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de Araújo EA, Cortez AA, Pellegrini VDOA, Vacilotto MM, Cruz AF, Batista PR, Polikarpov I. Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9. Carbohydr Polym 2024; 329:121739. [PMID: 38286536 DOI: 10.1016/j.carbpol.2023.121739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/31/2024]
Abstract
Carbohydrate-active enzymes from the glycoside hydrolase family 9 (GH9) play a key role in processing lignocellulosic biomass. Although the structural features of some GH9 enzymes are known, the molecular mechanisms that drive their interactions with cellulosic substrates remain unclear. To investigate the molecular mechanisms that the two-domain Bacillus licheniformis BlCel9A enzyme utilizes to depolymerize cellulosic substrates, we used a combination of biochemical assays, X-ray crystallography, small-angle X-ray scattering, and molecular dynamics simulations. The results reveal that BlCel9A breaks down cellulosic substrates, releasing cellobiose and glucose as the major products, but is highly inefficient in cleaving oligosaccharides shorter than cellotetraose. In addition, fungal lytic polysaccharide oxygenase (LPMO) TtLPMO9H enhances depolymerization of crystalline cellulose by BlCel9A, while exhibiting minimal impact on amorphous cellulose. The crystal structures of BlCel9A in both apo form and bound to cellotriose and cellohexaose were elucidated, unveiling the interactions of BlCel9A with the ligands and their contribution to substrate binding and products release. MD simulation analysis reveals that BlCel9A exhibits higher interdomain flexibility under acidic conditions, and SAXS experiments indicate that the enzyme flexibility is induced by pH and/or temperature. Our findings provide new insights into BlCel9A substrate specificity and binding, and synergy with the LPMOs.
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Affiliation(s)
- Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Giuseppe Maximo Scolfaro, 10000, Campinas, SP 13083-970, Brazil; Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Anelyse Abreu Cortez
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | | | - Milena Moreira Vacilotto
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Amanda Freitas Cruz
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Paulo Ricardo Batista
- Oswaldo Cruz Foundation, Scientific Computing Programme, Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Igor Polikarpov
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil.
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152
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Vela‐Rodríguez C, Yang C, Alanen HI, Eki R, Abbas TA, Maksimainen MM, Glumoff T, Duman R, Wagner A, Paschal BM, Lehtiö L. Oligomerization mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor. Protein Sci 2024; 33:e4945. [PMID: 38511494 PMCID: PMC10955461 DOI: 10.1002/pro.4945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Deltex proteins are a family of E3 ubiquitin ligases that encode C-terminal RING and DTC domains that mediate interactions with E2 ubiquitin-conjugating enzymes and recognize ubiquitination substrates. DTX3L is unique among the Deltex proteins based on its N-terminal domain architecture. The N-terminal D1 and D2 domains of DTX3L mediate homo-oligomerization, and the D3 domain interacts with PARP9, a protein that contains tandem macrodomains with ADP-ribose reader function. While DTX3L and PARP9 are known to heterodimerize, and assemble into a high molecular weight oligomeric complex, the nature of the oligomeric structure, including whether this contributes to the ADP-ribose reader function is unknown. Here, we report a crystal structure of the DTX3L N-terminal D2 domain and show that it forms a tetramer with, conveniently, D2 symmetry. We identified two interfaces in the structure: a major, conserved interface with a surface of 973 Å2 and a smaller one of 415 Å2. Using native mass spectrometry, we observed molecular species that correspond to monomers, dimers and tetramers of the D2 domain. Reconstitution of DTX3L knockout cells with a D1-D2 deletion mutant showed the domain is dispensable for DTX3L-PARP9 heterodimer formation, but necessary to assemble an oligomeric complex with efficient reader function for ADP-ribosylated androgen receptor. Our results suggest that homo-oligomerization of DTX3L is important for the DTX3L-PARP9 complex to read mono-ADP-ribosylation on a ligand-regulated transcription factor.
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Affiliation(s)
- Carlos Vela‐Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Chunsong Yang
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Heli I. Alanen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Rebeka Eki
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Tarek A. Abbas
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Bryce M. Paschal
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
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153
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An D, Chen X, Li Z, Dai L, Huang J, Xiao M, Liu H, Xu J, Ruan Y. Genetic variation in the BLM gene and its expression in the ovaries is closely related to kidding number in goats. Theriogenology 2024; 218:254-266. [PMID: 38367334 DOI: 10.1016/j.theriogenology.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Bloom (BLM) helicase plays an important role in DNA replication and the maintenance of genome integrity. BLM protein deficiency, which plays a vital role in the sperm-egg union and germ-cell development during reproduction, can lead to severe DNA damage in goats. However, the effect of BLM protein deficiency on goat litter size has not been reported. Herein, we studied the association between the genetic variation in the BLM gene and the number of kids per litter in Guizhou white goats. We explored differences in the expression of the BLM protein in the follicles of single and multi-kid nanny goats. We also analyzed the effects of dysregulated BLM gene expression on the proliferation and apoptosis of ovarian granulosa cells and the expression of genes related to follicle development in goats. Five single nucleotide polymorphism (SNP) loci, including the non-synonymous mutations g.38179 A > G, g.40626 G > C and g.89621 T > G; the intron synonymous mutation g.56961 G > A and the exon synonymous mutation g.65796 C > T were found in the BLM gene. All SNPs loci were in Hardy-Weinberg equilibrium, and correlation analysis showed that the g.65796 C > T and g.89621 T > G loci polymorphism was strongly associated with litter size in the first three litters (P < 0.05). The diplogenotype Hap 2/2 (AAGGAACCTT) showed no significant difference in litter size between different births, indicating that the diploid genotype is stable in different litter sizes. Bioinformatics analysis showed that three non-synonymous mutation loci (p.T488A, p.A662S, and p.S1373A) could affect BLM protein stability, and mutations in p.T488A and p.S1373A led to changes in amino acid polarity and associated interactions. qPCR results showed that the expression level of the BLM gene in the uterus and ovaries of TT genotype nanny goats was significantly higher than that of GG genotype nanny goats. Indirect immunofluorescence assay (IF) showed that the BLM protein was significantly overexpressed in both the primordial and growing follicles of nanny goats with multiple kids (P < 0.01). Disrupting BLM gene expression in the ovarian granulosa cells down-regulated the expression of the Cyp19A1 gene. It also significantly inhibited the proliferation of follicles and induces early apoptosis of the granulosa cells. These findings confirm that polymorphism in the BLM gene is closely related to the littering traits of Guizhou white goats, and it affects the reproductive performance of nanny goats by regulating the development of the oocytes and granulosa cells. This work provides new evidence on the regulatory effect of the BLM gene on the litter size of nanny goats.
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Affiliation(s)
- Dongwei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Ziyang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Huan Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China.
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154
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Ozden B, Şamiloğlu E, Özsan A, Erguven M, Yükrük C, Koşaca M, Oktayoğlu M, Menteş M, Arslan N, Karakülah G, Barlas AB, Savaş B, Karaca E. Benchmarking the accuracy of structure-based binding affinity predictors on Spike-ACE2 deep mutational interaction set. Proteins 2024; 92:529-539. [PMID: 37991066 DOI: 10.1002/prot.26645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023]
Abstract
Since the start of COVID-19 pandemic, a huge effort has been devoted to understanding the Spike (SARS-CoV-2)-ACE2 recognition mechanism. To this end, two deep mutational scanning studies traced the impact of all possible mutations across receptor binding domain (RBD) of Spike and catalytic domain of human ACE2. By concentrating on the interface mutations of these experimental data, we benchmarked six commonly used structure-based binding affinity predictors (FoldX, EvoEF1, MutaBind2, SSIPe, HADDOCK, and UEP). These predictors were selected based on their user-friendliness, accessibility, and speed. As a result of our benchmarking efforts, we observed that none of the methods could generate a meaningful correlation with the experimental binding data. The best correlation is achieved by FoldX (R = -0.51). When we simplified the prediction problem to a binary classification, that is, whether a mutation is enriching or depleting the binding, we showed that the highest accuracy is achieved by FoldX with a 64% success rate. Surprisingly, on this set, simple energetic scoring functions performed significantly better than the ones using extra evolutionary-based terms, as in Mutabind and SSIPe. Furthermore, we demonstrated that recent AI approaches, mmCSM-PPI and TopNetTree, yielded comparable performances to the force field-based techniques. These observations suggest plenty of room to improve the binding affinity predictors in guessing the variant-induced binding profile changes of a host-pathogen system, such as Spike-ACE2. To aid such improvements we provide our benchmarking data at https://github.com/CSB-KaracaLab/RBD-ACE2-MutBench with the option to visualize our mutant models at https://rbd-ace2-mutbench.github.io/.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Eda Şamiloğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Atakan Özsan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehmet Erguven
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Can Yükrük
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehdi Koşaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Melis Oktayoğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Muratcan Menteş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Nazmiye Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Büşra Savaş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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155
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Solaipriya S, Anbalagan M, Sivaramakrishnan V. Preclinical Targeting of the PGRMC1-CK2 Axis with Silmitasertib: A Potential Strategy for Lung Adenocarcinoma Therapy. Drug Res (Stuttg) 2024; 74:187-190. [PMID: 38508228 DOI: 10.1055/a-2273-2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Progesterone receptor membrane component 1 (PGRMC1) is a pleiotropic protein over-expressed in lung adenocarcinoma (LUAD). The precise molecular mechanisms underlying the signature motif of Casein kinase (CK2) presence in PGRMC1 and their role in LUAD remain unclear. X-ray crystallographic structure for CK2 and PGRMC1 from the PubChem database was obtained and subjected to protein-protein interaction (PPI) analysis to identify their interactions. In addition, the CK2 inhibitor - Silmitasertib was also utilised to understand the interaction between PGRMC1-CK2. The PPI complex (PGRMC1-CK2) and the PPI-ligand interaction analysis and their Molecular Dynamics (MD) studies revealed the stability of their interactions and critical amino acid contacts within the 5Ǻ vicinity of the CK2 signature motif "T/S-x-x-E/D". Moreover, in-vitro colony formation assay, migration assay, and gene expression analysis using quantitative Real-time PCR revealed that Silmitasertib (IC50-2.5 μM) was highly influential in suppressing the PGRMC1-CK2 expression axis. In conclusion, our study infers that PGRMC1-CK-2 axis inhibition could be a potential therapeutic option to limit the promotion and progression of lung cancer.
