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Wang X, Pu F, Yang X, Feng X, Zhang J, Duan K, Nian X, Ma Z, Ma XX, Yang XM. Immunosuppressants exert antiviral effects against influenza A(H1N1)pdm09 virus via inhibition of nucleic acid synthesis, mRNA splicing, and protein stability. Virulence 2024; 15:2301242. [PMID: 38170681 PMCID: PMC10854267 DOI: 10.1080/21505594.2023.2301242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Influenza A virus (IAV) poses a threat to patients receiving immunosuppressive medications since they are more susceptible to infection with severe symptoms, and even death. Understanding the direct effects of immunosuppressants on IAV infection is critical for optimizing immunosuppression in these patients who are infected or at risk of influenza virus infection. We profiled the effects of 10 immunosuppressants, explored the antiviral mechanisms of immunosuppressants, and demonstrated the combined effects of immunosuppressants with the antiviral drug oseltamivir in IAV-infected cell models. We found that mycophenolic acid (MPA) strongly inhibits viral RNA replication via depleting cellular guanosine pool. Treatment with 6-Thioguanine (6-TG) promoted viral protein degradation through a proteasomal pathway. Filgotinib blocked mRNA splicing of matrix protein 2, resulting in decreased viral particle assembly. Furthermore, combined treatment with immunosuppressants and oseltamivir inhibits IAV viral particle production in an additive or synergic manner. Our results suggest that MPA, 6-TG, and filgotinib could be the preferential choices for patients who must take immunosuppressants but are at risk of influenza virus infection.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Feiyang Pu
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xuanye Yang
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xili Feng
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Jiayou Zhang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China
- Wuhan Institute of Biological Products Co, Ltd, Wuhan, China
| | - Kai Duan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China
- Wuhan Institute of Biological Products Co, Ltd, Wuhan, China
| | - Xuanxuan Nian
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China
- Wuhan Institute of Biological Products Co, Ltd, Wuhan, China
| | - Zhongren Ma
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xiao-Xia Ma
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xiao-Ming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan, China
- China National Biotech Group Company Limited, Beijing, China
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2
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Moreira LDPD, Porcellato D, Marangon M, Nadai C, Duarte VDS, Devold TG, Giacomini A, Corich V. Interactions between Starmerella bacillaris and Saccharomyces cerevisiae during sequential fermentations influence the release of yeast mannoproteins and impact the protein stability of an unstable wine. Food Chem 2024; 440:138311. [PMID: 38160596 DOI: 10.1016/j.foodchem.2023.138311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/01/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Wine protein haze formation is a problem due to grape proteins aggregation during wine storage. The cell wall components of wine yeasts, particularly high molecular weight mannoproteins, have a protective effect against haze formation, although their involvement remains poorly understood. This study aimed at characterizing glycosylated proteins released by Starmerella bacillaris and Saccharomyces cerevisiae during single and sequential fermentations in a synthetic must, and testing their impact on wine protein stability. Mannoproteins-rich extracts from sequential fermentations showed an increase in the low MW polysaccharide fraction and, when added to an unstable wine, had a greater effect on protein stability than S. cerevisiae extracts. Shotgun proteomics approaches revealed that the identified cell wall proteins exclusively found in sequential fermentations were produced by both S. bacillaris (MKC7, ENG1) and S. cerevisiae (Bgl2p). Moreover, sequential fermentations significantly increased the expression of Scw4p and 1,3-beta-glucanosyltransferase (GAS5), produced by S. cerevisiae. Finally, some of the key proteins identified might play a positive role in increasing wine protein stability.
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Affiliation(s)
- Luiza de Paula Dias Moreira
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy; Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Live Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Live Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Matteo Marangon
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy; Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy
| | - Chiara Nadai
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy; Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padova, Legnaro, PD, Italy.
| | - Vinícius da Silva Duarte
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Live Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Tove Gulbrandsen Devold
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Live Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy; Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy; Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Conegliano, TV, Italy
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Patibandla C, van Aalten L, Dinkova-Kostova AT, Honda T, Cuadrado A, Fernández-Ginés R, McNeilly AD, Hayes JD, Cantley J, Sutherland C. Inhibition of glycogen synthase kinase-3 enhances NRF2 protein stability, nuclear localisation and target gene transcription in pancreatic beta cells. Redox Biol 2024; 71:103117. [PMID: 38479223 PMCID: PMC10950707 DOI: 10.1016/j.redox.2024.103117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Accumulation of reactive oxygen species (i.e., oxidative stress) is a leading cause of beta cell dysfunction and apoptosis in diabetes. NRF2 (NF-E2 p45-related factor-2) regulates the adaptation to oxidative stress, and its activity is negatively regulated by the redox-sensitive CUL3 (cullin-3) ubiquitin ligase substrate adaptor KEAP1 (Kelch-like ECH-associated protein-1). Additionally, NRF2 is repressed by the insulin-regulated Glycogen Synthase Kinase-3 (GSK3). We have demonstrated that phosphorylation of NRF2 by GSK3 enhances β-TrCP (beta-transducin repeat-containing protein) binding and ubiquitylation by CUL1 (cullin-1), resulting in increased proteasomal degradation of NRF2. Thus, we hypothesise that inhibition of GSK3 activity or β-TrCP binding upregulates NRF2 and so protects beta cells against oxidative stress. We have found that treating the pancreatic beta cell line INS-1 832/13 with the KEAP1 inhibitor TBE31 significantly enhanced NRF2 protein levels. The presence of the GSK3 inhibitor CT99021 or the β-TrCP-NRF2 protein-protein interaction inhibitor PHAR, along with TBE31, resulted in prolonged NRF2 stability and enhanced nuclear localisation (P < 0.05). TBE31-mediated induction of NRF2-target genes encoding NAD(P)H quinone oxidoreductase 1 (Nqo1), glutamate-cysteine ligase modifier (Gclm) subunit and heme oxygenase (Hmox1) was significantly enhanced by the presence of CT99021 or PHAR (P < 0.05) in both INS-1 832/13 and in isolated mouse islets. Identical results were obtained using structurally distinct GSK3 inhibitors and inhibition of KEAP1 with sulforaphane. In summary, we demonstrate that GSK3 and β-TrCP/CUL1 regulate the proteasomal degradation of NRF2, enhancing the impact of KEAP1 regulation, and so contributes to the redox status of pancreatic beta cells. Inhibition of GSK3, or β-TrCP/CUL1 binding to NRF2 may represent a strategy to protect beta cells from oxidative stress.
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Affiliation(s)
- Chinmai Patibandla
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom.
| | - Lidy van Aalten
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - Albena T Dinkova-Kostova
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - Tadashi Honda
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas Sols-Morreale UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz) and Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain; Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Raquel Fernández-Ginés
- Instituto de Investigaciones Biomédicas Sols-Morreale UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz) and Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain; Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Alison D McNeilly
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - John D Hayes
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - James Cantley
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
| | - Calum Sutherland
- Division of Cellular & Systems Medicine, James Arnott Drive, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, United Kingdom
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4
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Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C CDH1 governs mitotic protein stability and cell cycle entry. Nat Commun 2024; 15:3220. [PMID: 38622115 PMCID: PMC11018817 DOI: 10.1038/s41467-024-47427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Induced oncoproteins degradation provides an attractive anti-cancer modality. Activation of anaphase-promoting complex (APC/CCDH1) prevents cell-cycle entry by targeting crucial mitotic proteins for degradation. Phosphorylation of its co-activator CDH1 modulates the E3 ligase activity, but little is known about its regulation after phosphorylation and how to effectively harness APC/CCDH1 activity to treat cancer. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)-catalyzed phosphorylation-dependent cis-trans prolyl isomerization drives tumor malignancy. However, the mechanisms controlling its protein turnover remain elusive. Through proteomic screens and structural characterizations, we identify a reciprocal antagonism of PIN1-APC/CCDH1 mediated by domain-oriented phosphorylation-dependent dual interactions as a fundamental mechanism governing mitotic protein stability and cell-cycle entry. Remarkably, combined PIN1 and cyclin-dependent protein kinases (CDKs) inhibition creates a positive feedback loop of PIN1 inhibition and APC/CCDH1 activation to irreversibly degrade PIN1 and other crucial mitotic proteins, which force permanent cell-cycle exit and trigger anti-tumor immunity, translating into synergistic efficacy against triple-negative breast cancer.
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Affiliation(s)
- Shizhong Ke
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Lin Wang
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02215, USA
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
| | - Abhishek Thavamani
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nami Kim
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nandita M Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Huaxiu Sui
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen, 361023, China
| | - Wei Tang
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Chenxi Qiu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Kazuhiro Koikawa
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Felipe Batalini
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Medicine, Division of Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Emily Stern Gatof
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Daniela Arango Isaza
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jaymin M Patel
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Xiaodong Wang
- Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Xiao Zhen Zhou
- Departments of Pathology and Laboratory Medicine, Biochemistry, and Oncology, and Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
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Matsui Y, Imai A, Izumi H, Yasumura M, Makino T, Shimizu T, Sato M, Mori H, Yoshida T. Cancer-associated point mutations within the extracellular domain of PTPRD affect protein stability and HSPG interaction. FASEB J 2024; 38:e23609. [PMID: 38593345 DOI: 10.1096/fj.202302279rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
PTPRD, a well-established tumor suppressor gene, encodes the protein tyrosine phosphatase-type D. This protein consists of three immunoglobulin-like (Ig) domains, four to eight fibronectin type 3 (FN) domains, a single transmembrane segment, and two cytoplasmic tandem tyrosine phosphatase domains. PTPRD is known to harbor various cancer-associated point mutations. While it is assumed that PTPRD regulates cellular functions as a tumor suppressor through the tyrosine phosphatase activity in the intracellular region, the function of its extracellular domain (ECD) in cancer is not well understood. In this study, we systematically examined the impact of 92 cancer-associated point mutations within the ECD. We found that 69.6% (64 out of 92) of these mutations suppressed total protein expression and/or plasma membrane localization. Notably, almost all mutations (20 out of 21) within the region between the last FN domain and transmembrane segment affected protein expression and/or localization, highlighting the importance of this region for protein stability. We further found that some mutations within the Ig domains adjacent to the glycosaminoglycan-binding pocket enhanced PTPRD's binding ability to heparan sulfate proteoglycans (HSPGs). This interaction is proposed to suppress phosphatase activity. Our findings therefore suggest that HSPG-mediated attenuation of phosphatase activity may be involved in tumorigenic processes through PTPRD dysregulation.
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Affiliation(s)
- Yu Matsui
- Department of Dermatology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Ayako Imai
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Hironori Izumi
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Misato Yasumura
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Developmental Neuroscience, United Graduate School of Child Development (UGSCD), Osaka University, Osaka, Japan
| | - Teruhiko Makino
- Department of Dermatology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Tadamichi Shimizu
- Department of Dermatology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Makoto Sato
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Developmental Neuroscience, United Graduate School of Child Development (UGSCD), Osaka University, Osaka, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Tomoyuki Yoshida
- Department of Molecular Neuroscience, Faculty of Medicine, University of Toyama, Toyama, Japan
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
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Luo P, Liu Z, Lai C, Jin Z, Wang M, Zhao H, Liu Y, Zhang W, Wang X, Xiao C, Yang X, Wang F. Time-Resolved Ultraviolet Photodissociation Mass Spectrometry Probes the Mutation-Induced Alterations in Protein Stability and Unfolding Dynamics. J Am Chem Soc 2024; 146:8832-8838. [PMID: 38507251 DOI: 10.1021/jacs.4c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
How mutations impact protein stability and structure dynamics is crucial for understanding the pathological process and rational drug design. Herein, we establish a time-resolved native mass spectrometry (TR-nMS) platform via a rapid-mixing capillary apparatus for monitoring the acid-initiated protein unfolding process. The molecular details in protein structure unfolding are further profiled by a 193 nm ultraviolet photodissociation (UVPD) analysis of the structure-informative photofragments. Compared with the wild-type dihydrofolate reductase (WT-DHFR), the M42T/H114R mutant (MT-DHFR) exhibits a significant stability decrease in TR-nMS characterization. UVPD comparisons of the unfolding intermediates and original DHFR forms indicate the special stabilization effect of cofactor NADPH on DHFR structure, and the M42T/H114R mutations lead to a significant decrease in NADPH-DHFR interactions, thus promoting the structure unfolding. Our study paves the way for probing the mutation-induced subtle changes in the stability and structure dynamics of drug targets.
