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Nechushtai R, Rowland L, Karmi O, Marjault HB, Nguyen TT, Mittal S, Ahmed RS, Grant D, Manrique-Acevedo C, Morcos F, Onuchic JN, Mittler R. CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proc Natl Acad Sci U S A 2024; 121:e2405123121. [PMID: 38781208 PMCID: PMC11145280 DOI: 10.1073/pnas.2405123121] [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: 03/12/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria play a central role in muscle metabolism and function. A unique family of iron-sulfur proteins, termed CDGSH Iron Sulfur Domain-containing (CISD/NEET) proteins, support mitochondrial function in skeletal muscles. The abundance of these proteins declines during aging leading to muscle degeneration. Although the function of the outer mitochondrial CISD/NEET proteins, CISD1/mitoNEET and CISD2/NAF-1, has been defined in skeletal muscle cells, the role of the inner mitochondrial CISD protein, CISD3/MiNT, is currently unknown. Here, we show that CISD3 deficiency in mice results in muscle atrophy that shares proteomic features with Duchenne muscular dystrophy. We further reveal that CISD3 deficiency impairs the function and structure of skeletal muscles, as well as their mitochondria, and that CISD3 interacts with, and donates its [2Fe-2S] clusters to, complex I respiratory chain subunit NADH Ubiquinone Oxidoreductase Core Subunit V2 (NDUFV2). Using coevolutionary and structural computational tools, we model a CISD3-NDUFV2 complex with proximal coevolving residue interactions conducive of [2Fe-2S] cluster transfer reactions, placing the clusters of the two proteins 10 to 16 Å apart. Taken together, our findings reveal that CISD3/MiNT is important for supporting the biogenesis and function of complex I, essential for muscle maintenance and function. Interventions that target CISD3 could therefore impact different muscle degeneration syndromes, aging, and related conditions.
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Affiliation(s)
- Rachel Nechushtai
- Plant & Environmental Sciences, The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
| | - Linda Rowland
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Ola Karmi
- Plant & Environmental Sciences, The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
| | - Henri-Baptiste Marjault
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Thi Thao Nguyen
- Gehrke Proteomics Center, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211
| | - Shubham Mittal
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
| | - Raheel S. Ahmed
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
| | - DeAna Grant
- Electron Microscopy Core Facility, University of Missouri, NextGen Precision Health Institute, Columbia, MO65211
| | - Camila Manrique-Acevedo
- Division of Endocrinology and Metabolism, Department of Medicine, University of Missouri, Columbia, MO 65201
- NextGen Precision Health, University of Missouri, Columbia, MO 65201
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX75080
- Department of Physics, University of Texas at Dallas, Richardson, TX75080
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX75080
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Physics and Astronomy, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Biosciences, Rice University, Houston, TX77005
| | - Ron Mittler
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
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Maghsoud Y, Roy A, Leddin EM, Cisneros GA. Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ. J Chem Inf Model 2024; 64:4231-4249. [PMID: 38717969 PMCID: PMC11181361 DOI: 10.1021/acs.jcim.4c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
Human DNA polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy, which ensures the fidelity and stability of the human genomic blueprint. Several disease-associated mutations and their functional impact on DNA polymerases have been reported. One particular polymerase, human DNA polymerase kappa (Pol κ), has been reported to be susceptible to several cancer-associated mutations. The Y432S mutation in Pol κ, associated with various cancers, is of interest due to its impact on polymerization activity and markedly reduced thermal stability. Here, we have used computational simulations to investigate the functional consequences of the Y432S using classical molecular dynamics (MD) and coupled quantum mechanics/molecular mechanics (QM/MM) methods. Our findings suggest that Y432S induces structural alterations in domains responsible for nucleotide addition and ternary complex stabilization while retaining structural features consistent with possible catalysis in the active site. Calculations of the minimum energy path associated with the reaction mechanism of the wild type (WT) and Y432S Pol κ indicate that, while both enzymes are catalytically competent (in terms of energetics and the active site's geometries), the cancer mutation results in an endoergic reaction and an increase in the catalytic barrier. Interactions with a third magnesium ion and environmental effects on nonbonded interactions, particularly involving key residues, contribute to the kinetic and thermodynamic distinctions between the WT and mutant during the catalytic reaction. The energetics and electronic findings suggest that active site residues favor the catalytic reaction with dCTP3- over dCTP4-.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Arkanil Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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Park J, Herrmann GK, Roy A, Shumate CK, Cisneros GA, Yin YW. An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ. SCIENCE ADVANCES 2024; 10:eadl3214. [PMID: 38787958 PMCID: PMC11122685 DOI: 10.1126/sciadv.adl3214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.
