1
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Jones NH, Liu Q, Urnavicius L, Dahan NE, Vostal LE, Kapoor TM. Allosteric activation of VCP, an AAA unfoldase, by small molecule mimicry. Proc Natl Acad Sci U S A 2024; 121:e2316892121. [PMID: 38833472 PMCID: PMC11181084 DOI: 10.1073/pnas.2316892121] [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: 10/02/2023] [Accepted: 04/17/2024] [Indexed: 06/06/2024] Open
Abstract
The loss of function of AAA (ATPases associated with diverse cellular activities) mechanoenzymes has been linked to diseases, and small molecules that activate these proteins can be powerful tools to probe mechanisms and test therapeutic hypotheses. Unlike chemical inhibitors that can bind a single conformational state to block enzyme function, activator binding must be permissive to different conformational states needed for mechanochemistry. However, we do not know how AAA proteins can be activated by small molecules. Here, we focus on valosin-containing protein (VCP)/p97, an AAA unfoldase whose loss of function has been linked to protein aggregation-based disorders, to identify druggable sites for chemical activators. We identified VCP ATPase Activator 1 (VAA1), a compound that dose-dependently stimulates VCP ATPase activity up to ~threefold. Our cryo-EM studies resulted in structures (ranging from ~2.9 to 3.7 Å-resolution) of VCP in apo and ADP-bound states and revealed that VAA1 binds an allosteric pocket near the C-terminus in both states. Engineered mutations in the VAA1-binding site confer resistance to VAA1, and furthermore, modulate VCP activity. Mutation of a phenylalanine residue in the VCP C-terminal tail that can occupy the VAA1 binding site also stimulates ATPase activity, suggesting that VAA1 acts by mimicking this interaction. Together, our findings uncover a druggable allosteric site and a mechanism of enzyme regulation that can be tuned through small molecule mimicry.
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Affiliation(s)
- Natalie H. Jones
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
- Tri-Institutional PhD Program in Chemical Biology, New York, NY10065
| | - Qiwen Liu
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
| | - Linas Urnavicius
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
| | - Noa E. Dahan
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY10065
| | - Lauren E. Vostal
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
- Tri-Institutional PhD Program in Chemical Biology, New York, NY10065
| | - Tarun M. Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
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2
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Lai CH, Ko KT, Fan PJ, Yu TA, Chang CF, Draczkowski P, Hsu STD. Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance. J Biol Chem 2024; 300:107230. [PMID: 38537699 PMCID: PMC11047754 DOI: 10.1016/j.jbc.2024.107230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024] Open
Abstract
Arsenite-induced stress granule (SG) formation can be cleared by the ubiquitin-proteasome system aided by the ATP-dependent unfoldase p97. ZFAND1 participates in this pathway by recruiting p97 to trigger SG clearance. ZFAND1 contains two An1-type zinc finger domains (ZF1 and ZF2), followed by a ubiquitin-like domain (UBL); but their structures are not experimentally determined. To shed light on the structural basis of the ZFAND1-p97 interaction, we determined the atomic structures of the individual domains of ZFAND1 by solution-state NMR spectroscopy and X-ray crystallography. We further characterized the interaction between ZFAND1 and p97 by methyl NMR spectroscopy and cryo-EM. 15N spin relaxation dynamics analysis indicated independent domain motions for ZF1, ZF2, and UBL. The crystal structure and NMR structure of UBL showed a conserved β-grasp fold homologous to ubiquitin and other UBLs. Nevertheless, the UBL of ZFAND1 contains an additional N-terminal helix that adopts different conformations in the crystalline and solution states. ZFAND1 uses the C-terminal UBL to bind to p97, evidenced by the pronounced line-broadening of the UBL domain during the p97 titration monitored by methyl NMR spectroscopy. ZFAND1 binding induces pronounced conformational heterogeneity in the N-terminal domain of p97, leading to a partial loss of the cryo-EM density of the N-terminal domain of p97. In conclusion, this work paved the way for a better understanding of the interplay between p97 and ZFAND1 in the context of SG clearance.
