Article
Environmental Sciences
Junxia Mao, Xiaofang Huang, Hongyan Sun, Xin Jin, Wenjuan Guan, Jiahui Xie, Yiying Wang, Xubo Wang, Donghong Yin, Zhenlin Hao, Ying Tian, Jian Song, Jun Ding, Yaqing Chang
Summary: This study investigates the molecular response mechanism of scallops to a combination of high temperature and hypoxia stress. The research reveals that scallops exhibit different sensitivities to environmental stress, and high temperature and hypoxia have a synergistic effect on scallops. Immune and apoptosis-related pathways play important roles in scallops' response to environmental stress, and heat shock proteins play a key role in scallops' adaptation to altered environments.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Yan Wang, Peng Wang, Hai-Yan Cao, Hai-Tao Ding, Hai-Nan Su, Shi-Cheng Liu, Guangfeng Liu, Xia Zhang, Chun-Yang Li, Ming Peng, Fuchuan Li, Shengying Li, Yin Chen, Xiu-Lan Chen, Yu-Zhong Zhang
Summary: This study reports the structure and collagenolytic mechanism of Vibrio collagenase VhaC, providing new insights into bacterial collagenolysis.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Luisa R. Garcia Michel, Clara D. Keirns, Benjamin C. Ahlbrecht, Daniel A. Barr
Summary: A new method for estimating transfer entropy in biomolecular systems was developed by analyzing the variance-covariance matrix of atomic fluctuations. The results showed systematic consistency of the method for calculating transfer entropy and provided insights into the interconnected residue networks in proteins. Additionally, evidence of possible allosteric activity and different paths of activation in mutants were presented, highlighting the important role of transfer entropy analysis in understanding allosteric behavior.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Chunyan Tu, Xiaowa Nie, Jingguang G. Chen
Summary: This article critically assesses the progress of the catalytic reaction of CH4 and CO2 to produce acetic acid, focusing on identifying and constructing active sites. The differences in metal oxidation state can affect the activation of CH4 and CO2, thereby changing the efficiency of the reaction. By modifying the active sites and transition states through metal site placement, framework environment, and acid site promotion, the efficiency of heterogeneous catalysts can be improved for this reaction.
Article
Chemistry, Multidisciplinary
Rama K. Koppisetti, Yan G. Fulcher, Steven R. Van Doren
Summary: The fusion peptide of SARS-CoV-2 plays a crucial role in the fusion of viral and cell membranes, with its structure changes affecting the fusion process between the virus and the cell.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Dominique A. Doyle, Florencia N. Burian, Benjamin Aharoni, Annabelle J. Klinder, Melissa M. Menzel, Gerard Carlo C. Nifras, Ahad L. Shabazz-Henry, Bianca Ulrich Palma, Gisselle A. Hidalgo, Christopher J. Sottolano, Bianca M. Ortega, Matthew G. Niepielko
Summary: mRNA packaging into germ granules is a conserved strategy for posttranscriptional regulation of germline mRNAs. We studied the homotypic clustering of nos and pgc in four Drosophila species and found that clustering is a conserved process that enriches germ granule mRNAs. Natural variations in nos 3ʹ UTR sequence influence clustering, resulting in decreased nos levels and increased defective germ cells. Our findings highlight the impact of evolution on germ granules and provide insight into the diversity and regulation of biomolecular condensates.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Joseph S. Snowden, Jehad Alzahrani, Lee Sherry, Martin Stacey, David J. Rowlands, Neil A. Ranson, Nicola J. Stonehouse
Summary: This study reanalyzed the structure of type I fatty acid synthases (FASs) and identified several differences in both structural and enzymatic domains between P. pastoris FAS and the prototypical yeast FAS from S. cerevisiae. By using focussed classification, the researchers were able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is crucial for the function of FAS. The structure reported in this study will serve as a valuable resource for further engineering efforts to synthesize alternate products using yeast FAS.