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Affiliation(s)
- Pan Luo
- Institute of Advanced Science Facilities, Shenzhen 518107, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixiong Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Weiqing Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xingan Wang
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xueming Yang
- Institute of Advanced Science Facilities, Shenzhen 518107, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Wu M, Tie M, Hu L, Yang Y, Chen Y, Ferguson D, Chen Y, He A. Fatty liver disease protective MTARC1 p.A165T variant reduces the protein stability of MTARC1. Biochem Biophys Res Commun 2024; 702:149655. [PMID: 38340654 PMCID: PMC10940201 DOI: 10.1016/j.bbrc.2024.149655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the most common causes of liver disease worldwide. MTARC1, encoded by the MTARC1 gene, is a mitochondrial outer membrane-anchored enzyme. Interestingly, the MTARC1 p.A165T (rs2642438) variant is associated with a decreased risk of NAFLD, indicating that MTARC1 might be an effective target. It has been reported that the rs2642438 variant does not have altered enzymatic activity so we reasoned that this variation may affect MTARC1 stability. In this study, MTARC1 mutants were generated and stability was assessed using a protein stability reporter system both in vitro and in vivo. We found that the MTARC1 p.A165T variant has dramatically reduced the stability of MTARC1, as assessed in several cell lines. In mice, the MTARC1 A168T mutant, the equivalent of human MTARC1 A165T, had diminished stability in mouse liver. Additionally, several MTARC1 A165 mutants, including A165S, A165 N, A165V, A165G, and A165D, had dramatically decreased stability as well, suggesting that the alanine residue of MTARC1 165 site is essential for MTARC1 protein stability. Collectively, our data indicates that the MTARC1 p.A165T variant (rs2642438) leads to reduced stability of MTARC1. Given that carriers of rs2642438 show a decreased risk of NAFLD, the findings herein support the notion that MTARC1 inhibition may be a therapeutic target to combat NAFLD.
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Affiliation(s)
- Mengyue Wu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Meng Tie
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Liwei Hu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yunzhi Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yong Chen
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Daniel Ferguson
- Division of Nutritional Science and Obesity Medicine, Washington University in St. Louis, United States
| | - Yali Chen
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Anyuan He
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Anhui Medical University, Hefei, 230032, Anhui, China; Department of Biochemistry and Molecular Biology, College of Life Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
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8
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Zhang L, Zhou R, Liu D, Zhu M, Zhang G, Zhang L, Zhou SF, Jiang W. Multi-strategy orthogonal enhancement and analysis of aldo-keto reductase thermal stability. Int J Biol Macromol 2024; 264:130691. [PMID: 38458293 DOI: 10.1016/j.ijbiomac.2024.130691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Given their outstanding efficiency and selectivity, enzymes are integral in various domains such as drug synthesis, the food industry, and environmental management. However, the inherent instability of natural enzymes limits their widespread industrial application. In this study, we underscore the efficacy of enhancing protein thermal stability through comprehensive protein design strategies, encompassing elements such as the free energy of protein folding, internal forces within proteins, and the overall structural design. We also demonstrate the efficiency and precision of combinatorial screening in the thermal stability design of aldo-keto reductase (AKR7-2-1). In our research, three single-point mutations and five combinatorial mutations were strategically introduced into AKR7-2-1, using multiple computational techniques. Notably, the E12I/S235I mutant showed a significant increase of 25.4 °C in its melting temperature (Tm). Furthermore, the optimal mutant, E12V/S235I, maintained 80 % of its activity while realizing a 16.8 °C elevation in Tm. Remarkably, its half-life at 50 °C was increased to twenty times that of the wild type. Structural analysis indicates that this enhanced thermal stability primarily arises from reduced oscillation in the loop region and increased internal hydrogen bonding. The promising results achieved with AKR7-2-1 demonstrate that our strategy could serve as a valuable reference for enhancing the thermal stability of other industrial enzymes.
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Affiliation(s)
- Lingzhi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Rui Zhou
- Shanghai Marine Diesel Engine Research Institute, Shanghai 201108, PR China
| | - Dekai Liu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Meinan Zhu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Guangya Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Lijuan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Shu-Feng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| | - Wei Jiang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
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9
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Liu J, Isaji T, Komatsu S, Sun Y, Xu X, Fukuda T, Fujimura T, Takahashi S, Gu J. BRCC36 associates with FLT3-ITD to regulate its protein stability and intracellular signaling in acute myeloid leukemia. Cancer Sci 2024; 115:1196-1208. [PMID: 38288901 PMCID: PMC11007003 DOI: 10.1111/cas.16090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 04/12/2024] Open
Abstract
Fms-like tyrosine kinase-3 (FLT3) is a commonly mutated gene in acute myeloid leukemia (AML). The two most common mutations are the internal-tandem duplication domain (ITD) mutation and the tyrosine kinase domain (TKD) mutation. FLT3-ITD and FLT3-TKD exhibit distinct protein stability, cellular localization, and intracellular signaling. To understand the underlying mechanisms, we performed proximity labeling with TurboID to identify proteins that regulate FLT3-ITD or -TKD differently. We found that BRCA1/BRCA2-containing complex subunit 36 (BRCC36), a specific K63-linked polyubiquitin deubiquitinase, was exclusively associated with ITD, not the wild type of FLT3 and TKD. Knockdown of BRCC36 resulted in decreased signal transducers and activators of transcription 5 phosphorylation and cell proliferation in ITD cells. Consistently, treatment with thiolutin, an inhibitor of BRCC36, specifically suppressed cell proliferation and induced cell apoptosis in ITD cells. Thiolutin efficiently affected leukemia cell lines expressing FLT3-ITD cell viability and exhibited mutual synergies with quizartinib, a standard clinical medicine for AML. Furthermore, mutation of the lysine at 609 of ITD led to significant suppression of K63 polyubiquitination and decreased its stability, suggesting that K609 is a critical site for K63 ubiquitination specifically recognized by BRCC36. These data indicate that BRCC36 is a specific regulator for FLT3-ITD, which may shed light on developing a novel therapeutic approach for AML.
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Affiliation(s)
- Jianwei Liu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Tomoya Isaji
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Sachiko Komatsu
- Division of Bioanalytical ChemistryTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Yuhan Sun
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Xing Xu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Tomohiko Fukuda
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Tsutomu Fujimura
- Division of Bioanalytical ChemistryTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Shinichiro Takahashi
- Division of Laboratory Medicine, Faculty of MedicineTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
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10
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Dijkwel Y, Hart-Smith G, Kurscheid S, Tremethick DJ. ANP32e Binds Histone H2A.Z in a Cell Cycle-Dependent Manner and Regulates Its Protein Stability in the Cytoplasm. Mol Cell Biol 2024; 44:72-85. [PMID: 38482865 PMCID: PMC10950284 DOI: 10.1080/10985549.2024.2319731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
ANP32e, a chaperone of H2A.Z, is receiving increasing attention because of its association with cancer growth and progression. An unanswered question is whether ANP32e regulates H2A.Z dynamics during the cell cycle; this could have clear implications for the proliferation of cancer cells. We confirmed that ANP32e regulates the growth of human U2OS cancer cells and preferentially interacts with H2A.Z during the G1 phase of the cell cycle. Unexpectedly, ANP32e does not mediate the removal of H2A.Z from chromatin, is not a stable component of the p400 remodeling complex and is not strongly associated with chromatin. Instead, most ANP32e is in the cytoplasm. Here, ANP32e preferentially interacts with H2A.Z in the G1 phase in response to an increase in H2A.Z protein abundance and regulates its protein stability. This G1-specific interaction was also observed in the nucleoplasm but was unrelated to any change in H2A.Z abundance. These results challenge the idea that ANP32e regulates the abundance of H2A.Z in chromatin as part of a chromatin remodeling complex. We propose that ANP32e is a molecular chaperone that maintains the soluble pool of H2A.Z by regulating its protein stability and acting as a buffer in response to cell cycle-dependent changes in H2A.Z abundance.
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Affiliation(s)
- Yasmin Dijkwel
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Gene Hart-Smith
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David J. Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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11
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Ghassemi Z, Leach JB. Impact of Confinement within a Hydrogel Mesh on Protein Thermodynamic Stability and Aggregation Kinetics. Mol Pharm 2024; 21:1137-1148. [PMID: 38277273 DOI: 10.1021/acs.molpharmaceut.3c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Though protein stability and aggregation have been well characterized in dilute solutions, the influence of a confining environment that exists (e.g., in intercellular and tissue spaces and therapeutic formulations) on the protein structure is largely unknown. Herein, the effects of confinement on stability and aggregation were explored for proteins of different sizes, stability, and hydrophobicity when encapsulated in hydrophilic poly(ethylene glycol) hydrogels. Denaturation curves show linear correlations between confinement size (mesh size) and thermodynamic stability, i.e., unfolding free energy and surface area accessible for solvation (represented by m-value). Two clusters of protein types are identifiable from these correlations; the clusters are defined by differences in protein stability, surface area, and aggregation propensity. Proteins with higher stability, larger surface area, and lower aggregation propensity (e.g., lysozyme and myoglobin) are less affected by the confinement imposed by mesh size than proteins with lower stability, smaller surface area, and higher aggregation propensity (e.g., growth hormone and aldehyde dehydrogenase). According to aggregation kinetics measured by thioflavin T fluorescence, confinement in smaller mesh sizes resulted in slower aggregation rates than that in larger mesh sizes. Compared to that in buffer solution, the confinement of a hydrophobic protein (e.g., human insulin) in the hydrogels accelerates protein aggregation. Conversely, the confinement of a hydrophilic protein (e.g., human amylin) in the hydrogels decelerates or prevents aggregation, with the rates of aggregation inversely proportional to mesh size. These findings provide new insights into protein conformational stability in confined microenvironments relevant to various cellular, tissue, and therapeutics scenarios.
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Affiliation(s)
- Zahra Ghassemi
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, ECS 314, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Jennie B Leach
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, ECS 314, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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12
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Xu P, Liu Y, Liu C, Guey B, Li L, Melenec P, Ricci J, Ablasser A. The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Nature 2024; 627:873-879. [PMID: 38418882 PMCID: PMC10972748 DOI: 10.1038/s41586-024-07112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA8-15. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation.
