Editorial Material
Biochemistry & Molecular Biology
Seungmin Ahn, Hoyoung Jung, Jung-Min Kee
Summary: This article briefly summarizes a subset of the phosphoproteome called the cryptophosphoproteome, which has been underexplored due to technological challenges. The missing pieces for future studies on these elusive protein phosphorylations are identified in this Viewpoint.
Article
Multidisciplinary Sciences
Xiaoyu Guo, Xue Ding, Juan Dong
Summary: In this study, the authors found that BSL proteins in Arabidopsis have different functions in the cell cortex and nucleus, regulating stomatal formation through the activation or deactivation of different signaling pathways.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jared L. Johnson, Tomer M. Yaron, Emily M. Huntsman, Alexander Kerelsky, Junho Song, Amit Regev, Ting-Yu Lin, Katarina Liberatore, Daniel M. Cizin, Benjamin M. Cohen, Neil Vasan, Yilun Ma, Konstantin Krismer, Jaylissa Torres Robles, Bert van de Kooij, Anne E. van Vlimmeren, Nicole Andree-Busch, Norbert F. Kaeufer, Maxim Dorovkov, Alexey G. Ryazanov, Yuichiro Takagi, Edward R. Kastenhuber, Marcus D. Goncalves, Benjamin D. Hopkins, Olivier Elemento, Dylan J. Taatjes, Alexandre Maucuer, Akio Yamashita, Alexei Degterev, Mohamed Uduman, Jingyi Lu, Sean D. Landry, Bin Zhang, Ian Cossentino, Rune Linding, John Blenis, Peter Hornbeck, Benjamin E. Turk, Michael B. Yaffe, Lewis C. Cantley
Summary: Protein phosphorylation is a common post-translational modification, and thousands of phosphorylated sites have been associated with human diseases and biological processes. However, the responsible protein kinases for most phosphorylation events are currently unknown. This study used synthetic peptide libraries to profile the substrate specificity of 303 Ser/Thr kinases and identified the kinases capable of phosphorylating reported phosphorylation sites.
Article
Biochemical Research Methods
Marzieh Ayati, Serhan Yilmaz, Mark R. Chance, Mehmet Koyuturk
Summary: Protein phosphorylation is a critical regulatory mechanism in cellular signaling. Current technologies allow for high-throughput screening of thousands of phosphorylation sites. It has been discovered that functionally associated sites tend to exhibit significant positive or negative co-phosphorylation, which can be used to predict sites on the same pathway or targeted by the same kinase.
Article
Biochemistry & Molecular Biology
Emmanuel Baudouin, Juliette Puyaubert, Patrice Meimoun, Melisande Blein-Nicolas, Marlene Davanture, Michel Zivy, Christophe Bailly
Summary: This study investigated the remodeling of Arabidopsis seed phosphoproteome during imbibition using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. The study identified a large repertoire of phosphopeptides and phosphoproteins involved in seed germination control, including protein kinases and key regulators like DOG1. Gene ontology analysis revealed their involvement in various biological processes. The study provides evidence of the major role of phosphosignaling in the regulation of Arabidopsis seed germination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Microbiology
Aakriti Gangwal, Nishant Kumar, Nitika Sangwan, Neha Dhasmana, Uma Dhawan, Andaleeb Sajid, Gunjan Arora, Yogendra Singh
Summary: Protein phosphorylation is a universal mechanism that regulates cellular responses in all domains of life. Bacillus species, particularly with the availability of bacterial genome sequences, proteomics, and functional studies, have provided insights into the role of protein kinases and phosphatases in different physiological states of the organism. Phosphorylation of specific amino acid residues can alter protein activity, structure, and protein-protein interactions, ultimately impacting downstream pathways. This review summarizes the current knowledge of Bacillus signaling, focusing on the role of protein phosphorylation in physiological processes.
FEMS MICROBIOLOGY REVIEWS
(2023)
Review
Cell Biology
Claudio D'Incal, Jitse Broos, Thierry Torfs, R. Frank Kooy, Wim Vanden Berghe
Summary: FMRP plays a crucial role in neuronal development and synapse formation, with its absence affecting multiple cellular pathways, particularly neurotransmitter receptors and intracellular signaling molecules. By utilizing quantitative proteomic and phosphoproteomic studies, novel targets for treating Fragile X syndrome may be identified.
