines. RESULTS Neurodevelopmental delay and hypotonia were the commonest clinical signs of PDC deficiency. Structural brain abnormalities frequently included ventriculomegaly, dysgenesis of the corpus callosum and neuroimaging findings typical of Leigh syndrome. Neither gender nor any clinical or neuroimaging feature differentiated the various biochemical etiologies of the disease. Patients who died were younger, presented clinically earlier and had higher blood lactate levels and lower residual enzyme activities than subjects who were still alive at the time of reporting. Survival bore no relationship to the underlying biochemical or genetic abnormality or to gender. CONCLUSIONS Although the clinical spectrum of PDC deficiency is broad, the dominant clinical phenotype includes presentation during the first year of life; neurological and neuromuscular degeneration; structural lesions revealed by neuroimaging; lactic acidosis and a blood lactate:pyruvate ratio ≤20.
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Affiliation(s)
- Kavi P. Patel
- Department of Medicine (Division of Endocrinology and Metabolism), College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas W. O'Brien
- Department of Biochemistry and Molecular Biology College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | | | - Jonathan Shuster
- Epidemiology and Health Policy Research College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W. Stacpoole
- Department of Medicine (Division of Endocrinology and Metabolism), College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology College of Medicine, University of Florida, Gainesville, FL, 32611, USA
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Vaubel RA, Rustin P, Isaya G. Mutations in the dimer interface of dihydrolipoamide dehydrogenase promote site-specific oxidative damages in yeast and human cells. J Biol Chem 2011; 286:40232-45. [PMID: 21930696 PMCID: PMC3220568 DOI: 10.1074/jbc.m111.274415] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 09/13/2011] [Indexed: 12/31/2022] Open
Abstract
Dihydrolipoamide dehydrogenase (DLD) is a multifunctional protein well characterized as the E3 component of the pyruvate dehydrogenase and α-ketoglutarate dehydrogenase complexes. Previously, conditions predicted to destabilize the DLD dimer revealed that DLD could also function as a diaphorase and serine protease. However, the relevance of these cryptic activities remained undefined. We analyzed human DLD mutations linked to strikingly different clinical phenotypes, including E340K, D444V, R447G, and R460G in the dimer interface domain that are responsible for severe multisystem disorders of infancy and G194C in the NAD(+)-binding domain that is typically associated with milder presentations. In vitro, all of these mutations decreased to various degrees dihydrolipoamide dehydrogenase activity, whereas dimer interface mutations also enhanced proteolytic and/or diaphorase activity. Human DLD proteins carrying each individual mutation complemented fully the respiratory-deficient phenotype of yeast cells lacking endogenous DLD even when residual dihydrolipoamide dehydrogenase activity was as low as 21% of controls. However, under elevated oxidative stress, expression of DLD proteins with dimer interface mutations greatly accelerated the loss of respiratory function, resulting from enhanced oxidative damage to the lipoic acid cofactor of pyruvate dehydrogenase and α-ketoglutarate dehydrogenase and other mitochondrial targets. This effect was not observed with the G194C mutation or a mutation that disrupts the proteolytic active site of DLD. As in yeast, lipoic acid cofactor was damaged in human D444V-homozygous fibroblasts after exposure to oxidative stress. We conclude that the cryptic activities of DLD promote oxidative damage to neighboring molecules and thus contribute to the clinical severity of DLD mutations.