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Affiliation(s)
- Pengbiao Xu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Ying Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- School of Medicine, Jiangnan University, Wuxi, China
| | - Chong Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Baptiste Guey
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Lingyun Li
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Pauline Melenec
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Ricci
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Ablasser
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Institute for Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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13
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Liu X, Ye Z, Rao D, Chen Q, Zhang Z. DUSP4 maintains the survival and LSD1 protein stability in esophageal squamous cell carcinoma cells by inhibiting JNK signaling-dependent autophagy. In Vitro Cell Dev Biol Anim 2024; 60:115-122. [PMID: 38286920 DOI: 10.1007/s11626-023-00845-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/13/2023] [Indexed: 01/31/2024]
Abstract
DUSP4 is a biomarker of esophageal squamous cell carcinoma (ESCC), which is responsible for the prognosis in ESCC. However, the underlying mechanism of DUSP4-regulated ESCC carcinogenesis is unknown. As a negative regulator of JNK, DUSP4 can inhibit autophagy, which contributes to tumorigenesis. This study aimed to explore the role of autophagy in DUSP4-regulated ESCC carcinogenesis. Our results showed that DUSP4 overexpression inhibited autophagy and promoted LSD1 protein expression in ESCC cells, while DUSP4 silencing showed the opposite effects. However, DUSP4 overexpression and silencing did not affect LSD1 mRNA expression. But the regulatory ability of DUSP4 overexpression on autophagy, death level, and LSD1 protein was reversed by rapamycin. In addition, DUSP4 overexpression inhibited JNK and Bcl2 phosphorylation and the dissociation of Bcl2-Beclin1 complex, while DUSP4 silencing promoted JNK and Bcl2 phosphorylation. Moreover, the regulatory ability of DUSP4 overexpression on autophagy, death, and LSD1 protein was reversed by JNK activator anisomycin. The xenograft assays also showed that DUSP4 overexpression-promoted ESCC tumor growth in vivo and LC3II and LSD1 protein expression in tumor tissues were reversed by rapamycin or anisomycin. Overall, DUSP4 inhibits Bcl2-Beclin1-autophagy signal transduction through the negative regulation of JNK, thus suppressing autophagic death and the autophagic degradation of LSD1 in ESCC, by which DUSP4 promotes ESCC carcinogenesis.
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Affiliation(s)
- Xinxin Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
- Gannan Branch of National Clinical Research Center for Geriatrics Ganzhou 341000, Jiangxi, China
| | - Zhou Ye
- Department of Digestive, The 900Th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350001, Fujian, China
| | - Dingyu Rao
- Department of Thoracic Surgery, First Affiliated Hospital of Gannan Medical University, No. 3, Outangli, Xingannan Road, Zhanggong District, Ganzhou, 341000, Jiangxi, China
| | - Qianshun Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, China.
| | - Zuxiong Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of Gannan Medical University, No. 3, Outangli, Xingannan Road, Zhanggong District, Ganzhou, 341000, Jiangxi, China.
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, China.
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14
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Tamulaitiene G, Sabonis D, Sasnauskas G, Ruksenaite A, Silanskas A, Avraham C, Ofir G, Sorek R, Zaremba M, Siksnys V. Activation of Thoeris antiviral system via SIR2 effector filament assembly. Nature 2024; 627:431-436. [PMID: 38383786 DOI: 10.1038/s41586-024-07092-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems1-7. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and Thoeris) consist of two modules: a sensor responsible for infection recognition and an effector that stops viral replication by destroying key cellular components8-12. In the Thoeris system, a Toll/interleukin-1 receptor (TIR)-domain protein, ThsB, acts as a sensor that synthesizes an isomer of cyclic ADP ribose, 1''-3' glycocyclic ADP ribose (gcADPR), which is bound in the Smf/DprA-LOG (SLOG) domain of the ThsA effector and activates the silent information regulator 2 (SIR2)-domain-mediated hydrolysis of a key cell metabolite, NAD+ (refs. 12-14). Although the structure of ThsA has been solved15, the ThsA activation mechanism remained incompletely understood. Here we show that 1''-3' gcADPR, synthesized in vitro by the dimeric ThsB' protein, binds to the ThsA SLOG domain, thereby activating ThsA by triggering helical filament assembly of ThsA tetramers. The cryogenic electron microscopy (cryo-EM) structure of activated ThsA revealed that filament assembly stabilizes the active conformation of the ThsA SIR2 domain, enabling rapid NAD+ depletion. Furthermore, we demonstrate that filament formation enables a switch-like response of ThsA to the 1''-3' gcADPR signal.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Dziugas Sabonis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Audrone Ruksenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Carmel Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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15
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Grifagni D, Silva JM, Querci L, Lepoivre M, Vallières C, Louro RO, Banci L, Piccioli M, Golinelli-Cohen MP, Cantini F. Biochemical and cellular characterization of the CISD3 protein: Molecular bases of cluster release and destabilizing effects of nitric oxide. J Biol Chem 2024; 300:105745. [PMID: 38354784 PMCID: PMC10937110 DOI: 10.1016/j.jbc.2024.105745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
The NEET proteins, an important family of iron-sulfur (Fe-S) proteins, have generated a strong interest due to their involvement in diverse diseases such as cancer, diabetes, and neurodegenerative disorders. Among the human NEET proteins, CISD3 has been the least studied, and its functional role is still largely unknown. We have investigated the biochemical features of CISD3 at the atomic and in cellulo levels upon challenge with different stress conditions i.e., iron deficiency, exposure to hydrogen peroxide, and nitric oxide. The redox and cellular stability properties of the protein agree on a predominance of reduced form of CISD3 in the cells. Upon the addition of iron chelators, CISD3 loses its Fe-S clusters and becomes unstructured, and its cellular level drastically decreases. Chemical shift perturbation measurements suggest that, upon cluster oxidation, the protein undergoes a conformational change at the C-terminal CDGSH domain, which determines the instability of the oxidized state. This redox-associated conformational change may be the source of cooperative electron transfer via the two [Fe2S2] clusters in CISD3, which displays a single sharp voltammetric signal at -31 mV versus SHE. Oxidized CISD3 is particularly sensitive to the presence of hydrogen peroxide in vitro, whereas only the reduced form is able to bind nitric oxide. Paramagnetic NMR provides clear evidence that, upon NO binding, the cluster is disassembled but iron ions are still bound to the protein. Accordingly, in cellulo CISD3 is unaffected by oxidative stress induced by hydrogen peroxide but it becomes highly unstable in response to nitric oxide treatment.
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Affiliation(s)
- Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - José Malanho Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Querci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Michel Lepoivre
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cindy Vallières
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
| | | | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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16
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Chatterjee A, Sepuri NBV. Methionine sulfoxide reductase 2 regulates Cvt autophagic pathway by altering the stability of Atg19 and Ape1 in Saccharomyces cerevisiae. J Biol Chem 2024; 300:105662. [PMID: 38246354 PMCID: PMC10875273 DOI: 10.1016/j.jbc.2024.105662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The reversible oxidation of methionine plays a crucial role in redox regulation of proteins. Methionine oxidation in proteins causes major structural modifications that can destabilize and abrogate their function. The highly conserved methionine sulfoxide reductases protect proteins from oxidative damage by reducing their oxidized methionines, thus restoring their stability and function. Deletion or mutation in conserved methionine sulfoxide reductases leads to aging and several human neurological disorders and also reduces yeast growth on nonfermentable carbon sources. Despite their importance in human health, limited information about their physiological substrates in humans and yeast is available. For the first time, we show that Mxr2 interacts in vivo with two core proteins of the cytoplasm to vacuole targeting (Cvt) autophagy pathway, Atg19, and Ape1 in Saccharomyces cerevisiae. Deletion of MXR2 induces instability and early turnover of immature Ape1 and Atg19 proteins and reduces the leucine aminopeptidase activity of Ape1 without affecting the maturation process of Ape1. Additonally, Mxr2 interacts with the immature Ape1, dependent on Met17 present within the propeptide of Ape1 as a single substitution mutation of Met17 to Leu abolishes this interaction. Importantly, Ape1 M17L mutant protein resists oxidative stress-induced degradation in WT and mxr2Δ cells. By identifying Atg19 and Ape1 as cytosolic substrates of Mxr2, our study maps the hitherto unexplored connection between Mxr2 and the Cvt autophagy pathway and sheds light on Mxr2-dependent oxidative regulation of the Cvt pathway.
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Affiliation(s)
- Arpan Chatterjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Naresh Babu V Sepuri
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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17
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Koch J, Romero‐Romero S, Höcker B. Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels. Protein Sci 2024; 33:e4926. [PMID: 38380781 PMCID: PMC10880431 DOI: 10.1002/pro.4926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Over the past decades, the TIM-barrel fold has served as a model system for the exploration of how changes in protein sequences affect their structural, stability, and functional characteristics, and moreover, how this information can be leveraged to design proteins from the ground up. After numerous attempts to design de novo proteins with this specific fold, sTIM11 was the first validated de novo design of an idealized four-fold symmetric TIM barrel. Subsequent efforts to enhance the stability of this initial design resulted in the development of DeNovoTIMs, a family of de novo TIM barrels with various stabilizing mutations. In this study, we present an investigation into the biophysical and thermodynamic effects upon introducing a varying number of stabilizing mutations per quarter along the sequence of a four-fold symmetric TIM barrel. We compared the base design DeNovoTIM0 without any stabilizing mutations with variants containing mutations in one, two, three, and all four quarters-designated TIM1q, TIM2q, TIM3q, and DeNovoTIM6, respectively. This analysis revealed a stepwise and nonlinear change in the thermodynamic properties that correlated with the number of mutated quarters, suggesting positive nonadditive effects. To shed light on the significance of the location of stabilized quarters, we engineered two variants of TIM2q which contain the same number of mutations but positioned in different quarter locations. Characterization of these TIM2q variants revealed that the mutations exhibit varying effects on the overall protein stability, contingent upon the specific region in which they are introduced. These findings emphasize that the amount and location of stabilized interfaces among the four quarters play a crucial role in shaping the conformational stability of these four-fold symmetric TIM barrels. Analysis of de novo proteins, as described in this study, enhances our understanding of how sequence variations can finely modulate stability in both naturally occurring and computationally designed proteins.
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Affiliation(s)
| | | | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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18
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Huang YH, Jiang Z, Du Q, Yap K, Bigot A, Kaas Q, Wang CK, Craik DJ. Scanning mutagenesis identifies residues that improve the long-term stability and insecticidal activity of cyclotide kalata B1. J Biol Chem 2024; 300:105682. [PMID: 38272233 PMCID: PMC10877628 DOI: 10.1016/j.jbc.2024.105682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Cyclotides are plant-derived disulfide-rich cyclic peptides that have a natural function in plant defense and potential for use as agricultural pesticides. Because of their highly constrained topology, they are highly resistant to thermal, chemical, or enzymatic degradation. However, the stability of cyclotides at alkaline pH for incubation times of longer than a few days is poorly studied but important since these conditions could be encountered in the environment, during storage or field application as insecticides. In this study, kalata B1 (kB1), the prototypical cyclotide, was engineered to improve its long-term stability and retain its insecticidal activity via point mutations. We found that substituting either Asn29 or Gly1 to lysine or leucine increased the stability of kB1 by twofold when incubated in an alkaline buffer (pH = 9.0) for 7 days, while retaining its insecticidal activity. In addition, when Gly1 was replaced with lysine or leucine, the mutants could be cyclized using an asparaginyl endopeptidase, in vitro with a yield of ∼90% within 5 min. These results demonstrate the potential to manufacture kB1 mutants with increased stability and insecticidal activity recombinantly or in planta. Overall, the discovery of mutants of kB1 that have enhanced stability could be useful in leading to longer term activity in the field as bioinsecticides.
