Article
Chemistry, Medicinal
Marko Babic, Patrizia Jankovic, Silvia Marchesan, Goran Mausa, Daniela Kalafatovic
Summary: Ester hydrolysis is of biomedical interest, but existing peptide-based catalysts have low efficiency. In order to address this issue, statistical analysis was conducted on 22 hydrolases to identify patterns in the sequence for better catalyst design.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemical Research Methods
Pedro B. P. S. Reis, Djork-Arne Clevert, Miguel Machuqueiro
Summary: pK(a) values and isoelectric points of proteins can be estimated using computational methods with high accuracy, and the pKPDB database provides a vast amount of theoretical pK(a) values for over 120k protein structures. This database complements experimental data and provides insights on buried residues that are not well-represented in experimental measurements.
Article
Multidisciplinary Sciences
Oliviero Carugo
Summary: The novel procedure RaSPDB uses multiple PDB subsets to estimate and compute the average value and standard error of a protein feature F.
SCIENTIFIC REPORTS
(2021)
Article
Polymer Science
Ayana Bhaskaran, Heather M. Aitken, Zeyun Xiao, Mitchell Blyth, Mitchell D. Nothling, Shashank Kamdar, Megan L. O'Mara, Luke A. Connal
Summary: Controlling the local environment of the artificial catalytic triad affects catalytic activity. A polymeric catalyst shows enhanced esterolytic activity compared to a water-soluble artificial catalytic triad, possibly due to the hydrophobic microenvironment formed by the polymer backbone. Cross-linked catalytic triad functional polystyrene can be used as a reusable solid support catalyst for esterolysis.
Article
Biochemical Research Methods
Gabriel Abrahams, Janet Newman
Summary: Protein crystallization plays a critical role in macromolecular structure determination through X-ray diffraction. This study introduces a new screening method, Shotgun II, based on analysis of the Protein Data Bank, and shows the success of the previous Shotgun I approach. By applying a more effective algorithm for selecting conditions, the Shotgun method aims to cover the most diverse space of proteins found in the PDB.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jack Turner, Sanja Abbott, Neli Fonseca, Lucas Carrijo, Amudha Kumari Duraisamy, Osman Salih, Zhe Wang, Gerard J. Kleywegt, Kyle L. Morris, Ardan Patwardhan, Stephen K. Burley, Gregg Crichlow, Zukang Feng, Justin W. Flatt, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young, Sameer Velankar, David Armstrong, Marcus Bage, Wesley Morellato Bueno, Genevieve Evans, Romana Gaborova, Sudakshina Ganguly, Deepti Gupta, Deborah Harrus, Ahsan Tanweer, Manju Bansal, Vetriselvi Rangannan, Genji Kurisu, Hasumi Cho, Yasuyo Ikegawa, Yumiko Kengaku, Ju Yaen Kim, Satomi Niwa, Junko Sato, Ayako Takuwa, Jian Yu, Jeffrey C. Hoch, Kumaran Baskaran, Wenqing Xu, Weizhe Zhang, Xiaodan Ma
Summary: This article provides an overview of the Electron Microscopy Data Bank (EMDB), its significance as a global public archive, and its current holdings, recent updates, and future plans.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Chandranath Ghosh, Sneha Menon, Subhajit Bal, Surashree Goswami, Jagannath Mondal, Dibyendu Das
Summary: Through evolution, modern enzymes in metabolic pathways have become specialized, unlike their early ancestors which had broader substrate specificities. However, it is still unclear how these early enzymes displayed catalytic versatility without complex three-dimensional structures. This study reports the emergence of promiscuous catalytic triads in short amyloid peptide-based nanofibers that access paracrystalline folds of beta-sheets, allowing them to simultaneously catalyze multiple reactions and contribute to protometabolism and early evolutionary processes.
Article
Biochemistry & Molecular Biology
Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gerard Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F. Aoki-Kinoshita, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley, Jasmine Y. Young
Summary: The worldwide Protein Data Bank has collaborated with Global Phasing Ltd. and the Noguchi Institute to enhance validation reports for small molecules, including 2D diagrams and 3D electron density maps, to improve confidence in ligand conformation and interactions with macromolecules.
Article
Biochemical Research Methods
Joan Segura, Yana Rose, Sebastian Bittrich, Stephen K. Burley, Jose M. Duarte
Summary: This article presents a new library that allows for customizable interactive views between the positional features of protein and nucleic acid sequences and their 3D structures, providing researchers with a better understanding of the mechanisms underlying the functions of biological macromolecules at the atomic level.
Article
Biochemistry & Molecular Biology
Zhe Hu, Jincheng Ma, Yicai Chen, Wenhua Tong, Lei Zhu, Haihong Wang, John E. Cronan
Summary: The FabG protein of Escherichia coli is not a classic short-chain alcohol dehydrogenase/reductase, and mutagenesis experiments revealed an alternative mode of 3-ketoacyl-ACP reduction, suggesting a new research direction.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Bulat Faezov, Roland L. Dunbrack
Summary: The Protein Data Bank (PDB) is a repository for biological macromolecular crystal structures, with nearly 180,000 structures solved by various methods. However, inconsistencies in author numbering of amino acids in protein sequences within the PDB entries pose challenges for structure-function studies.