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Affiliation(s)
- Rachael A. Vaubel
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester Minnesota 55905
| | - Pierre Rustin
- INSERM U676 Hôpital Robert Debré, F-75019 Paris, France, and
- Université Paris 7, Faculté de Médecine Denis Diderot, IFR02 Paris, France
| | - Grazia Isaya
- From the Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester Minnesota 55905
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Ambrus A, Torocsik B, Tretter L, Ozohanics O, Adam-Vizi V. Stimulation of reactive oxygen species generation by disease-causing mutations of lipoamide dehydrogenase. Hum Mol Genet 2011; 20:2984-95. [PMID: 21558426 DOI: 10.1093/hmg/ddr202] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We investigated pathogenic mutations relevant in dihydrolipoamide dehydrogenase (LADH; gene: Dld) deficiency, a severe human disease, to elucidate how they alter reactive oxygen species (ROS) generation and associated biophysical characteristics of LADH. Twelve known disease-causing mutants of human LADH have been expressed and purified to homogeneity from E. coli. Detailed biophysical and biochemical characterization of the mutants has been performed applying circular dichroism (CD) spectroscopy, nano-spray mass spectrometry (MS), calibrated gel filtration and flavin adenine dinucleotide-content analysis. Functional analyses revealed that four of the pathogenic mutations significantly stimulated the ROS-generating activity of LADH and also increased its sensitivity to an acidic shift in pH. LADH activity was reduced by variable extents in the mutants exhibiting excessive ROS generation. It is remarkable that in the P453L mutant, enzyme activity was nearly completely lost with a ROS-forming activity becoming dominant, whereas the G194C mutation, common among Ashkenazi Jews, resulted in no alteration in LADH activity but a gain in the ROS-generating activity. There have been neither major conformational alterations nor monomerization of the functional homodimer of LADH associated with the higher ROS-generating capacity as measured by CD spectroscopy and size-exclusion chromatography combined with nano-spray MS, respectively. The excessive ROS generation of selected LADH mutants could be an important factor in the pathology and clinical presentation of human LADH deficiency and raises the possibility of an antioxidant therapy in the treatment of this condition.
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, Semmelweis University, Neurobiochemical Group of Hungarian Academy of Sciences, Budapest, 1094, Hungary
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Quintana E, Pineda M, Font A, Vilaseca MA, Tort F, Ribes A, Briones P. Dihydrolipoamide dehydrogenase (DLD) deficiency in a Spanish patient with myopathic presentation due to a new mutation in the interface domain. J Inherit Metab Dis 2010; 33 Suppl 3:S315-9. [PMID: 20652410 DOI: 10.1007/s10545-010-9169-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 06/30/2010] [Accepted: 07/01/2010] [Indexed: 11/29/2022]
Abstract
We present a 32-year-old patient who, from age 7 months, developed photophobia, left-eye ptosis and progressive muscular weakness. At age 7 years, she showed normal psychomotor development, bilateral ptosis and exercise-induced weakness with severe acidosis. Basal blood and urine lactate were normal, increasing dramatically after effort. PDHc deficiency was demonstrated in muscle and fibroblasts without detectable PDHA1 mutations. Ketogenic diet was ineffective, however thiamine gave good response although bilateral ptosis and weakness with acidosis on exercise persisted. Recently, DLD gene analysis revealed a homozygous missense mutation, c.1440 A>G (p.I480M), in the interface domain. Both parents are heterozygous and DLD activity in the patient's fibroblasts is undetectable. The five patients that have been reported with DLD-interface mutations suffered fatal deteriorations. Our patient's disease is milder, only myopathic, more similar to that due to mutation p.G229C in the NAD(+)-binding domain. Two of the five patients presented mutations (p.D479V and p.R482G) very close to the present case (p.I480M). Despite differing degrees of clinical severity, all three had minimal clues to DLD deficiency, with occasional minor increases in α-ketoglutarate and branched-chain amino acids. In the two other patients, hypertrophic cardiomyopathy was a significant feature that has been attributed to moonlighting proteolytic activity of monomeric DLD, which can degrade other mitochondrial proteins, such as frataxin. Our patient does not have cardiomyopathy, suggesting that p.I480M may not affect the DLD ability to dimerize to the same extent as p.D479V and p.R482G. Our patient, with a novel mutation in the DLD interface and mild clinical symptoms, further broadens the spectrum of this enzyme defect.