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Affiliation(s)
- S Solaipriya
- Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chennai - 603203, Tamil Nadu, India
| | - M Anbalagan
- Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - V Sivaramakrishnan
- Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chennai - 603203, Tamil Nadu, India
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156
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Li C, Gao X, Li H, Wang T, Lu F, Qin H. Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306478. [PMID: 38308132 PMCID: PMC11005681 DOI: 10.1002/advs.202306478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/22/2023] [Indexed: 02/04/2024]
Abstract
Fast screening strategies that enable high-throughput evaluation and identification of desired variants from diversified enzyme libraries are crucial to tailoring biocatalysts for the synthesis of D-allulose, which is currently limited by the poor catalytic performance of ketose 3-epimerases (KEases). Here, the study designs a minimally equipment-dependent, high-throughput, and growth-coupled in vivo screening platform founded on a redesigned D-allulose-dependent biosensor system. The genetic elements modulating regulator PsiR expression levels undergo systematic optimization to improve the growth-responsive dynamic range of the biosensor, which presents ≈30-fold facilitated growth optical density with a high signal-to-noise ratio (1.52 to 0.05) toward D-allulose concentrations from 0 to 100 mm. Structural analysis and evolutionary conservation analysis of Agrobacterium sp. SUL3 D-allulose 3-epimerase (ADAE) reveal a highly conserved catalytic active site and variable hydrophobic pocket, which together regulate substrate recognition. Structure-guided rational design and directed evolution are implemented using the growth-coupled in vivo screening platform to reprogram ADAE, in which a mutant M42 (P38N/V102A/Y201L/S207N/I251R) is identified with a 6.28-fold enhancement of catalytic activity and significantly improved thermostability with a 2.5-fold increase of the half-life at 60 °C. The research demonstrates that biosensor-assisted growth-coupled evolutionary pressure combined with structure-guided rational design provides a universal route for engineering KEases.
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Affiliation(s)
- Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyNational Engineering Laboratory for Industrial EnzymesCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457P. R. China
| | - Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyNational Engineering Laboratory for Industrial EnzymesCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457P. R. China
| | - Huimin Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyNational Engineering Laboratory for Industrial EnzymesCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457P. R. China
| | - Tong Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyNational Engineering Laboratory for Industrial EnzymesCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyNational Engineering Laboratory for Industrial EnzymesCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457P. R. China
| | - Hui‐Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyNational Engineering Laboratory for Industrial EnzymesCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457P. R. China
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157
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Li J, Khalid WA, Imtiaz H, Huang L, Ali Y, Yousaf R, Gul F, Mahmood A, Shah AA, Deng H, Khattak S. The deleterious variants of N-acetylgalactosamine-6-sulfatase (GalN6S) enzyme trigger Morquio a syndrome by disrupting protein foldings. J Biomol Struct Dyn 2024; 42:3700-3711. [PMID: 37222604 DOI: 10.1080/07391102.2023.2214234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Lysosomal enzymes degrade cellular macromolecules, while their inactivation causes human hereditary metabolic disorders. Mucopolysaccharidosis IVA (MPS IVA; Moquio A syndrome) is one of the lysosomal storage disorders caused by a defective Galactosamine-6-sulfatase (GalN6S) enzyme. In several populations, disease incidence is elevated due to missense mutations brought on by non-synonymous allelic variation in the GalN6S enzyme. Here, we studied the effect of non-synonymous single nucleotide polymorphism (nsSNPs) on the structural dynamics of the GalN6S enzyme and its binding with N-acetylgalactosamine (GalNAc) using all-atom molecular dynamics simulation and an essential dynamics approach. Consequently, in this study, we have identified three functionally disruptive mutations in domain-I and domain-II, that is, S80L, R90W, and S162F, which presumably contribute to post-translational modifications. The study delineated that both domains work cooperatively, and alteration in domain II (S80L, R90W) leads to conformational changes in the catalytic site in domain-I, while mutation S162F mainly provokes higher residual flexibility of domain II. These results show that these mutations impair the hydrophobic core, implying that Morquio A syndrome is caused by misfolding of the GalN6S enzyme. The results also show the instability of the GalN6S-GalNAc complex upon substitution. Overall, the structural dynamics resulting from point mutations give the molecular rationale for Moquio A syndrome and, more importantly, the Mucopolysaccharidoses (MPS) family of diseases, re-establishing MPS IVA as a protein-folding disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiuyi Li
- Department of Anesthesiology, The First People's Hospital of Chenzhou, Chenzhou, Hunan Province, PR China
| | - Waqas Ahmad Khalid
- Government Rana Abdul Raheem Memorial Hospital Sodiwal Lahore, Sodiwal, Punjab, Pakistan
| | - Hina Imtiaz
- Tehsil Headquarters Hospital Bhera, Sarghoda, Bhera, Punjab, Pakistan
| | - Lingkun Huang
- Department of Anesthesiology, The First People's Hospital of Chenzhou, Chenzhou, Hunan Province, PR China
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rimsha Yousaf
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fouzia Gul
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, PR China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, PR China
| | - Huiyin Deng
- Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, PR China
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
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158
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K P, Madhana PN, Eswaramoorthy R, Ramasamy M. A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis. Metab Brain Dis 2024; 39:545-558. [PMID: 38185715 DOI: 10.1007/s11011-024-01341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and - 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.
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Affiliation(s)
- Priyanka K
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Priya N Madhana
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, TamilNadu, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India.
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159
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Miller JE, Agdanowski MP, Dolinsky JL, Sawaya MR, Cascio D, Rodriguez JA, Yeates TO. AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography. Acta Crystallogr D Struct Biol 2024; 80:270-278. [PMID: 38451205 PMCID: PMC10994174 DOI: 10.1107/s205979832400072x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/19/2024] [Indexed: 03/08/2024] Open
Abstract
Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.
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Affiliation(s)
- Justin E. Miller
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew P. Agdanowski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua L. Dolinsky
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
| | - Jose A. Rodriguez
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Genomics and Proteomics, UCLA–DOE, Los Angeles, CA 90095, USA
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160
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Wittrien T, Ziegler A, Rühle A, Stomberg S, Meyer R, Bonneau D, Rodien P, Prunier-Mirebeau D, Coutant R, Behrends S. Heterozygous gain of function variant in GUCY1A2 may cause autonomous ovarian hyperfunction. Eur J Endocrinol 2024; 190:266-274. [PMID: 38578777 DOI: 10.1093/ejendo/lvae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024]
Abstract
PURPOSE The purpose of this study was to characterize the phenotype associated with a de novo gain-of-function variant in the GUCY1A2 gene. METHODS An individual carrying the de novo heterozygous variant c.1458G>T p.(E486D) in GUCY1A2 was identified by exome sequencing. The effect of the corresponding enzyme variant α2E486D/β1 was evaluated using concentration-response measurements with wild-type enzyme and the variant in cytosolic fractions of HEK293 cells, UV-vis absorbance spectra of the corresponding purified enzymes, and examination of overexpressed fluorescent protein-tagged constructs by confocal laser scanning microscopy. RESULTS The patient presented with precocious peripheral puberty resembling the autonomous ovarian puberty seen in McCune-Albright syndrome. Additionally, the patient displayed severe intellectual disability. In vitro activity assays revealed an increased nitric oxide affinity for the mutant enzyme. The response to carbon monoxide was unchanged, while thermostability was decreased compared to wild type. Heme content, susceptibility to oxidation, and subcellular localization upon overexpression were unchanged. CONCLUSION Our data define a syndromic autonomous ovarian puberty likely due to the activating allele p.(E486D) in GUCY1A2 leading to an increase in cGMP. The overlap with the ovarian symptoms of McCune-Albright syndrome suggests an impact of this cGMP increase on the cAMP pathway in the ovary. Additional cases will be needed to ensure a causal link.
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Affiliation(s)
- Theresa Wittrien
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Alban Ziegler
- Department of Genetics, University Hospital of Angers, 49933 Angers, France
- Department of Genetics, CRMR AnDDI-Rares, University Hospital of Reims, 51092 Reims, France
| | - Anne Rühle
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Svenja Stomberg
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Ruben Meyer
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Dominique Bonneau
- Department of Genetics, University Hospital of Angers, 49933 Angers, France
| | - Patrice Rodien
- Department of Endocrinology, Reference Center for Rare Thyroid and Hormone Receptor Diseases, University Hospital of Angers, 49933 Angers, France
| | - Delphine Prunier-Mirebeau
- Department of Biochemistry and Molecular Biology, University Hospital of Angers, 49933 Angers, France
| | - Régis Coutant
- Department of Pediatric Endocrinology, University Hospital, 49933 Angers, France
| | - Sönke Behrends
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
- Semmelweiss University Budapest, Asklepios Campus, 20099 Hamburg, Germany
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161
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Yang C, Sun X, Wu G. New insights into GATOR2-dependent interactions and its conformational changes in amino acid sensing. Biosci Rep 2024; 44:BSR20240038. [PMID: 38372438 PMCID: PMC10938194 DOI: 10.1042/bsr20240038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Eukaryotic cells coordinate growth under different environmental conditions via mechanistic target of rapamycin complex 1 (mTORC1). In the amino-acid-sensing signalling pathway, the GATOR2 complex, containing five evolutionarily conserved subunits (WDR59, Mios, WDR24, Seh1L and Sec13), is required to regulate mTORC1 activity by interacting with upstream CASTOR1 (arginine sensor) and Sestrin2 (leucine sensor and downstream GATOR1 complex). GATOR2 complex utilizes β-propellers to engage with CASTOR1, Sestrin2 and GATOR1, removal of these β-propellers results in substantial loss of mTORC1 capacity. However, structural information regarding the interface between amino acid sensors and GATOR2 remains elusive. With the recent progress of the AI-based tool AlphaFold2 (AF2) for protein structure prediction, structural models were predicted for Sentrin2-WDR24-Seh1L and CASTOR1-Mios β-propeller. Furthermore, the effectiveness of relevant residues within the interface was examined using biochemical experiments combined with molecular dynamics (MD) simulations. Notably, fluorescence resonance energy transfer (FRET) analysis detected the structural transition of GATOR2 in response to amino acid signals, and the deletion of Mios β-propeller severely impeded that change at distinct arginine levels. These findings provide structural perspectives on the association between GATOR2 and amino acid sensors and can facilitate future research on structure determination and function.
