Review
Biochemistry & Molecular Biology
Yukihiro Itoh, Yuri Takada, Yasunobu Yamashita, Takayoshi Suzuki
Summary: For many years, drug discovery studies in the field of epigenetics have primarily focused on specific enzymes. However, there has recently been increasing interest in small molecules targeting multiprotein enzyme/transcription factor complexes. This review explores small molecules that modulate the function of well-known epigenetic complexes, such as PRC2, PRC1, and CoREST.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Edem Gavor, Yeu Khai Choong, Chacko Jobichen, Yu Keung Mok, R. Manjunatha Kini, J. Sivaraman
Summary: The study examined the sensitivity of metallocarboxypeptidases (MCPs) in the mosquito midgut to a plant protease inhibitor (PCI). The results indicated that the sensitivity of PCI is largely determined by key differences in the active-site regions of MCPs, providing insights for mosquito population/parasite control strategies.
Article
Chemistry, Multidisciplinary
Ronan P. Hanley, David Y. Nie, John R. Tabor, Fengling Li, Amin Sobh, Chenxi Xu, Natalie K. Barker, David Dilworth, Taraneh Hajian, Elisa Gibson, Magdalena M. Szewczyk, Peter J. Brown, Dalia Barsyte-Lovejoy, Laura E. Herring, Gang Greg Wang, Jonathan D. Licht, Masoud Vedadi, Cheryl H. Arrowsmith, Lindsey I. James
Summary: Nuclear receptor-binding SET domain-containing 2 (NSD2) is involved in gene regulation by dimethylating lysine 36 of histone 3 (H3K36me2). UNC8153 is a novel NSD2-targeted degrader that effectively reduces NSD2 protein and H3K36me2 levels. It works by degrading NSD2 through a unique mechanism and has demonstrated positive effects on pathological phenotypes in multiple myeloma cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Koh Takeuchi, Imai Misaki, Yuji Tokunaga, Miwa Fujisaki, Hajime Kamoshida, Takeshi Takizawa, Hiroyuki Hanzawa, Ichio Shimada
Summary: By using solution NMR, the study compared the three-dimensional structures of cyclorasins 9A5 and 9A54, revealing that 9A5 has the ability to adopt an amphipathic structure in water, which is important for its cell permeabilization activity. On the other hand, 9A54 is unable to form this structure due to steric hindrance between bulky amino-acid sidechains at positions 2 and 3. It was also found that the bulkiness of sidechains at these positions negatively affects cell permeabilization activities.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Food Science & Technology
Mohammad Alrosan, Thuan-Chew Tan, Azhar Mat Easa, Sana Gammoh, Muhammad H. Alu'datt
Summary: The application of protein-protein interaction (PPI) has been widely used in various industries, requiring a deeper understanding of molecular forces in PPI and the relationship between protein structure, functional properties, and influencing factors. Methods for identifying molecular forces and characterizing protein structure are summarized in this review.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Article
Chemistry, Physical
Jia-Liang Chen, Xiao Wang, Feng Yang, Bin Li, Gottfried Otting, Xun-Cheng Su
Summary: We report the solution structure of an authentic sortaseA thioester intermediate with the bound substrate. Through advanced techniques, we determined the 3D structure of this short-lived enzymatic reaction intermediate at atomic resolution. The formation and stability of the intermediate are influenced by calcium binding and its interaction with the substrate, highlighting the importance of calcium in the function of sortase A.
Article
Biochemistry & Molecular Biology
William Karsten, Leonard M. Thomas, Christian Fleming, Priscilla Seabourn, Christina Bruxvoort, Lilian Chooback
Summary: Dihydrodipicolinate synthase (DHDPS) catalyzes the initial step in the biosynthesis of L-lysine, and is a potential drug target due to its absence in mammals. Acetopyruvate is a slow-binding inhibitor of DHDPS that competes with pyruvate to form a covalent enamine complex, confirmed by spectral studies and crystal structure analysis.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Chemistry, Analytical
Siyu Jin, Dongru Li, Xingjia Feng, Guoqi Fu
Summary: Molecularly imprinted polymers combined with fluorescence sensing have potential applications in biological analysis and disease diagnosis. A versatile strategy for the synthesis of surface protein-imprinted nanoparticles is illustrated, using sandwich-structured template pre-assemble and post-imprinting modification (PIM) to enhance fluorescence detection.
