Article
Cardiac & Cardiovascular Systems
Naixin Wang, Weiwei Wang, Xiaoqi Wang, Ge Mang, Jianfeng Chen, Xiangyu Yan, Zhonghua Tong, Qiannan Yang, Mengdi Wang, Liangqi Chen, Ping Sun, Yupeng Yang, Jingxuan Cui, Mian Yang, Yafei Zhang, Dongni Wang, Jian Wu, Maomao Zhang, Bo Yu
Summary: Histone lactylation promotes early remote activation of reparative transcriptional response in monocytes, which is essential for establishing immune homeostasis and timely activation of the cardiac repair process post-MI.
CIRCULATION RESEARCH
(2022)
Article
Immunology
Anasuya C. Pal, Isaline Renard, Pallavi Singh, Pratap Vydyam, Joy E. Chiu, Sovitj Pou, Rolf W. Winter, Rozalia Dodean, Lisa Frueh, Aaron C. Nilsen, Michael K. Riscoe, J. Stone Doggett, Choukri Ben Mamoun
Summary: This study describes an optimized method for culturing Babesia duncani in a mouse model, which can be used to study the virulence of Babesia and develop new therapies for human babesiosis. The model combines continuous parasite replication in human erythrocytes with lethal infection in mice.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
Dakota L. Jones, Grey F. Hallstroem, Xi Jiang, Ryan C. Locke, Mary Kate Evans, Edward D. Bonnevie, Anjana Srikumar, Thomas P. Leahy, Madhura P. Nijsure, Joel D. Boerckel, Robert L. Mauck, Nathaniel A. Dyment
Summary: Cells integrate mechanical cues to maintain tissue function and homeostasis, but the underlying mechanisms are not well understood. This study shows that loss of tensile cues changes nuclear morphology, positioning, and gene expression, resulting in weakening of tendons.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Evangelia Koutelou, Aimee T. Farria, Sharon Y. R. Dent
Summary: Researchers have accumulated a wealth of biochemical and cellular data over the years to gain insight into the molecular mechanisms of GCN5 and PCAF in gene activation, as well as their roles in developmental processes and disease states.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Multidisciplinary Sciences
Alfonso Carlos Barragan-Rosillo, Carlos Alberto Peralta-Alvarez, Jonathan Odilon Ojeda-Rivera, Rodrigo G. Arzate-Mejia, Felix Recillas-Targa, Luis Herrera-Estrella
Summary: Plants have evolved strategies to cope with phosphorus scarcity, with genetic approaches identifying key regulators like PHR1 and PHL2 in the transcriptional response to phosphate starvation. Chromatin accessibility undergoes genome-wide remodeling in root cells during Pi starvation, with PHR1 and PHL2 playing a crucial role in this process. These transcription factors directly activate a second wave of epigenetic changes needed for the transcriptional activation of low-Pi-responsive genes in Pi-starved root cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Alexander Munden, Mary Lauren Benton, John A. Capra, Jared T. Nordman
Summary: R-loops play important roles in various biological processes. This study reveals that R-loop abundance and genome localization change during Drosophila embryogenesis and that RNaseH1 activity is crucial for embryonic development. The findings also demonstrate the developmental plasticity of R-loops in gene formation and their relative positioning.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
James E. Brownell, C. David Allis
Summary: The maintenance of eukaryotic genomes within DNA-protein complexes known as chromatin is regulated by post-translational modifications of chromatin proteins. GCN5 has been identified as a histone acetyltransferase, linking it to a transcription co-activator complex in yeast, emphasizing the importance of histone modifying activity in gene regulation.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Microbiology
Shikha Shikha, Mariana Ferreira Silva, Lilach Sheiner
Summary: Mitochondrial ribosomes are crucial for the function and survival of eukaryotes, but different lineages have evolved divergent features in their mitochondrial ribosomes. The study of apicomplexan mitochondrial ribosomes, which are essential for the parasites, is still limited due to the unknown composition. In this study, the components of the mitoribosomal large subunit in the model apicomplexan Toxoplasma gondii were identified and validated to facilitate further research.
Review
Parasitology
Joshua Seun Olajide, Zigang Qu, Shunli Yang, Oyeseyi Joshua Oyelade, Jianping Cai
Summary: This review provides a comprehensive overview of constitutively expressed Eimeria proteins in Apicomplexans parasites. It discusses the importance of these proteins in different developmental stages, organelles, and sub-cellular components, and also highlights the existing trends and suggestions for future studies on Eimeria protein characterization.