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Affiliation(s)
- Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhihao Jiang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Qingdan Du
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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19
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Weinberg J, Whitcomb E, Bohm A, Chekkilla UK, Taylor A. The E3 ligase SMURF1 stabilizes p27 via UbcH7 catalyzed K29-linked ubiquitin chains to promote cell migration SMURF1-UbcH7 K29 ubiquitination of p27 and cell migration. J Biol Chem 2024; 300:105693. [PMID: 38301893 PMCID: PMC10897894 DOI: 10.1016/j.jbc.2024.105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Ubiquitination is a key regulator of protein stability and function. The multifunctional protein p27 is known to be degraded by the proteasome following K48-linked ubiquitination. However, we recently reported that when the ubiquitin-conjugating enzyme UbcH7 (UBE2L3) is overexpressed, p27 is stabilized, and cell cycle is arrested in multiple diverse cell types including eye lens, retina, HEK-293, and HELA cells. However, the ubiquitin ligase associated with this stabilization of p27 remained a mystery. Starting with an in vitro ubiquitination screen, we identified RSP5 as the yeast E3 ligase partner of UbcH7 in the ubiquitination of p27. Screening of the homologous human NEDD4 family of E3 ligases revealed that SMURF1 but not its close homolog SMURF2, stabilizes p27 in cells. We found that SMURF1 ubiquitinates p27 with K29O but not K29R or K63O ubiquitin in vitro, demonstrating a strong preference for K29 chain formation. Consistent with SMURF1/UbcH7 stabilization of p27, we also found that SMURF1, UbcH7, and p27 promote cell migration, whereas knockdown of SMURF1 or UbcH7 reduces cell migration. We further demonstrated the colocalization of SMURF1/p27 and UbcH7/p27 at the leading edge of migrating cells. In sum, these results indicate that SMURF1 and UbcH7 work together to produce K29-linked ubiquitin chains on p27, resulting in the stabilization of p27 and promoting its cell-cycle independent function of regulating cell migration.
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Affiliation(s)
- Jasper Weinberg
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Elizabeth Whitcomb
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Andrew Bohm
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Uday Kumar Chekkilla
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Allen Taylor
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University.
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20
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Thakur A, Gizzio J, Levy RM. Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability. J Phys Chem B 2024; 128:1656-1667. [PMID: 38350894 PMCID: PMC10939730 DOI: 10.1021/acs.jpcb.3c08097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Single-point mutations in kinase proteins can affect their stability and fitness, and computational analysis of these effects can provide insights into the relationships among protein sequence, structure, and function for this enzyme family. To assess the impact of mutations on protein stability, we used a sequence-based Potts Hamiltonian model trained on a kinase family multiple-sequence alignment (MSA) to calculate the statistical energy (fitness) effects of mutations and compared these against relative folding free energies (ΔΔGs) calculated from all-atom molecular dynamics free energy perturbation (FEP) simulations in explicit solvent. The fitness effects of mutations in the Potts model (ΔEs) showed good agreement with experimental thermostability data (Pearson r = 0.68), similar to the correlation we observed with ΔΔGs predicted from structure-based relative FEP simulations. Recognizing the possible advantages of using Potts models to rapidly estimate protein stability effects of kinase mutations seen in cancer genomics data, we used the Potts statistical energy model to estimate the stability effects of 65 conservative and nonconservative mutations across three distinct kinases (Wee1, Abl1, and Cdc7) with somatic mutations reported in the Genomic Data Commons (GDC) database. The ΔEs of these mutations calculated from the Potts model are consistent with the corresponding ΔΔGs from FEP simulations (Pearson ratio of 0.72). The agreement between these methods suggests that the Potts model may be used as a sequence-based tool for high-throughput screening of mutational effects as part of a computational pipeline for predicting the stability effects of mutations. We also demonstrate how the scalability of the fitness-based Potts model calculations permits analyses that are not easily accessed using FEP simulations. To this end, we employed site-saturation mutagenesis in the Potts model in order to investigate the relative stability effects of mutations seen in different cancer evolutionary scenarios. We used this approach to analyze the effects of drug pressure in Abl kinase by contrasting the relative fitness penalties of somatic mutations seen in miscellaneous cancer types with those calculated for mutations associated with cancer drug resistance. We observed that, in contrast to somatic mutations of Abl seen in various tumors that appear to have evolved neutrally, cancer mutations that evolved under drug pressure in Abl-targeted therapies tend to preserve enzyme stability.
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Affiliation(s)
- Abhishek Thakur
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Joan Gizzio
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
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21
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Jos S, Poulose R, Kambaru A, Gogoi H, Dalavaikodihalli Nanjaiah N, Padmanabhan B, Mehta B, Padavattan S. Tau-S214 Phosphorylation Inhibits Fyn Kinase Interaction and Increases the Decay Time of NMDAR-mediated Current. J Mol Biol 2024; 436:168445. [PMID: 38218365 DOI: 10.1016/j.jmb.2024.168445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Fyn kinase SH3 domain interaction with PXXP motif in the Tau protein is implicated in AD pathology and is central to NMDAR function. Among seven PXXP motifs localized in proline-rich domain of Tau protein, tandem 5th and 6th PXXP motifs are critical to Fyn-SH3 domain interaction. Here, we report the crystal structure of Fyn-SH3 -Tau (207-221) peptide consisting of 5th and 6th PXXP motif complex to 1.01 Å resolution. Among five AD-specific phosphorylation sites encompassing the 5th and 6th PXXP motifs, only S214 residue showed interaction with SH3 domain. Biophysical studies showed that Tau (207-221) with S214-phosphorylation (pS214) inhibits its interaction with Fyn-SH3 domain. The individual administration of Tau (207-221) with/without pS214 peptides to a single neuron increased the decay time of evoked NMDA current response. Recordings of spontaneous NMDA EPSCs at +40 mV indicate an increase in frequency and amplitude of events for the Tau (207-221) peptide. Conversely, the Tau (207-221) with pS214 peptide exhibited a noteworthy amplitude increase alongside a prolonged decay time. These outcomes underscore the distinctive modalities of action associated with each peptide in the study. Overall, this study provides insights into how Tau (207-221) with/without pS214 affects the molecular framework of NMDAR signaling, indicating its involvement in Tau-related pathogenesis.
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Affiliation(s)
- Sneha Jos
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Roshni Poulose
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Archanalakshmi Kambaru
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Hemanga Gogoi
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | | | - Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Bhupesh Mehta
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.
| | - Sivaraman Padavattan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.
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22
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Pandey P, Alexov E. Most Monogenic Disorders Are Caused by Mutations Altering Protein Folding Free Energy. Int J Mol Sci 2024; 25:1963. [PMID: 38396641 PMCID: PMC10888012 DOI: 10.3390/ijms25041963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Revealing the molecular effect that pathogenic missense mutations have on the corresponding protein is crucial for developing therapeutic solutions. This is especially important for monogenic diseases since, for most of them, there is no treatment available, while typically, the treatment should be provided in the early development stages. This requires fast targeted drug development at a low cost. Here, we report an updated database of monogenic disorders (MOGEDO), which includes 768 proteins and the corresponding 2559 pathogenic and 1763 benign mutations, along with the functional classification of the corresponding proteins. Using the database and various computational tools that predict folding free energy change (ΔΔG), we demonstrate that, on average, 70% of pathogenic cases result in decreased protein stability. Such a large fraction indicates that one should aim at in silico screening for small molecules stabilizing the structure of the mutant protein. We emphasize that knowledge of ΔΔG is essential because one wants to develop stabilizers that compensate for ΔΔG, but do not make protein over-stable, since over-stable protein may be dysfunctional. We demonstrate that, by using ΔΔG and predicted solvent exposure of the mutation site, one can develop a predictive method that distinguishes pathogenic from benign mutations with a success rate even better than some of the leading pathogenicity predictors. Furthermore, hydrophobic-hydrophobic mutations have stronger correlations between folding free energy change and pathogenicity compared with others. Also, mutations involving Cys, Gly, Arg, Trp, and Tyr amino acids being replaced by any other amino acid are more likely to be pathogenic. To facilitate further detection of pathogenic mutations, the wild type of amino acids in the 768 proteins mentioned above was mutated to other 19 residues (14,847,817 mutations), the ΔΔG was calculated with SAAFEC-SEQ, and 5,506,051 mutations were predicted to be pathogenic.
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Affiliation(s)
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA;
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23
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Dieckhaus H, Brocidiacono M, Randolph NZ, Kuhlman B. Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proc Natl Acad Sci U S A 2024; 121:e2314853121. [PMID: 38285937 PMCID: PMC10861915 DOI: 10.1073/pnas.2314853121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/26/2023] [Indexed: 01/31/2024] Open
Abstract
Amino acid mutations that lower a protein's thermodynamic stability are implicated in numerous diseases, and engineered proteins with enhanced stability can be important in research and medicine. Computational methods for predicting how mutations perturb protein stability are, therefore, of great interest. Despite recent advancements in protein design using deep learning, in silico prediction of stability changes has remained challenging, in part due to a lack of large, high-quality training datasets for model development. Here, we describe ThermoMPNN, a deep neural network trained to predict stability changes for protein point mutations given an initial structure. In doing so, we demonstrate the utility of a recently released megascale stability dataset for training a robust stability model. We also employ transfer learning to leverage a second, larger dataset by using learned features extracted from ProteinMPNN, a deep neural network trained to predict a protein's amino acid sequence given its three-dimensional structure. We show that our method achieves state-of-the-art performance on established benchmark datasets using a lightweight model architecture that allows for rapid, scalable predictions. Finally, we make ThermoMPNN readily available as a tool for stability prediction and design.
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Affiliation(s)
- Henry Dieckhaus
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC27599
| | - Michael Brocidiacono
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC27599
| | - Nicholas Z. Randolph
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC27599
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC27599
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24
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Xu S, Xu X, Wang Z, Wu R. A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability. Angew Chem Int Ed Engl 2024; 63:e202315286. [PMID: 38117010 PMCID: PMC10981938 DOI: 10.1002/anie.202315286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
The N-termini of proteins can regulate their degradation, and the same protein with different N-termini may have distinct dynamics. Recently, it was found that N-terminal glycine can serve as a degron recognized by two E3 ligases, but N-terminal glycine was also reported to stabilize proteins. Here we developed a chemoenzymatic method for selective enrichment of proteoforms with N-terminal glycine and integrated dual protease cleavage to further improve the enrichment specificity. Over 2000 unique peptides with protein N-terminal glycine were analyzed from >1000 proteins, and most of them are previously unknown, indicating the effectiveness of the current method to capture low-abundance proteoforms with N-terminal glycine. The degradation rates of proteoforms with N-terminal glycine were quantified along with those of proteins from the whole proteome. Bioinformatic analyses reveal that proteoforms with N-terminal glycine with the fastest and slowest degradation rates have different functions and localizations. Membrane proteins with N-terminal glycine and proteins with N-terminal glycine from the N-terminal methionine excision degrade more rapidly. Furthermore, the secondary structures, adjacent amino acid residues, and protease specificities for N-terminal glycine are also vital for protein degradation. The results advance our understanding of the effects of N-terminal glycine on protein properties and functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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25
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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26
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Guo Y, Cheng R, Wang Y, Gonzalez ME, Zhang H, Liu Y, Kleer CG, Xue L. Regulation of EZH2 protein stability: new mechanisms, roles in tumorigenesis, and roads to the clinic. EBioMedicine 2024; 100:104972. [PMID: 38244292 PMCID: PMC10835131 DOI: 10.1016/j.ebiom.2024.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The importance of EZH2 as a key methyltransferase has been well documented theoretically. Practically, the first EZH2 inhibitor Tazemetostat (EPZ6438), was approved by FDA in 2020 and is used in clinic. However, for most solid tumors it is not as effective as desired and the scope of clinical indications is limited, suggesting that targeting its enzymatic activity may not be sufficient. Recent technologies focusing on the degradation of EZH2 protein have drawn attention due to their potential robust effects. This review focuses on the molecular mechanisms that regulate EZH2 protein stability via post-translational modifications (PTMs), mainly including ubiquitination, phosphorylation, and acetylation. In addition, we discuss recent advancements of multiple proteolysis targeting chimeras (PROTACs) strategies and the latest degraders that can downregulate EZH2 protein. We aim to highlight future directions to expand the application of novel EZH2 inhibitors by targeting both EZH2 enzymatic activity and protein stability.
