Article
Plant Sciences
Jing Chen, Guifen Zhou, Yan Dong, Xiaodong Qian, Jing Li, Xuting Xu, Huilian Huang, Limin Xu, Liqin Li
Summary: This study used iTRAQ technology to analyze protein expression profiles of saffron under cold stress and a normal environment, revealing the important roles of sucrose/starch biosynthesis pathways in floral development. Under cold stress, saffron non-flowering buds showed significantly decreased sucrose contents, while starch contents remained unchanged.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Zoology
Tharathip Hemthanon, Boonhiang Promdonkoy, Panadda Boonserm
Summary: Bacillus thuringiensis (Bt) isolates collected from Thailand were screened for high Vip3A and Cry protein production levels and high thermostability to control Spodoptera spp. The selected Bt isolate 506 showed high toxicity against S. exigua and S. frugiperda second-instar larvae and the insecticidal proteins retained their activity after heat treatment.
JOURNAL OF INVERTEBRATE PATHOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yusi Liu, Shanna Bastiaan-Net, Yuebin Zhang, Tamara Hoppenbrouwers, Yingying Xie, Yulu Wang, Xue Wei, Guoming Du, Haowen Zhang, Khandader M. D. Sharif Uddin Imam, Harry Wichers, Zhen Li
Summary: This study evaluated the correlation between thermal stability and protein structural features of rFIP-nha, which has significant anti-tumor activity. The results showed that higher thermostability was correlated to higher oligomerization states, larger interface area, and more interactions. The findings suggest that the thermostability of FIPs is dependent on their oligomerization state, and is correlated with their cytotoxicity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Songtao Ye, Han Zhang, Jinyu Fei, Charles H. Wolstenholme, Xin Zhang
Summary: By chemically installing extended pi-rich alternating carbon-carbon linkages between the rotational electron donors and acceptors of RBFs, the lack of control of their viscosity sensitivity has been resolved. The length of the linkage strongly influences the viscosity sensitivity, providing the possibility to design RBFs with different viscosity sensitivities. RBFs can differentiate misfolded protein oligomers and insoluble aggregates in test tubes and live cells through a dual-color imaging strategy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Lauren J. Rice, Heath Ecroyd, Antoine M. van Oijen
Summary: Single-molecule approaches have advantages in studying amyloid fibril formation, providing insights into the mechanism and interactions involved. Fluorescence-based single-molecule methods have proven to be particularly effective in studying amyloid fibril formation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Mohd Younus Bhat, Maqsood Ahmad Malik, Laishram Rajendrakumar Singh, Tanveer Ali Dar
Summary: This study investigated the effect of osmolytes on beta-casein and found that trimethylamine N-oxide induced a compact structural state with slightly decreased chaperone activity, while sarcosine and betaine had no significant effect. This suggests a possible evolutionary selection for higher structural disorder in beta-casein compared to alpha-casein for stability of the casein complex and prevention of amyloidosis in the mammary gland.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Multidisciplinary
Wang Wan, Yanan Huang, Qiuxuan Xia, Yulong Bai, Yuwen Chen, Wenhan Jin, Mengdie Wang, Di Shen, Haochen Lyu, Yuqi Tang, Xuepeng Dong, Zhenming Gao, Qun Zhao, Lihua Zhang, Yu Liu
Summary: The study reveals that covalent Michael addition can occur during protein aggregation, offering a new pathway for chemical reactions. By designing covalent probes for imaging, chemical proteomics, and therapeutic purposes, different fluorescence color-switch responses can be achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Andrius Sakalauskas, Kamile Mikalauskaite, Ruta Snieckute, Vytautas Smirnovas
Summary: Prion protein aggregation into amyloid fibrils is linked to prion diseases, but the polymorphism of these aggregates complicates the search for anti-amyloid compounds. Research shows that prion protein fibrils can form multiple types under different temperature conditions, depending on the initial state of the protein molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Polymer Science
Agusti Emperador
Summary: Using the PACSAB protein model, researchers simulated protein-protein recognition and studied the impact of helical structure on the association of aggregating peptides. The optimized PACSAB force field accurately reproduced the correct binding interface in ubiquitin dimerization and the conformational ensemble of the disordered protein activator for hormone and retinoid receptor (ACTR). The PACSAB model allowed for the prediction of the native binding of ACTR with its binding partner, reproducing the refolding mechanism of the disordered protein upon binding.
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Kamile Mikalauskaite, Lukas Krasauskas, Vytautas Smirnovas
Summary: Protein aggregation into amyloid fibrils plays a role in neurodegenerative diseases such as Alzheimer's and Parkinson's. Despite significant research, the process remains poorly understood, hindering the development of treatments. Recent reports of cross-interactions between amyloidogenic proteins, including Tau and prion, have further complicated the process. This study observed a conformation-specific association between Tau and prion fibrils, increasing their aggregate formation and amyloid binding capacity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Derrick Lau, James C. Walsh, Claire F. Dickson, Andrew Tuckwell, Jeffrey H. Stear, Dominic J. B. Hunter, Akshay Bhumkar, Vaibhav Shah, Stuart G. Turville, Emma Sierecki, Yann Gambin, Till Bocking, David A. Jacques
Summary: The study developed a fluorescence analysis method using HIV capsid as bait to screen for fluorescence-labeled binding molecules. By using a scanning stage, rapid detection was achieved without compromising sensitivity, providing a new approach for screening potential interactors.
