Assessing the martini 3 protein model: A review of its path and potential
Biochim Biophys Acta Proteins Proteom. 2024 Apr 24:141014. doi: 10.1016/j.bbapap.2024.141014. Online ahead of print.ABSTRACTCoarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field - Martini 3 - a new...
Source: Biochimica et Biophysica Acta - April 26, 2024 Category: Biochemistry Authors: Lu ís Borges-Araújo Gilberto P Pereira Mariana Val ério Paulo C T Souza Source Type: research
A mouse model of autoimmune inner ear disease without endolymphatic hydrops
Biochim Biophys Acta Mol Basis Dis. 2024 Apr 24:167198. doi: 10.1016/j.bbadis.2024.167198. Online ahead of print.ABSTRACTAutoimmune inner ear disease (AIED) is an organ-specific disease characterized by irreversible, prolonged, and progressive hearing and equilibrium dysfunctions. The primary symptoms of AIED include asymmetric sensorineural hearing loss accompanied by vertigo, aural fullness, and tinnitus. AIED is divided into primary and secondary types. Research has been conducted using animal models of rheumatoid arthritis (RA), a cause of secondary AIED. However, current models are insufficient to accurately analyze v...
Source: Biochimica et Biophysica Acta - April 26, 2024 Category: Biochemistry Authors: Shotaro Harada Yoshihisa Koyama Takao Imai Yoshichika Yoshioka Takuya Sumi Hidenori Inohara Shoichi Shimada Source Type: research
CILP2 promotes hypertrophic scar through Snail acetylation by interaction with ACLY
CONCLUSION: CILP2 exerts a vital role in hypertrophic scar formation and might be a detectable biomarker reflecting the progression of hypertrophic scar and a therapeutic target for hypertrophic scar.PMID:38670440 | DOI:10.1016/j.bbadis.2024.167202 (Source: Biochimica et Biophysica Acta)
Source: Biochimica et Biophysica Acta - April 26, 2024 Category: Biochemistry Authors: Jianzhang Wang Juan Du Yuanyong Wang Yajuan Song Junzheng Wu Tong Wang Zhou Yu Baoqiang Song Source Type: research
TAT38 and TAT38 mimics potently inhibit adipogenesis by repressing C/EBP α, PPARγ, Pi-PPARγ, and SREBP1 expression
Biochim Biophys Acta Gene Regul Mech. 2024 Apr 24:195030. doi: 10.1016/j.bbagrm.2024.195030. Online ahead of print.ABSTRACTAntiretroviral therapy-naive people living with HIV possess less fat than people without HIV. Previously, we found that HIV-1 transactivator of transcription (TAT) decreases fat in ob/ob mice. The TAT38 (a.a. 20-57) is important in the inhibition of adipogenesis and contains three functional domains: Cys-ZF domain (a.a. 20-35 TACTNCYCAKCCFQVC), core-domain (a.a. 36-46, FITKALGISYG), and protein transduction domain (PTD)(a.a. 47-57, RAKRRQRRR). Interestingly, the TAT38 region interacts with the Cyclin T...
Source: Biochimica et Biophysica Acta - April 26, 2024 Category: Biochemistry Authors: Sun-Young Park Dongyoon Shin Young So Yoon Sujin Park Seung Soon Im Yeongshin Kim Young-Soo Kim CheolSoo Choi Man-Wook Hur Source Type: research
RBM3 enhances the stability of MEF2C mRNA and modulates blood-brain barrier permeability in AD microenvironment
This study found the reduced RNA binding motif protein 3 (RBM3) expression in brain microvascular endothelial cells (BMECs) incubated with Aβ1-42. This downregulation of RBM3 caused a decrease in the levels of ZO-1 and occludin and increased the permeability of BBB cell model in AD microenvironment. Myocyte enhancer factor 2C (MEF2C) expression was also inhibited in BMECs incubated with Aβ1-42. A decrease in MEF2C expression led to increased permeability of BBB cell model in AD microenvironment and reductions in the levels of ZO-1 and occludin. Further analysis of the underlying mechanism revealed that RBM3 binds to and ...
Source: Biochimica et Biophysica Acta - April 26, 2024 Category: Biochemistry Authors: Ye Ding Meiqing Lin Jirui Wang Xiuli Shang Source Type: research
Copper enhances aggregational toxicity of mutant huntingtin in a Drosophila model of Huntington's Disease
Biochim Biophys Acta Mol Basis Dis. 2024 Jan;1870(1):166928. doi: 10.1016/j.bbadis.2023.166928. Epub 2023 Oct 28.ABSTRACTHuntington's disease (HD) is a progressive neurodegenerative disorder with clinical presentations of moderate to severe cognitive, motor, and psychiatric disturbances. HD is caused by the trinucleotide repeat expansion of CAG of the huntingtin (HTT) gene. The mutant HTT protein containing pathological polyglutamine (polyQ) extension is prone to misfolding and aggregation in the brain. It has previously been observed that copper and iron concentrations are increased in the striata of post-mortem human HD ...