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Affiliation(s)
- Yunyun Guo
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Rui Cheng
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Yuqing Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Maria E Gonzalez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Hongshan Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yang Liu
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
| | - Celina G Kleer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Lixiang Xue
- Cancer Center of Peking University Third Hospital, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
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27
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Monticelli M, Wright DM, Cubellis MV, Andreotti G. ReBaTSA: A simplified CeTSA protocol for studying recombinant mutant proteins in bacterial extracts. Biochim Biophys Acta Gen Subj 2024; 1868:130526. [PMID: 38049040 DOI: 10.1016/j.bbagen.2023.130526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023]
Abstract
INTRODUCTION The study of protein stability is crucial to biochemistry and relies on different methodologies. Recently, the Cellular Thermal Shift Assay has been introduced to study protein stability in whole cells. METHODS We report a novel application of CeTSA named ReBaTSA. This Recombinant Bacterial TSA was performed using clear extracts from bacteria expressing a recombinant protein, incubated at different temperatures, centrifuged and analyzed via SDS-PAGE. RESULTS AND CONCLUSIONS We demonstrated the feasibility and reliability of this simplified approach. We validated the method using the protein phosphomannomutase-2 and its common mutants, which were compared in the presence or the absence of a known ligand.
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Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy.
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
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28
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Lu J, Ge P, Sawaya MR, Hughes MP, Boyer DR, Cao Q, Abskharon R, Cascio D, Tayeb-Fligelman E, Eisenberg DS. Cryo-EM structures of the D290V mutant of the hnRNPA2 low-complexity domain suggests how D290V affects phase separation and aggregation. J Biol Chem 2024; 300:105531. [PMID: 38072051 PMCID: PMC10844680 DOI: 10.1016/j.jbc.2023.105531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 02/02/2024] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2) is a human ribonucleoprotein that transports RNA to designated locations for translation via its ability to phase separate. Its mutated form, D290V, is implicated in multisystem proteinopathy known to afflict two families, mainly with myopathy and Paget's disease of bone. Here, we investigate this mutant form of hnRNPA2 by determining cryo-EM structures of the recombinant D290V low complexity domain. We find that the mutant form of hnRNPA2 differs from the WT fibrils in four ways. In contrast to the WT fibrils, the PY-nuclear localization signals in the fibril cores of all three mutant polymorphs are less accessible to chaperones. Also, the mutant fibrils are more stable than WT fibrils as judged by phase separation, thermal stability, and energetic calculations. Similar to other pathogenic amyloids, the mutant fibrils are polymorphic. Thus, these structures offer evidence to explain how a D-to-V missense mutation diverts the assembly of reversible, functional amyloid-like fibrils into the assembly of pathogenic amyloid, and may shed light on analogous conversions occurring in other ribonucleoproteins that lead to neurological diseases such as amyotrophic lateral sclerosis and frontotemporal dementia.
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Affiliation(s)
- Jiahui Lu
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Peng Ge
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David R Boyer
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Duilio Cascio
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - Einav Tayeb-Fligelman
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, Molecular Biology Institute, Howard Hughes Medical Institute, Los Angeles, California, USA.
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Chaudhuri D, Chowdhury D, Chakraborty S, Bhatt M, Chowdhury R, Dutta A, Mistry A, Haldar S. Structurally different chemical chaperones show similar mechanical roles with independent molecular mechanisms. Nanoscale 2024; 16:2540-2551. [PMID: 38214221 DOI: 10.1039/d3nr00398a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Osmolytes are well known to protect the protein structure against different chemical and physical denaturants. Since their actions with protein surfaces are mechanistically complicated and context dependent, the underlying molecular mechanism is not fully understood. Here, we combined single-molecule magnetic tweezers and molecular dynamics (MD) simulation to explore the mechanical role of osmolytes from two different classes, trimethylamine N-oxide (TMAO) and trehalose, as mechanical stabilizers of protein structure. We observed that these osmolytes increase the protein L mechanical stability by decreasing unfolding kinetics while accelerating the refolding kinetics under force, eventually shifting the energy landscape toward the folded state. These osmolytes mechanically stabilize the protein L and plausibly guide them to more thermodynamically robust states. Finally, we observed that osmolyte-modulated protein folding increases mechanical work output up to twofold, allowing the protein to fold under a higher force regime and providing a significant implication for folding-induced structural stability in proteins.
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Affiliation(s)
- Deep Chaudhuri
- Department of Chemistry, Ashoka University, Sonepat, Haryana, India.
| | - Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Madhu Bhatt
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Rudranil Chowdhury
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Aakashdeep Dutta
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Ayush Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
| | - Shubhasis Haldar
- Department of Chemistry, Ashoka University, Sonepat, Haryana, India.
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal, India
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, India
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30
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Zhao H, Lu Y, Zhang J, Sun Z, Cheng C, Liu Y, Wu L, Zhang M, He W, Hao S, Li K. NCOA4 requires a [3Fe-4S] to sense and maintain the iron homeostasis. J Biol Chem 2024; 300:105612. [PMID: 38159858 PMCID: PMC10831263 DOI: 10.1016/j.jbc.2023.105612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
NCOA4 is a selective cargo receptor for ferritinophagy, the autophagic turnover of ferritin (FTH), a process critical for regulating intracellular iron bioavailability. However, how ferritinophagy flux is controlled through NCOA4 in iron-dependent processes needs to be better understood. Here, we show that the C-terminal FTH-binding domain of NCOA4 harbors a [3Fe-4S]-binding site with a stoichiometry of approximately one labile [3Fe-4S] cluster per NCOA4 monomer. By analyzing the interaction between NCOA4 and HERC2 ubiquitin ligase or NCOA4 and FTH, we demonstrate that NCOA4 regulates ferritinophagy by sensing the intracellular iron-sulfur cluster levels. Under iron-repletion conditions, HERC2 recognizes and recruits holo-NCOA4 as a substrate for polyubiquitination and degradation, favoring ferritin iron storage. Under iron-depletion conditions, NCOA4 exists in the form of apo-protein and binds ferritin to promote the occurrence of ferritinophagy and release iron. Thus, we identify an iron-sulfur cluster [3Fe-4S] as a critical cofactor in determining the fate of NCOA4 in favoring iron storage in ferritin or iron release via ferritinophagy and provide a dual mechanism for selective interaction between HERC2 and [3Fe-4S]-NCOA4 for proteasomal degradation or between ferritin and apo-NCOA4 for ferritinophagy in the control of iron homeostasis.
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Affiliation(s)
- Hongting Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Yao Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Jinghua Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Zichen Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Chen Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Yutong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Lin Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Meng Zhang
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Weijiang He
- School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Shuangying Hao
- School of Medicine, Henan Polytechnic University, Jiaozuo, China.
| | - Kuanyu Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China.
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31
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Xu X, Mao Y, Feng Z, Dai F, Gu T, Zheng J. SENP1 inhibits ferroptosis and promotes head and neck squamous cell carcinoma by regulating ACSL4 protein stability via SUMO1. Oncol Rep 2024; 51:34. [PMID: 38186303 PMCID: PMC10777466 DOI: 10.3892/or.2023.8693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/01/2023] [Indexed: 01/09/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is currently one of the most common malignancies with a poor prognosis worldwide. Meanwhile, small ubiquitin‑like modifier (SUMO) specific peptidase 1 (SENP1) was associated with ferroptosis. However, the specific functions and underlying mechanisms of action of SENP1 in ferroptosis and tumor progression of HNSCC remain to be established. The findings of the present study implicated a novel ferroptosis pathway in the initiation and progression of HNSCC, providing new functional targets to guide future therapy. In the present study, The Cancer Genome Atlas database was employed to establish a gene model related to ferroptosis and verified SENP1 as a key gene via transcriptome sequencing. Expression of SENP1 in HNSCC tissue and CAL‑27 cells was detected based on reverse transcription‑quantitative PCR and western blot analysis. Proliferation and migration abilities of cells were determined using Cell Counting Kit‑8, wound healing and Transwell experiments. Expression levels of iron, glutathione (GSH) and lipid peroxidation end‑product malondialdehyde (MDA) under conditions of silencing of SENP1 with shRNA lentivirus were assayed. Additionally, the relationship between SENP1 and long‑chain acyl‑coenzyme A synthase 4 (ACSL4) was validated with the aid of immunoblotting and co‑immunoprecipitation (co‑IP). Finally, the influence of shSENP1 on the expression of key ferroptosis proteins, glutathione peroxidase 4 (GPX4) and solute carrier family 7 member 11, was evaluated via western blotting. It was revealed that SENP1 was significantly overexpressed in HNSCC and associated with low patient survival. Silencing of SENP1 led to significant suppression of cell proliferation, migration and invasion, increase in the contents of iron ions and MDA and decline in GSH levels in HNSCC cells, thereby enhancing ferroptosis and inhibiting disease progression. Conversely, overexpression of SENP1 suppressed ferroptosis and promoted progression of HNSCC. Co‑IP and western blot analyses revealed a SUMOylation link between SENP1 and ACSL4. SENP1 reduced the stability of ACSL4 protein through deSUMOylation, leading to inhibition of ferroptosis. SENP1 silencing further inhibited the expression of the key iron death protein, GPX4, to regulate ferroptosis. Taken together, SENP1 deficiency promoted ferroptosis and inhibited tumor progression through reduction of SUMOylation of ACSL4 in HNSCC. The collective results of the present study supported the utility of SENP1 as an effective predictive biomarker for targeted treatment of HNSCC.
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Affiliation(s)
- Xianzhi Xu
- School of Stomatology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Yiting Mao
- School of Stomatology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Zhaowei Feng
- Department of Neurology, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, P.R. China
| | - Feng Dai
- Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, P.R. China
| | - Teng Gu
- School of Stomatology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Jiwei Zheng
- School of Stomatology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
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32
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Majumdar S, Rastogi H, Chowdhury PK. Bridging Soft Interaction and Excluded Volume in Crowded Milieu through Subtle Protein Dynamics. J Phys Chem B 2024; 128:716-730. [PMID: 38226816 DOI: 10.1021/acs.jpcb.3c07266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The impact of macromolecular crowding on biological macromolecules has been elucidated through the excluded volume phenomenon and soft interactions. However, it has often been difficult to provide a clear demarcation between the two regions. Here, using temperature-dependent dynamics (local and global) of the multidomain protein human serum albumin (HSA) in the presence of commonly used synthetic crowders (Dextran 40, PEG 8, Ficoll 70, and Dextran 70), we have shown the presence of a transition that serves as a bridge between the soft and hard regimes. The bridging region is independent of the crowder identity and displays no apparent correlation with the critical overlap concentration of the polymeric crowding agents. Moreover, the dynamics of domains I and II and the protein gating motion respond differently, thereby bringing to the fore the asymmetry underlying the crowder influence on HSA. In addition, solvent-coupled and decoupled protein motions indicate the heterogeneity of the dynamic landscape in the crowded milieu. We also propose an intriguing correlation between protein stability and dynamics, with increased global stability being accompanied by eased local domain motion.