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Affiliation(s)
- Can Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, the Joint International Research Laboratory of Metabolic and Developmental Sciences MOE, Shanghai Jiao Tong University, Shanghai, China
| | - Xuan Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, the Joint International Research Laboratory of Metabolic and Developmental Sciences MOE, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, the Joint International Research Laboratory of Metabolic and Developmental Sciences MOE, Shanghai Jiao Tong University, Shanghai, China
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162
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Ayodele AO, Udosen B, Oluwagbemi OO, Oladipo EK, Omotuyi I, Isewon I, Nash O, Soremekun O, Fatumo S. An in-silico analysis of OGT gene association with diabetes mellitus. BMC Res Notes 2024; 17:89. [PMID: 38539217 PMCID: PMC10976716 DOI: 10.1186/s13104-024-06744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
O-GlcNAcylation is a nutrient-sensing post-translational modification process. This cycling process involves two primary proteins: the O-linked N-acetylglucosamine transferase (OGT) catalysing the addition, and the glycoside hydrolase OGA (O-GlcNAcase) catalysing the removal of the O-GlCNAc moiety on nucleocytoplasmic proteins. This process is necessary for various critical cellular functions. The O-linked N-acetylglucosamine transferase (OGT) gene produces the OGT protein. Several studies have shown the overexpression of this protein to have biological implications in metabolic diseases like cancer and diabetes mellitus (DM). This study retrieved 159 SNPs with clinical significance from the SNPs database. We probed the functional effects, stability profile, and evolutionary conservation of these to determine their fit for this research. We then identified 7 SNPs (G103R, N196K, Y228H, R250C, G341V, L367F, and C845S) with predicted deleterious effects across the four tools used (PhD-SNPs, SNPs&Go, PROVEAN, and PolyPhen2). Proceeding with this, we used ROBETTA, a homology modelling tool, to model the proteins with these point mutations and carried out a structural bioinformatics method- molecular docking- using the Glide model of the Schrodinger Maestro suite. We used a previously reported inhibitor of OGT, OSMI-1, as the ligand for these mutated protein models. As a result, very good binding affinities and interactions were observed between this ligand and the active site residues within 4Å of OGT. We conclude that these mutation points may be used for further downstream analysis as drug targets for treating diabetes mellitus.
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Affiliation(s)
- Abigail O Ayodele
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Brenda Udosen
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
| | - Olugbenga O Oluwagbemi
- Department of Computer Science and Information Technology, Faculty of Natural and Applied Sciences, Sol Plaatje University, 8301, Kimberley, South Africa
- Department of Mathematical Sciences, Stellenbosch University, 7602, Stellenbosch, South Africa
| | - Elijah K Oladipo
- Laboratory of Molecular Biology, Immunology and Bioinformatics, Department of Microbiology, Adeleke University, 232104, Ede, Nigeria
- Genomics Unit, Helix Biogen Institute, 210214, Ogbomoso, Nigeria
| | - Idowu Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti, Nigeria
- Molecular Biology and Molecular Simulation Center (Mols&Sims), Ado Ekiti, Nigeria
| | - Itunuoluwa Isewon
- Computer and Information Sciences Department, Covenant University, Ota, Ogun State, Nigeria
| | - Oyekanmi Nash
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
- MRC/UVRI and London School of Hygiene and Tropical Medicine London (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Segun Fatumo
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria.
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda.
- MRC/UVRI and London School of Hygiene and Tropical Medicine London (LSHTM) Uganda Research Unit, Entebbe, Uganda.
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163
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Li XL, Tei R, Uematsu M, Baskin JM. Ultralow Background Membrane Editors for Spatiotemporal Control of Phosphatidic Acid Metabolism and Signaling. ACS CENTRAL SCIENCE 2024; 10:543-554. [PMID: 38559292 PMCID: PMC10979500 DOI: 10.1021/acscentsci.3c01105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 04/04/2024]
Abstract
Phosphatidic acid (PA) is a multifunctional lipid with important metabolic and signaling functions, and efforts to dissect its pleiotropy demand strategies for perturbing its levels with spatiotemporal precision. Previous membrane editing approaches for generating local PA pools used light-mediated induced proximity to recruit a PA-synthesizing enzyme, phospholipase D (PLD), from the cytosol to the target organelle membrane. Whereas these optogenetic PLDs exhibited high activity, their residual activity in the dark led to undesired chronic lipid production. Here, we report ultralow background membrane editors for PA wherein light directly controls PLD catalytic activity, as opposed to localization and access to substrates, exploiting a light-oxygen-voltage (LOV) domain-based conformational photoswitch inserted into the PLD sequence and enabling their stable and nonperturbative targeting to multiple organelle membranes. By coupling organelle-targeted LOVPLD activation to lipidomics analysis, we discovered different rates of metabolism for PA and its downstream products depending on the subcellular location of PA production. We also elucidated signaling roles for PA pools on different membranes in conferring local activation of AMP-activated protein kinase signaling. This work illustrates how membrane editors featuring acute, optogenetic conformational switches can provide new insights into organelle-selective lipid metabolic and signaling pathways.
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Affiliation(s)
- Xiang-Ling Li
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Reika Tei
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Masaaki Uematsu
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Jeremy M. Baskin
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
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164
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Karagöl T, Karagöl A, Zhang S. Structural bioinformatics studies of serotonin, dopamine and norepinephrine transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F. PLoS One 2024; 19:e0300340. [PMID: 38517879 PMCID: PMC10959339 DOI: 10.1371/journal.pone.0300340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/26/2024] [Indexed: 03/24/2024] Open
Abstract
Monoamine transporters including transporters for serotonin, dopamine, and norepinephrine play key roles in monoaminergic synaptic signaling, involving in the molecular etiology of a wide range of neurological and physiological disorders. Despite being crucial drug targets, the study of transmembrane proteins remains challenging due to their localization within the cell membrane. To address this, we present the structural bioinformatics studies of 7 monoamine transporters and their water-soluble variants designed using the QTY code, by systematically replacing the hydrophobic amino acids leucine (L), valine (V), isoleucine (I) and phenylalanine (F) with hydrophilic amino acids (glutamine (Q), threonine (T) and tyrosine (Y). The resulting QTY variants, despite significant protein transmembrane sequence differences (44.27%-51.85%), showed similar isoelectric points (pI) and molecular weights. While their hydrophobic surfaces significantly reduced, this change resulted in a minimal structural alteration. Quantitatively, Alphafold2 predicted QTY variant structures displayed remarkable similarity with RMSD 0.492Å-1.619Å. Accompanied by the structural similarities of substituted amino acids in the context of 1.5Å electron density maps, our study revealed multiple QTY and reverse QTY variations in genomic databases. We further analyzed their phenotypical and topological characteristics. By extending evolutionary game theory to the molecular foundations of biology, we provided insights into the evolutionary dynamics of chemically distinct alpha-helices, their usage in different chemotherapeutic applications, and open possibilities of diagnostic medicine. Our study rationalizes that QTY variants of monoamine transporters may not only become distinct tools for medical, structural, and evolutionary research, but these transporters may also emerge as contemporary therapeutic targets, providing a new approach to treatment for several conditions.
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Affiliation(s)
- Taner Karagöl
- Istanbul University Istanbul Medical Faculty, Istanbul, Turkey
| | - Alper Karagöl
- Istanbul University Istanbul Medical Faculty, Istanbul, Turkey
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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165
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Jones JA, Andreas MP, Giessen TW. Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae. Nat Commun 2024; 15:2558. [PMID: 38519509 PMCID: PMC10960027 DOI: 10.1038/s41467-024-46880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen Klebsiella pneumoniae. By combining cryo-electron microscopy with TP and TP-binding site mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
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166
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Muthukumar G, Stevens TA, Inglis AJ, Esantsi TK, Saunders RA, Schulte F, Voorhees RM, Guna A, Weissman JS. Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology. Mol Cell 2024; 84:1101-1119.e9. [PMID: 38428433 DOI: 10.1016/j.molcel.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse proteins remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways that act on substrates based on their topology. NAC is required for the efficient targeting of polytopic proteins, whereas signal-anchored proteins require TTC1, a cytosolic chaperone that physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, the targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.
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Affiliation(s)
- Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alina Guna
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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167
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Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG. Molecular dynamics of the human RhD and RhAG blood group proteins. Front Chem 2024; 12:1360392. [PMID: 38566898 PMCID: PMC10985258 DOI: 10.3389/fchem.2024.1360392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Blood group antigens of the RH system (formerly known as "Rhesus") play an important role in transfusion medicine because of the severe haemolytic consequences of antibodies to these antigens. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown. Methods: To analyse their structural properties, the trimers formed by RhD and/or RhAG subunits were generated by protein modelling and molecular dynamics simulations were performed. Results: No major differences in structural behaviour were found between trimers of different compositions. The conformation of the subunits is relatively constant during molecular dynamics simulations, except for three large disordered loops. Discussion: This work makes it possible to propose a reasonable stoichiometry and demonstrates the potential of studying the structural behaviour of these proteins to investigate the hundreds of genetic variants relevant to transfusion medicine.
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Affiliation(s)
- Aline Floch
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
| | - France Pirenne
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Christophe Tournamille
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
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168
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Deitch I, Itskov S, Panneman D, Abu Shtaya A, Saban T, Goldberg Y, Ehrenberg M, Cremers FPM, Roosing S, Ben-Yosef T. Autosomal Recessive Rod-Cone Dystrophy with Mild Extra-Ocular Manifestations Due to a Splice-Affecting Variant in BBS9. Curr Issues Mol Biol 2024; 46:2566-2575. [PMID: 38534779 DOI: 10.3390/cimb46030163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
Bardet-Biedl syndrome (BBS), one of the most common forms of syndromic inherited retinal diseases (IRDs), is characterized by the combination of retinal degeneration with additional extra-ocular manifestations, including obesity, intellectual disability, kidney disease, polydactyly and other skeletal abnormalities. We observed an Israeli patient with autosomal recessive apparently non-syndromic rod-cone dystrophy (RCD). Extra-ocular findings were limited to epilepsy and dental problems. Genetic analysis with a single molecule molecular inversion probes-based panel that targets the exons and splice sites of 113 genes associated with retinitis pigmentosa and Leber congenital amaurosis revealed a homozygous rare missense variant in the BBS9 gene (c.263C>T;p.(Ser88Leu)). This variant, which affects a highly conserved amino acid, is also located in the last base of Exon 3, and predicted to be splice-altering. An in vitro minigene splice assay demonstrated that this variant leads to the partial aberrant splicing of Exon 3. Therefore, we suggest that this variant is likely hypomorphic. This is in agreement with the relatively mild phenotype observed in the patient. Hence, the findings in our study expand the phenotypic spectrum associated with BBS9 variants and indicate that variants in this gene should be considered not only in BBS patients but also in individuals with non-syndromic IRD or IRD with very mild extra-ocular manifestations.