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben Webb, John D. Westbrook, Shamara Whetstone, Jasmine Y. Young, Arthur Zalevsky, Christine Zardecki
Summary: The Protein Data Bank (PDB) is an open-access global archive that houses three-dimensional biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the US data center for wwPDB and is responsible for processing and ensuring the security of PDB data. It provides free access to PDB data and supports training and education through its web portals.
Article
Biochemistry & Molecular Biology
Vinicius G. Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman-Aiden, Peter G. Wolynes, Michele Di Pierro, Jose N. Onuchic
Summary: The Nucleome Data Bank (NDB) is a web-based platform for simulating and analyzing the 3D organization of genomes, allowing users to generate chromosomal sub-compartment annotations and access experimental and computational structural genomics data for free. Users can also analyze and visualize data through custom-designed web-based tools.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Paola Turina, Piero Fariselli, Emidio Capriotti
Summary: In recent years, the increase in DNA sequencing and protein mutagenesis studies has generated a large amount of variation data. The manual curation of data from literature is time-consuming and costly, prompting the development of tools like ThermoScan for extracting relevant thermodynamic data on protein stability from full-text articles. ThermoScan's text mining approach has shown accurate predictions and outperformed other text-mining algorithms based on publication abstracts.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Physical
Sergi Burguera, Antonio Frontera, Antonio Bauza
Summary: This study provides the first evidence of favorable noncovalent interactions between ADP metavanadate and ADP orthovanadate with electron rich atoms, and explores the physical nature, directionality and biological implications of these interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biotechnology & Applied Microbiology
Balazs Szalkai, Vince Grolmusz
Article
Biochemical Research Methods
Balazs Szalkai, Vince Grolmusz
Article
Neuroimaging
Balazs Szalkai, Balint Varga, Vince Grolmusz
BRAIN IMAGING AND BEHAVIOR
(2019)
Article
Neurosciences
Balazs Szalkai, Balint Varga, Vince Grolmusz
COGNITIVE NEURODYNAMICS
(2018)
Article
Neurosciences
Mate Fellner, Balint Varga, Vince Grolmusz
COGNITIVE NEURODYNAMICS
(2019)
Article
Multidisciplinary Sciences
Balazs Szalkai, Csaba Kerepesi, Balint Varga, Vince Grolmusz
Article
Multidisciplinary Sciences
Mate Fellner, Balint Varga, Vince Grolmusz
Article
Multidisciplinary Sciences
Mate Fellner, Balint Varga, Vince Grolmusz
Article
Neurosciences
Balint Varga, Vince Grolmusz
Summary: The study of the human brain, the most complex object of study today, involves mapping neuronal-level connections and macroscopic connections using advanced MRI technology. This research paper presents a dataset of 1064 human connectomes obtained from the Human Connectome Project, allowing scientists to access and analyze brain graphs for further research and study. The dataset, available for download online, provides a valuable resource for mathematicians, physicists, engineers, brain scientists, and computational neuroscientists to study the connections of the human brain.
COGNITIVE NEURODYNAMICS
(2021)
Article
Neurosciences
Balazs Szalkai, Balint Varga, Vince Grolmusz
Summary: Graph theory has been widely applied in the study of human brain connections, with diffusion MRI allowing for detailed mapping of these connections between regions. Research has shown statistically significant differences in graph parameters between male and female brains, indicating distinct characteristics in brain connectivity.
Article
Biochemistry & Molecular Biology
Laszlo Keresztes, Evelin Szogi, Balint Varga, Viktor Farkas, Andras Perczel, Vince Grolmusz
Summary: The amyloid state of proteins is a well-defined structure consisting of parallel and antiparallel beta-sheets. Understanding of this state is improving with the development of molecular imaging tools like cryogenic electron microscopy. Sequence-based amyloid predictors have been developed using artificial neural networks (ANNs).
Article
Neurosciences
Laszlo Keresztes, Evelin Szogi, Balint Varga, Vince Grolmusz
Summary: Diffusion magnetic resonance imaging (dMRI) techniques have enabled the discovery and study of thousands of cerebral connections. By identifying specific brain connections, it is possible to accurately determine the sex of the subject.
COGNITIVE NEURODYNAMICS
(2021)
Article
Chemistry, Multidisciplinary
Laszlo Keresztes, Evelin Szogi, Balint Varga, Viktor Farkas, Andras Perczel, Vince Grolmusz
Summary: Hexapeptides are widely used to study the amyloid-forming properties of polypeptides. By utilizing artificial intelligence classifiers, researchers have successfully predicted the amyloid state of peptides. In this study, the Budapest Amyloid Predictor was applied to discover amyloidogenic and nonamyloidogenic hexapeptide patterns with high accuracy, providing novel rules for understanding the amyloid state of peptides.
Article
Biochemistry & Molecular Biology
Kristof Takacs, Vince Grolmusz
Summary: Multiple sequence alignment (MSA) is increasingly important in bioinformatics, often focusing on long sequences, while the optimization of MSA for short sequences is a neglected area that can contribute to improving algorithms for long sequence alignment. This study demonstrates that the optimum solution for the MSA problem can be achieved by trivial alignment for sequences of different lengths.
Article
Neuroimaging
Balazs Szalkai, Balint Varga, Vince Grolmusz
BRAIN IMAGING AND BEHAVIOR
(2018)
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