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Affiliation(s)
- Joon Park
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Geoffrey K. Herrmann
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Arkanil Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Christie K. Shumate
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - G. Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Physics, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
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Mills KR, Misra J, Torabifard H. Allosteric Modulation of the YAP/TAZ-TEAD Interaction by Palmitoylation and Small-Molecule Inhibitors. J Phys Chem B 2024; 128:3795-3806. [PMID: 38606592 DOI: 10.1021/acs.jpcb.3c07073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
The Hippo signaling pathway is a highly conserved signaling network that plays a central role in regulating cellular growth, proliferation, and organ size. This pathway consists of a kinase cascade that integrates various upstream signals to control the activation or inactivation of YAP/TAZ proteins. Phosphorylated YAP/TAZ is sequestered in the cytoplasm; however, when the Hippo pathway is deactivated, it translocates into the nucleus, where it associates with TEAD transcription factors. This partnership is instrumental in regulating the transcription of progrowth and antiapoptotic genes. Thus, in many cancers, aberrantly hyperactivated YAP/TAZ promotes oncogenesis by contributing to cancer cell proliferation, metastasis, and therapy resistance. Because YAP and TAZ exert their oncogenic effects by binding with TEAD, it is critical to understand this key interaction to develop cancer therapeutics. Previous research has indicated that TEAD undergoes autopalmitoylation at a conserved cysteine, and small molecules that inhibit TEAD palmitoylation disrupt effective YAP/TAZ binding. However, how exactly palmitoylation contributes to YAP/TAZ-TEAD interactions and how the TEAD palmitoylation inhibitors disrupt this interaction remains unknown. Utilizing molecular dynamics simulations, our investigation not only provides detailed atomistic insight into the YAP/TAZ-TEAD dynamics but also unveils that the inhibitor studied influences the binding of YAP and TAZ to TEAD in distinct manners. This discovery has significant implications for the design and deployment of future molecular interventions targeting this interaction.
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Affiliation(s)
- Kira R Mills
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jyoti Misra
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Hedieh Torabifard
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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He Y, Liu K, Cao F, Song R, Liu J, Zhang Y, Li W, Han W. Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase. Sci Rep 2024; 14:174. [PMID: 38168773 PMCID: PMC10761953 DOI: 10.1038/s41598-023-50686-0] [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: 10/24/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynamics simulations for the Apo, LWM, and ALPM systems. The results reveal a stronger binding affinity of the LWM peptide to XO, potentially due to increased hydrogen bond formation. Notable changes were observed in the XO tunnel upon inhibitor binding, particularly with LWM, which showed a thinner, longer, and more twisted configuration compared to ALPM. The study highlights the importance of residue F914 in the allosteric pathway. Methodologically, we utilized the perturbed response scan (PRS) based on Python, enhancing tools for MD analysis. These findings deepen our understanding of food-derived anti-XO inhibitors and could inform the development of food-based therapeutics for reducing uric acid levels with minimal side effects.
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Affiliation(s)
- Yi He
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Renxiu Song
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Jianxuan Liu
- Jilin Academy of Chinese Medicine Sciences, Chuangju Road 155, Changchun, 130012, China
| | - Yinghua Zhang
- Jilin Academy of Chinese Medicine Sciences, Chuangju Road 155, Changchun, 130012, China.
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China.
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Maghsoud Y, Jayasinghe-Arachchige VM, Kumari P, Cisneros GA, Liu J. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. J Chem Inf Model 2023; 63:6834-6850. [PMID: 37877218 DOI: 10.1021/acs.jcim.3c01284] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium-dependent nuclease domains of the Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH domain is believed to determine the DNA cleavage activity of both endonuclease domains and is sensitive to complementary RNA-DNA base pairing. However, the underlying molecular mechanisms of CRISPR-Cas9, by which it rebukes or accepts mismatches, are poorly understood. Thus, investigation of the structure and dynamics of the catalytic state of Cas9 with either matched or mismatched t-DNA can provide insights into improving its specificity by reducing off-target cleavages. Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical molecular dynamics and coupled quantum mechanics/molecular mechanics simulations to study two possible mechanisms of t-DNA cleavage reaction catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA structure called MM5 (C to G at the fifth position from the protospacer adjacent motif region), the impact of single-guide RNA (sgRNA) and t-DNA complementarity on the catalysis process was investigated. Based on these simulations, our calculated binding affinities, minimum energy paths, and analysis of catalytically important residues provide atomic-level details of the differences between matched and mismatched cleavage reactions. In addition, several residues exhibit significant differences in their catalytic roles for the two studied systems, including K253, K263, R820, K896, and K913.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Vindi M Jayasinghe-Arachchige
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Pratibha Kumari
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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Maghsoud Y, Dong C, Cisneros GA. Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study. J Chem Inf Model 2023; 63:4190-4206. [PMID: 37319436 PMCID: PMC10405278 DOI: 10.1021/acs.jcim.3c00624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Xanthine oxidoreductase (XOR) is an enzyme found in various organisms. It converts hypoxanthine to xanthine and urate, which are crucial steps in purine elimination in humans. Elevated uric acid levels can lead to conditions like gout and hyperuricemia. Therefore, there is significant interest in developing drugs that target XOR for treating these conditions and other diseases. Oxipurinol, an analogue of xanthine, is a well-known inhibitor of XOR. Crystallographic studies have revealed that oxipurinol directly binds to the molybdenum cofactor (MoCo) in XOR. However, the precise details of the inhibition mechanism are still unclear, which would be valuable for designing more effective drugs with similar inhibitory functions. In this study, molecular dynamics and quantum mechanics/molecular mechanics calculations are employed to investigate the inhibition mechanism of XOR by oxipurinol. The study examines the structural and dynamic effects of oxipurinol on the pre-catalytic structure of the metabolite-bound system. Our results provide insights on the reaction mechanism catalyzed by the MoCo center in the active site, which aligns well with experimental findings. Furthermore, the results provide insights into the residues surrounding the active site and propose an alternative mechanism for developing alternative covalent inhibitors.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Chao Dong
- Department of Chemistry and Physics, The University of Texas Permian Basin, Odessa, Texas 79762, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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