Editorial Material
Hematology
Monika Haemmerle
Summary: This study explores the role of Mnk1 in megakaryocytes and platelets, showing that it regulates protein synthesis and affects megakaryocyte ploidy and platelet production. These findings have clinical implications and contribute to our understanding of platelet function and thrombosis.
Article
Biochemical Research Methods
Xu Yan, Xinbao Gong, Tao Lin, Maosen Lin, Ping Qin, Jing Ye, Hailing Li, Qiwen Hong, Mengxian Li, Ya Liu, Yunsheng Li, Xiujuan Wang, Yunhai Zhang, Yinghui Ling, Hongguo Cao, Xiaorong Zhang, Fugui Fang
Summary: The study investigates the molecular changes controlling the onset of puberty in goats by identifying differentially phosphorylated proteins (DPPs) and phosphorylation sites (DPSs). The results provide evidence for a complex interaction network in goat hypothalamus proteins that affects puberty. This data may help identify new puberty-regulating candidates and contribute to understanding the physiological mechanism of puberty onset in mammals.
JOURNAL OF PROTEOMICS
(2022)
Article
Hematology
Yuanliang Peng, Li Tang, Yanan Li, Jianhui Song, Hong Liu, Pan Wang, Zhizhou Zhong, Yifei Yang, Shihui Wang, Lixiang Chen, Ji Zhang, Shijie Zhang, Zi Wang, Min Li, Long Liang, Jing Liu
Summary: This study characterized the quantitative and qualitative analysis of phosphorylated proteins during human early erythropoiesis using tandem mass-tagging technology. The results revealed the important regulatory role of phosphorylated proteins in erythroid development and identified functional modules related to cell cycle and signaling pathways.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Hui-Liang Zhang, Xiao-Chuan Wang, Rong Liu
Summary: Zinc is crucial for human growth and development, particularly in regulating the mechanisms of neurodegenerative diseases.
Review
Biochemistry & Molecular Biology
Adriana Costa, Ana C. Cruz, Filipa Martins, Sandra Rebelo
Summary: Protein phosphorylation alterations in DM1 contribute to the various manifestations and symptoms of the disease. A systematic review identified abnormal levels of protein kinases, phosphatases, and phosphoproteins in DM1. Multiple signaling pathways involved in cell functions such as glucose metabolism, cell cycle, myogenesis, and apoptosis were impaired in DM1 samples, explaining the complexity and diverse symptoms of the disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Malathi Bheri, Swati Mahiwal, Sibaji K. Sanyal, Girdhar K. Pandey
Summary: Protein phosphorylation and dephosphorylation are important reversible post-translational modifications, with protein phosphatases playing a key role in signaling networks. The classification and mechanism of phosphatases in plant systems still require further investigation.
Review
Biochemistry & Molecular Biology
Antonio Casamayor, Joaquin Arino
Summary: Overexpression of yeast Ser/Thr protein phosphatase Ppz1 leads to a halt in cell proliferation due to changes in gene expression, altered phosphorylation state of proteins, and diverse cellular processes. However, overexpression of the Ppz1 regulatory subunit Hal3 can fully counteract the toxic effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Andrea Riba, Attila Oravecz, Matej Durik, Sara Jimenez, Violaine Alunni, Marie Cerciat, Matthieu Jung, Celine Keime, William M. Keyes, Nacho Molina
Summary: This study utilizes single-cell RNA-sequencing technology to analyze the dynamics of gene regulation during the cell cycle. The authors propose a deep learning method, DeepCycle, to infer the cell cycle state in single cells based on scRNA-seq data. By generating scRNA-seq libraries in different cell systems and observing cycling patterns in cell cycle-related genes, the authors establish a high-resolution map of the entire cell cycle transcriptome and identify major waves of transcription during the G1 phase.