PARASITES & VECTORS
(2022)
Review
Parasitology
Rajshekhar Y. Gaji, Amanda K. Sharp, Anne M. Brown
Summary: Toxoplasma gondii is a life-threatening intracellular pathogen that depends on protein kinases for its life cycle. Research on Toxoplasma kinases aims to understand their functions and potentially develop therapeutics against this parasite.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2021)
Review
Multidisciplinary Sciences
Jason H. Brickner
Summary: This article discusses the mechanisms by which histone modifications can be inherited and relates them to the phenomenon of epigenetic transcriptional memory. Recent studies have found that the histone H3 lysine 4 dimethylation associated with this memory plays a critical role in sustaining memory and can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism involves a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1(-) COMPASS. This is the first example of chromatin-mediated inheritance of a mark that promotes transcription.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Multidisciplinary Sciences
Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A. Doudna
Summary: The fusion of PRDM9 and Cas9 in CRISPR-Cas genome editing can increase the efficiency of homology-directed repair (HDR) and avoid off-target editing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biology
Kavitha Govarthanan, Piyush Kumar Gupta, Binita Zipporahe, Rekha Gahtori, Soumya Pandit, Ram Prasad
Summary: Stem cells are essential for replenishing damaged cells in tissues and understanding the molecular events driving successful differentiation is crucial. The stable inheritance of the epigenome is vital for cell development, modulation, and maintenance. The epigenetic regulatory network dictates lineage commitment and differentiation, with emerging roles of epigenetic modifiers in lineage differentiation and epigenetic markers as potential targets for cancer therapy.
Article
Microbiology
Samuel S. Porter, Jennifer C. Liddle, Kristen Browne, Diana Pastrana, Benjamin A. Garcia, Christopher B. Buck, Matthew D. Weitzman, Alison A. McBride
Summary: Papillomaviruses package their genomes with host histones into virions, with specific histone modifications being acquired late in infection that benefit viral replication and gene expression. The viral minichromosome is enriched in posttranslational modifications associated with active chromatin, potentially aiding in evasion of detection and promoting early infection stages.
Review
Chemistry, Medicinal
Kundlik Gadhave, Deepak Kumar, Vladimir N. Uversky, Rajanish Giri
Summary: The exact molecular mechanisms associated with Alzheimer's disease remain a mystery, making the utilization of signaling pathways as potential drug targets limited. It is necessary to find correlations and cross-talk between these pathways and establish different therapeutic targets for a better understanding of the biological events responsible for AD-related neurodegeneration. Consideration should be given to the central role of autophagy in AD and its interplay with other pathways as the finest therapeutic strategy.
MEDICINAL RESEARCH REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Bi Zhao, Akila Katuwawala, Vladimir N. Uversky, Lukasz Kurgan
Summary: The study found that human proteins are significantly enriched in intrinsic disorder, with proteins localized in the nucleus and cytoskeleton having higher levels of disorder. On average, human proteins are assigned to 2.3 subcellular compartments, with proteins localized to fewer compartments being more disordered. Disordered proteins in the most disorder-enriched subcellular compartments primarily interact with nucleic acids and protein partners, adding a missing piece to the puzzle of functional disorder within the cell.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Eduard Y. Kostetsky, Vladimir N. Uversky
Summary: This study discusses the formation of the matrix mechanism in protocells, focusing on the involvement of mineral complexes and gas phase radicals. The structures of apatite and carbonate-apatite play a role in determining the formation of DNA and RNA, while organic matter gradually replaces the mineral matrix. The study provides a detailed description of the preparation and launch of the matrix mechanism, as well as discussing several related issues.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Letter
Biochemistry & Molecular Biology
Vladimir N. Uversky, Fatma Elrashdy, Abdullah Aljadawi, Elrashdy M. Redwan
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Zhihua Du, Xiangdong Xiao, Vladimir N. Uversky
Summary: In this article, the authors propose a new deep learning method called DeepA-RBPBS for predicting the binding site of RNA-binding proteins (RBP) using RNA sequences and structural features. The performance of DeepA-RBPBS is found to be better than the state-of-the-art predictor iDeepS in terms of MCC and AUC scores. The method is also successfully applied to predict target RNA data of RBPs related to diabetes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Gerard Kian-Meng Goh, Vladimir N. Uversky
Summary: This article discusses the significant impact of intrinsic disorder in the outer shell of HIV on vaccine development and proposes a new model for vaccine design. Traditional viruses typically do not have high levels of intrinsic disorder in their outer shells, allowing for successful establishment of effective vaccines.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Murat Caliskan, Sunay Y. Mandaci, Vladimir N. Uversky, Orkid Coskuner-Weber
Summary: The choice of force field parameters and simulation techniques significantly influences the results of molecular dynamics simulations for amyloid-beta(1-40) peptide, with simulations using a99sb*-ildn, charmm36m, and a99sb-disp parameters showing better agreement with experimental results.