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Affiliation(s)
- Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuang-Ting Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Ju Fan
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | - Tsun-Ai Yu
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | | | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability With Knotted Chiral Meta Matter (SKCM(2)), Hiroshima University, Higashihiroshima, Japan.
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3
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Feng MF, Chen YX, Shen HB. DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score. J Struct Biol 2024; 216:108059. [PMID: 38160703 DOI: 10.1016/j.jsb.2023.108059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local quality for 3D cryo-EM density maps, using a deep-learning algorithm based on map-model fit score. DeepQs is a parameter-free method for users and incorporates structural information between map and its related atomic model into well-trained models by deep learning. More specifically, the DeepQs approach leverages the interplay between map and atomic model through predefined map-model fit score, Q-score. DeepQs can get close results to the ground truth map-model fit scores with only cryo-EM map as input. In experiments, DeepQs demonstrates the lowest root mean square error with standard method Fourier shell correlation metric and high correlation with map-model fit score, Q-score, when compared with other local quality estimation methods in high-resolution dataset (<=5 Å). DeepQs can also be applied to evaluate the quality of the post-processed maps. In both cases, DeepQs runs faster by using GPU acceleration. Our program is available at http://www.csbio.sjtu.edu.cn/bioinf/DeepQs for academic use.
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Affiliation(s)
- Ming-Feng Feng
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Yu-Xuan Chen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
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4
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Shein M, Hitzenberger M, Cheng TC, Rout SR, Leitl KD, Sato Y, Zacharias M, Sakata E, Schütz AK. Characterizing ATP processing by the AAA+ protein p97 at the atomic level. Nat Chem 2024; 16:363-372. [PMID: 38326645 PMCID: PMC10914628 DOI: 10.1038/s41557-024-01440-0] [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: 03/24/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.
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Affiliation(s)
- Mikhail Shein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany
- Bavarian NMR Center, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manuel Hitzenberger
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Germany.
| | - Tat Cheung Cheng
- Institute for Neuropathology, University Medical Center Göttingen, Göttingen, Germany
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
| | - Smruti R Rout
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
| | - Kira D Leitl
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany
- Bavarian NMR Center, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Graduate School of Engineering, Tottori University, Tottori, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Germany.
| | - Eri Sakata
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany.
- Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany.
| | - Anne K Schütz
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany.
- Bavarian NMR Center, Technical University of Munich, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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5
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Soontrapa P, Seven NA, Liewluck T, Cui G, Mer G, Milone M. Adolescent-onset multisystem proteinopathy due to a novel VCP variant. Neuromuscul Disord 2024; 34:89-94. [PMID: 38159460 DOI: 10.1016/j.nmd.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
Valosin-containing protein (VCP) pathogenic variants are the most common cause of multisystem proteinopathy presenting with inclusion body myopathy, amyotrophic lateral sclerosis/frontotemporal dementia, and Paget disease of bone in isolation or in combination. We report a patient manifesting with adolescent-onset myopathy caused by a novel heterozygous VCP variant (c.467G > T, p.Gly156Val). The myopathy manifested asymmetrically in lower limbs and extended to proximal, axial, and upper limb muscles, with loss of ambulation at age 35. Creatine kinase value was normal. Alkaline phosphatase was elevated. Electromyography detected mixed low amplitude, short duration and high amplitude, long duration motor unit potentials. Muscle biopsy showed features of inclusion body myopathy, which in combination with newly diagnosed Paget disease of bone, supported the VCP variant pathogenicity. In conclusion, VCP-multisystem proteinopathy is not only a disease of adulthood but can have a pediatric onset and should be considered in differential diagnosis of neuromuscular weakness in the pediatric population.