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Affiliation(s)
- Ester Quintana
- Sección de Errores Congénitos del Metabolismo, Servicio de Bioquímica y Genética Molecular, Hospital Clínic, Instituto de Bioquímica Clínica, Barcelona, Spain
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Quintana E, Gort L, Busquets C, Navarro-Sastre A, Lissens W, Moliner S, Lluch M, Vilaseca MA, De Meirleir L, Ribes A, Briones P. Mutational study in thePDHA1gene of 40 patients suspected of pyruvate dehydrogenase complex deficiency. Clin Genet 2010; 77:474-82. [DOI: 10.1111/j.1399-0004.2009.01313.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Cloning and purification of recombinant silkworm dihydrolipoamide dehydrogenase expressed in Escherichia coli. Protein Expr Purif 2010; 72:95-100. [PMID: 20093189 DOI: 10.1016/j.pep.2010.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 11/20/2022]
Abstract
Dihydrolipoamide dehydrogenase (DLDH), a flavin-dependent oxidoreductase is essential for energy metabolism. As an oxidoreductase it catalyzes the NAD(+)-dependent oxidation of dihydrolipoamide. In this study, a putative Bombyx mori dihydrolipoamide dehydrogenase (BmDLDH) gene was cloned, expressed, purified and characterized for the first time. The BmDLDH gene was amplified from a pool of silkworm cDNAs by PCR and cloned into Escherichia coli expression vector pET-28a(+). The recombinant His-tagged BmDLDH protein was expressed in E. coli BL21 (DE3) and purified by metal chelating affinity chromatography. The amino acid sequence of recombinant protein was confirmed by mass spectroscopic analysis. Furthermore, the oxidoreductase activity in the reverse reaction indicated that the soluble recombinant BmDLDH produced at lower growth temperature was able to catalyze the lipoamide-dependent oxidation of NADH.
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Interaction of E1 and E3 components with the core proteins of the human pyruvate dehydrogenase complex. ACTA ACUST UNITED AC 2009; 61:2-6. [PMID: 20160912 DOI: 10.1016/j.molcatb.2009.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human (h) pyruvate dehydrogenase complex (hPDC) consists of multiple copies of several components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), dihydrolipoamide dehydrogenase (E3), E3-binding protein (BP), and specific kinases and phosphatases. Mammalian PDC has a well organized structure with an icosahedral symmetry of the central E2/BP core to which the other component proteins bind non-covalently. Both hE2 and hBP consist of three well defined domains, namely the lipoyl domain, the subunit-binding domain and the inner domain, connected with flexible linkers. hE1 (alpha(2)beta(2)) binds to the subunit-binding domain of hE2; whereas hE3 binds to the E3-binding domain of hBP. Among several residues of the C-terminal surface of the hE1beta E1betaD289 was found to interact with hE2K276. The C-terminal residue I329 of the hE1beta did not participate in binding to hE2. This latter finding shows specificity in the interaction between E1beta and E2 in hPDC. The selective binding between hE3 and the E3-binding domain of hBP was investigated using specific mutants. E3R460G and E3340K showed significant reductions in affinity for hBP as determined by surface plasmon resonance. Both residues are involved in the structural organization of the binding site on hE3. Substitution of I157, N137 and R155 of hBP resulted in variable increases in the K(D) for binding with wild-type hE3, suggesting that the binding results from several weak electrostatic bonds and hydrophobic interactions among residues of hBP with residues at the interface of dimeric hE3. These results provide insight in the mono-specificity of binding of E1 to E2 and E3 to BP in hPDC and showed the differences in the binding of peripheral components (E1 and E3) in human and bacterial PDCs.
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TAT-mediated Delivery of LAD Restores Pyruvate Dehydrogenase Complex Activity in the Mitochondria of Patients with LAD Deficiency. Mol Ther 2008; 16:691-7. [DOI: 10.1038/mt.2008.4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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26
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Rapoport M, Saada A, Elpeleg O, Lorberboum-Galski H. TAT-mediated Delivery of LAD Restores Pyruvate Dehydrogenase Complex Activity in the Mitochondria of Patients with LAD Deficiency. Mol Ther 2008. [DOI: 10.1038/sj.mt.6300410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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27
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Wang YC, Wang ST, Li C, Chen LY, Liu WH, Chen PR, Chou MC, Liu TC. The role of amino acids T148 and R281 in human dihydrolipoamide dehydrogenase. J Biomed Sci 2007; 15:37-46. [PMID: 17960497 DOI: 10.1007/s11373-007-9208-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/20/2007] [Indexed: 11/25/2022] Open
Abstract
Human dihydrolipoamide dehydrogenase (hE3) is a common component of alpha-ketoacid dehydrogenase complexes. Mutations of this homodimeric protein cause E3 deficiency and are always fatal. To investigate its reaction mechanism, we first performed multiple sequence alignment with other 17 eukaryotic E3s. According to hE3 structure and the result of multiple sequence alignment, two amino acids, T148 and R281, were subjected to mutagenesis and four hE3 mutants, T148G, T148S, R281N, and R281K, were expressed and assayed. The specific activities of T148G, T148S, R281N, and R281K are 76.34%, 88.62%, 12.50%, and 11.93% to that of wild-type E3, respectively. The FAD content analysis indicated that the FAD content of these mutant E3s were about 71.0%, 92%, 96%, and 93% that of wild-type E3, respectively. The molecular weight analysis showed that these three mutant proteins form the dimer. Kinetic data demonstrated that the K(cat) of forward reaction of all mutants, except T148 mutants, were decreased dramatically. The results of kinetic study suggest that T148 is not important to E3 catalytic function and R281 play a role in the catalytic function of the E3.