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Affiliation(s)
- Shubhangi Majumdar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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33
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Li G, Yao S, Fan L. ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks. J Chem Inf Model 2024; 64:340-347. [PMID: 38166383 PMCID: PMC10806799 DOI: 10.1021/acs.jcim.3c01697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024]
Abstract
Protein thermodynamic stability is essential to clarify the relationships among structure, function, and interaction. Therefore, developing a faster and more accurate method to predict the impact of the mutations on protein stability is helpful for protein design and understanding the phenotypic variation. Recent studies have shown that protein embedding will be particularly powerful at modeling sequence information with context dependence, such as subcellular localization, variant effect, and secondary structure prediction. Herein, we introduce a novel method, ProSTAGE, which is a deep learning method that fuses structure and sequence embedding to predict protein stability changes upon single point mutations. Our model combines graph-based techniques and language models to predict stability changes. Moreover, ProSTAGE is trained on a larger data set, which is almost twice as large as the most used S2648 data set. It consistently outperforms all existing state-of-the-art methods on mutation-affected problems as benchmarked on several independent data sets. The protein embedding as the prediction input achieves better results than the previous results, which shows the potential of protein language models in predicting the effect of mutations on proteins. ProSTAGE is implemented as a user-friendly web server.
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Affiliation(s)
- Gen Li
- Production and R&D Center
I of LSS, GenScript (Shanghai) Biotech Co.,
Ltd., Shanghai 200131, China
| | - Sijie Yao
- Production and R&D Center
I of LSS, GenScript (Shanghai) Biotech Co.,
Ltd., Shanghai 200131, China
| | - Long Fan
- Production and R&D Center
I of LSS, GenScript (Shanghai) Biotech Co.,
Ltd., Shanghai 200131, China
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34
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Xie CTY, Pastore SF, Vincent JB, Frankland PW, Hamel PA. Nonsynonymous Mutations in Intellectual Disability and Autism Spectrum Disorder Gene PTCHD1 Disrupt N-Glycosylation and Reduce Protein Stability. Cells 2024; 13:199. [PMID: 38275824 PMCID: PMC10814814 DOI: 10.3390/cells13020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
PTCHD1 has been implicated in Autism Spectrum Disorders (ASDs) and/or intellectual disability, where copy-number-variant losses or loss-of-function coding mutations segregate with disease in an X-linked recessive fashion. Missense variants of PTCHD1 have also been reported in patients. However, the significance of these mutations remains undetermined since the activities, subcellular localization, and regulation of the PTCHD1 protein are currently unknown. This paucity of data concerning PTCHD1 prevents the effective evaluation of sequence variants identified during diagnostic screening. Here, we characterize PTCHD1 protein binding partners, extending previously reported interactions with postsynaptic scaffolding protein, SAP102. Six rare missense variants of PTCHD1 were also identified from patients with neurodevelopmental disorders. After modelling these variants on a hypothetical three-dimensional structure of PTCHD1, based on the solved structure of NPC1, PTCHD1 variants harboring these mutations were assessed for protein stability, post-translational processing, and protein trafficking. We show here that the wild-type PTCHD1 post-translational modification includes complex N-glycosylation and that specific mutant proteins disrupt normal N-link glycosylation processing. However, regardless of their processing, these mutants still localized to PSD95-containing dendritic processes and remained competent for complexing SAP102.
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Affiliation(s)
- Connie T. Y. Xie
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephen F. Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Paul W. Frankland
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Psychology, University of Toronto, Toronto, ON M5S 3G3, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul A. Hamel
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
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35
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Ogawa Y, Ueda TP, Obara K, Nishimura K, Kamura T. Targeted Protein Degradation Systems: Controlling Protein Stability Using E3 Ubiquitin Ligases in Eukaryotic Species. Cells 2024; 13:175. [PMID: 38247866 PMCID: PMC10814424 DOI: 10.3390/cells13020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This review explores various methods for modulating protein stability to achieve target protein degradation, which is a crucial aspect in the study of biological processes and drug design. Thirty years have passed since the introduction of heat-inducible degron cells utilizing the N-end rule, and methods for controlling protein stability using the ubiquitin-proteasome system have moved from academia to industry. This review covers protein stability control methods, from the early days to recent advancements, and discusses the evolution of techniques in this field. This review also addresses the challenges and future directions of protein stability control techniques by tracing their development from the inception of protein stability control methods to the present day.
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Affiliation(s)
| | | | | | - Kohei Nishimura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan; (Y.O.); (T.P.U.); (K.O.)
| | - Takumi Kamura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan; (Y.O.); (T.P.U.); (K.O.)
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36
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Liu Q, Yang H, Luo J, Peng C, Wang K, Zhang G, Lin H, Ji Z. 14-3-3 protein augments the protein stability of phosphorylated spastin and promotes the recovery of spinal cord injury through its agonist intervention. eLife 2024; 12:RP90184. [PMID: 38231910 PMCID: PMC10945579 DOI: 10.7554/elife.90184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
Axon regeneration is abortive in the central nervous system following injury. Orchestrating microtubule dynamics has emerged as a promising approach to improve axonal regeneration. The microtubule severing enzyme spastin is essential for axonal development and regeneration through remodeling of microtubule arrangement. To date, however, little is known regarding the mechanisms underlying spastin action in neural regeneration after spinal cord injury. Here, we use glutathione transferase pulldown and immunoprecipitation assays to demonstrate that 14-3-3 interacts with spastin, both in vivo and in vitro, via spastin Ser233 phosphorylation. Moreover, we show that 14-3-3 protects spastin from degradation by inhibiting the ubiquitination pathway and upregulates the spastin-dependent severing ability. Furthermore, the 14-3-3 agonist Fusicoccin (FC-A) promotes neurite outgrowth and regeneration in vitro which needs spastin activation. Western blot and immunofluorescence results revealed that 14-3-3 protein is upregulated in the neuronal compartment after spinal cord injury in vivo. In addition, administration of FC-A not only promotes locomotor recovery, but also nerve regeneration following spinal cord injury in both contusion and lateral hemisection models; however, the application of spastin inhibitor spastazoline successfully reverses these phenomena. Taken together, these results indicate that 14-3-3 is a molecular switch that regulates spastin protein levels, and the small molecule 14-3-3 agonist FC-A effectively mediates the recovery of spinal cord injury in mice which requires spastin participation.
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Affiliation(s)
- Qiuling Liu
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Hua Yang
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Jianxian Luo
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Cheng Peng
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Ke Wang
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Guowei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Hongsheng Lin
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Zhisheng Ji
- Department of Orthopedics, The First Affiliated Hospital of Jinan UniversityGuangzhouChina
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37
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Precupas A, Popa VT. Impact of Sinapic Acid on Bovine Serum Albumin Thermal Stability. Int J Mol Sci 2024; 25:936. [PMID: 38256010 PMCID: PMC10815719 DOI: 10.3390/ijms25020936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The thermal stability of bovine serum albumin (BSA) in Tris buffer, as well as the effect of sinapic acid (SA) on protein conformation were investigated via calorimetric (differential scanning microcalorimetry-μDSC), spectroscopic (dynamic light scattering-DLS; circular dichroism-CD), and molecular docking approaches. μDSC data revealed both the denaturation (endotherm) and aggregation (exotherm) of the protein, demonstrating the dual effect of SA on protein thermal stability. With an increase in ligand concentration, (i) protein denaturation shifts to a higher temperature (indicating native form stabilization), while (ii) the aggregation process shifts to a lower temperature (indicating enhanced reactivity of the denatured form). The stabilization effect of SA on the native structure of the protein was supported by CD results. High temperature (338 K) incubation induced protein unfolding and aggregation, and increasing the concentration of SA altered the size distribution of the protein population, as DLS measurements demonstrated. Complementary information offered by molecular docking allowed for the assessment of the ligand binding within the Sudlow's site I of the protein. The deeper insight into the SA-BSA interaction offered by the present study may serve in the clarification of ligand pharmacokinetics and pharmacodynamics, thus opening paths for future research and therapeutic applications.
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Affiliation(s)
| | - Vlad Tudor Popa
- “Ilie Murgulescu” Institute of Physical Chemistry, Romanian Academy, Splaiul Independentei 202, 060021 Bucharest, Romania;
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38
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Liu B, Jiang Y, Yang Y, Chen JX. OmeDDG: Improved Protein Mutation Stability Prediction Based on Predicted 3D Structures. J Phys Chem B 2024; 128:67-76. [PMID: 38130113 DOI: 10.1021/acs.jpcb.3c05601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Determining changes in the protein's thermal stability following mutations is critical in protein engineering and understanding pathogenic missense mutations. Despite the development of various computational methods to predict the effects of single-point mutations, their accuracy remains limited. In this study, we propose a new computational method, OmeDDG, that more accurately predicts mutation-induced Gibbs free energy changes in protein folding (ΔΔG). OmeDDG takes the sequences of wild-type and mutant proteins as input, utilizes OmegaFold to obtain the 3D structure, employs a convolutional neural network to extract structural features, and combines them with protein mutation features and pretraining features to predict the stability of single-point mutations in proteins. We performed a comprehensive comparison between OmeDDG and other available prediction methods on four blind test datasets, confirming that OmeDDG can effectively enhance protein mutation prediction performance. Notably, on the antisymmetric dataset Ssym, OmeDDG achieves the best performance, demonstrating favorable antisymmetry with PCC = 0.79 and RMSE = 0.96 for forward mutations and PCC = 0.77 and RMSE = 0.97 for reverse mutant types.
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Affiliation(s)
- Baoying Liu
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
| | - Yongquan Jiang
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
- Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
| | - Yan Yang
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
- Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
| | - Jim X Chen
- Department of Computer Science, George Mason University, Fairfax, Virginia 22030-4444, United States
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39
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Chen CH, Lin HW, Huang MF, Chiang CW, Lee KH, Phuong NT, Cai ZY, Chang WC, Lin DY. Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function. BMC Mol Cell Biol 2024; 25:2. [PMID: 38172660 PMCID: PMC10765799 DOI: 10.1186/s12860-023-00498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Fas-associated factor 1 (FAF1) is a multidomain protein that interacts with diverse partners to affect numerous cellular processes. Previously, we discovered two Small Ubiquitin-like Modifier (SUMO)-interacting motifs (SIMs) within FAF1 that are crucial for transcriptional modulation of mineralocorticoid receptor. Recently, we identified Sin3A-associated protein 130 (SAP130), a putative sumoylated protein, as a candidate FAF1 interaction partner by yeast two-hybrid screening. However, it remained unclear whether SAP130 sumoylation might occur and functionally interact with FAF1. RESULTS In this study, we first show that SAP130 can be modified by SUMO1 at Lys residues 794, 878 and 932 both in vitro and in vivo. Mutation of these three SUMO-accepting Lys residues to Ala had no impact on SAP130 association with Sin3A or its nuclear localization, but the mutations abrogated the association of SAP130 with the FAF1. The mutations also potentiated SAP130 trans-repression activity and attenuated SAP130-mediated promotion of cell growth. Additionally, SUMO1-modified SAP130 was less stable than unmodified SAP130. Transient transfection experiments further revealed that FAF1 mitigated the trans-repression and cell proliferation-promoting functions of SAP130, and promoted SAP130 degradation by enhancing its polyubiquitination in a sumoylation-dependent manner. CONCLUSIONS Together, these results demonstrate that sumoylation of SAP130 regulates its biological functions and that FAF1 plays a crucial role in controlling the SUMO-dependent regulation of transcriptional activity and protein stability of SAP130.