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Affiliation(s)
- Iris Deitch
- Rabin Medical Center, Department of Ophthalmology, Petach Tikva 4941492, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sofia Itskov
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109601, Israel
| | - Daan Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Aasem Abu Shtaya
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva 4941492, Israel
- Unit of Gastroenterology, Carmel Medical Center, Haifa 3436212, Israel
| | - Tal Saban
- Rabin Medical Center, Department of Ophthalmology, Petach Tikva 4941492, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Goldberg
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva 4941492, Israel
| | - Miriam Ehrenberg
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Schneider Children's Medical Center of Israel, Department of Ophthalmology, Petach Tikva 4920235, Israel
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109601, Israel
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169
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Shrivastava A, Magani SKJ, Lokhande KB, Chintakhindi M, Singh A. Exploring the role of TLK2 mutation in tropical calcific pancreatitis: an in silico and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-20. [PMID: 38500246 DOI: 10.1080/07391102.2024.2329797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Tropical calcific pancreatitis (TCP) is a juvenile form of non-alcoholic chronic pancreatitis seen exclusively in tropical countries. The disease poses a high risk of complications, including pancreatic diabetes and cancer, leading to significant mortality due to poor diagnosis and ineffective treatments. This study employed whole exome sequencing (WES) of 5 TCP patient samples to identify genetic variants associated with TCP. Advanced computational techniques were used to gain atomic-level insights into disease progression, including microsecond-scale long MD simulations and essential dynamics. In silico virtual screening was performed to identify potential therapeutic compounds targeting the mutant protein using the Asinex and DrugBank compound library. WES analysis predicted several single nucleotide variants (SNVs) associated with TCP, including a novel missense variant (c.T1802A or p.V601E) in the TLK2 gene. Computational analysis revealed that the p.V601E mutation significantly affected the structure of the TLK2 kinase domain and its conformational dynamics, altering the interaction profile between ATP and the binding pocket. These changes could impact TLK2's kinase activity and functions, potentially correlating with TCP progression. Promising lead compounds that selectively bind to the TLK2 mutant protein were identified, offering potential for therapeutic interventions in TCP. These findings hold great potential for future research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Sri Krishna Jayadev Magani
- Cancer Biology Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Kiran Bharat Lokhande
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | | | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
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170
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Gerber JL, Morales Guzmán SI, Worf L, Hubbe P, Kopp J, Peschek J. Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease. Nat Commun 2024; 15:2378. [PMID: 38493148 PMCID: PMC10944509 DOI: 10.1038/s41467-024-46568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
RNA ligases of the RTCB-type play an essential role in tRNA splicing, the unfolded protein response and RNA repair. RTCB is the catalytic subunit of the pentameric human tRNA ligase complex. RNA ligation by the tRNA ligase complex requires GTP-dependent activation of RTCB. This active site guanylylation reaction relies on the activation factor Archease. The mechanistic interplay between both proteins has remained unknown. Here, we report a biochemical and structural analysis of the human RTCB-Archease complex in the pre- and post-activation state. Archease reaches into the active site of RTCB and promotes the formation of a covalent RTCB-GMP intermediate through coordination of GTP and metal ions. During the activation reaction, Archease prevents futile RNA substrate binding to RTCB. Moreover, monomer structures of Archease and RTCB reveal additional states within the RNA ligation mechanism. Taken together, we present structural snapshots along the reaction cycle of the human tRNA ligase.
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Affiliation(s)
- Janina Lara Gerber
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | | | - Lorenz Worf
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Petra Hubbe
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Jirka Peschek
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany.
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171
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Zambrano-Román M, Padilla-Gutiérrez JR, Valle Y, Muñoz-Valle JF, Guevara-Gutiérrez E, López-Olmos PA, Sepúlveda-Loza LC, Bautista-Herrera LA, Valdés-Alvarado E. PTCH1 Gene Variants, mRNA Expression, and Bioinformatics Insights in Mexican Cutaneous Squamous Cell Carcinoma Patients. BIOLOGY 2024; 13:191. [PMID: 38534460 DOI: 10.3390/biology13030191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Skin cancer is one of the most frequent types of cancer, and cutaneous squamous cell carcinoma (cSCC) constitutes 20% of non-melanoma skin cancer (NMSC) cases. PTCH1, a tumor suppressor gene involved in the Sonic hedgehog signaling pathway, plays a crucial role in neoplastic processes. METHODS An analytical cross-sectional study, encompassing 211 cSCC patients and 290 individuals in a control group (CG), was performed. A subgroup of samples was considered for the relative expression analysis, and the results were obtained using quantitative real-time PCR (qPCR) with TaqMan® probes. The functional, splicing, and disease-causing effects of the proposed variants were explored via bioinformatics. RESULTS cSCC was predominant in men, especially in sun-exposed areas such as the head and neck. No statistically significant differences were found regarding the rs357564, rs2236405, rs2297086, and rs41313327 variants of PTCH1, or in the risk of cSCC, nor in the mRNA expression between the cSCC group and CG. A functional effect of rs357564 and a disease-causing relation to rs41313327 was identified. CONCLUSION The proposed variants were not associated with cSCC risk in this Mexican population, but we recognize the need for analyzing larger population groups to elucidate the disease-causing role of rare variants.
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Affiliation(s)
- Marianela Zambrano-Román
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Jorge R Padilla-Gutiérrez
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Yeminia Valle
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Elizabeth Guevara-Gutiérrez
- Departamento de Dermatología, Instituto Dermatológico de Jalisco "Dr. José Barba Rubio", Secretaría de Salud Jalisco, Zapopan 45190, Mexico
| | - Patricia Aidé López-Olmos
- Departamento de Dermatología, Instituto Dermatológico de Jalisco "Dr. José Barba Rubio", Secretaría de Salud Jalisco, Zapopan 45190, Mexico
| | | | | | - Emmanuel Valdés-Alvarado
- Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico
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172
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Witek W, Sliwiak J, Rawski M, Ruszkowski M. Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting. FRONTIERS IN PLANT SCIENCE 2024; 15:1343980. [PMID: 38559763 PMCID: PMC10978614 DOI: 10.3389/fpls.2024.1343980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of Medicago truncatula HISN5 (MtHISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. MtHISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure MtHISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.
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Affiliation(s)
- Wojciech Witek
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Sliwiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Michal Rawski
- Cryo-EM Facility, SOLARIS National Synchrotron Radiation Centre, Krakow, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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173
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Panchal NK, Samdani P, Sengupta T, Prince SE. Computational Analysis of Non-synonymous SNPs in ATM Kinase: Structural Insights, Functional Implications, and Inhibitor Discovery. Mol Biotechnol 2024:10.1007/s12033-024-01120-x. [PMID: 38489015 DOI: 10.1007/s12033-024-01120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
Ataxia telangiectasia-mutated (ATM) protein kinase, a key player in cellular integrity regulation, is known for its role in DNA damage response. This study investigates the broader impact of ATM on cellular processes and potential clinical manifestations arising from mutations, aiming to expand our understanding of ATM's diverse functions beyond conventional roles. The research employs a comprehensive set of computational techniques for a thorough analysis of ATM mutations. The mutation data are curated from dbSNP and HuVarBase databases. A meticulous assessment is conducted, considering factors such as deleterious effects, protein stability, oncogenic potential, and biophysical characteristics of the identified mutations. Conservation analysis, utilizing diverse computational tools, provides insights into the evolutionary significance of these mutations. Molecular docking and dynamic simulation analyses are carried out for selected mutations, investigating their interactions with Y2080D, AZD0156, and quercetin inhibitors to gauge potential therapeutic implications. Among the 419 mutations scrutinized, five (V1913C, Y2080D, L2656P, C2770G, and C2930G) are identified as both disease causing and protein destabilizing. The study reveals the oncogenic potential of these mutations, supported by findings from the COSMIC database. Notably, Y2080D is associated with haematopoietic and lymphoid cancers, while C2770G shows a correlation with squamous cell carcinomas. Molecular docking and dynamic simulation analyses highlight strong binding affinities of quercetin for Y2080D and AZD0156 for C2770G, suggesting potential therapeutic options. In summary, this computational analysis provides a comprehensive understanding of ATM mutations, revealing their potential implications in cellular integrity and cancer development. The study underscores the significance of Y2080D and C2770G mutations, offering valuable insights for future precision medicine targeting-specific ATM. Despite informative computational analyses, a significant research gap exists, necessitating essential in vitro and in vivo studies to validate the predicted effects of ATM mutations on protein structure and function.
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Affiliation(s)
- Nagesh Kishan Panchal
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Poorva Samdani
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Tiasa Sengupta
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sabina Evan Prince
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India.
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174
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Levillayer L, Brighelli C, Demeret C, Sakuntabhai A, Bureau JF. Role of two modules controlling the interaction between SKAP1 and SRC kinases comparison with SKAP2 architecture and consequences for evolution. PLoS One 2024; 19:e0296230. [PMID: 38483858 PMCID: PMC10939263 DOI: 10.1371/journal.pone.0296230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
SRC kinase associated phosphoprotein 1 (SKAP1), an adaptor for protein assembly, plays an important role in the immune system such as stabilizing immune synapses. Understanding how these functions are controlled at the level of the protein-protein interactions is necessary to describe these processes and to develop therapeutics. Here, we dissected the SKAP1 modular organization to recognize SRC kinases and compared it to that of its paralog SRC kinase associated phosphoprotein 2 (SKAP2). Different conserved motifs common to either both proteins or specific to SKAP2 were found using this comparison. Two modules harboring different binding properties between SKAP1 and SKAP2 were identified: one composed of two conserved motifs located in the second interdomain interacting at least with the SH2 domain of SRC kinases and a second one composed of the DIM domain modulated by the SH3 domain and the activation of SRC kinases. This work suggests a convergent evolution of the binding properties of some SRC kinases interacting specifically with either SKAP1 or SKAP2.