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Affiliation(s)
- Yi-Chun Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan, ROC
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28
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Brown AM, Gordon D, Lee H, Wavrant-De Vrièze F, Cellini E, Bagnoli S, Nacmias B, Sorbi S, Hardy J, Blass JP. Testing for linkage and association across the dihydrolipoyl dehydrogenase gene region with Alzheimer's disease in three sample populations. Neurochem Res 2007; 32:857-69. [PMID: 17342416 DOI: 10.1007/s11064-006-9235-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 11/20/2006] [Indexed: 12/01/2022]
Abstract
Prior case-control studies from our laboratory of a population enriched with individuals of Ashkenazi Jewish descent suggested that association exists between Alzheimer's disease (AD) and the chromosomal region near the DLD gene, which encodes the mitochondrial dihydrolipoamide dehydrogenase enzyme. In support of this finding, we found that linkage analysis restricted to autopsy-proven patients in the National Institute of Mental Health-National Cell Repository for Alzheimer's Disease (NIMH-NCRAD) Genetics Initiative pedigree data resulted in point-wise significant evidence for linkage (minimum p-value = 0.024) for a marker position close to the DLD locus. We now report case-control replication studies in two independent Caucasian series from the US and Italy, as well as a linkage analysis from the NIMH-NCRAD Genetics Initiative Database. Pair-wise analysis of the SNPs in the case-control series indicated there was strong linkage disequilibrium across the DLD locus in these populations, as previously reported. These findings suggest that testing for association of complex diseases with DLD locus should have considerable statistical power. Analysis of multi-locus genotypes or haplotypes based upon three SNP loci combined with results from our previous report provided trends toward significant evidence of association of DLD with AD, although neither of the present studies' association showed significance at the 0.05 level. Combining linkage and association findings for all AD patients (males and females) results in a p-value that is more significant than any of the individual findings' p-values. Finally, minimum sample size calculations using parameters from the DLD locus suggest that sample sizes on the order of 1,000 total cases and controls are needed to detect association for a wide range of genetic model parameters.
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Affiliation(s)
- Abraham M Brown
- Burke Medical Research Institute, 785 Mamaroneck Avenue, White Plains, NY 10605, USA
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29
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Cameron JM, Levandovskiy V, Mackay N, Raiman J, Renaud DL, Clarke JTR, Feigenbaum A, Elpeleg O, Robinson BH. Novel mutations in dihydrolipoamide dehydrogenase deficiency in two cousins with borderline-normal PDH complex activity. Am J Med Genet A 2006; 140:1542-52. [PMID: 16770810 DOI: 10.1002/ajmg.a.31313] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We have diagnosed dihydrolipoamide dehydrogenase (DLD) deficiency in two male second cousins, who presented with markedly different clinical phenotypes. Patient 1 had a recurrent encephalopathy, and patient 2 had microcephaly and lactic acidosis. Their presentation is unusual, in that the DLD subunit deficiency had little effect on pyruvate dehydrogenase complex activity, but caused a severe reduction in the activities of other enzymes that utilize this subunit. We have identified two mutations in the DLD gene in each patient. The second cousins have one novel mutation in common resulting in a substitution of isoleucine for threonine (I47T), which has not been previously reported in the literature. Patient 1 has a second mutation that has been reported to be common in the Ashkenazi Jewish population, G229C. Patient 2 has a second mutation, E375K, which has also been previously reported in the literature. Enzyme kinetic measurements on patient fibroblasts show that under certain conditions, one heteroallelic mutation may have a higher K(m). This may account for the differing clinical phenotypes. These findings have important repercussions for other patients with similar clinical phenotypes, as DLD activity is not normally measured in cases with normal PDHc activity.
