Article
Multidisciplinary Sciences
Andrey G. Baranovskiy, Nigar D. Babayeva, Alisa E. Lisova, Lucia M. Morstadt, Tahir H. Tahirov
Summary: This study focused on the structure and function of human DNA polymerase alpha (Pol alpha) in its interaction with a mismatched template:primer. It was found that Pol alpha has low affinity to DNA in the absence of deoxynucleotide triphosphate (dNTP), but shows higher selectivity for a correct duplex in the presence of cognate dNTP. The efficiency of Pol alpha in extending a T-C mismatch is significantly reduced. This research is important for understanding the mechanism of Pol alpha infidelity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Ashleigh Shannon, Bhawna Sama, Pierre Gauffre, Theo Guez, Francoise Debart, Jean-Jacques Vasseur, Etienne Decroly, Bruno Canard, Francois Ferron
Summary: In this study, we discovered that the ORF1a region of certain members of the large genome Tobaniviridae family indeed harbors N7-specific methyltransferase activity. We presented its structure as the first N7-specific Rossmann-fold (RF) methyltransferase identified for (+)RNA viruses, which is remarkably different from that of the known Coronaviridae ORF1b N7-MTase gene. The appearance of this methyltransferase in an unexpected location in the genome introduces a split-off in the classification of Tobaniviridae.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Katja Leben, Ziga Strmsek, Tina Lebar, Anze Verbic, Matej Dragovan, Neza Omersa, Gregor Anderluh, Roman Jerala
Summary: DNA transcription is regulated by various mechanisms, mainly through the recruitment of RNA polymerase complex by transcription factors. In this study, we found that a TALE lacking an activation domain can enhance transcription in mammalian cells without direct interaction with multiple transcription factors. TALEs can exert their effects over a long distance and enhance the transcriptional regulation of other factors. This mechanism may involve an allosteric effect on DNA structure or dynamics.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Afreen Kamal Farooqui, Haleema Ahmad, Mohd Umar Rehmani, Afzal Husain
Summary: The polymerase chain reaction is a widely used technique in biology, and Pfu-Sso7d is a fusion DNA polymerase known for its high processivity and fidelity. This study reports a quick and cost-efficient purification protocol as well as an optimized buffer system for Pfu-Sso7d.
PROTEIN EXPRESSION AND PURIFICATION
(2023)
Article
Biochemistry & Molecular Biology
Avigail Stokar-Avihail, Taya Fedorenko, Jens Hor, Jeremy Garb, Azita Leavitt, Adi Millman, Gabriela Shulman, Nicole Wojtania, Sarah Melamed, Gil Amitai, Rotem Sorek
Summary: In recent years, various defense systems against phages have been found in bacteria. However, the mechanism of how these systems sense phage infection remains unknown. To address this question, the researchers isolated 177 phage mutants that can evade 15 different defense systems. These mutants were found to have mutations in the gene sensed by the defense system, providing insights into the determinants of phage sensitivity. The study identifies specific determinants of different retron systems and reveals phage-encoded triggers for abortive infection systems, shedding light on how bacterial immune systems sense phage invaders.
Article
Multidisciplinary Sciences
Qixiang He, Xiuhua Lin, Bianca L. Chavez, Sourav Agrawal, Benjamin L. Lusk, Ci Ji Lim
Summary: This study reveals that the CST accessory protein helps organize the Pol alpha-primase enzyme for efficient primer synthesis. Cryogenic electron microscopy structures show that CST separates the DNA and RNA catalytic centers of Pol alpha-primase into two domains and arranges them in the correct order for RNA-DNA synthesis. The study also provides insights into the template-binding specificity of CST and its role in the assembly and activation of the CST-Pol alpha-primase complex.