Source: Biochimica et Biophysica Acta - April 25, 2024 Category: Biochemistry Authors: Amanda G Lobato Natalie Ortiz-Vega Yi Zhu Deepa Neupane Katlyn K Meier R Grace Zhai Source Type: research
Targeting JUNB to modulate M2 macrophage polarization in preeclampsia
This study utilized single-cell RNA sequencing (scRNA-seq) to delineate the cellular landscape of the placenta in PE, identifying 11 distinct cell subpopulations, with macrophages playing a pivotal role in mediating cell-cell communication. Specifically, the transcription factor JUNB was found to be a key gene in macrophages from PE samples, influencing the interaction between macrophages and both epithelial and endothelial cells. Functional experiments indicated that interference with JUNB expression promoted macrophage polarization towards an M2 phenotype, which facilitated trophoblast invasion, migration, and angiogenes...
Source: Biochimica et Biophysica Acta - April 25, 2024 Category: Biochemistry Authors: Peiyue Jiang Xiaojun Zhu Ying Jiang Hetong Li Qiong Luo Source Type: research
Knockdown of heat shock protein family D member 1 (HSPD1) in lung cancer cell altered secretome profile and cancer-associated fibroblast induction
This study established stable HSPD1-knockdown A549 lung cancer cells using a lentivirus-mediated shRNA transduction. A targeted label-free proteomic analysis identified six significantly altered secretory proteins in the shHSPD1-A549 secretome compared to shControl-A549. Functional enrichment analysis highlighted their involvement in cell-to-cell communication and immune responses within the tumor microenvironment. Additionally, most altered proteins exhibited positive correlations and significant prognostic impacts on LUAD patient survival. Investigations on the effects of lung cancer secretomes on lung fibroblast WI-38 c...
Source: Biochimica et Biophysica Acta - April 25, 2024 Category: Biochemistry Authors: Siripat Aluksanasuwan Keerakarn Somsuan Jatuporn Ngoenkam Wararat Chiangjong Artitaya Rongjumnong Atthapan Morchang Somchai Chutipongtanate Sutatip Pongcharoen Source Type: research
Copper enhances aggregational toxicity of mutant huntingtin in a Drosophila model of Huntington's Disease
Biochim Biophys Acta Mol Basis Dis. 2024 Jan;1870(1):166928. doi: 10.1016/j.bbadis.2023.166928. Epub 2023 Oct 28.ABSTRACTHuntington's disease (HD) is a progressive neurodegenerative disorder with clinical presentations of moderate to severe cognitive, motor, and psychiatric disturbances. HD is caused by the trinucleotide repeat expansion of CAG of the huntingtin (HTT) gene. The mutant HTT protein containing pathological polyglutamine (polyQ) extension is prone to misfolding and aggregation in the brain. It has previously been observed that copper and iron concentrations are increased in the striata of post-mortem human HD ...
Source: Biochimica et Biophysica Acta - April 25, 2024 Category: Biochemistry Authors: Amanda G Lobato Natalie Ortiz-Vega Yi Zhu Deepa Neupane Katlyn K Meier R Grace Zhai Source Type: research
Targeting JUNB to modulate M2 macrophage polarization in preeclampsia
This study utilized single-cell RNA sequencing (scRNA-seq) to delineate the cellular landscape of the placenta in PE, identifying 11 distinct cell subpopulations, with macrophages playing a pivotal role in mediating cell-cell communication. Specifically, the transcription factor JUNB was found to be a key gene in macrophages from PE samples, influencing the interaction between macrophages and both epithelial and endothelial cells. Functional experiments indicated that interference with JUNB expression promoted macrophage polarization towards an M2 phenotype, which facilitated trophoblast invasion, migration, and angiogenes...