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Affiliation(s)
- Pannathat Soontrapa
- Department of Neurology, Division of Neuromuscular Medicine, Mayo Clinic, Rochester, MN, United States of America; Department of Medicine, Division of Neurology, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nathan A Seven
- Department of Neurology, Division of Neuromuscular Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Teerin Liewluck
- Department of Neurology, Division of Neuromuscular Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Margherita Milone
- Department of Neurology, Division of Neuromuscular Medicine, Mayo Clinic, Rochester, MN, United States of America.
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6
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Yu G, Bai Y, Zhang ZY. Valosin-Containing Protein (VCP)/p97 Oligomerization. Subcell Biochem 2024; 104:485-501. [PMID: 38963497 DOI: 10.1007/978-3-031-58843-3_18] [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
Valosin-containing protein (VCP), also known as p97, is an evolutionarily conserved AAA+ ATPase essential for cellular homeostasis. Cooperating with different sets of cofactors, VCP is involved in multiple cellular processes through either the ubiquitin-proteasome system (UPS) or the autophagy/lysosomal route. Pathogenic mutations frequently found at the interface between the NTD domain and D1 ATPase domain have been shown to cause malfunction of VCP, leading to degenerative disorders including the inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia (IBMPFD), amyotrophic lateral sclerosis (ALS), and cancers. Therefore, VCP has been considered as a potential therapeutic target for neurodegeneration and cancer. Most of previous studies found VCP predominantly exists and functions as a hexamer, which unfolds and extracts ubiquitinated substrates from protein complexes for degradation. However, recent studies have characterized a new VCP dodecameric state and revealed a controlling mechanism of VCP oligomeric states mediated by the D2 domain nucleotide occupancy. Here, we summarize our recent knowledge on VCP oligomerization, regulation, and potential implications of VCP in cellular function and pathogenic progression.
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Affiliation(s)
- Guimei Yu
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, China
| | - Yunpeng Bai
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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7
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Jones NH, Liu Q, Urnavicius L, Dahan NE, Vostal LE, Kapoor TM. Allosteric activation of VCP, a AAA unfoldase, by small molecule mimicry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560478. [PMID: 37873168 PMCID: PMC10592943 DOI: 10.1101/2023.10.02.560478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The loss of function of AAA (ATPases associated with diverse cellular activities) mechanoenzymes has been linked to diseases, and small molecules that activate these proteins can be powerful tools to probe mechanisms and test therapeutic hypotheses. Unlike chemical inhibitors that can bind a single conformational state to block enzyme activity, activator binding must be permissive to different conformational states needed for enzyme function. However, we do not know how AAA proteins can be activated by small molecules. Here, we focus on valosin-containing protein (VCP)/p97, a AAA unfoldase whose loss of function has been linked to protein aggregation-based disorders, to identify druggable sites for chemical activators. We identified VCP Activator 1 (VA1), a compound that dose-dependently stimulates VCP ATPase activity up to ∼3-fold. Our cryo-EM studies resulted in structures (∼2.9-3.5 Å-resolution) of VCP in apo and ADP-bound states, and revealed VA1 binding an allosteric pocket near the C-terminus in both states. Engineered mutations in the VA1 binding site confer resistance to VA1, and furthermore, modulate VCP activity to a similar level as VA1-mediated activation. The VA1 binding site can alternatively be occupied by a phenylalanine residue in the VCP C-terminal tail, a motif that is post-translationally modified and interacts with cofactors. Together, our findings uncover a druggable allosteric site and a mechanism of enzyme regulation that can be tuned through small molecule mimicry. Significance The loss of function of valosin-containing protein (VCP/p97), a mechanoenzyme from the AAA superfamily that hydrolyzes ATP and uses the released energy to extract or unfold substrate proteins, is linked to protein aggregation-based disorders. However, druggable allosteric sites to activate VCP, or any AAA mechanoenzyme, have not been identified. Here, we report cryo-EM structures of VCP in two states in complex with VA1, a compound we identified that dose-dependently stimulates VCP's ATP hydrolysis activity. The VA1 binding site can also be occupied by a phenylalanine residue in the VCP C-terminal tail, suggesting that VA1 acts through mimicry of this interaction. Our study reveals a druggable allosteric site and a mechanism of enzyme regulation.