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Affiliation(s)
- Jessie M Cameron
- Metabolism Research Programme, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
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30
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Fedotcheva NI, Sokolov AP, Kondrashova MN. Nonezymatic formation of succinate in mitochondria under oxidative stress. Free Radic Biol Med 2006; 41:56-64. [PMID: 16781453 DOI: 10.1016/j.freeradbiomed.2006.02.012] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 02/03/2006] [Accepted: 02/18/2006] [Indexed: 11/26/2022]
Abstract
The products of the reactions of mitochondrial 2-oxo acids with hydrogen peroxide and tert-butyl hydroperoxide (tert-BuOOH) were studied in a chemical system and in rat liver mitochondria. It was found by HPLC that the decarboxylation of alpha-ketoglutarate (KGL), pyruvate (PYR), and oxaloacetate (OA) by both oxidants results in the formation of succinate, acetate, and malonate, respectively. The two latter products do not metabolize in rat liver mitochondria, whereas succinate is actively oxidized, and its nonenzymatic formation from KGL may shunt the tricarboxylic acid (TCA) cycle upon inactivation of alpha-ketoglutarate dehydrogenase (KGDH) under oxidative stress, which is inherent in many diseases and aging. The occurrence of nonenzymatic oxidation of KGL in mitochondria was established by an increase in the CO(2) and succinate levels in the presence of the oxidants and inhibitors of enzymatic oxidation. H(2)O(2) and menadione as an inductor of reactive oxygen species (ROS) caused the formation of CO(2) in the presence of sodium azide and the production of succinate, fumarate, and malate in the presence of rotenone. These substrates were also formed from KGL when mitochondria were incubated with tert-BuOOH at concentrations that completely inhibit KGDH. The nonenzymatic oxidation of KGL can support the TCA cycle under oxidative stress, provided that KGL is supplied via transamination. This is supported by the finding that the strong oxidant such as tert-BuOOH did not impair respiration and its sensitivity to the transaminase inhibitor aminooxyacetate when glutamate and malate were used as substrates. The appearance of two products, KGL and fumarate, also favors the involvement of transamination. Thus, upon oxidative stress, nonenzymatic decarboxylation of KGL and transamination switch the TCA cycle to the formation and oxidation of succinate.
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Affiliation(s)
- Nadezhda I Fedotcheva
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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31
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Brautigam CA, Wynn RM, Chuang JL, Machius M, Tomchick DR, Chuang DT. Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex. Structure 2006; 14:611-21. [PMID: 16442803 PMCID: PMC2879633 DOI: 10.1016/j.str.2006.01.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 01/04/2006] [Accepted: 01/06/2006] [Indexed: 11/17/2022]
Abstract
The 9.5 MDa human pyruvate dehydrogenase complex (PDC) utilizes the specific dihydrolipoamide dehydrogenase (E3) binding protein (E3BP) to tether the essential E3 component to the 60-meric core of the complex. Here, we report crystal structures of the binding domain (E3BD) of human E3BP alone and in complex with human E3 at 1.6 angstroms and 2.2 angstroms, respectively. The latter structure shows that residues from E3BD contact E3 across its 2-fold axis, resulting in one E3BD binding site on the E3 homodimer. Negligible conformational changes occur in E3BD upon its high-affinity binding to E3. Modifications of E3BD residues at the center of the E3BD/E3 interface impede E3 binding far more severely than those of residues on the periphery, validating the "hot spot" paradigm for protein interactions. A cluster of disease-causing E3 mutations located near the center of the E3BD/E3 interface prevents the efficient recruitment of these E3 variants by E3BP into the PDC, leading to the dysfunction of the PDC catalytic machine.