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Affiliation(s)
- Chang-Han Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, 407219, Taiwan, ROC
- Department of Applied Chemistry, and Graduate Institute of Biomedicine and Biomedical Technology, National Chi Nan University, Nantou, 545301, Taiwan, ROC
| | - Hung-Wei Lin
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC
| | - Meng-Fang Huang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC
| | - Chi-Wu Chiang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC
| | - Kuen-Haur Lee
- Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan, ROC
| | - Nguyen Thanh Phuong
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC
| | - Zong-Yan Cai
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC
| | - Wen-Chang Chang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei Medical University, Taipei, 11031, Taiwan, ROC
| | - Ding-Yen Lin
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan, ROC.
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40
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Javanshad R, Panth R, Venter AR. Effects of Amino Acid Additives on Protein Stability during Electrothermal Supercharging in ESI-MS. J Am Soc Mass Spectrom 2024; 35:151-157. [PMID: 38078777 DOI: 10.1021/jasms.3c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The surprising formation of highly charged protein ions from aqueous ammonium bicarbonate solution is a fascinating phenomenon referred to as electrothermal supercharging (ETS). Although the precise mechanism involved is not clearly understood, previous studies predominantly suggest that ETS is due to native protein destabilization in the presence of bicarbonate anion inside the electrospray ionization droplets under high temperatures and spray voltages. To evaluate existing hypotheses surrounding the underlying mechanism of ETS, the effects of several additives on protein charging under ETS conditions were investigated. The changes in the protein charge state distributions were compared by measuring the ratios between the intensities of highest intensity charge states of native and unfolded protein envelopes and shifts in the lowest and highest observed charge states. This study demonstrated that source temperature plays a more important role in ETS compared to spray voltage, especially when using a nebulized microelectrospray ionization source. Moreover, the effect of amino acids on ETS were generally in good agreement with the extensive literature available on the stabilization or destabilization of proteins by these additives in bulk solution. Among the natural amino acids, protein supercharging was significantly reduced by proline and glycine; however, imidazole provided the highest degree of noncovalent complex stabilization against ETS, outperforming the amino acids. Overall, our study shows that the simple addition of stabilizing reagents such as proline and imidazole can reduce the extent of apparent protein unfolding and supercharging in ammonium bicarbonate solution and provide evidence against the roles of charge depletion and thermal unfolding during ETS.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Rajendra Panth
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
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41
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Dai L, Davis J, Nagapudi K, Mantik P, Zhang K, Pellett JD, Wei B. Predicting Long-Term Stability of an Oral Delivered Antibody Drug Product with Accelerated Stability Assessment Program Modeling. Mol Pharm 2024; 21:325-332. [PMID: 38060811 DOI: 10.1021/acs.molpharmaceut.3c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2024]
Abstract
The oral delivery of protein therapeutics offers numerous advantages for patients but also presents significant challenges in terms of development. Currently, there is limited knowledge available regarding the stability and shelf life of orally delivered protein therapeutics. In this study, a comprehensive assessment of the stability of an orally delivered solid dosage variable domain of heavy-chain antibody (VHH antibody) drug product was conducted. Four stability related quality attributes that undergo change as a result of thermal and humidity stress were identified. Subsequently, these attributes were modeled using an accelerated stability approach facilitated by ASAPprime software. To the best of our knowledge, this is the first time that this approach has been reported for an antibody drug product. We observed overall good model quality and accurate predictions regarding the protein stability during storage. Notably, we discovered that protein aggregation, formed through a degradation pathway, requires additional adjustments to the modeling method. In summary, the ASAP approach demonstrated promising results in predicting the stability of this complex solid-state protein formulation. This study sheds light on the stability and shelf life of orally delivered protein therapeutics, addressing an important knowledge gap in the field.
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Affiliation(s)
- Lulu Dai
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
| | - Jeff Davis
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
| | - Karthik Nagapudi
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
| | - Priscilla Mantik
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
| | - Jackson D Pellett
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
| | - Bingchuan Wei
- Synthetic Molecule Pharmaceutical Science, Early Research and Development, Genentech, South San Francisco, California 94080, United States
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42
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Pearce A, Ponnam S, Holt MR, Randall T, Beckingham R, Kho AL, Kampourakis T, Ehler E. Missense mutations in the central domains of cardiac myosin binding protein-C and their potential contribution to hypertrophic cardiomyopathy. J Biol Chem 2024; 300:105511. [PMID: 38042491 PMCID: PMC10772716 DOI: 10.1016/j.jbc.2023.105511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023] Open
Abstract
Myosin binding protein-C (MyBP-C) is a multidomain protein that regulates muscle contraction. Mutations in MYBPC3, the gene encoding for the cardiac variant (henceforth called cMyBP-C), are amongst the most frequent causes of hypertrophic cardiomyopathy. Most mutations lead to a truncated version of cMyBP-C, which is most likely unstable. However, missense mutations have also been reported, which tend to cluster in the central domains of the cMyBP-C molecule. This suggests that these central domains are more than just a passive spacer between the better characterized N- and C-terminal domains. Here, we investigated the potential impact of four different missense mutations, E542Q, G596R, N755K, and R820Q, which are spread over the domains C3 to C6, on the function of MyBP-C on both the isolated protein level and in cardiomyocytes in vitro. Effect on domain stability, interaction with thin filaments, binding to myosin, and subcellular localization behavior were assessed. Our studies show that these missense mutations result in slightly different phenotypes at the molecular level, which are mutation specific. The expected functional readout of each mutation provides a valid explanation for why cMyBP-C fails to work as a brake in the regulation of muscle contraction, which eventually results in a hypertrophic cardiomyopathy phenotype. We conclude that missense mutations in cMyBP-C must be evaluated in context of their domain localization, their effect on interaction with thin filaments and myosin, and their effect on protein stability to explain how they lead to disease.
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Affiliation(s)
- Amy Pearce
- School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, United Kingdom; British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom
| | - Saraswathi Ponnam
- British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics (School of Basic and Biosciences), King's College London, London, United Kingdom
| | - Mark R Holt
- School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, United Kingdom; British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom
| | - Thomas Randall
- School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, United Kingdom; British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom
| | - Rylan Beckingham
- School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, United Kingdom; British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom
| | - Ay Lin Kho
- British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics (School of Basic and Biosciences), King's College London, London, United Kingdom
| | - Thomas Kampourakis
- British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics (School of Basic and Biosciences), King's College London, London, United Kingdom
| | - Elisabeth Ehler
- School of Cardiovascular and Metabolic Medicine and Sciences, King's College London, London, United Kingdom; British Heart Foundation Centre of Research Excellence, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics (School of Basic and Biosciences), King's College London, London, United Kingdom.
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43
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Monteiro APF, Pérez-Jiménez A, Spitzlei C, Caucheteux J, Alves VD, Lambert S, Grandfils C. Interpenetrating alginate network as drug delivery matrix: Effects on protein stability and release. J Biomed Mater Res B Appl Biomater 2024; 112:e35354. [PMID: 37986690 DOI: 10.1002/jbm.b.35354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/26/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
The study investigates the rheological properties and protein release capacity of a uniform hydrogel composed of sodium alginate (SA) and poloxamer (P407). The hydrogel is prepared through the sustained release of calcium ions, resulting in a reinforced and homogeneous interpenetrating networks (IPNs) of SA and P407 polymeric chains. By adjusting the amount of crosslink agent, the hydrogel exhibites an adjustable dissolution ratio and adaptable gelling time. Moreover, the composite showed a well-structured network and superior mechanical strength, enabling the sustained release of both calcium ions and Soybean Trypsin Inhibitor (STI) protein, a model of Bone Morphogenic Protein (BMP). Importantly, the protein release kinetic can be tuned based on the SA content in the polymeric blend, highlighting the versatile nature of this hydrogel for drug delivery purposes.
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Affiliation(s)
- Ana P F Monteiro
- Interfaculty Research Center of Biomaterials (CEIB), University of Liège, Liège, Belgium
- Department of Chemical Engineering - Nanomaterials, Catalysis and Electrochemistry (NCE), University of Liège, Liège, Belgium
| | - Aurora Pérez-Jiménez
- Interfaculty Research Center of Biomaterials (CEIB), University of Liège, Liège, Belgium
| | - Claire Spitzlei
- Interfaculty Research Center of Biomaterials (CEIB), University of Liège, Liège, Belgium
| | - Joachim Caucheteux
- Interfaculty Research Center of Biomaterials (CEIB), University of Liège, Liège, Belgium
| | - Vitor Delgado Alves
- LEAF-Linking Landscape Environment Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Stéphanie Lambert
- Department of Chemical Engineering - Nanomaterials, Catalysis and Electrochemistry (NCE), University of Liège, Liège, Belgium
| | - Christian Grandfils
- Interfaculty Research Center of Biomaterials (CEIB), University of Liège, Liège, Belgium
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Holler CV, Petersson NM, Brohus M, Niemelä MA, Iversen ED, Overgaard MT, Iwaï H, Wimmer R. Allosteric changes in protein stability and dynamics as pathogenic mechanism for calmodulin variants not affecting Ca 2+ coordinating residues. Cell Calcium 2024; 117:102831. [PMID: 37995470 DOI: 10.1016/j.ceca.2023.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023]
Abstract
Mutations in the small, calcium-sensing, protein calmodulin cause cardiac arrhythmia and can ultimately prove lethal. Here, we report the impact of the G113R variant on the structure and dynamics of the calmodulin molecule, both in the presence and in the absence of calcium. We show that the mutation introduces minor changes into the structure of calmodulin and that it changes the thermostability and thus the degree of foldedness at human body temperature. The mutation also severely impacts the intramolecular mobility of calmodulin, especially in the apo form. Glycine 113 acts as an alpha-helical C-capping residue in both apo/ - and Ca2+/calmodulin, but its exchange to arginine has very different effects on the apo and Ca2+ forms. The majority of arrhythmogenic calmodulin variants identified affects residues in the Ca2+ coordinating loops of the two C-domain EF-Hands, causing a 'direct impact on Ca2+ binding'. However, G113R lies outside a Ca2+ coordinating loop and acts differently and more similar to the previously characterized arrhythmogenic N53I. Therefore, we suggest that altered apo/CaM dynamics may be a novel general disease mechanism, defining low-calcium target affinity - or Ca2+ binding kinetics - critical for timely coordination of essential ion-channels in the excitation-contraction cycle.
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Affiliation(s)
- Christina Vallentin Holler
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg, Denmark
| | - Nina Møller Petersson
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg, Denmark
| | - Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg, Denmark
| | | | - Emil Drivsholm Iversen
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg, Denmark
| | - Michael Toft Overgaard
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg, Denmark
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers vej 7H, 9220 Aalborg, Denmark.