Source: Biochimica et Biophysica Acta - April 25, 2024 Category: Biochemistry Authors: Peiyue Jiang Xiaojun Zhu Ying Jiang Hetong Li Qiong Luo Source Type: research
Knockdown of heat shock protein family D member 1 (HSPD1) in lung cancer cell altered secretome profile and cancer-associated fibroblast induction
This study established stable HSPD1-knockdown A549 lung cancer cells using a lentivirus-mediated shRNA transduction. A targeted label-free proteomic analysis identified six significantly altered secretory proteins in the shHSPD1-A549 secretome compared to shControl-A549. Functional enrichment analysis highlighted their involvement in cell-to-cell communication and immune responses within the tumor microenvironment. Additionally, most altered proteins exhibited positive correlations and significant prognostic impacts on LUAD patient survival. Investigations on the effects of lung cancer secretomes on lung fibroblast WI-38 c...
Source: Biochimica et Biophysica Acta - April 25, 2024 Category: Biochemistry Authors: Siripat Aluksanasuwan Keerakarn Somsuan Jatuporn Ngoenkam Wararat Chiangjong Artitaya Rongjumnong Atthapan Morchang Somchai Chutipongtanate Sutatip Pongcharoen Source Type: research
Ubiquitin ligase TRIM15 promotes the progression of pancreatic cancer via the upregulation of the IGF2BP2-TLR4 axis
CONCLUSIONS: TRIM15 could ubiquitinate IGF2BP2 to enhance the function of phase separation and the maintenance of mRNA stability of TLR4. TRIM15 is a potential therapeutic target against pancreatic cancer.PMID:38657551 | DOI:10.1016/j.bbadis.2024.167183 (Source: Biochimica et Biophysica Acta)
Source: Biochimica et Biophysica Acta - April 24, 2024 Category: Biochemistry Authors: Hongkun Cai Jingyuan Zhao Qiyue Zhang Heyu Wu Yan Sun Feng Guo Yingke Zhou Gengdu Qin Wentao Xia Yuhan Zhao Xueyi Liang Shilin Yin Yang Qin Dan Li Heshui Wu Dianyun Ren Source Type: research
Vitamin C and inhibition of the fibroblast growth factor pathway synergistically enhance myogenesis
Biochim Biophys Acta Mol Cell Res. 2024 Apr 22:119737. doi: 10.1016/j.bbamcr.2024.119737. Online ahead of print.NO ABSTRACTPMID:38657910 | DOI:10.1016/j.bbamcr.2024.119737 (Source: Biochimica et Biophysica Acta)
Source: Biochimica et Biophysica Acta - April 24, 2024 Category: Biochemistry Authors: Xiajie Fu Masayuki Funaba Source Type: research
Pan-neuronal expression of human mutant SOD1 in Drosophila impairs survival and motor performance, induces early neuroinflammation and chromosome aberrations
Biochim Biophys Acta Mol Basis Dis. 2024 Apr 22:167192. doi: 10.1016/j.bbadis.2024.167192. Online ahead of print.ABSTRACTSeveral mutations in the SOD1 gene encoding for the antioxidant enzyme Superoxide Dismutase 1, are associated with amyotrophic lateral sclerosis, a rare and devastating disease characterized by motor neuron degeneration and patients' death within 2-5 years from diagnosis. Motor neuron loss and related symptomatology manifest mostly in adult life and, to date, there is still a gap of knowledge on the precise cellular and molecular events preceding neurodegeneration. To deepen our awareness of the early ph...
Source: Biochimica et Biophysica Acta - April 24, 2024 Category: Biochemistry Authors: Francesco Liguori Francesca Alberti Susanna Amadio Daniela Francesca Angelini Eleonora Pilesi Giuseppe Vitale Giulia Tesoriere Giovanna Borsellino Fiammetta Vern ì Cinzia Volont é Source Type: research
MTH1 inhibition synergizes with ROS-inducing agents to trigger cervical cancer cells undergoing parthanatos
Biochim Biophys Acta Mol Basis Dis. 2024 Apr 22:167190. doi: 10.1016/j.bbadis.2024.167190. Online ahead of print.ABSTRACTCervical cancer cells possess high levels of reactive oxygen species (ROS); thus, increasing oxidative stress above the toxicity threshold to induce cell death is a promising chemotherapeutic strategy. However, the underlying mechanisms of cell death are elusive, and efficacy and toxicity issues remain. Within DNA, 8-oxo-7,8-dihydroguanine (8-oxoG) is the most frequent base lesion repaired by 8-oxoguanine glycosylase 1 (OGG1)-initiated base excision repair. Cancer cells also express high levels of MutT h...
Source: Biochimica et Biophysica Acta - April 24, 2024 Category: Biochemistry Authors: Chunshuang Li Yaoyao Xue Jiaxin Wu Lihong Zhang Tianming Yang Mengtao Ai Jinling Han Xu Zheng Ruoxi Wang Istvan Boldogh Xueqing Ba Source Type: research