NATURE COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Jie Sun, Tanupong Rattanasawatesun, Penghao Tang, Zhaoxia Bi, Santosh Pandit, Lisa Lam, Caroline Wasen, Malin Erlandsson, Maria Bokarewa, Jichen Dong, Feng Ding, Fangzhu Xiong, Ivan Mijakovic
Summary: The study reveals that vertically oriented graphene preferentially grows in areas with stronger local electric fields during plasma-enhanced chemical vapor deposition. The electric field helps accumulate charges on graphene, transforming cohesive graphene layers into separate three-dimensional VG flakes. Additionally, the field attracts charged precursors to protruding areas on the substrate, aiding in the formation of VG.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Microbiology
Priyanka Singh, Ivan Mijakovic
Summary: Green silver nanoparticles (G-AgNPs) have garnered attention in medical science for their strong antimicrobial properties against multidrug-resistant microorganisms. This study demonstrates a simple and environmentally friendly method to produce G-AgNPs from an environmental isolate of Viridibacillus sp. The produced G-AgNPs were stable for over 1 year in an aqueous solution and exhibited remarkable antimicrobial activity against Gram-negative pathogens.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Priyanka Singh, Ivan Mijakovic
Summary: In this study, rowanberries were found to be effective in reducing gold and silver salts into nanoparticles. The produced nanoparticles were highly monodisperse, spherical, and stable over long periods. However, the antimicrobial activity of these nanoparticles was found to be low.
Review
Chemistry, Applied
Sri Renukadevi Balusamy, Shadi Rahimi, Johan Sukweenadhi, Sneha Sunderraj, Rajeshkumar Shanmugam, Lakshmi Thangavelu, Ivan Mijakovic, Haribalan Perumalsamy
Summary: This research review discusses the effects of chitosan, chitosan nanoparticles, and modified chitosan biomaterials on plant growth parameters, enzymes, and gene expression under salt stress. The study suggests that chitosan nanoparticles and modified chitosan biomaterials have a greater potential for improving plant function under salinity stress compared to chitosan.
CARBOHYDRATE POLYMERS
(2022)
Review
Microbiology
Fazlurrahman Khan, Priyanka Singh, Abhayraj S. Joshi, Nazia Tabassum, Geum-Jae Jeong, Nilushi Indika Bamunuarachchi, Ivan Mijakovic, Young-Mog Kim
Summary: This review discusses the antimicrobial properties of nisin and its derivatives, as well as various strategies employed to enhance its activity and stability. The underlying mechanisms of action and evolutionary relationships of nisin genes are also explored. The review provides valuable insights into the research on nisin as an antimicrobial agent.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Biophysics
Omur Acet, Emrah Dikici, Burcu Onal Acet, Mehmet Odabasi, Ivan Mijakovic, Santosh Pandit
Summary: Microbial adhesion and formation of biofilms pose serious problems in various areas. Preventing microbial adhesion and biofilm formation is a promising strategy to address these issues. In this study, attaching EGCG to membranes effectively prevented bacterial colonization.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Pharmacology & Pharmacy
Shadi Rahimi, Daniel van Leeuwen, Fariba Roshanzamir, Santosh Pandit, Lei Shi, Nima Sasanian, Jens Nielsen, Elin K. Esbjoerner, Ivan Mijakovic
Summary: To enhance the delivery of doxorubicin (DOX) and minimize its side effects, researchers developed a pH-responsive delivery system based on graphene oxide (GO) that can release drugs specifically in acidic tumor environments.
Review
Microbiology
Pragati Rajendra More, Santosh Pandit, Anna De Filippis, Gianluigi Franci, Ivan Mijakovic, Massimiliano Galdiero
Summary: This review focuses on the synthesis of silver nanoparticles (AgNPs) and their mechanism of action against antibiotic-resistant and biofilm-forming bacteria. AgNPs exert their antibacterial effects through oxidative stress, protein dysfunction, membrane disruption, and DNA damage in bacteria. They also prevent biofilm formation by altering bacterial cell adhesion. However, the medical use of AgNPs is limited by their harmful effects on humans and the environment. The review compiles recent studies on the antibacterial activity of AgNPs and discusses their potential applications in medicine.
