Article
Multidisciplinary Sciences
Dmitry A. Nedosekin, TsungYen Chen, Srinivas Ayyadevara, Vladimir P. Zharov, Robert J. Shmookler Reis
Summary: The study introduces a laser-based photothermal treatment method for aggregates, which successfully delays their accumulation and enhances the lifespan of treated nematodes. This drug-free therapy, combining photothermal treatment with advanced imaging techniques, effectively disrupts aggregates and initiates systemic recovery, validating the concept of aggregate-disruption treatments for neurodegenerative diseases in humans.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Dahyun Yu, Nicole Zarate, Angel White, De'jah Coates, Wei Tsai, Carmen Nanclares, Francesco Cuccu, Johnny S. Yue, Taylor G. Brown, Rachel H. Mansky, Kevin Jiang, Hyuck Kim, Tessa Nichols-Meade, Sarah N. Larson, Katherine Gundry, Ying Zhang, Cristina Tomas-Zapico, Jose J. Lucas, Michael Benneyworth, Gulin Oz, Marija Cvetanovic, Alfonso Araque, Rocio Gomez-Pastor
Summary: This study investigated the role of protein kinase CK2 alpha' in the regulation of neuroinflammation and synaptic function in Huntington's disease. The results showed that CK2 alpha' haploinsufficiency can decrease pro-inflammatory cytokines, improve synaptic activity, and enhance motor coordination in a mouse model of Huntington's disease. These findings provide important clues for developing effective therapeutic strategies for Huntington's disease.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Alvaro Martinez-Camarena, Marian Merino, Ana Virginia Sanchez-Sanchez, Salvador Blasco, Jose M. Llinares, Jose L. Mullor, Enrique Garcia-Espana
Summary: A novel amino-nanozyme based on boehmite nanoparticles has been designed to address important issues in Huntington disease. The amino-nanozyme exhibits SOD activity, mitoROS scavenging properties, and the ability to disaggregate mutant huntingtin deposits in cells.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Premila P. Samuel Russell, Meredith M. Rickard, Mayank Boob, Martin Gruebele, Taras V. Pogorelov
Summary: This study examines the influence of cellular interactions on the early folding events of a three-helix bundle protein in the cytoplasm. It is found that even fast-folding proteins can get stuck in non-native states in the cell, making them useful models for studying protein-chaperone interactions and early stages of aggregate formation relevant to cellular disease.
Article
Biochemistry & Molecular Biology
Mohammed Khaled, Birgit Strodel, Abdallah Sayyed-Ahmad
Summary: Polyglutamine expansion in the huntingtin protein exon 1 is associated with neurodegenerative diseases. Molecular dynamics simulations revealed differences between nonpathogenic and pathogenic forms of Htt-ex1. The nonpathogenic monomer adopts a long alpha-helix, while the pathogenic monomer has a disordered polyglutamine region and forms compact structures with beta-sheets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sanda Nastasia Moldovean, Vasile Chis
Summary: The study reveals that m-HTT proteins and CaM interact in the cerebral cortex, affecting intracellular calcium levels. The 9P(EM) model has the most significant impact on the structure and fluctuation rate of CaM, with lower interaction energies compared to the 45Qs-HTT mutant model.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
S. M. Ayala Mariscal, M. L. Pigazzini, Y. Richter, M. Ozel, I. L. Grothaus, J. Protze, K. Ziege, M. Kulke, M. ElBediwi, J. V. Vermaas, L. Colombi Ciacchi, S. Koppen, F. Liu, J. Kirstein
Summary: Huntington's disease is a neurodegenerative disorder caused by aggregation-prone mutant HTT protein. The trimeric chaperone complex formed by Hsc70, DNAJB1, and Apg2 can suppress and reverse the aggregation of HTTExon1Q(48) by binding to the HTT protein's poly-proline region through DNAJB1. The mutation of the conserved H244 in DNAJB1's HBM specifically affects the suppression and disaggregation of HTT fibrils, highlighting the importance of this interaction site for Huntington's disease.