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Affiliation(s)
- Laurine Levillayer
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Camille Brighelli
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Caroline Demeret
- Institut Pasteur, Université de Paris-Cité, Laboratoire Interactomique, ARN et Immunité ‐ Interactomics, RNA and Immunity, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Jean-François Bureau
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
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175
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Nishio S, Emori C, Wiseman B, Fahrenkamp D, Dioguardi E, Zamora-Caballero S, Bokhove M, Han L, Stsiapanava A, Algarra B, Lu Y, Kodani M, Bainbridge RE, Komondor KM, Carlson AE, Landreh M, de Sanctis D, Yasumasu S, Ikawa M, Jovine L. ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat. Cell 2024; 187:1440-1459.e24. [PMID: 38490181 DOI: 10.1016/j.cell.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/07/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
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Affiliation(s)
- Shunsuke Nishio
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Benjamin Wiseman
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisa Dioguardi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Marcel Bokhove
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Alena Stsiapanava
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Blanca Algarra
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Yonggang Lu
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Mayo Kodani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Rachel E Bainbridge
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kayla M Komondor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne E Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | | | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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176
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Singla A, Boesch DJ, Joyce Fung HY, Ngoka C, Enriquez AS, Song R, Kramer DA, Han Y, Juneja P, Billadeau DD, Bai X, Chen Z, Turer EE, Burstein E, Chen B. Structural basis for Retriever-SNX17 assembly and endosomal sorting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584676. [PMID: 38559023 PMCID: PMC10980035 DOI: 10.1101/2024.03.12.584676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms underlying this interaction have remained elusive. Here, we report the structure of the Retriever-SNX17 complex determined using cryogenic electron microscopy (cryo-EM). Our structure reveals that the C-terminal tail of SNX17 engages with a highly conserved interface between the VPS35L and VPS26C subunits of Retriever. Through comprehensive biochemical, cellular, and proteomic analyses, we demonstrate that disrupting this interface impairs the Retriever-SNX17 interaction, subsequently affecting the recycling of SNX17-dependent cargos and altering the composition of the plasma membrane proteome. Intriguingly, we find that the SNX17-binding pocket on Retriever can be utilized by other ligands that share a consensus acidic C-terminal tail motif. By showing how SNX17 is linked to Retriever, our findings uncover a fundamental mechanism underlying endosomal trafficking of critical cargo proteins and reveal a mechanism by which Retriever can engage with other regulatory factors.
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Affiliation(s)
- Amika Singla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Daniel J. Boesch
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Ho Yee Joyce Fung
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Chigozie Ngoka
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Avery S. Enriquez
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Ran Song
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Daniel A. Kramer
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Puneet Juneja
- Cryo-EM facility, Office of Biotechnology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Daniel D. Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester MN, 55905, USA
| | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Emre E. Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA 50011, USA
- On sabbatical leave at Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
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177
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Saha S, Mandal SK, Kanaujia SP. Distinct characteristics of putative archaeal 5-methylcytosine RNA methyltransferases unveil their substrate specificities and evolutionary ancestries. J Biomol Struct Dyn 2024:1-18. [PMID: 38450736 DOI: 10.1080/07391102.2024.2325670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
5-Methylcytosine methyltransferases (m5C MTases) are known to be involved in the modification of RNA. Although these enzymes have been relatively well characterized in bacteria and eukarya, a complete understanding of the archaeal counterparts is lacking. In this study, the identification and characterization of archaeal RNA m5C MTases were performed. As a case study, a hyperthermophilic archaeon, Pyrococcus horikoshii OT3, which possesses five putative RNA m5C MTases, was chosen. Among the five putative RNA m5C MTases, two proteins (PH0851 and PH1991) have been characterized as homologs of a bacterial rRNA MTase (RsmB) and eukaryal tRNA MTase (NSUN6), respectively. The in-depth characterization of the remaining three putative RNA m5C MTases (PH1078, PH1374, and PH1537) in this study suggests the presence of the signature architecture and catalytic residues plausibly involved in the binding of their cognate RNA substrates. Additionally, the results also suggest the existence of two RsmB-like proteins (PH0851 and PH1078) belonging to the same subfamily IV of m5C RNA MTase. However, the proteins PH1374 and PH1537 belong to the same subfamily V but bind to different substrates, rRNA and tRNA, respectively. The findings further indicate that archaeal RNA m5C MTases link those from bacteria and eukarya.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayan Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Suraj Kumar Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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178
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Brownfield BA, Richardson BC, Halaby SL, Fromme JC. Sec7 regulatory domains scaffold autoinhibited and active conformations. Proc Natl Acad Sci U S A 2024; 121:e2318615121. [PMID: 38416685 PMCID: PMC10927569 DOI: 10.1073/pnas.2318615121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/16/2024] [Indexed: 03/01/2024] Open
Abstract
The late stages of Golgi maturation involve a series of sequential trafficking events in which cargo-laden vesicles are produced and targeted to multiple distinct subcellular destinations. Each of these vesicle biogenesis events requires activation of an Arf GTPase by the Sec7/BIG guanine nucleotide exchange factor (GEF). Sec7 localization and activity is regulated by autoinhibition, positive feedback, and interaction with other GTPases. Although these mechanisms have been characterized biochemically, we lack a clear picture of how GEF localization and activity is modulated by these signals. Here, we report the cryogenic electron microscopy structure of full-length Sec7 in its autoinhibited form, revealing the architecture of its multiple regulatory domains. We use functional experiments to determine the basis for autoinhibition and use structural predictions to produce a model for an active conformation of the GEF that is supported empirically. This study therefore elucidates the conformational transition that Sec7 undergoes to become active on the organelle membrane surface.
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Affiliation(s)
- Bryce A. Brownfield
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - Brian C. Richardson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - Steve L. Halaby
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - J. Christopher Fromme
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
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179
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Cao R, Gozlan O, Tveriakhina L, Zhou H, Jiang H, Cole PA, Aster JC, Sprinzak D, Blacklow SC. Structural Requirements for Activity of Mind bomb1 in Notch Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582834. [PMID: 38464278 PMCID: PMC10925295 DOI: 10.1101/2024.03.01.582834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mind bomb 1 (MIB1) is a RING E3 ligase that ubiquitinates Notch ligands, a necessary step for induction of Notch signaling. The structural basis for binding of the JAG1 ligand by the N-terminal region of MIB1 is known, yet how the ankyrin (ANK) and RING domains of MIB1 cooperate to catalyze ubiquitin transfer from E2~Ub to Notch ligands remains unclear. Here, we show that the third RING domain and adjacent coiled coil region of MIB1 (ccRING3) drives MIB1 dimerization and that ubiquitin transfer activity of MIB1 relies solely on RING3. We report x-ray crystal structures of a UbcH5B-ccRING3 complex as a fusion protein and of the ANK region. Directly tethering the N-terminal region to ccRING3 forms a minimal MIB1 protein, which is sufficient to induce a Notch response in receiver cells. Together, these studies define the functional elements of an E3 ligase needed for ligands to induce a Notch signaling response.
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Affiliation(s)
- Ruili Cao
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Oren Gozlan
- George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lena Tveriakhina
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Haixia Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hanjie Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Philip A Cole
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Jon C Aster
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - David Sprinzak
- George S. Wise Faculty of Life Sciences, School of Neurobiology, Biochemistry, and Biophysics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Lead contact
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180
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Yates M, Marois I, St-Hilaire E, Ronato DA, Djerir B, Brochu C, Morin T, Hammond-Martel I, Gezzar-Dandashi S, Casimir L, Drobetsky E, Cappadocia L, Masson JY, Wurtele H, Maréchal A. SMARCAL1 ubiquitylation controls its association with RPA-coated ssDNA and promotes replication fork stability. PLoS Biol 2024; 22:e3002552. [PMID: 38502677 PMCID: PMC10950228 DOI: 10.1371/journal.pbio.3002552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Impediments in replication fork progression cause genomic instability, mutagenesis, and severe pathologies. At stalled forks, RPA-coated single-stranded DNA (ssDNA) activates the ATR kinase and directs fork remodeling, 2 key early events of the replication stress response. RFWD3, a recently described Fanconi anemia (FA) ubiquitin ligase, associates with RPA and promotes its ubiquitylation, facilitating late steps of homologous recombination (HR). Intriguingly, RFWD3 also regulates fork progression, restart and stability via poorly understood mechanisms. Here, we used proteomics to identify putative RFWD3 substrates during replication stress in human cells. We show that RFWD3 interacts with and ubiquitylates the SMARCAL1 DNA translocase directly in vitro and following DNA damage in vivo. SMARCAL1 ubiquitylation does not trigger its subsequent proteasomal degradation but instead disengages it from RPA thereby regulating its function at replication forks. Proper regulation of SMARCAL1 by RFWD3 at stalled forks protects them from excessive MUS81-mediated cleavage in response to UV irradiation, thereby limiting DNA replication stress. Collectively, our results identify RFWD3-mediated SMARCAL1 ubiquitylation as a novel mechanism that modulates fork remodeling to avoid genome instability triggered by aberrant fork processing.
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Affiliation(s)
- Maïlyn Yates
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Isabelle Marois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Edlie St-Hilaire
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Billel Djerir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Chloé Brochu
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Théo Morin
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | | | | | - Lisa Casimir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Elliot Drobetsky
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Laurent Cappadocia
- Faculty of Sciences, Department of Chemistry, Université du Québec à Montréal, Montréal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Hugo Wurtele
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
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181
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Gutiérrez-Fernández J, Hersleth HP, Hammerstad M. The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria. Acta Crystallogr D Struct Biol 2024; 80:181-193. [PMID: 38372589 PMCID: PMC10910545 DOI: 10.1107/s205979832400113x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reductases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future antituberculosis drug development.