ANALYTICAL CHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Johanna Giovannini, Willy Smeralda, Marie Jouanne, Jana Sopkova-de Oliveira Santos, Marco Catto, Anne Sophie Voisin-Chiret
Summary: Tauopathies are neurodegenerative disorders characterized by the accumulation of abnormal tau protein in the brain, with Alzheimer's disease being the most common form. The pathophysiological mechanisms of AD are still not fully understood, and there is currently no curative treatment available. Therefore, targeting tau protein aggregation has become an important focus for therapeutic approaches.
DRUG DISCOVERY TODAY
(2022)
Article
Neurosciences
Viet Hoang Man, Da Lin, Xibing He, Jie Gao, Junmei Wang
Summary: This study aimed to develop a joint computational/cell-based protocol for screening tau assembly inhibitors. The virtual oligomerization inhibition experiment and tau seeding assay were used to evaluate a ligand's ability to inhibit tau assembly. The findings suggest that traditional biochemical assays may not be as accurate as tau seeding activities in cells for predicting therapeutic outcomes.
JOURNAL OF ALZHEIMERS DISEASE
(2022)
Article
Multidisciplinary Sciences
Archana Vishwakarma, Yogesan Meganathan, Mohandass Ramya
Summary: This study presents the development of an aptamer-based assay for rapid, sensitive, and cost-effective detection of pathogenic Leptospira. The aptamer is conjugated to gold nanoparticles, resulting in a colorimetric response in the presence of L. interrogans. The assay exhibits a detection limit of 57 CFU/mL and demonstrates high specificity and reproducibility in detecting pathogenic Leptospira in water samples.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Analytical
Mariacristina Gagliardi, Laura Colagiorgio, Marco Cecchini
Summary: This study proposes a QCM-D method to investigate the interactions between polymeric nanoparticles and three different human blood proteins. The results indicate that bare nanoparticles have a high affinity towards fibrinogen and γ-globulin, while PEGylation greatly reduces these interactions and surfactant coating appears to increase them. These findings suggest that the proposed approach is valid for studying the interactions between nanoparticles and blood proteins.
Article
Biochemistry & Molecular Biology
Anastasiia D. Gonchar, Galina V. Kopylova, Anastasia M. Kochurova, Valentina Y. Berg, Daniil V. Shchepkin, Natalia A. Koubasova, Andrey K. Tsaturyan, Sergey Y. Kleymenov, Alexander M. Matyushenko, Dmitrii I. Levitsky
Summary: Mutations in the TPM3 gene cause structural changes and impaired functional properties in the gamma gamma-Tpm molecule, shedding light on the molecular mechanism of CFTD development and slow skeletal muscle weakness in this inherited disease.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Victoria V. Nefedova, Natalia A. Koubassova, Vera A. Borzova, Sergey Y. Kleymenov, Andrey K. Tsaturyan, Alexander M. Matyushenko, Dmitrii Levitsky
Summary: This study investigated the effects of mutations mimicking phosphorylation of Tpm on the structural and functional properties of cardiac Tpm carrying cardiomyopathy-associated mutations. The results showed that these mutations can alter the affinity of Tpm for F-actin, potentially influencing the development of heart diseases.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Marina Marchenko, Victoria Nefedova, Natalia Artemova, Sergey Kleymenov, Dmitrii Levitsky, Alexander Matyushenko
Summary: This study investigates the structural and functional differences of five cytoplasmic Tpm isoforms, revealing that sequence variations in alternatively spliced regions of these isoforms can significantly impact their interaction with actin filaments, thus playing a crucial role in cytoskeleton organization and dynamics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Marina A. Marchenko, Victoria V. Nefedova, Daria S. Yampolskaya, Vera A. Borzova, Sergey Y. Kleymenov, Salavat R. Nabiev, Larisa V. Nikitina, Alexander M. Matyushenko, Dmitrii I. Levitsky
Summary: This study investigated the properties of five low molecular weight Tpm isoforms and found significant differences in their sequences variations in alternatively spliced regions, which may be important for further research on the organization and dynamics of the cytoskeleton.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biology
Dmitry E. Petrenko, Vladimir I. Timofeev, Vladimir V. Britikov, Elena V. Britikova, Sergey Y. Kleymenov, Anna V. Vlaskina, Inna P. Kuranova, Anna G. Mikhailova, Tatiana V. Rakitina
Summary: This study presented the crystal structure of bacterial oligopeptidase B and identified an intermediate conformation between open and closed states, suggesting a potential impact on computational studies. The modification of the interdomain linker and the presence of spermine were crucial for crystallization success.