CHEMICAL BIOLOGY & DRUG DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Alexander Denesyuk, Sergei E. Permyakov, Mark S. Johnson, Eugene A. Permyakov, Vladimir N. Uversky, Konstantin Denessiouk
Summary: This study identified a universal structural motif NBCZone in proteinases and revealed a complete Structural Catalytic Core (SCC) consisting of different classes and groups. Comparative analysis showed that amino acid variations at specific positions can modulate enzymatic activity by affecting the interaction between catalytic acid core and supplementary core. The findings contribute significantly to the analysis and systematization of (chymo)trypsin-like serine/cysteine fold proteinases' 3D structures.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Microbiology
Kelly L. Hawley, Jairo M. Montezuma-Rusca, Kristina N. Delgado, Navreeta Singh, Vladimir N. Uversky, Melissa J. Caimano, Justin D. Radolf, Amit Luthra
Summary: The outer membrane of Treponema pallidum exhibits unique properties and composition compared to other bacteria. Through structural modeling and computational tools, the outer membrane protein repertoire of T. pallidum has been characterized, revealing multiple families of proteins involved in various functions related to OM biogenesis and small molecule transport. This research provides insights into the intricate structure of T. pallidum's outer membrane and its potential implications for vaccine development.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Environmental Sciences
Sk Sarif Hassan, Pallab Basu, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Angel Serrano-Aroca, Gajendra Kumar Azad, Alaa A. A. Aljabali, Giorgio Palu, Tarek Mohamed Abd El-Aziz, Debmalya Barh, Bruce D. Uhal, Parise Adadi, Kazuo Takayama, Nicolas G. Bazan, Murtaza Tambuwala, Amos Lal, Gaurav Chauhan, Wagner Baetas-da-Cruz, Samendra P. Sherchan, Vladimir N. Uversky
Summary: This study tracked the emergence of mutations in SARS-CoV-2 proteins globally and in six model countries, revealing that since October 2020, frequent mutations have been observed mainly in ORF7b and ORF8. Interestingly, no high-frequency mutations were found in the UK, India, and Brazil, which does not correlate with the virus's transmission in these countries.
ENVIRONMENTAL RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Parveen Salahuddin, Rizwan Hasan Khan, Mohammad Furkan, Vladimir N. Uversky, Zeyaul Islam, Munazza Tamkeen Fatima
Summary: Protein misfolding and aggregation can be induced by various factors, leading to neurodegenerative diseases. To inhibit protein aggregation, different molecules and strategies have been designed.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Faisal Nabi, Owais Ahmad, Yawar Ali Khan, Anas Nabi, Hashmi Md Amiruddin, Faizan Abul Qais, Aiman Masroor, Malik Hisamuddin, Vladimir N. Uversky, Rizwan Hasan Khan
Summary: The study screened FDA-approved drugs against SARS-CoV-2 proteins and found potential interactions with anticancer, antipsychotic, and antiviral drugs. Molecular dynamics simulations revealed protein evolution upon drug interaction, and a phylogenetic analysis was conducted on 43 coronavirus strains infecting 12 mammalian species.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Biochemistry & Molecular Biology
Liberato Marzullo, Maria C. Turco, Vladimir N. Uversky
Summary: The Bcl-2 associated athanogene (BAG) family of proteins in humans exhibit exceptional multifunctionality and binding promiscuity, playing a role in the pathogenesis of various diseases. The presence of multiple isoforms and extensive posttranslational modifications can be explained through the concept of intrinsic disorder, which allows for a broad spectrum of interactions with diverse binding partners. Understanding the functional roles of BAG proteins from a perspective of protein intrinsic disorder provides insights into their multifunctionality and relation to disease pathogenesis.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Oyku Irem Balli, Vladimir N. Uversky, Serdar Durdagi, Orkid Coskuner-Weber
Summary: Experimenters face challenges in analyzing glycoproteins due to their structural complexity, but computational studies have been used to complement experimental results. However, recent investigations have shown that computational studies also have significant challenges. Future developments in computational biochemistry and biology are necessary to provide more accurate analyses of glycoprotein structures.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Sk Sarif Hassan, Kenneth Lundstrom, Debmalya Barh, Raner Jose Santana Silva, Bruno Silva Andrade, Vasco Azevedo, Pabitra Pal Choudhury, Giorgio Palu, Bruce D. Uhal, Ramesh Kandimalla, Murat Seyran, Amos Lal, Samendra P. Sherchan, Gajendra Kumar Azad, Alaa A. A. Aljabali, Adam M. Brufsky, Angel Serrano-Aroca, Parise Adadi, Tarek Mohamed Abd El-Aziz, Elrashdy M. Redwan, Kazuo Takayama, Nima Rezaei, Murtaza Tambuwala, Vladimir N. Uversky
Summary: The spike protein of SARS-CoV-2 plays a critical role in infectivity and antigenicity. Unique variants of the spike protein have been identified on different continents, with North America exhibiting significant differences compared to others. International travel may facilitate the spread of new variants, suggesting the importance of travel restrictions and mass vaccination in controlling the pandemic. Reviewing and potentially re-engineering vaccines to address emerging spike protein variants is also recommended.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)