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45
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Ma X, Wan R, Wen Y, Liu T, Song Y, Zhu Y. Deubiquitinating enzyme OTUD4 regulates metastasis in triple-negative breast cancer by stabilizing Snail1. Exp Cell Res 2024; 434:113864. [PMID: 38040050 DOI: 10.1016/j.yexcr.2023.113864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
Metastasis is the primary cause of cancer-related deaths and remains poorly understood. Deubiquitinase OTU domain containing 4 (OTUD4) has been reported to regulate antiviral immune responses and resistance to radio- or chemo-therapies in certain cancers. However, the role of OTUD4 in cancer metastasis remain unknown. Here, we demonstrate that the depletion of OTUD4 in triple-negative breast cancer (TNBC) cells markedly suppress cell clonogenic ability, migration, invasion and cancer stem cell population in vitro as well as metastasis in vivo. Mechanistically, the tumor promoting function of OTUD4 is mainly mediated by deuiquitinating and stabilizing Snail1, one key transcriptional factor in the epithelial-mesenchymal transition. The inhibitory effect of targeting OTUD4 could be largely reversed by the reconstitution of Snail1 in OTUD4-deficient cells. Overall, our study establishes the OTUD4-Snail1 axis as an important regulatory mechanism of breast cancer metastasis and provides a rationale for potential therapeutic interventions in the treatment of TNBC.
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Affiliation(s)
- Xiuqing Ma
- College of Pharmacy/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, China
| | - Rui Wan
- College of Pharmacy/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, China
| | - Yalei Wen
- Guangdong Second Provincial General Hospital, Research Institute for Maternal and Child Health, Jinan University, Guangzhou, China
| | - Tongzheng Liu
- College of Pharmacy/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, China.
| | - Yan Song
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical, Sciences and Peking Union Medical College, Beijing, China.
| | - Yingjie Zhu
- College of Pharmacy/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou, China.
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46
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Ling X, Liu L, Jiang A, Shi X, Liu L, Wang X, Lu C, Ren C, Yu Z. PFKFB3 promotes endometriosis cell proliferation via enhancing the protein stability of β-catenin. Mol Cell Endocrinol 2024; 579:112083. [PMID: 37820851 DOI: 10.1016/j.mce.2023.112083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023]
Abstract
Endometriosis is a common inflammatory disease in women of reproductive age and is highly associated with infertility. However, the molecular mechanism of endometriosis remains unclear. 6-Phosphofructose-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) is a key enzyme in glycolysis and plays an important regulatory role in the development of cancer. Here we found that PFKFB3 is highly expressed in endometriotic tissues. PFKFB3 promotes the proliferation and growth of endometriosis cells. Meanwhile, PFKFB3 promotes glycolysis in endometriosis cells. Furthermore, PFKFB3 promotes migration and invasion of endometriosis cells. On this basis, we found that PFKFB3 promotes epithelial-mesenchymal transition (EMT) in endometriosis cells. PFKFB3 interacts with the essential factor of EMT, β-catenin, and promotes the protein stability of β-catenin. In addition, the PFKFB3 inhibitor PFK-015 inhibites the growth of endometriosis cells and the development of endometrial tissue. In conclusion, our study shows that PFKFB3 plays an important role in the development of endometriosis and provides new ideas for the clinical diagnosis or treatment of endometriosis.
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Affiliation(s)
- Xi Ling
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China; School of Clinical Medicine, Weifang Medical University, Weifang, Shandong Province, PR China
| | - Lan Liu
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China; School of Clinical Medicine, Weifang Medical University, Weifang, Shandong Province, PR China
| | - Aifang Jiang
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China
| | - Xiaodan Shi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, PR China
| | - Lu Liu
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China; School of Clinical Medicine, Weifang Medical University, Weifang, Shandong Province, PR China
| | - Xiaoyun Wang
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China; School of Clinical Medicine, Weifang Medical University, Weifang, Shandong Province, PR China
| | - Chao Lu
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China
| | - Chune Ren
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China.
| | - Zhenhai Yu
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, PR China.
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Zheng F, Liu Y, Yang Y, Wen Y, Li M. Assessing computational tools for predicting protein stability changes upon missense mutations using a new dataset. Protein Sci 2024; 33:e4861. [PMID: 38084013 PMCID: PMC10751734 DOI: 10.1002/pro.4861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/14/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
Insight into how mutations affect protein stability is crucial for protein engineering, understanding genetic diseases, and exploring protein evolution. Numerous computational methods have been developed to predict the impact of amino acid substitutions on protein stability. Nevertheless, comparing these methods poses challenges due to variations in their training data. Moreover, it is observed that they tend to perform better at predicting destabilizing mutations than stabilizing ones. Here, we meticulously compiled a new dataset from three recently published databases: ThermoMutDB, FireProtDB, and ProThermDB. This dataset, which does not overlap with the well-established S2648 dataset, consists of 4038 single-point mutations, including over 1000 stabilizing mutations. We assessed these mutations using 27 computational methods, including the latest ones utilizing mega-scale stability datasets and transfer learning. We excluded entries with overlap or similarity to training datasets to ensure fairness. Pearson correlation coefficients for the tested tools ranged from 0.20 to 0.53 on unseen data, and none of the methods could accurately predict stabilizing mutations, even those performing well in anti-symmetric property analysis. While most methods present consistent trends for predicting destabilizing mutations across various properties such as solvent exposure and secondary conformation, stabilizing mutations do not exhibit a clear pattern. Our study also suggests that solely addressing training dataset bias may not significantly enhance accuracy of predicting stabilizing mutations. These findings emphasize the importance of developing precise predictive methods for stabilizing mutations.
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Affiliation(s)
- Feifan Zheng
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Yang Liu
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Yan Yang
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Yuhao Wen
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Minghui Li
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
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Lan T, Geng XJ, Zhang SJ, Zeng XX, Ying JJ, Xu Y, Liu SY, Li P, Tong YH, Wang W, Mao ZJ, Wang SW. Si-Ni-San inhibits hepatic Fasn expression and lipid accumulation in MAFLD mice through AMPK/p300/SREBP-1c axis. Phytomedicine 2024; 123:155209. [PMID: 37984123 DOI: 10.1016/j.phymed.2023.155209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/22/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Soothing the liver and regulating qi is one of the core ideas of traditional Chinese medicine (TCM) in the treatment of fatty liver. Si-Ni-San (SNS) is a well-known herbal formula in TCM for liver soothing and qi regulation in fatty liver treatment. However, its efficacy lacks modern scientific evidence. PURPOSE This study was aimed to investigate the impact of SNS on metabolic associated fatty liver disease (MAFLD) in mice and explore the underlying molecular mechanisms, particularly its effects on lipid metabolism in hepatocytes. METHODS The therapeutic effect of SNS was evaluated using in vivo and in vitro models of high-fat/high-cholesterol (HFHC) diet-induced mice and palmitic acid (PA)-induced hepatocytes, respectively. Molecular biological techniques such as RNA-sequencing (RNA-seq), co-immunoprecipitation (co-IP), and western blotting were employed to elucidate the molecular mechanism of SNS in regulating lipid metabolism in hepatocytes. RESULTS Our findings revealed that SNS effectively reduced lipid accumulation in the livers of HFHC diet-induced mice and PA-induced hepatocytes. RNA-seq analysis demonstrated that SNS significantly down-regulated the expression of fatty acid synthase (Fasn) in the livers of HFHC-fed mice. Mechanistically, SNS inhibited Fasn expression and lipid accumulation by activating adenosine monophosphate (AMP)-activated protein kinase (AMPK). Activation of AMPK suppressed the activity of the transcriptional coactivator p300 and modulated the protein stability of sterol regulatory element-binding protein-1c (SREBP-1c). Importantly, p300 was required for the inhibition of Fasn expression and lipid accumulation by SNS. Furthermore, SNS activated AMPK by decreasing adenosine triphosphate (ATP) production in hepatocytes. CONCLUSION This study provided novel evidence on the regulatory mechanisms underlying the effects of SNS on Fasn expression. Our findings demonstrate, for the first time, that SNS exerts suppressive effects on Fasn expression through modulation of the AMPK/p300/SREBP-1c axis. Consequently, this regulatory pathway mitigates excessive lipid accumulation and ameliorates MAFLD in mice.
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Affiliation(s)
- Tian Lan
- The Joint Innovation Center for Health & Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Xiao-Juan Geng
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Si-Jia Zhang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xi-Xi Zeng
- The Joint Innovation Center for Health & Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Jun-Jie Ying
- The Joint Innovation Center for Health & Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Yi Xu
- The Joint Innovation Center for Health & Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Shi-Yu Liu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ping Li
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yu-Hua Tong
- The Joint Innovation Center for Health & Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China; Department of Ophthalmology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Wen Wang
- Preventive Treatment Center, Zhejiang Chinese Medical University Affiliated Four-provinces Marginal Hospital of Traditional Chinese Medicine, Quzhou Hospital of Traditional Chinese Medicine, Quzhou 324000, China.
| | - Zhu-Jun Mao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China; Department of Ophthalmology, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China.
| | - Si-Wei Wang
- The Joint Innovation Center for Health & Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China.
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49
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Lin N, Zhang Y, Song X, Xu J, Luo C, Tian Q, Yao K, Wu W, Chen X, Hu L. Cataract-causing mutations S78F and S78P of γD-crystallin decrease protein conformational stability and drive aggregation. Int J Biol Macromol 2023; 253:126910. [PMID: 37739288 DOI: 10.1016/j.ijbiomac.2023.126910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/28/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
Congenital cataract is the leading cause of childhood blindness, which primarily results from genetic factors. γD-crystallin is the most abundant γ-crystallin and is essential for maintaining lens transparency and refractivity. Numerous mutations in γD-crystallin have been reported with unclear pathogenic mechanism. Two different cataract-causing mutations Ser78Phe and Ser78Pro in γD-crystallin were previously identified at the same conserved Ser78 residue. In this work, firstly, we purified the mutants and characterized for the structural change using fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and size-exclusion chromatography (SEC). Both mutants were prone to form insoluble precipitates when expressed in Escherichia coli strain BL21 (DE3) cells. Compared with wild-type (WT), both mutations caused structural disruption, increased hydrophobic exposure, decreased solubility, and reduced thermal stability. Next, we investigated the aggregation of the mutants at the cellular level. Overexpression the mutants in HLE-B3 and HEK 293T cells could induce aggresome formations. The environmental stresses (including heat, ultraviolet irradiation and oxidative stress) promoted the formation of aggregates. Moreover, the intracellular S78F and S78P aggregates could be reversed by lanosterol. Molecular dynamic simulation indicated that both mutations disrupted the structural integrity of Greek-key motif 2. Hence, our results reveal the vital role of conserved Ser78 in maintaining the structural stability, which can offer new insights into the mechanism of cataract formation.
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Affiliation(s)
- Ningqin Lin
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, China; Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310020, China
| | - Ying Zhang
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310020, China
| | - Xiaohui Song
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China
| | - Jingjie Xu
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China
| | - Chenqi Luo
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China
| | - Qing Tian
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310020, China
| | - Ke Yao
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China
| | - Wei Wu
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China.
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou 310009, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310020, China.
| | - Lidan Hu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, China.
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Gomes I, Galamba N. Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving? J Chem Phys 2023; 159:235101. [PMID: 38099555 DOI: 10.1063/5.0177095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:ζ; ζ = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes' preferential exclusion/preferential hydration mechanism. Although the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where β-fluctuations are key, with the non-monotonic hydration of some amino acids with the water content providing an explanation to the non-monotonic folding of some proteins in aqueous DESs. A major thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism.
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Affiliation(s)
- Inês Gomes
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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