SCIENTIFIC REPORTS
(2021)
News Item
Medicine, General & Internal
Revital Marcus
Summary: This Medical News article explores the potential link between hormonal fluctuations, calcitonin gene-related peptide (CGRP), and migraines in women.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Oncology
Felicity Newell, Peter A. Johansson, James S. Wilmott, Katia Nones, Vanessa Lakis, Antonia L. Pritchard, Serigne N. Lo, Robert Rawson, Stephen H. Kazakoff, Andrew J. Colebatch, Lambros T. Koufariotis, Peter M. Ferguson, Scott Wood, Conrad Leonard, Matthew H. Law, Kelly M. Brooks, Natasa Broit, Jane M. Palmer, Kasey L. Couts, Ismael A. Vergara, Georgina Long, Andrew P. Barbour, Omgo E. Nieweg, Brindha Shivalingam, William A. Robinson, Jonathan R. Stretch, Andrew J. Spillane, Robyn P. M. Saw, Kerwin F. Shannon, John F. Thompson, Graham J. Mann, John Pearson, Richard A. Scolyer, Nicola Waddell, Nicholas K. Hayward
Summary: This is the largest whole-genome analysis of melanoma to date, comprehensively comparing the genomics of the four major melanoma subtypes. This study highlights both similarities and differences between the subtypes, providing insights into the etiology and biology of melanoma.
Article
Multidisciplinary Sciences
Timothy H. Tran, Albert H. Chan, Lucy C. Young, Lakshman Bindu, Chris Neale, Simon Messing, Srisathiyanarayanan Dharmaiah, Troy Taylor, John-Paul Denson, Dominic Esposito, Dwight V. Nissley, Andrew G. Stephen, Frank McCormick, Dhirendra K. Simanshu
Summary: This study presents molecular details of the RAS-RAF interaction, including the crystal structures of KRAS binding with RAF1 and a proposed model of membrane-bound RAS-RAF complex formation.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Tao Zeng, Jianmei Yin, Peishi Feng, Feiran Han, Yong Tian, Yuntong Wang, Tiantian Gu, Yuhui Xu, Yali Liu, Guohui Li, Liang Qu, Li Chen, Lihong Gu, Wenwu Xu, Qian Xue, Qingyu Wei, Yongqing Cao, Peifeng Li, Huiyong Zhang, Guoqin Li, Lijun Liu, Chenghao Zhou, Zhengrong Tao, Junda Shen, Wei Han, Lizhi Lu
Summary: Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jianxiang Ma, Pengchuan Sun, Dandan Wang, Zhenyue Wang, Jiao Yang, Ying Li, Wenjie Mu, Renping Xu, Ying Wu, Congcong Dong, Nawal Shrestha, Jianquan Liu, Yongzhi Yang
Summary: The study reports the high-quality genome of Chloranthus sessilifolius, revealing the genome duplication within the species and the phylogenetic relationships with other Mesangiospermae lineages. Additionally, the findings suggest that both hybridization and incomplete lineage sorting may have contributed to the phylogenetic incongruities.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Katie Leap, Iveta Yotova, Steve Horvath, Julian A. Martinez-Agosto
Summary: Endometriosis is a common disease with various presentations. The use of DNA methylation age can help distinguish the origin of ectopic lesions, contributing to clinical classification.
SCIENTIFIC REPORTS
(2022)
Article
Ophthalmology
Wilson Luu, Barbara Zangerl, Michael Kalloniatis, Stephen Palmisano, Juno Kim
Summary: This study found that participants with AMD exhibited stronger vection and spatial presence in self-motion perception, while individuals with glaucoma showed lower vection strength and spatial presence. Both AMD and glaucoma groups reported reduced severity in cybersickness compared to healthy normals.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Plant Sciences
Miao Sun, Xiao-Lan Yang, Zhi-Peng Zhu, Qin-Yi Xu, Ke-Xin Wu, Yi-Jun Kang, Hao Wang, Ai-Sheng Xiong
Summary: Nitric oxide plays a crucial role in improving cold stress resistance in okra by inhibiting lignin accumulation and delaying lignification, promoting endogenous NO biosynthesis, reducing ethylene and ABA content, and protecting the plant from cold stress damage.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Valeriy P. Shendrikov, Anna S. Alekseeva, Erik F. Kot, Konstantin S. Mineev, Daria S. Tretiakova, Abdulilah Ece, Ivan A. Boldyrev
Summary: This study describes azophenylindane based molecular motors, which have different rotamers in trans and cis configurations. The behaviors of these motors were investigated experimentally and computationally, revealing that the conversion of the motor results in a mixture of isomers. Some cis-rotamers can directly convert to each other, while others require conversion via trans-configuration. The motion of these motors is similar to a mixing machine, with the indane group acting as a base and the phenol group as a beater. These aphin-switches may have promising applications in advanced biological systems or in cases where molecular packing disordering is desired, such as lipid bilayers.