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Affiliation(s)
- Javier Gutiérrez-Fernández
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Hans-Petter Hersleth
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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182
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Kaizuka T, Hirouchi T, Saneyoshi T, Shirafuji T, Collins MO, Grant SGN, Hayashi Y, Takumi T. FAM81A is a postsynaptic protein that regulates the condensation of postsynaptic proteins via liquid-liquid phase separation. PLoS Biol 2024; 22:e3002006. [PMID: 38452102 PMCID: PMC10919877 DOI: 10.1371/journal.pbio.3002006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/17/2024] [Indexed: 03/09/2024] Open
Abstract
Proteome analyses of the postsynaptic density (PSD), a proteinaceous specialization beneath the postsynaptic membrane of excitatory synapses, have identified several thousands of proteins. While proteins with predictable functions have been well studied, functionally uncharacterized proteins are mostly overlooked. In this study, we conducted a comprehensive meta-analysis of 35 PSD proteome datasets, encompassing a total of 5,869 proteins. Employing a ranking methodology, we identified 97 proteins that remain inadequately characterized. From this selection, we focused our detailed analysis on the highest-ranked protein, FAM81A. FAM81A interacts with PSD proteins, including PSD-95, SynGAP, and NMDA receptors, and promotes liquid-liquid phase separation of those proteins in cultured cells or in vitro. Down-regulation of FAM81A in cultured neurons causes a decrease in the size of PSD-95 puncta and the frequency of neuronal firing. Our findings suggest that FAM81A plays a crucial role in facilitating the interaction and assembly of proteins within the PSD, and its presence is important for maintaining normal synaptic function. Additionally, our methodology underscores the necessity for further characterization of numerous synaptic proteins that still lack comprehensive understanding.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Taisei Hirouchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshihiko Shirafuji
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
| | - Mark O. Collins
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- biOMICS Facility, Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom
| | - Seth G. N. Grant
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, Japan
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183
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Graffam D, Cutlan M, Storm AR, Hulse-Kemp AM, Stoeckman AK. Gossypium hirsutum gene of unknown function Gohir.A02G161000 encodes a potential transmembrane Root UVB Sensitive 4 Protein with a putative protein-protein interaction interface. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000869. [PMID: 38495582 PMCID: PMC10943365 DOI: 10.17912/micropub.biology.000869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 02/05/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
A gene of unknown function, Gohir.A02G161000.1, identified in Gossypium hirsutum was studied using computational sequence and structure bioinformatics tools. The associated protein GhRUS4-A0A1U8JPV7 (UniProt A0A1U8JPV7) is predicted to be a plastid-localized, transmembrane root UVB-sensitive 4 (RUS4) protein with a newly identified potential dimerization surface. Evidence from homology and sequence conservation suggest involvement in auxin transport and pollen maturation.
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Affiliation(s)
| | - Marissa Cutlan
- Chemistry Department, Bethel University, Saint Paul, MN USA
| | - Amanda R Storm
- Department of Biology, Western Carolina University, Cullowhee, NC USA
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture, Raleigh, NC USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC USA
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184
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Kim H, Park J, Roh SH. The structural basis of eukaryotic chaperonin TRiC/CCT: Action and folding. Mol Cells 2024; 47:100012. [PMID: 38280673 PMCID: PMC11004407 DOI: 10.1016/j.mocell.2024.100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/29/2024] Open
Abstract
Accurate folding of proteins in living cells often requires the cooperative support of molecular chaperones. Eukaryotic group II chaperonin Tailless complex polypeptide 1-Ring Complex (TRiC) accomplishes this task by providing a folding chamber for the substrate that is regulated by an Adenosine triphosphate (ATP) hydrolysis-dependent cycle. Once delivered to and recognized by TRiC, the nascent substrate enters the folding chamber and undergoes folding and release in a stepwise manner. During the process, TRiC subunits and cochaperones such as prefoldin and phosducin-like proteins interact with the substrate to assist the overall folding process in a substrate-specific manner. Coevolution between the components is supposed to consult the binding specificity and ultimately expand the substrate repertoire assisted by the chaperone network. This review describes the TRiC chaperonin and the substrate folding process guided by the TRiC network in cooperation with cochaperones, specifically focusing on recent progress in structural analyses.
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Affiliation(s)
- Hyunmin Kim
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsun Park
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Soung-Hun Roh
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea.
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185
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Taglini F, Kafetzopoulos I, Rolls W, Musialik KI, Lee HY, Zhang Y, Marenda M, Kerr L, Finan H, Rubio-Ramon C, Gautier P, Wapenaar H, Kumar D, Davidson-Smith H, Wills J, Murphy LC, Wheeler A, Wilson MD, Sproul D. DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Rep 2024; 25:1130-1155. [PMID: 38291337 PMCID: PMC7615734 DOI: 10.1038/s44319-024-00061-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here, we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1α and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3-marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.
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Affiliation(s)
- Francesca Taglini
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Altos Labs, Cambridge Institute, Cambridge, UK
| | - Willow Rolls
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kamila Irena Musialik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Imperial College London, London, UK
| | - Heng Yang Lee
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Endocrine Oncology Research Group, Department of Surgery, The Royal College of Surgeons RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Yujie Zhang
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Mattia Marenda
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hannah Finan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Swiss Federal Institute of Technology, ETH Zürich, Institute of Molecular Health Sciences, Zürich, Switzerland
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Dhananjay Kumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Hazel Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ann Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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186
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Sun H, Bai H, Hu Y, He S, Wei R, Meng D, Jiang Q, Pan H, Shen P, Ou Q, Jiang C. Regulatory mechanisms of dopamine metabolism in a marine Meyerozyma guilliermondii GXDK6 under NaCl stress as revealed by integrative multi-omics analysis. Synth Syst Biotechnol 2024; 9:115-126. [PMID: 38292761 PMCID: PMC10825490 DOI: 10.1016/j.synbio.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Dopamine can be used to treat depression, myocardial infarction, and other diseases. However, few reports are available on the de novo microbial synthesis of dopamine from low-cost substrate. In this study, integrated omics technology was used to explore the dopamine metabolism of a novel marine multi-stress-tolerant aromatic yeast Meyerozyma guilliermondii GXDK6. GXDK6 was found to have the ability to biosynthesize dopamine when using glucose as the substrate. 14 key genes for the biosynthesis of dopamine were identified by whole genome-wide analysis. Transcriptomic and proteomic data showed that the expression levels of gene AAT2 encoding aspartate aminotransferase (regulating dopamine anabolism) were upregulated, while gene AO-I encoding copper amine oxidase (involved in dopamine catabolism) were downregulated under 10 % NaCl stress compared with non-NaCl stress, thereby contributing to biosynthesis of dopamine. Further, the amount of dopamine under 10 % NaCl stress was 2.51-fold higher than that of zero NaCl, which was consistent with the multi-omics results. Real-time fluorescence quantitative PCR (RT-qPCR) and high-performance liquid chromatography (HPLC) results confirmed the metabolic model of dopamine. Furthermore, by overexpressing AAT2, AST enzyme activity was increased by 24.89 %, the expression of genes related to dopamine metabolism was enhanced, and dopamine production was increased by 56.36 % in recombinant GXDK6AAT2. In conclusion, Meyerozyma guilliermondii GXDK6 could utilize low-cost carbon source to synthesize dopamine, and NaCl stress promoted the biosynthesis of dopamine.
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Affiliation(s)
- Huijie Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
| | - Huashan Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yonghong Hu
- College of Food Science and Light Industry, Nanjing Tech University, No. 30, South Puzhu Road, Nanjing, 211816, China
| | - Sheng He
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, 530033, China
| | - Ruihang Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Duotao Meng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Qiong Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Hongping Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Peihong Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory for Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
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187
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Salvador GHM, Fernandes CAH, Borges RJ, Soares AM, Fontes MRM. Structural studies with crotoxin B from Crotalus durissus collilineatus venom suggest a heterodimeric assembly formed by two new isoforms. Biochimie 2024; 218:46-56. [PMID: 37659716 DOI: 10.1016/j.biochi.2023.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/07/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
In accidents involving Crotalus snakes, the crotoxin complex (CTX) plays lethal action due to its neurotoxic activity. On the other hand, CTX have potential biotechnological application due to its anti-tumoral, anti-inflammatory, antimicrobial, analgesic and immunomodulatory properties. CTX is a heterodimer composed of Crotoxin A (CA or crotapotin), the acidic nontoxic and non-enzymatic component and; Crotoxin B (CB), a basic, toxic and catalytic PLA2. Currently, there are two classes of CTX isoforms, whose differences in their biological activities have been attributed to features presented in CB isoforms. Here, we present the crystal structure of CB isolated from the Crotalus durissus collilineatus venom. It amino acid sequence was assigned using the SEQUENCE SLIDER software, which revealed that the crystal structure is a heterodimer composed of two new CB isoforms (colCB-A and colCB-B). Bioinformatic and biophysical analyses showed that the toxin forms a tetrameric assembly in solution similar to CB from Crotalus durissus terrificus venom, despite some differences observed at the dimeric interface. By the previously proposed classification, the colCB-B presents features of the class I isoforms while colCB-A cannot be classified into classes I and II based on its amino acid sequence. Due to similar features observed for other CB isoforms found in the NCBI database and the results obtained for colCB-A, we suggest that there are more than two classes of CTX and CB isoforms in crotalic venoms.
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Affiliation(s)
- Guilherme H M Salvador
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Carlos A H Fernandes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; UMR 7590, CNRS, Muséum National d'Histoire Naturelle, IRD, Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Paris, France
| | - Rafael J Borges
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Centro de Química Medicina (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade de Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Andreimar M Soares
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos Aplicados, Fundação Oswaldo Cruz (FIOCRUZ), Unidade Rondônia, Porto Velho, RO, Brazil; Inst Nac. de Epidemiologia da Amazônia Ocidental (INCT-EPIAMO), Rede de Pesquisa e Conhecimento de Excelência na Amazônia Ocidental (RED-CONEXAO), Brazil
| | - Marcos R M Fontes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Instituto de Estudos Avançados do Mar (IEAMar), Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil.