NATURE COMMUNICATIONS
(2022)
Article
Biophysics
Sharon E. Groover, Adewale Adegbuyiro, Caleb K. Fan, Breanna L. Hodges, Maryssa Beasley, Katelyn Taylor, Alyssa R. Stonebraker, Chathuranga Siriwardhana, Justin Legleiter
Summary: This study investigated the impact of macromolecular crowding on the aggregation of Huntington's disease-related protein htt in bulk solution and at interfaces. It was found that crowding agents influenced the aggregation characteristics of htt on different interfaces, highlighting the importance of crowding in the aqueous phase on this process.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Priyanka Borah, Airy Sanjeev, Venkata Satish Kumar Mattaparthi
Summary: Parkinson's disease is a common progressive neurodegenerative disorder caused by misfolding and aggregation of alpha-synuclein. Recent research shows that Oleuropein aglycone (OleA) stabilizes the monomeric structure of alpha-synuclein, preventing the formation of toxic aggregates and favoring the growth of stable ones, highlighting a potential therapeutic approach.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Multidisciplinary
Surajit Kalita, Hagai Bergman, Kshatresh Dutta Dubey, Sason Shaik
Summary: Alzheimer's disease and other neurodegenerative diseases characterized by senile plaques are caused by the accumulation of s-amyloid peptides. This study investigates the behavior of these plaques in the presence of static and oscillating oriented external electric fields using molecular dynamics simulations. The results show that long-term disintegration of the plaques is desirable for therapeutic treatments. Furthermore, the use of oscillating oriented external electric fields leads to irreversible disintegration of the aggregated s-amyloid peptides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Yunxiang Sun, Aleksandr Kakinen, Xulin Wan, Niamh Moriarty, Cameron P. J. Hunt, Yuhuan Li, Nicholas Andrikopoulos, Aparna Nandakumar, Thomas P. Davis, Clare L. Parish, Yang Song, Pu Chun Ke, Feng Ding
Summary: This study provides evidence of the structure, dynamics and toxicity of A beta 42 oligomers through synergistic in silico, in vitro and in vivo validations, highlighting their role as toxic intermediates in the early aggregation of amyloid peptides.
Article
Chemistry, Medicinal
Huan He, Yuying Liu, Yunxiang Sun, Feng Ding
Summary: Pathological aggregation of intrinsically disordered tau protein, driven by the interactions between microtubule-binding (MTB) domains, is associated with Alzheimer's disease. Our results from atomistic discrete molecular dynamics simulations show that all four repeat monomers of tau are dynamic, with R3 displaying the strongest aggregation propensity. R1 is the least prone to aggregation, while R2 and R4 dimers contain both helix and beta-sheet structures.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Ryuji Owada, Shinichi Mitsui, Kazuhiro Nakamura
Summary: The study revealed that aggregated polyS and polyL peptides can spontaneously enter neuron-like cells and astrocytes, causing cell degeneration, aberrant differentiation, and cell death. Injecting these aggregates into the ventricles of adult mice resulted in behavioral changes, with polyS injection leading to extensive vacuolar degeneration in the brain. This suggests that RAN translation-related proteins containing polyS and polyL have the potential to propagate and exert universal toxicity in recipient cells.
SCIENTIFIC REPORTS
(2022)
Review
Multidisciplinary Sciences
Harleen Kohli, Pravir Kumar, Rashmi K. Ambasta
Summary: Huntington's disease is a neurodegenerative disorder caused by a genetic mutation, with no current cure available, but peptide therapy may help in recovering brain damage. This study focuses on using peptide-based therapy to target mutated proteins and prevent aggregation, potentially ameliorating disease symptoms.
Article
Biochemistry & Molecular Biology
Exequiel E. Barrera, Francesco Zonta, Sergio Pantano
Summary: Poly glutamine and glutamine-rich peptides are central in pathological aggregation events, their biophysical properties can be characterized using coarse-grained simulations. A double role for glutamines was found in the study, mediating seeding and optimizing hydrogen bond networks for aggregates maturation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Hisae Tateishi-Karimata, Miki Nakano, Smritimoy Pramanik, Shigenori Tanaka, Naoki Sugimoto
CHEMICAL COMMUNICATIONS
(2015)
Article
Chemistry, Physical
Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Florence Tama, Osamu Miyashita, Shu-ichi Nakano, Naoki Sugimoto
CHEMICAL PHYSICS LETTERS
(2016)
Article
Chemistry, Medicinal
Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J. Parker, Yoshio Okiyama, Hitomi Yuki, Shigeyuki Yokoyama, Hirofumi Nakano, Shigenori Tanaka, Teruki Honma
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2017)
Article
Instruments & Instrumentation
Miki Nakano, Osamu Miyashita, Slavica Jonic, Changyong Song, Daewoong Nam, Yasumasa Joti, Florence Tama
JOURNAL OF SYNCHROTRON RADIATION
(2017)
Article
Virology
Fengqi Xu, Shigenori Tanaka, Hirofumi Watanabe, Yasuhiro Shimane, Misako Iwasawa, Kazue Ohishi, Tadashi Maruyama
Article
Chemistry, Physical
Keiya Maruyama, Yinglei Sheng, Hirofumi Watanabe, Kaori Fukuzawa, Shigenori Tanaka
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2018)
Article
Instruments & Instrumentation
Miki Nakano, Osamu Miyashita, Slavica Jonic, Atsushi Tokuhisa, Florence Tama
JOURNAL OF SYNCHROTRON RADIATION
(2018)
Article
Chemistry, Medicinal
Fumiyuki Shirai, Takeshi Tsumura, Yoko Yashiroda, Hitomi Yuki, Hideaki Niwa, Shin Sato, Tsubasa Chikada, Yasuko Koda, Kenichi Washizuka, Nobuko Yoshimoto, Masako Abe, Tetsuo Onuki, Yui Mazaki, Chizuko Hirama, Takehiro Fukami, Hirofumi Watanabe, Teruki Honma, Takashi Umehara, Mikako Shirouzu, Masayuki Okue, Yuko Kano, Takashi Watanabe, Kouichi Kitamura, Eiki Shitara, Yukiko Muramatsu, Haruka Yoshida, Anna Mizutani, Hiroyuki Seimiya, Minoru Yoshida, Hiroo Koyama
JOURNAL OF MEDICINAL CHEMISTRY
(2019)
Review
Chemistry, Multidisciplinary
Evgeni B. Starikov
Summary: The research re-analyzed the two hundred years of thermodynamics' history and emphasized Carnot's priority in modern scientific research on thermodynamics.