Article
Pharmacology & Pharmacy
Alexey I. Kuzmenkov, Steve Peigneur, Joshua A. Nasburg, Konstantin S. Mineev, Maxim V. Nikolaev, Ernesto Lopes Pinheiro-Junior, Alexander S. Arseniev, Heike Wulff, Jan Tytgat, Alexander A. Vassilevski
Summary: Apamin is a selective inhibitor of K(Ca)2 channels with no significant effects on other molecular targets. The spatial structure of apamin and its potential use as a pharmacological tool and drug design template for K(Ca)2 channels are supported by this study.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Vladislav V. Motov, Erik F. Kot, Alexandra V. Shabalkina, Sergey A. Goncharuk, Alexander S. Arseniev, Marina V. Goncharuk, Konstantin S. Mineev
Summary: Membrane proteins are essential in molecular biology, but studying their structures requires finding suitable membranes and refolding protocols. Isotropic bicelles are commonly used as membrane mimetics, but the refolding process is still not well understood. To find the best refolding methods for helical membrane proteins, we studied the interactions between proteins, lipids, and detergents in trifluoroethanol-water mixtures. Using NMR spectroscopy and light scattering, we determined key states of the compounds and proposed optimal protocols. These protocols were tested on various membrane domains with successful results.
JOURNAL OF BIOMOLECULAR NMR
(2023)
Article
Biochemistry & Molecular Biology
Eugene P. Kramarova, Sophia S. Borisevich, Edward M. Khamitov, Alexander A. Korlyukov, Pavel Dorovatovskii, Anastasia D. Shagina, Konstantin S. Mineev, Dmitri Tarasenko, Roman A. Novikov, Alexey A. Lagunin, Ivan Boldyrev, Aiarpi A. Ezdoglian, Natalia Yu Karpechenko, Tatiana A. Shmigol, Yuri Baukov, Vadim V. Negrebetsky
Summary: The synthesis of products from the interaction of 1,3-propanesultone ring with amides of pyridinecarboxylic acids was investigated. The position of the substituent in the heteroaromatic fragment and temperature condition influenced the yield of the reaction products. A mechanism and transition-state model were proposed based on spectroscopic, X-Ray, and quantum-chemical calculation data. The synthesized compounds showed promising pharmacological effects and low acute toxicity.
Article
Biophysics
Bruno Hargittay, Konstantin S. Mineev, Christian Richter, Sridhar Sreeramulu, Hendrik R. A. Jonker, Krishna Saxena, Harald Schwalbe
Summary: We report the NMR chemical shift assignment of FGF8b, an important regulator of brain embryonic development in humans. The obtained chemical shifts agree with X-ray data, except for the N-terminal gN helix which forms only when complexed with the receptor. This data serves as a starting point for investigating the interaction of FGF8b with its receptors and potential drugs or inhibitors.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biochemistry & Molecular Biology
Yulia A. Bogdanova, Elvira R. Zaitseva, Alexander Yu. Smirnov, Nadezhda S. Baleeva, Alexey S. Gavrikov, Ivan N. Myasnyanko, Sergey A. Goncharuk, Erik F. Kot, Konstantin S. Mineev, Alexander S. Mishin, Mikhail S. Baranov
Summary: In this study, we demonstrated that NanoLuc luciferase, a well-known enzyme, can serve as a fluorogen activating protein for arylidene-imidazolones analogs of the Kaede protein chromophore. We showed that these compounds can be utilized as fluorescent sensors for this particular protein and can also be employed alongside it as a genetically encoded tag in fluorescent microscopy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Rafael Moliner, Mykhailo Girych, Cecilia A. Brunello, Vera Kovaleva, Caroline Biojone, Giray Enkavi, Lina Antenucci, Erik F. Kot, Sergey A. Goncharuk, Katja Kaurinkoski, Mirjami Kuutti, Senem M. Fred, Lauri V. Elsila, Sven Sakson, Cecilia Cannarozzo, Cassiano R. A. F. Diniz, Nina Seiffert, Anna Rubiolo, Hele Haapaniemi, Elsa Meshi, Elina Nagaeva, Tiina Ohman, Tomasz Rog, Esko Kankuri, Marcal Vilar, Markku Varjosalo, Esa R. Korpi, Perttu Permi, Konstantin S. Mineev, Mart Saarma, Ilpo Vattulainen, Plinio C. Casarotto, Eero Castren
Summary: Moliner et al. demonstrate that psychedelics can bind directly to the BDNF receptor TrkB and enhance its plasticity and antidepressant-like effects, while their hallucinogenic effects are unrelated to TrkB binding. These findings suggest that psychedelics have potential as fast-acting antidepressants with lasting effects, similar to clinically approved antidepressants. The study also reveals that LSD and psilocin have higher affinity for TrkB than other antidepressants, and both psychedelics and antidepressants bind to specific sites within the transmembrane domain of TrkB dimers.