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188
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Khanppnavar B, Schuster D, Lavriha P, Uliana F, Özel M, Mehta V, Leitner A, Picotti P, Korkhov VM. Regulatory sites of CaM-sensitive adenylyl cyclase AC8 revealed by cryo-EM and structural proteomics. EMBO Rep 2024; 25:1513-1540. [PMID: 38351373 PMCID: PMC10933263 DOI: 10.1038/s44319-024-00076-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/19/2024] Open
Abstract
Membrane adenylyl cyclase AC8 is regulated by G proteins and calmodulin (CaM), mediating the crosstalk between the cAMP pathway and Ca2+ signalling. Despite the importance of AC8 in physiology, the structural basis of its regulation by G proteins and CaM is not well defined. Here, we report the 3.5 Å resolution cryo-EM structure of the bovine AC8 bound to the stimulatory Gαs protein in the presence of Ca2+/CaM. The structure reveals the architecture of the ordered AC8 domains bound to Gαs and the small molecule activator forskolin. The extracellular surface of AC8 features a negatively charged pocket, a potential site for unknown interactors. Despite the well-resolved forskolin density, the captured state of AC8 does not favour tight nucleotide binding. The structural proteomics approaches, limited proteolysis and crosslinking mass spectrometry (LiP-MS and XL-MS), allowed us to identify the contact sites between AC8 and its regulators, CaM, Gαs, and Gβγ, as well as to infer the conformational changes induced by these interactions. Our results provide a framework for understanding the role of flexible regions in the mechanism of AC regulation.
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Affiliation(s)
- Basavraj Khanppnavar
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Dina Schuster
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Pia Lavriha
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biological Chemistry, ETH Zurich, Zurich, Switzerland
| | - Merve Özel
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Ved Mehta
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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189
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Hafez M, Gourlie R, McDonald M, Telfer M, Carmona MA, Sautua FJ, Moffat CS, Moolhuijzen PM, See PT, Aboukhaddour R. Evolution of the Toxb Gene in Pyrenophora tritici-repentis and Related Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:327-337. [PMID: 37759383 DOI: 10.1094/mpmi-08-23-0114-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mohamed Hafez
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
- Botany and Microbiology Department, Faculty of Science, Suez University, Suez, Egypt
| | - Ryan Gourlie
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Megan McDonald
- School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, U.K
| | - Melissa Telfer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Marcelo A Carmona
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Francisco J Sautua
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Paula M Moolhuijzen
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Pao Theen See
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
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190
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Abok JI, Garver WS, Edwards JS. Bioinformatic analysis of human ZPR1 gene pathogenic exome mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582196. [PMID: 38464185 PMCID: PMC10925172 DOI: 10.1101/2024.02.27.582196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Advanced sequencing technologies enable rapid detection of sequence variants, aiming to uncover the molecular foundations of human genetic disorders. The challenge lies in interpreting the influence of new exome variants that lead to diverse phenotypes. Our study introduces a detailed, multi-tiered method for assessing the impact of novel variants, particularly focusing on the zinc finger protein 1 (ZPR1) gene. Herein, we employed a combination of variant effect predictors, protein stability analyses, and the American College of Medical Genetics and Association of Molecular Pathology (ACMG/AMP) guidelines. Our structural analysis pinpoints specific amino acid residues in the ZPR1 zinc finger domains that are sensitive to changes, distinguishing between benign and disease-causing coding variants using rigorous in silico tools. We examined 223 germline ZPR1 exome variants, uncovering significant ethnic disparities in the frequency of heterozygous harmful ZPR1 variants, ranging from 0.04% in the Ashkenazi Jewish population to 0.34% in African/African Americans. Additionally, the discovery of three homozygous carriers in European and South Asian groups suggests a higher occurrence of ZPR1 variants in these demographics, meriting further exploration. This research provides insights into the prevalence and implications of amino acid substitutions in the ZPR1 protein.
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Affiliation(s)
- Jeremiah I. Abok
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - William S. Garver
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
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191
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Kumar R, R R, Diwakar V, Khan N, Kumar Meghwanshi G, Garg P. Structural-functional analysis of drug target aspartate semialdehyde dehydrogenase. Drug Discov Today 2024; 29:103908. [PMID: 38301800 DOI: 10.1016/j.drudis.2024.103908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Aspartate β-semialdehyde dehydrogenase (ASADH) is a key enzyme in the biosynthesis of essential amino acids in microorganisms and some plants. Inhibition of ASADHs can be a potential drug target for developing novel antimicrobial and herbicidal compounds. This review covers up-to-date information about sequence diversity, ligand/inhibitor-bound 3D structures, potential inhibitors, and key pharmacophoric features of ASADH useful in designing novel and target-specific inhibitors of ASADH. Most reported ASADH inhibitors have two highly electronegative functional groups that interact with two key arginyl residues present in the active site of ASADHs. The structural information, active site binding modes, and key interactions between the enzyme and inhibitors serve as the basis for designing new and potent inhibitors against the ASADH family.
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Affiliation(s)
- Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Rajkumar R
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar 160062, Punjab, India
| | - Vineet Diwakar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar 160062, Punjab, India
| | - Nazam Khan
- Clinical Laboratory Science Department, Applied Medical Science College, Shaqra University, Shaqra, Kingdom of Saudi Arabia
| | | | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar 160062, Punjab, India.
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192
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Chiduza GN, Garza-Garcia A, Almacellas E, De Tito S, Pye VE, van Vliet AR, Cherepanov P, Tooze SA. ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A. Autophagy 2024; 20:557-576. [PMID: 37938170 PMCID: PMC10936676 DOI: 10.1080/15548627.2023.2275905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophagy-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A vertebrates encode ATG9B, a poorly characterized paralog expressed in a subset of tissues. Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. By establishing the molecular structure and function of ATG9B, our results inform the exploration of niche roles for autophagy machinery in more complex eukaryotes and reveal insights relevant across species.Abbreviation: ATG: autophagy related; CHS: cholesteryl hemisuccinate; cryo-EM: single-particle cryogenic electron microscopy; CTF: contrast transfer function: CTH: C- terminal α helix; FSC: fourier shell correlation; HDIR: HORMA domain interacting region; LMNG: lauryl maltose neopentyl glycol; MD: molecular dynamics simulations; MSA: multiple sequence alignment; NBD-PE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl ammonium salt); POPC: palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; RBG: repeating beta groove domain; RMSD: root mean square deviation; SEC: size-exclusion chromatography; TMH: transmembrane helix.
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Affiliation(s)
- George N. Chiduza
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Eugenia Almacellas
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | | | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
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193
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da Silva ANR, Pereira GRC, Bonet LFS, Outeiro TF, De Mesquita JF. In silico analysis of alpha-synuclein protein variants and posttranslational modifications related to Parkinson's disease. J Cell Biochem 2024; 125:e30523. [PMID: 38239037 DOI: 10.1002/jcb.30523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 03/12/2024]
Abstract
Parkinson's disease (PD) is among the most prevalent neurodegenerative disorders, affecting over 10 million people worldwide. The protein encoded by the SNCA gene, alpha-synuclein (ASYN), is the major component of Lewy body (LB) aggregates, a histopathological hallmark of PD. Mutations and posttranslational modifications (PTMs) in ASYN are known to influence protein aggregation and LB formation, possibly playing a crucial role in PD pathogenesis. In this work, we applied computational methods to characterize the effects of missense mutations and PTMs on the structure and function of ASYN. Missense mutations in ASYN were compiled from the literature/databases and underwent a comprehensive predictive analysis. Phosphorylation and SUMOylation sites of ASYN were retrieved from databases and predicted by algorithms. ConSurf was used to estimate the evolutionary conservation of ASYN amino acids. Molecular dynamics (MD) simulations of ASYN wild-type and variants A30G, A30P, A53T, and G51D were performed using the GROMACS package. Seventy-seven missense mutations in ASYN were compiled. Although most mutations were not predicted to affect ASYN stability, aggregation propensity, amyloid formation, and chaperone binding, the analyzed mutations received relatively high rates of deleterious predictions and predominantly occurred at evolutionarily conserved sites within the protein. Moreover, our predictive analyses suggested that the following mutations may be possibly harmful to ASYN and, consequently, potential targets for future investigation: K6N, T22I, K34E, G36R, G36S, V37F, L38P, G41D, and K102E. The MD analyses pointed to remarkable flexibility and essential dynamics alterations at nearly all domains of the studied variants, which could lead to impaired contact between NAC and the C-terminal domain triggering protein aggregation. These alterations may have functional implications for ASYN and provide important insight into the molecular mechanism of PD, supporting the design of future biomedical research and improvements in existing therapies for the disease.
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Affiliation(s)
- Aloma N R da Silva
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel R C Pereira
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiz Felippe Sarmento Bonet
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Joelma F De Mesquita
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
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194
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Rajagopal BS, Yates N, Smith J, Paradisi A, Tétard-Jones C, Willats WGT, Marcus S, Knox JP, Firdaus-Raih M, Henrissat B, Davies GJ, Walton PH, Parkin A, Hemsworth GR. Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae. IUCRJ 2024; 11:260-274. [PMID: 38446458 PMCID: PMC10916295 DOI: 10.1107/s2052252524001386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about polysaccharide oxidation. In bacteria, less is known about the interplay between redox proteins and LPMOs, or how the interaction between the two contributes to polysaccharide degradation. We therefore set out to characterize two previously unstudied proteins from the shipworm symbiont Teredinibacter turnerae that were initially identified by the presence of carbohydrate binding domains appended to uncharacterized domains with probable redox functions. Here, X-ray crystal structures of several domains from these proteins are presented together with initial efforts to characterize their functions. The analysis suggests that the target proteins are unlikely to function as LPMO electron donors, raising new questions as to the potential redox functions that these large extracellular multi-haem-containing c-type cytochromes may perform in these bacteria.
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Affiliation(s)
- Badri S. Rajagopal
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nick Yates
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake Smith
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | | | - Catherine Tétard-Jones
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - William G. T. Willats
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Susan Marcus
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gideon J. Davies
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Paul H. Walton
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Alison Parkin
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Glyn R. Hemsworth
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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195
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Hernández-Prieto JH, Martini VP, Iulek J. Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie 2024; 218:20-33. [PMID: 37709188 DOI: 10.1016/j.biochi.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The pathogen Paracoccidioides lutzii (Pb01) is found in South America countries Colombia, Ecuador, Venezuela and Brazil, especially in the central, west, and north regions of the latter. It belongs to the Ajellomycetaceae family, Onygenales order, and is typically thermodimorphic, presenting yeast cells when it grows in animal tissues, but mycelia when in the environment, where it produces the infectious propagule. This fungus is one of the etiologic agents of Paracoccidioidomycosis (PCM), the most important endemic fungal infection in Latin America. Investigations on its genome have contributed to a better understanding about its metabolism and revealed the complexity of several metabolic glycolytic pathways. Glyceraldehyde-3-Phosphate Dehydrogenase from Paracoccidioides lutzii (PlGAPDH) is considered a moonlighting protein and participates in several biological processes of this pathogen. The enzyme was expressed and purified, as seen in SDS-PAGE gel, crystallized and had its three dimensional structure (3D) determined in complex with NAD+, a sulphate ion and d-galactonic acid, therefore, a type of 'GAA site'. It is the first GAPDH structure to show this chemical type in this site and how this protein can bind an acid derived from oxidation of a linear hexose.