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Affiliation(s)
- Chad A. Brautigam
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Corresponding authors: ,
| | - R. Max Wynn
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Department of Internal Medicine, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Jacinta L. Chuang
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Mischa Machius
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Diana R. Tomchick
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - David T. Chuang
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Department of Internal Medicine, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
- Corresponding authors: ,
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32
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Brautigam CA, Chuang JL, Tomchick DR, Machius M, Chuang DT. Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations. J Mol Biol 2005; 350:543-52. [PMID: 15946682 DOI: 10.1016/j.jmb.2005.05.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 05/02/2005] [Accepted: 05/06/2005] [Indexed: 01/08/2023]
Abstract
Human dihydrolipoamide dehydrogenase (hE3) is an enzymatic component common to the mitochondrial alpha-ketoacid dehydrogenase and glycine decarboxylase complexes. Mutations to this homodimeric flavoprotein cause the often-fatal human disease known as E3 deficiency. To catalyze the oxidation of dihydrolipoamide, hE3 uses two molecules: non-covalently bound FAD and a transiently bound substrate, NAD+. To address the catalytic mechanism of hE3 and the structural basis for E3 deficiency, the crystal structures of hE3 in the presence of NAD+ or NADH have been determined at resolutions of 2.5A and 2.1A, respectively. Although the overall fold of the enzyme is similar to that of yeast E3, these two structures differ at two loops that protrude from the proteins and at their FAD-binding sites. The structure of oxidized hE3 with NAD+ bound demonstrates that the nicotinamide moiety is not proximal to the FAD. When NADH is present, however, the nicotinamide base stacks directly on the isoalloxazine ring system of the FAD. This is the first time that this mechanistically requisite conformation of NAD+ or NADH has been observed in E3 from any species. Because E3 structures were previously available only from unicellular organisms, speculations regarding the molecular mechanisms of E3 deficiency were based on homology models. The current hE3 structures show directly that the disease-causing mutations occur at three locations in the human enzyme: the dimer interface, the active site, and the FAD and NAD(+)-binding sites. The mechanisms by which these mutations impede the function of hE3 are discussed.
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Affiliation(s)
- Chad A Brautigam
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.
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33
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Brown AM, Gordon D, Lee H, Caudy M, Hardy J, Haroutunian V, Blass JP. Association of the dihydrolipoamide dehydrogenase gene with Alzheimer's disease in an Ashkenazi Jewish population. Am J Med Genet B Neuropsychiatr Genet 2004; 131B:60-6. [PMID: 15389771 DOI: 10.1002/ajmg.b.30008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abundant biochemical evidence links deficient activity of mitochondrial alpha-ketoglutarate dehydrogenase with neuropathologically confirmed Alzheimer's disease (AD). Reduced alpha-ketoglutarate dehydrogenase activity has also been associated with anti-mortem measures of clinical disability. One of the genes encoding this complex, namely, DLD, lies within a chromosome 7 region that is in linkage disequilibrium with AD. We therefore examined the hypothesis that variation in DLD is associated with AD risk. Denaturing HPLC was used to search for sequence variations in the coding and flanking regions of all exons of DLD, but no abundant variants that alter protein sequence were found. However, four common SNPs were identified and genotyped in a case-control series of 297 Caucasians from New York City, including 229 residents of a Jewish nursing home. Logistic regression analysis was performed for the four-locus DLD genotype, sex, and ApoE4 status to determine the association of these independent variables with AD. Significant associations with AD were observed for ApoE4 (P < 10(-6)) and sex combined with DLD genotype (P = 0.013). The association with the DLD genotypes appears only in the male population in both the Caucasian series (P = 0.0009, n = 83) and the Ashkenazi Jewish subseries (P = 0.017, n = 49). The DLD genotype appears to operate independently of APOE in conferring AD risk.
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Affiliation(s)
- Abraham M Brown
- Dementia Research Service, Burke Medical Research Institute, 785 Mamaroneck Ave, White Plains, New York 10605, USA.