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8
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Columbres RCA, Chin Y, Pratti S, Quinn C, Gonzalez-Cuyar LF, Weiss M, Quintero-Rivera F, Kimonis V. Novel Variants in the VCP Gene Causing Multisystem Proteinopathy 1. Genes (Basel) 2023; 14:genes14030676. [PMID: 36980948 PMCID: PMC10048343 DOI: 10.3390/genes14030676] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Valosin-containing protein (VCP) gene mutations have been associated with a rare autosomal dominant, adult-onset progressive disease known as multisystem proteinopathy 1 (MSP1), or inclusion body myopathy (IBM), Paget's disease of bone (PDB), frontotemporal dementia (FTD), (IBMPFD), and amyotrophic lateral sclerosis (ALS). We report the clinical and genetic analysis findings in five patients, three from the same family, with novel VCP gene variants: NM_007126.5 c.1106T>C (p.I369T), c.478G>A (p.A160T), and c.760A>T (p.I254F), associated with cardinal MSP1 manifestations including myopathy, PDB, and FTD. Our report adds to the spectrum of heterozygous pathogenic variants found in the VCP gene and the high degree of clinical heterogeneity. This case series prompts increased awareness and early consideration of MSP1 in the differential diagnosis of myopathies and/or PDB, dementia, or ALS to improve the diagnosis and early management of clinical symptoms.
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Affiliation(s)
- Rod Carlo Agram Columbres
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Yue Chin
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Sanjana Pratti
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, USA
| | - Colin Quinn
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis F Gonzalez-Cuyar
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Michael Weiss
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
| | - Fabiola Quintero-Rivera
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
- Department of Neurology, University of California, Irvine, CA 92697, USA
- Department of Pathology, University of California, Irvine, CA 92697, USA
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9
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Ahlstedt BA, Ganji R, Raman M. The functional importance of VCP to maintaining cellular protein homeostasis. Biochem Soc Trans 2022; 50:1457-1469. [PMID: 36196920 PMCID: PMC9704522 DOI: 10.1042/bst20220648] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022]
Abstract
The AAA-ATPase (ATPases associated with diverse cellular activities) valosin-containing protein (VCP), is essential for many cellular pathways including but not limited to endoplasmic reticulum-associated degradation (ERAD), DNA damage responses, and cell cycle regulation. VCP primarily identifies ubiquitylated proteins in these pathways and mediates their unfolding and degradation by the 26S proteasome. This review summarizes recent research on VCP that has uncovered surprising new ways that this ATPase is regulated, new aspects of recognition of substrates and novel pathways and substrates that utilize its activity.
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Affiliation(s)
- Brittany A. Ahlstedt
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, U.S.A
| | - Rakesh Ganji
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, U.S.A
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, U.S.A
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10
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Mirzadeh A, Kobakhidze G, Vuillemot R, Jonic S, Rouiller I. In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor. BMC Mol Cell Biol 2022; 23:39. [PMID: 36088301 PMCID: PMC9464413 DOI: 10.1186/s12860-022-00437-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The AAA + ATPase p97 is an essential unfoldase/segragase involved in a multitude of cellular processes. It functions as a molecular machine critical for protein homeostasis, homotypic membrane fusion events and organelle biogenesis during mitosis in which it acts in concert with cofactors p47 and p37. Cofactors assist p97 in extracting and unfolding protein substrates through ATP hydrolysis. In contrast to other p97ʼs cofactors, p37 uniquely increases the ATPase activity of p97. Disease-causing mutations in p97, including mutations that cause neurodegenerative diseases, increase cofactor association with its N-domain, ATPase activity and improper substrate processing. Upregulation of p97 has also been observed in various cancers. This study aims towards the characterization of the protein–protein interaction between p97 and p37 at the atomic level. We defined the interacting residues in p97 and p37. The knowledge will facilitate the design of unique small molecules inhibiting this interaction with insights into cancer therapy and drug design.