NATURE NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
F. D. Kornilov, A. V. Shabalkina, Cong Lin, P. E. Volynsky, E. F. Kot, A. L. Kayushin, V. A. Lushpa, M. V. Goncharuk, A. S. Arseniev, S. A. Goncharuk, Xiaohui Wang, K. S. Mineev
Summary: Toll-like receptors (TLRs) play a crucial role in the innate immune system. In this study, the researchers investigated the spatial structures of the transmembrane and cytoplasmic juxtamembrane regions of TLR2, TLR3, TLR5, and TLR9 using solution NMR spectroscopy and computer simulations. They discovered a previously unreported structural element, the cytoplasmic hydrophobic juxtamembrane alpha-helix, which is important for receptor activation and serves as a more complex connection between the transmembrane and cytoplasmic parts of the proteins.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Fedor D. Kornilov, Yury B. Slonimskiy, Daria A. Lunegova, Nikita A. Egorkin, Anna G. Savitskaya, Sergey Yu. Kleymenov, Eugene G. Maksimov, Sergey A. Goncharuk, Konstantin S. Mineev, Nikolai N. Sluchanko
Summary: This study explains the ligand promiscuity of AstaPo1 by determining its NMR structure and validating it through various experiments. The FAS1 domain of AstaPo1 binds carotenoids by embracing their polyene structure, but cannot cap the beta-ionone rings to dictate specificity. This research also suggests the neofunctionalization of FAS1 in a subset of AstaP-like proteins in green algae.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Medicinal
Alix Troster, Nathalie Jores, Konstantin S. Mineev, Sridhar Sreeramulu, Michael DiPrima, Giovanna Tosato, Harald Schwalbe
Summary: This concept paper describes the general strategies for EPHA2 inhibition with small molecules and summarizes the potential of targeting EPHA2 in CRC. EPHA2 plays a crucial role in the development and resistance mechanisms of CRC.
Article
Biochemistry & Molecular Biology
Marina V. Goncharuk, Ekaterina V. Vasileva, Egor A. Ananiev, Andrey Y. Gorokhovatsky, Eduard V. Bocharov, Konstantin S. Mineev, Sergey A. Goncharuk
Summary: Integral membrane proteins are essential for cell function and require large amounts of protein for their structural and functional studies. Cell-free protein synthesis using Facade detergents has been shown to significantly increase the yield of active rhodopsin, making it a promising method for the production of membrane proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Renata I. Zagitova, Konstantin V. Purtov, Aleksandr S. Shcheglov, Konstantin S. Mineev, Maxim A. Dubinnyi, Ivan N. Myasnyanko, Olga A. Belozerova, Vera G. Pakhomova, Valentin N. Petushkov, Natalia S. Rodionova, Vladislav A. Lushpa, Elena B. Guglya, Sergey Kovalchuk, Valeri B. Kozhemyako, Jeremy D. Mirza, Anderson G. Oliveira, Ilia V. Yampolsky, Zinaida M. Kaskova, Aleksandra S. Tsarkova
Summary: In this study, three compounds were isolated and structurally elucidated from the Chaetomorpha linum algae. These compounds showed bioluminescence activity with Chaetopterus luciferase in the presence of Fe2+ ions. They are derivatives of polyunsaturated fatty acid peroxides. The study also confirmed the broad substrate specificity of the luciferase by obtaining and demonstrating the activity of their structural analogues in the bioluminescence reaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