MICROCHEMICAL JOURNAL
(2022)
Article
Biochemical Research Methods
Yunda Si, Chengfei Yan
Summary: AlphaFold2 is able to predict protein complex structures using multiple sequence alignments of interologs. A simplified phylogeny-based approach was applied to generate the alignments, resulting in successful predictions for a high percentage of bacterial and eukaryotic protein-protein interactions. Restricting the interologs to specific taxonomic ranks further improved the success rates.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Kiran Lata, Jyoti Vishwakarma, Sanjay Kumar, Taran Khanam, Ravishankar Ramachandran
Summary: Nei2 is a BER glycosylase that forms a complex with the beta-clamp, enhancing its activity. The interaction between Nei2 and the beta-clamp is mediated by a specific motif in the C-terminal zinc-finger domain. Inhibitors such as Tubulosine disrupt Nei2-beta-clamp interactions, providing insights into the role of Nei2 in bacterial prereplicative BER.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Susanne Kramer, Natalia Katarzyna Karolak, Johanna Odenwald, Bernardo Gabiatti, Paula Andrea Castaneda Londono, Anna Zavrelova, Eden Ribeiro Freire, Kayo Schemiko Almeida, Silke Braune, Claudia Moreira, Amelie Eder, Carina Goos, Mark Field, Mark Carrington, Fabiola Holetz, Maria Wiktoria Gorna, Martin Zoltner
Summary: The removal of the mRNA 5' cap is essential for controlling gene expression in eukaryotes. Unlike other eukaryotes, kinetoplastida rely on a unique complex involving ALPH1, XRNA, and other proteins for decapping. This complex has a specific and dynamic localization at the posterior pole of the cell. This unique composition sets the trypanosome decapping complex apart from other eukaryotes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Food Science & Technology
Xiaoxue Lu, Ranran Chang, Hao Lu, Lizhong Qiu, Yaoqi Tian
Summary: The study demonstrated that amino acids released from rice proteins during digestion inhibited the digestion of starch and led to the formation of a new starch structure, slowing down the digestion process. This finding provides insights into the relationship between amino acids and starch digestion, offering a theoretical basis for developing starch-based foods with a low glycemic index.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Miaomiao Liu, Yunhong Song, Yi-Heng P. Job Zhang, Chun You
Summary: A method for carrier-free immobilization of multi-enzyme complexes with more than four enzymes is developed using polypeptide interactions and enzyme component self-oligomerization. The self-assembled enzyme complexes show higher initial reaction rates than the four-enzyme cocktail. Water-insoluble self-assembled multi-enzyme complexes are observed, serving as carrier-free immobilized multi-enzyme complex aggregates. These immobilized enzyme complexes can be easily recycled and obtained from either purified enzyme components or crude cell extracts. This strategy sheds light on improving the catalytic capability of in vitro synthetic enzymatic biosystems.
Article
Chemistry, Medicinal
Francini Fonseca Lopez, Jiayuan Miao, Jovan Damjanovic, Luca Bischof, Michael B. Braun, Yingjie Ling, Marcus D. Hartmann, Yu-Shan Lin, Joshua A. Kritzer
Summary: The Nrf2 transcription factor regulates the response to oxidative stress, and Keap1 is its main negative regulator. This study used molecular dynamics simulations to predict the preorganization of cyclic peptides and correlated it with binding affinities for Keap1. The findings provide insights into designing selective inhibitors of protein-protein interactions using cyclic peptides.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Hamida Laroussi, Ariadna B. Juarez-Martinez, Aline Le Roy, Elisabetta Boeri Erba, Frank Gabel, Bernard de Massy, Jan Kadlec
Summary: Meiotic recombination in mice is initiated by DNA double-strand breaks (DSBs), catalyzed by the TOPOVIL complex. This complex's activity is regulated by meiotic factors such as REC114, MEI4, and IHO1, but the mechanism is not well understood. This study reveals the molecular details of these factors and their interactions, including REC114 forming homodimers, associating with MEI4 as a heterotrimer, and IHO1 forming tetramers. The study also shows that IHO1 directly interacts with REC114 and shares a binding surface with TOPOVIBL and another meiotic factor ANKRD31. These findings suggest the existence of a ternary IHO1-REC114-MEI4 complex and highlight the potential regulatory role of REC114 in mediating interactions with multiple partners.