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Affiliation(s)
| | | | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil.
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196
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Harracksingh AN, Singh A, Mayorova T, Bejoy B, Hornbeck J, Elkhatib W, McEdwards G, Gauberg J, Taha ARW, Islam IM, Erclik T, Currie MA, Noyes M, Senatore A. The binding of Mint/X11 PDZ domains to Ca V 2 calcium channels predates bilaterian animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582151. [PMID: 38463976 PMCID: PMC10925089 DOI: 10.1101/2024.02.26.582151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
PDZ domain mediated interactions with voltage-gated calcium (Ca V ) channel C-termini play important roles in localizing and compartmentalizing membrane Ca 2+ signaling. The first such interaction discovered was between the neuronal multi-domain protein Mint-1, and the presynaptc calcium channel Ca V 2.2 in mammals. Although the physiological significance of this interaction is unclear, its occurrence in vertebrates and bilaterian invertebrates suggests important and conserved functions. In this study, we explore the evolutionary origins of Mint and its interaction with Ca V 2 channels. Phylogenetic and structural in silico analyses revealed that Mint is an animal-specific gene, like Ca V 2 channels, which bears a highly divergent N-terminus but strongly conserved C-terminus comprised of a phosphotyrosine binding domain, two tandem PDZ domains (PDZ-1 and PDZ-2), and a C-terminal auto-inhibitory element that binds and inhibits PDZ-1. Also deeply conserved are other Mint interacting proteins, namely amyloid precursor and related proteins, presenilins, neurexin, as well as CASK and Veli which form a tripartite complex with Mint in bilaterians. Through yeast 2-hybrid and bacterial 2-hybrid experiments, we show that Mint and Ca V 2 channels from cnidarians and placozoans interact in vitro , and in situ hybridization revealed co-expression of corresponding transcripts in dissociated neurons from the cnidarian Nematostella vectensis . Unexpectedly, the Mint orthologue from the ctenophore Hormiphora californiensis was able to strongly bind the divergent C-terminal ligands of cnidarian and placozoan Ca V 2 channels, despite neither the ctenophore Mint, nor the placozoan and cnidarian orthologues, binding the ctenophore Ca V 2 channel C-terminus. Altogether, our analyses provide a model for the emergence of this interaction in early animals first via adoption of a PDZ ligand by Ca V 2 channels, followed by sequence changes in the ligand that caused a modality switch for binding to Mint.
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Alcorlo M, Luque-Ortega JR, Gago F, Ortega A, Castellanos M, Chacón P, de Vega M, Blanco L, Hermoso J, Serrano M, Rivas G, Hermoso J. Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29. Nucleic Acids Res 2024; 52:2045-2065. [PMID: 38281216 PMCID: PMC10899789 DOI: 10.1093/nar/gkae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024] Open
Abstract
The genome-organizing protein p6 of Bacillus subtilis bacteriophage φ29 plays an essential role in viral development by activating the initiation of DNA replication and participating in the early-to-late transcriptional switch. These activities require the formation of a nucleoprotein complex in which the DNA adopts a right-handed superhelix wrapping around a multimeric p6 scaffold, restraining positive supercoiling and compacting the viral genome. Due to the absence of homologous structures, prior attempts to unveil p6's structural architecture failed. Here, we employed AlphaFold2 to engineer rational p6 constructs yielding crystals for three-dimensional structure determination. Our findings reveal a novel fold adopted by p6 that sheds light on its self-association mechanism and its interaction with DNA. By means of protein-DNA docking and molecular dynamic simulations, we have generated a comprehensive structural model for the nucleoprotein complex that consistently aligns with its established biochemical and thermodynamic parameters. Besides, through analytical ultracentrifugation, we have confirmed the hydrodynamic properties of the nucleocomplex, further validating in solution our proposed model. Importantly, the disclosed structure not only provides a highly accurate explanation for previously experimental data accumulated over decades, but also enhances our holistic understanding of the structural and functional attributes of protein p6 during φ29 infection.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, CSIC, 28006 Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas “Margarita Salas”, CSIC, 28040Madrid, Spain
| | - Federico Gago
- Departamento de Farmacología and CSIC-IQM Associate Unit, Universidad de Alcalá, Alcalá de Henares, 28871Madrid, Spain
| | - Alvaro Ortega
- Department of Biochemistry and Molecular Biology ‘B’ and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence ‘Campus Mare Nostrum, Murcia, Spain
| | - Milagros Castellanos
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Nanotechnology for Health-Care, 28049 Madrid, Spain
| | - Pablo Chacón
- Department of Biological Physical-Chemistry, Institute of Physical-Chemistry “Blas Cabrera”, CSIC, 28006Madrid, Spain
| | - Miguel de Vega
- Genome maintenance and instability, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049Cantoblanco, Madrid, Spain
| | - Luis Blanco
- Genome maintenance and instability, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049Cantoblanco, Madrid, Spain
| | - José M Hermoso
- Genome maintenance and instability, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, 28049Cantoblanco, Madrid, Spain
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
- Cambridge Institute of Science, Altos Labs, Cambridge, UK
| | - Germán Rivas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas “Margarita Salas”, CSIC, 28040Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, CSIC, 28006 Madrid, Spain
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198
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Kulshreshtha A, Bhatnagar S. Structural effect of the H992D/H418D mutation of angiotensin-converting enzyme in the Indian population: implications for health and disease. J Biomol Struct Dyn 2024:1-18. [PMID: 38411559 DOI: 10.1080/07391102.2024.2321246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
The Non synonymous SNPs (nsSNPs) of the renin-angiotensin-system (RAS) pathway, unique to the Indian population were investigated in view of its importance as an endocrine system. nsSNPs of the RAS pathway genes were mined from the IndiGenome database. Damaging nsSNPs were predicted using SIFT, PredictSNP, SNP and GO, Snap2 and Protein Variation Effect Analyzer. Loss of function was predicted based on protein stability change using I mutant, PremPS and CONSURF. The structural impact of the nsSNPs was predicted using HOPE and Missense3d followed by modeling, refinement, and energy minimization. Molecular Dynamics studies were carried out using Gromacsv2021.1. 23 Indian nsSNPs of the RAS pathway genes were selected for structural analysis and 8 were predicted to be damaging. Further sequence analysis showed that HEMGH zinc binding motif changes to HEMGD in somatic ACE-C domain (sACE-C) H992D and Testis ACE (tACE) H418D resulted in loss of zinc coordination, which is essential for enzymatic activity in this metalloprotease. There was a loss of internal interactions around the zinc coordination residues in the protein structural network. This was also confirmed by Principal Component Analysis, Free Energy Landscape and residue contact maps. Both mutations lead to broadening of the AngI binding cavity. The H992D mutation in sACE-C is likely to be favorable for cardiovascular health, but may lead to renal abnormalities with secondary impact on the heart. H418D in tACE is potentially associated with male infertility.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akanksha Kulshreshtha
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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199
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Vincenzi M, Mercurio FA, Autiero I, Leone M. Cancer-Related Mutations in the Sam Domains of EphA2 Receptor and Ship2 Lipid Phosphatase: A Computational Study. Molecules 2024; 29:1024. [PMID: 38474536 DOI: 10.3390/molecules29051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The lipid phosphatase Ship2 interacts with the EphA2 receptor by forming a heterotypic Sam (sterile alpha motif)-Sam complex. Ship2 works as a negative regulator of receptor endocytosis and consequent degradation, and anti-oncogenic effects in cancer cells should be induced by hindering its association with EphA2. Herein, a computational approach is presented to investigate the relationship between Ship2-Sam/EphA2-Sam interaction and cancer onset and further progression. A search was first conducted through the COSMIC (Catalogue of Somatic Mutations in Cancer) database to identify cancer-related missense mutations positioned inside or close to the EphA2-Sam and Ship2-Sam reciprocal binding interfaces. Next, potential differences in the chemical-physical properties of mutant and wild-type Sam domains were evaluated by bioinformatics tools based on analyses of primary sequences. Three-dimensional (3D) structural models of mutated EphA2-Sam and Ship2-Sam domains were built as well and deeply analysed with diverse computational instruments, including molecular dynamics, to classify potentially stabilizing and destabilizing mutations. In the end, the influence of mutations on the EphA2-Sam/Ship2-Sam interaction was studied through docking techniques. This in silico approach contributes to understanding, at the molecular level, the mutation/cancer relationship by predicting if amino acid substitutions could modulate EphA2 receptor endocytosis.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
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200
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Kamble A, Singh R, Singh H. Structural and Functional Characterization of Obesumbacterium proteus Phytase: A Comprehensive In-Silico Study. Mol Biotechnol 2024:10.1007/s12033-024-01069-x. [PMID: 38393631 DOI: 10.1007/s12033-024-01069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/09/2024] [Indexed: 02/25/2024]
Abstract
Phytate, also known as myoinositol hexakisphosphate, exhibits anti-nutritional properties and possesses a negative environmental impact. Phytase enzymes break down phytate, showing potential in various industries, necessitating thorough biochemical and computational characterizations. The present study focuses on Obesumbacterium proteus phytase (OPP), indicating its similarities with known phytases and its potential through computational analyses. Structure, functional, and docking results shed light on OPP's features, structural stability, strong and stable interaction, and dynamic conformation, with flexible sidechains that could adapt to different temperatures or specific functions. Root Mean Square fluctuation (RMSF) highlighted fluctuating regions in OPP, indicating potential sites for stability enhancement through mutagenesis. The systematic approach developed here could aid in enhancing enzyme properties via a rational engineering approach. Computational analysis expedites enzyme discovery and engineering, complementing the traditional biochemical methods to accelerate the quest for superior enzymes for industrial applications.
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Affiliation(s)
- Asmita Kamble
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Vile Parle (W), Mumbai, Maharashtra, India
| | - Rajkumar Singh
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Station 19, Lausanne, Switzerland
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Vile Parle (W), Mumbai, Maharashtra, India.
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