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34
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Ames BN, Elson-Schwab I, Silver EA. High-dose vitamin therapy stimulates variant enzymes with decreased coenzyme binding affinity (increased K(m)): relevance to genetic disease and polymorphisms. Am J Clin Nutr 2002; 75:616-58. [PMID: 11916749 DOI: 10.1093/ajcn/75.4.616] [Citation(s) in RCA: 218] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
As many as one-third of mutations in a gene result in the corresponding enzyme having an increased Michaelis constant, or K(m), (decreased binding affinity) for a coenzyme, resulting in a lower rate of reaction. About 50 human genetic dis-eases due to defective enzymes can be remedied or ameliorated by the administration of high doses of the vitamin component of the corresponding coenzyme, which at least partially restores enzymatic activity. Several single-nucleotide polymorphisms, in which the variant amino acid reduces coenzyme binding and thus enzymatic activity, are likely to be remediable by raising cellular concentrations of the cofactor through high-dose vitamin therapy. Some examples include the alanine-to-valine substitution at codon 222 (Ala222-->Val) [DNA: C-to-T substitution at nucleo-tide 677 (677C-->T)] in methylenetetrahydrofolate reductase (NADPH) and the cofactor FAD (in relation to cardiovascular disease, migraines, and rages), the Pro187-->Ser (DNA: 609C-->T) mutation in NAD(P):quinone oxidoreductase 1 [NAD(P)H dehy-drogenase (quinone)] and FAD (in relation to cancer), the Ala44-->Gly (DNA: 131C-->G) mutation in glucose-6-phosphate 1-dehydrogenase and NADP (in relation to favism and hemolytic anemia), and the Glu487-->Lys mutation (present in one-half of Asians) in aldehyde dehydrogenase (NAD + ) and NAD (in relation to alcohol intolerance, Alzheimer disease, and cancer).
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Affiliation(s)
- Bruce N Ames
- Department of Molecular and Cellular Biology, University of California, Berkeley, USA.
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35
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Patel MS, Hong YS, Kerr DS. Genetic defects in E3 component of alpha-keto acid dehydrogenase complexes. Methods Enzymol 2001; 324:453-64. [PMID: 10989452 DOI: 10.1016/s0076-6879(00)24253-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- M S Patel
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York, Buffalo 14214, USA
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36
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Saada A, Aptowitzer I, Link G, Elpeleg ON. ATP synthesis in lipoamide dehydrogenase deficiency. Biochem Biophys Res Commun 2000; 269:382-6. [PMID: 10708561 DOI: 10.1006/bbrc.2000.2310] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lipoamide dehydrogenase deficiency is an inborn error of several metabolic pathways, including pyruvate metabolism, Krebs cycle, and branched-chain amino acid degradation. The clinical course is variable, ranging from infantile neurodegenerative disease to recurrent episodes of liver failure or myoglobinuria starting later in life. In contrast, residual enzymatic activity in muscle tissue spans over a narrow range. Despite the recent elucidation of the underlying molecular pathology in most patients, relationships between the genotype and the biochemical and clinical phenotype remain unclear. In order to find a suitable assay for the prediction of clinical outcome and assessment of treatment, we have evaluated enzymatic activities and energetic states in fibroblasts from lipoamide dehydrogenase-deficient patients representing three different phenotypes and genotypes. Direct relationships between clinical parameters such as age of onset and disease severity and biochemical characteristics, including lipoamide dehydrogenase activity, pyruvate dehydrogenase complex activity, and ATP production ratio in fibroblasts, were identified. Clinical parameters were not reflected by lactate/pyruvate ratio. ATP production rate was in direct relationship with the severity of the neurological involvement; the patient with reduced ATP synthesis to 30% of the control mean had a severe neurodegenerative disease, whereas ATP synthesis values above 45% were associated with a more favorable course. Incubation of the patients' fibroblasts with dichloroacetate coupled with thiamin resulted in slight but significant improvement of the cell energetic state.