Article
Biochemistry & Molecular Biology
A. G. Mikhailova, A. N. Nekrasov, A. A. Zinchenko, T. V. Rakitina, D. A. Korzhenevsky, A. V. Lipkin, O. A. Razguljaeva, M. V. Ovchinnikova, V. A. Gorlenko, L. D. Rumsh
BIOCHEMISTRY-MOSCOW
(2015)
Article
Multidisciplinary Sciences
Rita V. Chertkova, Nadezda A. Brazhe, Tatiana V. Bryantseva, Alexey N. Nekrasov, Dmitry A. Dolgikh, Alexander I. Yusipovich, Olga Sosnovtseva, Georgy V. Maksimov, Andrei B. Rubin, Mikhail P. Kirpichnikov
Article
Biochemistry & Molecular Biology
Yves Briers, Konstantin Miroshnikov, Oleg Chertkov, Alexei Nekrasov, Vadim Mesyanzhinov, Guido Volckaert, Rob Lavigne
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2008)
Article
Biochemistry & Molecular Biology
A. N. Nekrasov, L. E. Petrovskaya, V. A. Toporova, E. A. Kryukova, A. V. Rodina, E. Yu. Moskaleva, M. P. Kirpichnikov
BIOCHEMISTRY-MOSCOW
(2009)
Article
Genetics & Heredity
Veronika E. Anisimova, Alex S. Shcheglov, Ekaterina A. Bogdanova, Denis V. Rebrikov, Alexey N. Nekrasov, Ekaterina V. Barsova, Dmitry A. Shagin, Sergey A. Lukyanov
Article
Biochemistry & Molecular Biology
Alexei N. Nekrasov, Alexei A. Zinchenko
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2008)
Article
Multidisciplinary Sciences
Nicole Hartwig Trier, Bettina Eide Holm, Ole Slot, Henning Locht, Hanne Lindegaard, Anders Svendsen, Gunnar Houen
Article
Biochemistry & Molecular Biology
L. N. Shingarova, L. E. Petrovskaya, A. N. Nekrasov, E. A. Kryukova, E. F. Boldyreva, S. A. Yakimov, S. V. Guryanova, D. A. Dolgih, M. P. Kirpichnikov
RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY
(2010)
Article
Mathematics, Applied
Anastasia A. Anashkina, Alexei N. Nekrasov
RUSSIAN JOURNAL OF NUMERICAL ANALYSIS AND MATHEMATICAL MODELLING
(2014)
Article
Biochemistry & Molecular Biology
Alexei N. Nekrasov, Ludmila G. Alekseeva, Rudolf A. Pogosyan, Dmitry A. Dolgikh, M. P. Kirpichnikov, Alexandre G. de Brevern, Anastasia A. Anashkina
Article
Mathematics, Applied
A. Mikhalskii, I. Petrov, V. V. Tsurko, A. A. Anashkina, A. N. Nekrasov
RUSSIAN JOURNAL OF NUMERICAL ANALYSIS AND MATHEMATICAL MODELLING
(2020)
Article
Biochemistry & Molecular Biology
Alexei N. Nekrasov, Vitaly V. Radchenko, Tatiana M. Shuvaeva, Vladimir I. Novoselov, Eugenyi E. Fesenko, Valery M. Lipkin
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2007)
Article
Immunology
Ludmila Alekseeva, Aleksei Nekrasov, Aleksei Marchenko, Marina Shevchenko, Sergei Benevolenskii, Alexander Sapozhnikov, Viswanath P. Kurup, Elena Svirshchevskaya
Article
Biochemistry & Molecular Biology
AN Nekrasov
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2004)