Article
Multidisciplinary Sciences
Chung-Chi Liao, Yi-Sen Wang, Wen-Chieh Pi, Chun-Hsiung Wang, Yi-Min Wu, Wei-Yi Chen, Kuo-Chiang Hsia
Summary: The authors present a cryo-EM structure of Kap114p, revealing a non-canonical function beyond nuclear transport that modulates yTBP-dependent transcription.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Robert P. Hayes, Mee Ra Heo, Mark Mason, John Reid, Christine Burlein, Kira A. Armacost, David M. Tellers, Izzat Raheem, Anthony W. Shaw, Edward Murray, Philip M. McKenna, Pravien Abeywickrema, Sujata Sharma, Stephen M. Soisson, Daniel Klein
Summary: Herpesviruses encode a DNA polymerase crucial for viral genome replication, targeted by nucleoside and non-nucleoside inhibitors. The study revealed that PNU inhibits replication by blocking dNTP association and inducing enzyme inactivation. The crystal structure of herpesvirus polymerase in complex with PNU-183792 provides insights for drug design.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Andy Schneider, Jan Bergsch, Georg Lipps
Summary: The marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase that combines the conserved domains of archaeoeukaryotic heterodimeric primases in one protein. This primase displays sequence specificity typically seen in bacterial type primases and can synthesize short RNA primers with high activity. The compact monomeric primase NEQ395 could serve as a functional and structural model for the study of heterodimeric archaeoeukaryotic primases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Radhika Malik, Robert E. Johnson, Louise Prakash, Satya Prakash, Iban Ubarretxena-Belandia, Aneel K. Aggarwal
Summary: The study investigates the structure of the DNA-Pol zeta complex and its ability to extend DNA synthesis past mismatched base pairs. The results reveal the conformational changes in the Pol zeta active site and how it responds to mismatched DNA, allowing for the proper binding and extension of nucleotides. This study provides valuable insights into the regulation of DNA synthesis in eukaryotes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Yang Yang, Chang Liu, Wei Zhou, Wei Shi, Ming Chen, Baoyue Zhang, David G. Schatz, Yangbo Hu, Bin Liu
Summary: The MerR family of transcriptional regulators, such as EcmrR, activate promoters with a suboptimal structure for recognition by RNA polymerase holoenzyme. Structural insights into the EcmrR-dependent transcription process elucidate the mechanisms enabling optimal promoter recognition and transition from initiation to elongation.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Zuanning Yuan, Roxana Georgescu, Huilin Li, Michael E. E. O'Donnell
Summary: DNA polymerase α has separate RNA and DNA polymerase subunits to form a unique-length RNA-DNA primer. Cryo-EM structures of each stage in primer synthesis reveal large conformational changes among the four subunits and explain how primer length is limited.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Xinglu Jiang, Beibei Xie, Kangjing Li, Fengyuan Zhou
Summary: This study achieved controlled release of Taq DNA polymerase in qPCR by introducing BSA hydrogel, resulting in over 20 cycles of linear amplification. The slope of linear amplification was found to have a significant negative correlation with Ct values, and an exponential equation between Ct values and the slopes was fitted by varying primer concentrations. The slopes and Ct values of each qPCR system were corrected using this equation to ensure consistency in amplification efficiency.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Tim Pasch, Alexander Schroeder, Sabrina Kattelmann, Miriam Eisenstein, Shmuel Pietrokovski, Daniel Kuemmel, Henning D. Mootz
Summary: This article reports a new cysteine-independent split intein that plays an important role in protein splicing. By rational engineering, a higher-yielding split intein mutant was obtained, and a histidine residue critical for splicing was identified. These findings advance the toolbox, as well as the structural and mechanistic understanding of cysteine-less inteins.
Article
Chemistry, Multidisciplinary
Asmat Ullah, Atia-tul-Wahab, Peng Gong, Abdul Mateen Khan, M. Iqbal Choudhary
Summary: The rapid spread of dengue virus is a major health problem worldwide. This study evaluated 75 compounds for their ability to interact with NS5 protein and identified 12 potential antiviral agents against dengue virus.
Article
Biochemistry & Molecular Biology
Wei-Han Hui, Yen-Lin Chen, Shu-Wei Chang
Summary: Crosslinking affects the mechanical behavior and tissue metabolism of collagen-based tissues. Aging and diabetes alter the crosslinking type and density, thus changing tissue properties. High-connectivity enzymatic crosslinking and advanced-glycation end-products result in uniform deformation under daily activity, while low-connectivity enzymatic crosslinking does not. High-connectivity model displays more sliding, while AGEs induce instability in structures near the binding sites.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Yao-Bin Ma, Xiao-Qiu Zhou, Wei-Dan Jiang, Pei Wu, Yang Liu, Shu-Wei Li, Ling Tang, Lu Zhang, Hai-Feng Mi, Lin Feng
Summary: Tea polyphenols (TPs) are an inexpensive feed additive that can protect the gill function of fish against Flavobacterium columnare (F. columnare) through various mechanisms, including suppression of oxidative stress, apoptosis, and inflammation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Yan-Jia Guo, Jing-Ru Pang, Yu Zhang, Zhong-Rui Li, Xiao-Lin Zi, Hong-Min Liu, Ning Wang, Li-Juan Zhao, Ya Gao, Bo Wang, Piet Herdewijn, Cheng-Yun Jin, Ying Liu, Yi-Chao Zheng
Summary: This study identifies the conjugation of NEDD8 to LSD1 and its impact on GC cells, revealing the significance of LSD1 neddylation in GC.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Review
Biochemistry & Molecular Biology
Geum-Jae Jeong, Fazlurrahman Khan, Nazia Tabassum, Young-Mog Kim