Results
The homology model of human p37 UBX domain was built from the X-ray crystal structure of p47 C-terminus from rat (PDB code:1S3S, G) as a template and assessed by model validation analysis. According to the HDOCK, HAWKDOCK, MM-GBSA binding free energy calculations and Arpeggio, we found that there are several hydrophobic and two hydrogen-bonding interactions between p37 UBX and p97 N-D1 domain. Residues of p37 UBX predicted to be involved in the interactions with p97 N-D1 domain interface are highly conserved among UBX cofactors.
Conclusion
This study provides a reliable structural insight into the p37-p97 complex binding sites at the atomic level though molecular docking coupled with molecular dynamics simulation. This can guide the rational design of small molecule drugs for inhibiting mutant p97 activity.
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11
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DeVore K, Chiu PL. Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity. Biomolecules 2022; 12:biom12050628. [PMID: 35625556 PMCID: PMC9138638 DOI: 10.3390/biom12050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.
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12
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Cryo-EM structures of human p97 double hexamer capture potentiated ATPase-competent state. Cell Discov 2022; 8:19. [PMID: 35190543 PMCID: PMC8861141 DOI: 10.1038/s41421-022-00379-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022] Open
Abstract
The conserved ATPase p97 (Cdc48 in yeast) and adaptors mediate diverse cellular processes through unfolding polyubiquitinated proteins and extracting them from macromolecular assemblies and membranes for disaggregation and degradation. The tandem ATPase domains (D1 and D2) of the p97/Cdc48 hexamer form stacked rings. p97/Cdc48 can unfold substrates by threading them through the central pore. The pore loops critical for substrate unfolding are, however, not well-ordered in substrate-free p97/Cdc48 conformations. How p97/Cdc48 organizes its pore loops for substrate engagement is unclear. Here we show that p97/Cdc48 can form double hexamers (DH) connected through the D2 ring. Cryo-EM structures of p97 DH reveal an ATPase-competent conformation with ordered pore loops. The C-terminal extension (CTE) links neighboring D2s in each hexamer and expands the central pore of the D2 ring. Mutations of Cdc48 CTE abolish substrate unfolding. We propose that the p97/Cdc48 DH captures a potentiated state poised for substrate engagement.
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13
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Yu G, Bai Y, Li K, Amarasinghe O, Jiang W, Zhang ZY. Cryo-electron microscopy structures of VCP/p97 reveal a new mechanism of oligomerization regulation. iScience 2021; 24:103310. [PMID: 34765927 PMCID: PMC8571493 DOI: 10.1016/j.isci.2021.103310] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/01/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
VCP/p97 is an evolutionarily conserved AAA+ ATPase important for cellular homeostasis. Previous studies suggest that VCP predominantly exists as a homohexamer. Here, we performed structural and biochemical characterization of VCP dodecamer, an understudied state of VCP. The structure revealed an apo nucleotide status that has rarely been captured, a tail-to-tail assembly of two hexamers, and the up-elevated N-terminal domains akin to that seen in the ATP-bound hexamer. Further analyses elucidated a nucleotide status-dependent dodecamerization mechanism, where nucleotide dissociation from the D2 AAA domains induces and promotes VCP dodecamerization. In contrast, nucleotide-free D1 AAA domains are associated with the up-rotation of N-terminal domains, which may prime D1 for ATP binding. These results therefore reveal new nucleotide status-dictated intra- and interhexamer conformational changes and suggest that modulation of D2 domain nucleotide occupancy may serve as a mechanism in controlling VCP oligomeric states.
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Affiliation(s)
- Guimei Yu
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Yunpeng Bai
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Department of Biological Sciences, Purdue University, 240 S Martin Jischke Drive, West Lafayette, IN 47907, USA
| | - Ovini Amarasinghe
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, 240 S Martin Jischke Drive, West Lafayette, IN 47907, USA
| | - Zhong-Yin Zhang
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
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