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Affiliation(s)
- A Saada
- Metabolic Disease Unit, Shaare-Zedek Medical Center, Jerusalem, 91031, Israel
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37
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Gibson GE, Park LC, Sheu KF, Blass JP, Calingasan NY. The alpha-ketoglutarate dehydrogenase complex in neurodegeneration. Neurochem Int 2000; 36:97-112. [PMID: 10676873 DOI: 10.1016/s0197-0186(99)00114-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Altered energy metabolism is characteristic of many neurodegenerative disorders. Reductions in the key mitochondrial enzyme complex, the alpha-ketoglutarate dehydrogenase complex (KGDHC), occur in a number of neurodegenerative disorders including Alzheimer's Disease (AD). The reductions in KGDHC activity may be responsible for the decreases in brain metabolism, which occur in these disorders. KGDHC can be inactivated by several mechanisms, including the actions of free radicals (Reactive Oxygen Species, ROS). Other studies have associated specific forms of one of the genes encoding KGDHC (namely the DLST gene) with AD, Parkinson's disease, as well as other neurodegenerative diseases. Reductions in KGDHC activity can be plausibly linked to several aspects of brain dysfunction and neuropathology in a number of neurodegenerative diseases. Further studies are needed to assess mechanisms underlying the sensitivity of KGDHC to oxidative stress and the relation of KGDHC deficiency to selective vulnerability in neurodegenerative diseases.
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Affiliation(s)
- G E Gibson
- Department of Neurology and Neuroscience, Weill Medical College of Cornell University, Burke Medical Research Institute, White Plains, NY 10605, USA.
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38
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Rouillac C, Aral B, Fouque F, Marchant D, Saudubray JM, Dumez Y, Lindsay G, Abitbol M, Dufier JL, Marsac C, Benelli C. First prenatal diagnosis of defects in the HsPDX1 gene encoding protein X, an additional lipoyl-containing subunit of the human pyruvate dehydrogenase complex. Prenat Diagn 1999; 19:1160-4. [PMID: 10590436 DOI: 10.1002/(sici)1097-0223(199912)19:12<1160::aid-pd712>3.0.co;2-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have previously reported a genetic study of a neonatal lactic acidosis linked to a pyruvate dehydrogenase complex deficiency due to the absence of the protein X subunit. This rare autosomal recessive disorder is associated with specific deletions in this polypeptide which is encoded by the HsPDX1 gene, located on chromosome 11p1.3. The pathology of the patient was considered to arise from a large homozygous deletion (78del85) found at the 5' end of the HsPDX1 coding sequence. Her heterozygous mother underwent prenatal diagnosis during a subsequent pregnancy. Chorionic villus samples were used for three independent studies: (1) normal levels of the protein X component of the PDH complex were detected by immunoblotting; (2) RT-PCR analysis showed no deletion at the 5' end of the cDNA but the presence of a distinct heterozygous deletion (965del59) at its 3' end inherited from the father; (3) haplotype analysis revealed the presence of the father's mutated allele and the mother's normal allele. It was concluded that the fetus was heterozygous for this separate 3' deletion, so, it was likely to be not affected. This study permitted us to characterize more precisely the genetic abnormalities of the HsPDX1 cDNA occurring in each family's member.
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Affiliation(s)
- C Rouillac
- Centre de Recherches Thérapeutiques en Ophtalmologie (CERTO), Faculté de Médecine Necker, Paris, France
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39
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Shany E, Saada A, Landau D, Shaag A, Hershkovitz E, Elpeleg ON. Lipoamide dehydrogenase deficiency due to a novel mutation in the interface domain. Biochem Biophys Res Commun 1999; 262:163-6. [PMID: 10448086 DOI: 10.1006/bbrc.1999.1133] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An infant with a neurodegenerative disorder accompanied by lactic acidemia is described. In muscle homogenate, the activity of lipoamide dehydrogenase (LAD), the third catalytic subunit of pyruvate dehydrogenase complex (PDHc), alpha-ketoglutarate dehydrogenase complex (KGDHc), and branched-chain keto acid dehydrogenase complex was reduced to 15% of the control. The activity of PDHc was undetectable and the activity of KGDHc was 2% of the control mean. The immunoreactive LAD protein was reduced to about 10% of the control. Direct sequencing of LAD cDNA revealed only one mutation, substituting Asp for Val at position 479 of the precursor form. The mutation resides within the interface domain and likely perturbs stable dimerization. The phenotypic heterogeneity in LAD deficiency is not directly correlated with the residual LAD activity but rather with its impact on the multienzymatic complex activity.
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Affiliation(s)
- E Shany
- Neonatology and Pediatric Departments, Soroka Medical Center, Beer-Sheva, Israel
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