Summary: Vibrio species are motile gram-negative bacteria commonly found in aquatic environments. They can adapt to environmental fluctuations and develop protective mechanisms against host immune systems. Different types of sigma and anti-sigma factors play important roles in regulating gene expression and virulence in Vibrio species.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Zahra Mohammadbagheri, Behrooz Movahedi, Shaghayegh Saeedi, Abbas Rahmati
Summary: In this study, a reusable biobased composite hydrogel was successfully synthesized and used for the removal of Tl(I) from aqueous solutions. The hydrogel exhibited high adsorption capacity and thermal stability, and the adsorption process was found to be thermodynamically spontaneous. The results demonstrated that the hydrogel can be reused multiple times without significant loss of its adsorption capacity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Iqra Batool, Muhammad Imran, Ayesha Anwar, Farhan Ahmed Khan, Afrah E. Mohammed, Ashwag Shami, Hafiz Iqbal
Summary: Enzyme immobilization on ZnO/SnO2 and ZnO/SnO2/SA nanocomposites was studied, and the catalytic and biochemical characteristics of the immobilized enzyme were investigated. The results showed that ZnO/SnO2 and ZnO/SnO2/SA nanostructures are suitable carriers for enzyme immobilization.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Elias Mosaffa, Dhruvi Patel, Nasim Amiri Ramsheh, Rishikumar Indravadan Patel, Atanu Banerjee, Hossein Ghafuri
Summary: In this study, a unique 3D bead structure of adsorbent, composed of bacterial cellulose microfilaments reinforced chitosan adorned with melamine 2D plates, was synthesized for anionic dye removal. The adsorbent showed high specific surface area and abundant functional groups, resulting in exceptional adsorption capacity. The characteristics and optimal conditions of the adsorbent were assessed and analyzed.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Carolina Gismene, Jorge Enrique Hernandez Gonzalez, Marilia de Freitas Calmon, Andrey Fabricio Ziem Nascimento, Angela Rocio Nino Santisteban, Felipe Antunes Calil, Alana Della Torre da Silva, Paula Rahal, Rejane Maira Goes, Raghuvir Krishnaswamy Arni, Ricardo Barros Mariutti
Summary: Mammaliicoccus sciuri, a bacterium of clinical and veterinary relevance, expresses the virulence factor Exfoliative Toxin C (ExhC), which binds specifically to desmoglein-1 (Dsg1) and plays a role in tissue integrity. This study investigates the necrotic activity of ExhC and identifies a variant lacking necrotic potential but retaining enzymatic activity through mutagenesis experiments and crystal structure determination.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Bibhas K. Bhunia, Ashutosh Bandyopadhyay, Souradeep Dey, Biman B. Mandal
Summary: Intervertebral disc degeneration is a major cause of chronic low back pain and disability. Researchers have developed a bioactive silk-based hybrid hydrogel system functionalized with decellularized human Wharton's jelly extracellular matrix as bioactive cues. The hydrogels mimic the rheological and mechanical properties of the native nucleus pulposus tissue and support cell viability, proliferation, and tissue maturation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Qun Zhang, Yonggan Yan, Zhao Li, Jing Du, Kai Zhang, Liguo Zhang, Ting Wang, Alberto Bianco, Shaohua Ge, Baojin Ma
Summary: A new crosslinking strategy has been devised to construct injectable sodium alginate hydrogels, which can be regulated for injectability and have great potential in biomedical applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Seong Eun Hong, Ji-Soo Lee, Hyeon Gyu Lee
Summary: The potential of multi-layer nanoemulsions for improving the cellular uptake, antioxidant activity, and in vitro bioaccessibility of alpha-tocopherol was examined. The results showed that the multi-layer nanoemulsions significantly enhanced the cellular uptake and antioxidant activity of alpha-tocopherol compared to free coumarin 6. Furthermore, the use of chitosan and dextran sulfate as wall materials in the multi-layer nanoemulsions led to even higher cellular uptake, in vitro bioaccessibility, and antioxidant activity of alpha-tocopherol.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Jingjing Yu, Yanhui Zhang, Ruoning Zhang, Yanxiang Gao, Like Mao
Summary: High internal phase emulsions (HIPEs) based on beeswax (BW) oleogels and octenyl succinic acid starch (OSA starch) were prepared by a simple one-step method. The results showed that oleogelation improved the stability and encapsulation capability of the HIPEs, which is significant for the development of novel healthy food.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Review
Biochemistry & Molecular Biology
Bi-Feng Yao, Xiu-Ju Luo, Jun Peng
Summary: The balanced and continuous fission and fusion of mitochondria, regulated by OPA1, are important for maintaining mitochondrial dynamics in cardiovascular disorders. Understanding the role of OPA1 in mitochondrial fusion can provide insights into the pathogenesis of cardiovascular diseases.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Review
Biochemistry & Molecular Biology
Gokul Paramasivam, Anandhavelu Sanmugam, Vishnu Vardhan Palem, Murugan Sevanan, Ananda Babu Sairam, Nachiappan Nachiappan, Buhyun Youn, Jung Sub Lee, Muthuchamy Nallal, Kang Hyun Park
Summary: Nanomaterials are being used to deliver therapeutic agents in living systems. Different nanotechnological applications such as immunosensors, immune assays, and drug delivery are being implemented using nanotechnology. Genomics plays a crucial role in selecting appropriate drugs for personalized cancer therapy. It helps in analyzing gene and protein expression, disease classification, and designing disease models. Delivering drugs to specific areas using nanoparticles is a challenging issue.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Jing Li, Wei Wang, Han Wu, Feng Peng, Hui Gao, Ying Guan
Summary: In this study, CMH-based CPF films were prepared and their thermal and barrier properties were successfully regulated. The tensile strength and water vapor barrier property of CPF films were significantly improved, making them promising for food packaging applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)