MONATSHEFTE FUR CHEMIE
(2021)
Review
Chemistry, Multidisciplinary
Nils Engelbrektsson, Karl Franzen, Evgeni B. Starikov
Summary: This passage discusses how a Swedish schoolteacher, Nils Engelbrektsson, was able to theoretically derive a universally valid thermodynamic equation of state over 100 years ago. His colleague, Karl Franzen, experimentally verified his inferences, leading to a victorious outcome after a century-long struggle. Their trains of thoughts deserve careful consideration and analysis.
MONATSHEFTE FUR CHEMIE
(2021)
Article
Biophysics
Miki Nakano, Osamu Miyashita, Florence Tama
BIOPHYSICS AND PHYSICOBIOLOGY
(2019)
Article
Chemistry, Physical
Carl-Mikael Suomivuori, Heike Fliegl, Evgeni B. Starikov, T. Silviu Balaban, Ville R. I. Kaila, Dage Sundholm
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)
Article
Biochemistry & Molecular Biology
Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma
CHEM-BIO INFORMATICS JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2018)
Article
Physics, Multidisciplinary
Evgeni B. Starikov
FRONTIERS IN PHYSICS
(2018)
Article
Biology
Kunal Bhattacharya, Shikha Mahato, Satyendra Deka, Nongmaithem Randhoni Chanu, Amit Kumar Shrivastava, Pukar Khanal
Summary: Chemoresistance, a major challenge in cancer treatment, is associated with the cellular glutathione-related detoxification system. A study has identified GSTP1 enzyme as critical in the inactivation of anticancer drugs and suggests the need for GSTP1 inhibitors to combat chemoresistance. Through molecular docking and simulations, the study found that quercetin 7-O-beta-D-glucoside showed promise as a potential candidate for addressing chemoresistance in cancer patients.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Manwi Shankar, Majji Sai Sudha Rani, Priyanka Gopi, P. Arsha, Prateek Pandya
Summary: This study investigates the interaction between the food dye BBY and the serum protein BSA. The results show that BBY binds to a specific site on BSA through hydrophobic interactions, affecting the structural stability of the protein. These findings enhance our understanding of the molecular-level interactions between BBY and BSA.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Chi Zhang, Qian Gao, Ming Li, Tianfei Yu
Summary: In this study, we propose a graph neural network-based autoencoder model, AGraphSAGE, that effectively predicts protein-protein interactions across diverse biological species by integrating gene ontology.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Kangjie Wu, Liqian Xu, Xinxiang Li, Youhua Zhang, Zhenyu Yue, Yujia Gao, Yiqiong Chen
Summary: Named Entity Recognition (NER) is a crucial task in natural language processing (NLP) and big data analysis, with wide application range. This paper proposes an improved neural network method for NER of rice genes and phenotypes, which can learn semantic information in the context without feature engineering. Experimental results show that the proposed model outperforms other models.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Suman Hait, Sudip Kundu
Summary: Interactions between amino acids in proteins are crucial for stability and structural integrity. Thermophiles have more and more stable interactions to survive in extreme environments. Different types of interactions are enriched in different structural regions.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Kountay Dwivedi, Ankit Rajpal, Sheetal Rajpal, Virendra Kumar, Manoj Agarwal, Naveen Kumar
Summary: This study aims to identify biomarkers for non-small cell lung cancer (NSCLC) using copy number variation (CNV) data. A novel deep learning architecture, XL1R-Net, is proposed to improve the classification accuracy for NSCLC subtyping. Twenty NSCLC-relevant biomarkers are uncovered using explainable AI (XAI)-based feature identification. The results show that the identified biomarkers have high classification performance and clinical relevance. Additionally, twelve of the biomarkers are potentially druggable and eighteen of them have a high probability of predicting NSCLC patients' survival likelihood according to the Drug-Gene Interaction Database and the K-M Plotter tool, respectively. This research suggests that investigating these seven novel biomarkers can contribute to NSCLC therapy, and the integration of multiomics data and other sources will help better understand NSCLC heterogeneity.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)
Article
Biology
Pengli Lu, Wenqi Zhang, Jinkai Wu
Summary: Researchers have developed a computational method, AMPCDA, to predict circRNA-disease associations using predefined metapaths, achieving high predictive accuracy. This method effectively combines node embeddings with higher-order neighborhood representations and provides valuable guidance for revealing new disease mechanisms in biological research.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2024)