Article
Biochemistry & Molecular Biology
Vera A. Borzova, Natalia A. Chebotareva, Nikolai N. Sluchanko, Sergey Yu Kleymenov, Kira A. Markossian, Boris Kurganov
Summary: Chemical chaperones are low-molecular compounds that counteract protein aggregation. The aggregation process of bovine liver glutamate dehydrogenase (GDH) at different temperatures was studied, and the unfolding of the protein was found to be the rate-limiting stage of the overall aggregation process. The anti-aggregation activity of chemical chaperones was quantified, and arginine ethyl ester showed the highest activity.
Article
Biochemistry & Molecular Biology
Tatiana B. Eronina, Valeriya V. Mikhaylova, Natalia A. Chebotareva, Sergey Y. Kleymenov, Anastasia V. Pivovarova, Boris I. Kurganov
Summary: Chemical chaperones are small molecules that enhance protein stability and folding. They have significant effects on the stability, oligomeric state, and aggregation of muscle glycogen phosphorylase b (Phb).
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Andrey K. Tsaturyan, Elena V. Zaklyazminskaya, Margarita E. Polyak, Galina V. Kopylova, Daniil V. Shchepkin, Anastasia M. Kochurova, Anastasiia D. Gonchar, Sergey Y. Kleymenov, Natalia A. Koubasova, Sergey Y. Bershitsky, Alexander M. Matyushenko, Dmitrii I. Levitsky
Summary: The study identified a new variant in the TPM1 gene, which is associated with HCM. The variant increased the thermal stability of the Tpm molecule and its affinity for F-actin was unaffected. However, it increased the Ca2+ sensitivity of filament sliding and impaired its inhibition at low Ca2+ concentration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Victoria V. Nefedova, Galina V. Kopylova, Daniil V. Shchepkin, Anastasia M. Kochurova, Olga I. Kechko, Vera A. Borzova, Natalia S. Ryabkova, Ivan A. Katrukha, Vladimir A. Mitkevich, Sergey Y. Bershitsky, Dmitrii I. Levitsky, Alexander M. Matyushenko
Summary: By investigating the role of cardiac troponin T (TnT) in Tpm mutations associated with cardiomyopathy, it was found that TnT1 stabilizes Tpm WT and all mutants except Tpm M8R. The study also demonstrated that Tpm mutations likely exert their pathogenic effects through interactions with Tn, cardiac myosin, or other protein partners.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Vera A. Borzova, Svetlana G. Roman, Anastasiya V. Pivovarova, Natalia A. Chebotareva
Summary: Intracellular proteins aggregation can be enhanced under stress. Heat-shock proteins (HSPs) and accumulation of osmolytes are cellular protective mechanisms. The antiaggregation activity of HSPB5 can be affected by crowding agents and osmolytes, and different additives can either improve or impair its activity against different protein targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Galina V. V. Kopylova, Anastasia M. M. Kochurova, Daria S. S. Yampolskaya, Victoria V. V. Nefedova, Andrey K. K. Tsaturyan, Natalia A. A. Koubassova, Sergey Y. Y. Kleymenov, Dmitrii I. I. Levitsky, Sergey Y. Y. Bershitsky, Alexander M. M. Matyushenko, Daniil V. V. Shchepkin
Summary: The TPM1 gene expresses two isoforms of tropomyosin (Tpm) in the myocardium, alpha (aTpm; Tpm 1.1) and kappa (?Tpm; Tpm 1.2), with ?Tpm being the result of alternative splicing. In this study, the structural features and regulatory function of ?Tpm in the atrial and ventricular myocardium were investigated using an in vitro motility assay. The formation of a?Tpm heterodimer was found to be thermodynamically favorable, indicating that ?Tpm most likely exists as a?Tpm heterodimer in the myocardium.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alexander M. Matyushenko, Victoria V. Nefedova, Anastasia M. Kochurova, Galina V. Kopylova, Natalia A. Koubassova, Anna G. Shestak, Daria S. Yampolskaya, Daniil V. Shchepkin, Sergey Y. Kleymenov, Natalia S. Ryabkova, Ivan A. Katrukha, Sergey Y. Bershitsky, Elena V. Zaklyazminskaya, Andrey K. Tsaturyan, Dmitrii I. Levitsky
Summary: We characterized a novel genetic variant c.292G > A (p.E98K) in the TPM1 gene encoding cardiac tropomyosin 1.1 isoform (Tpm1.1), which is associated with complex cardiomyopathy, conduction dysfunction, and neuromuscular involvement. We found that the E98K substitution in Tpm1.1 significantly destabilizes its structure and impairs its regulatory properties. This study provides insights into the mechanism by which the E98K Tpm mutation affects myocardial function and relaxation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
A. A. Pometun, P. D. Parshin, N. P. Galanicheva, L. A. Shaposhnikov, D. L. Atroshenko, E. Pometun, V. V. Burmakin, S. Yu Kleymenov, S. S. Savin, V. Tishkov
Summary: A mutant formate dehydrogenase (PseFDH) from Pseudomonas sp. 101 bacterium with improved thermal stability has been generated through single-point amino acid replacements. The mutant with E170D substitution exhibits increased thermal stability compared to the starting mutant and the wild-type enzyme.