Article
Chemistry, Multidisciplinary
Shadi Rahimi, Teo Lovmar, Alexandra Aulova, Santosh Pandit, Martin Lovmar, Sven Forsberg, Magnus Svensson, Roland Kadar, Ivan Mijakovic
Summary: To combat bacterial infections in the post-antibiotic era, efforts are being made to engineer new materials with antibacterial properties. A new automated pipeline based on scanning electron microscopy images has been developed to predict the antibacterial potential of these materials. The density of sharp exposed edges of graphite-oriented nanoplatelets (GNPs) is a key factor in killing bacteria on contact.
Article
Energy & Fuels
Muthusankar Eswaran, Shadi Rahimi, Santosh Pandit, Bavatharani Chokkiah, Ivan Mijakovic
Summary: In this work, a flexible, multifunctional polyimide (PI)/Au-polyaniline (PAN)/Pd nanocomposite electrode with excellent electrochemical properties was fabricated. The electrode showed high conductivity, rapid response, and high electron transfer rate due to the strong metal-polymer interaction between PAN and Pd. It demonstrated successful biomedical sensing of glucose and electrooxidation of alcohols such as methanol and ethanol, making it promising for healthcare diagnostics and alternative energy conversion devices.
Article
Chemistry, Multidisciplinary
Zhejian Cao, Xiaozhi Fu, Hao Li, Santosh Pandit, Francoise M. Amombo Noa, Lars Ohrstrom, Aleksej Zelezniak, Ivan Mijakovic
Summary: This study successfully synthesized MOFs using enzymatically recycled PET, demonstrating the feasibility of this approach. Compared to conventional methods, this approach avoids the use of strong acids or bases and high temperatures, leading to reduced environmental and energy penalties.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Jian Zhang, Nisha Neupane, Puspa Raj Dahal, Shadi Rahimi, Zhejian Cao, Santosh Pandit, Ivan Mijakovic
Summary: Developed antibiotic-loaded boron nitride nanoconjugates with strong antimicrobial properties for combating bacterial biofilms.
ACS APPLIED BIO MATERIALS
(2023)
Article
Nanoscience & Nanotechnology
Hengzhi Ruan, Marko Bek, Santosh Pandit, Alexandra Aulova, Jian Zhang, Philip Bjellheim, Martin Lovmar, Ivan Mijakovic, Roland Kadar
Summary: This study presents a facile approach of incorporating dopamine and [2-(methacryloyloxy) ethyl] dimethyl-(3-sulfopropyl) ammonium hydroxide via in situ synthesis into gelatin hydrogels. The resulting hydrogels show exceptional antibacterial efficiency and multifunctional performance, making them highly promising for various biomedical applications.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Review
Chemistry, Multidisciplinary
Fazlurrahman Khan, Geum-Jae Jeong, Priyanka Singh, Nazia Tabassum, Ivan Mijakovic, Young-Mog Kim
Summary: Emerging nanotechnology has successfully synthesized and applied nanoparticles using the green-chemistry approach, which offers simplicity, cost-effectiveness, environmental friendliness, stability, and biocompatibility. Researchers have turned to pure-compound-based synthesis due to the diverse and environmentally influenced composition of natural extracts, investigating the biological activities and mechanisms of these nanoparticles.
Article
Multidisciplinary Sciences
Priyanka Singh, Ivan Mijakovic
Summary: The increasing demand for green and biological nanoparticles has led to the exploration of medicinal plants and other green resources. In this study, Ligustrum vulgare berries were used to reduce gold and silver salts into nanoparticles. The resulting nanoparticles showed stability and antimicrobial properties.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Trang Van Tran, Hoa Nguyen, Luyen Vu, ChangWoo Lee
Summary: Glutaredoxin 3 (Grx3) is a redox protein that maintains structural integrity and glutathione (GSH) binding capabilities across different temperatures. This study investigates the roles of specific bonds in Grx3's structure and function, and how psychrophilic Grx3 variants adapt to cold environments. The highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the structure and catalytic activity of Grx3. Psychrophilic variants of Grx3 have adapted to cold environments by reducing GSH binding and increasing structural flexibility.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Amanda Lais de Souza Coto, Arthur Alexandre Pereira, Sabrina Dorta Oliveira, Milene Nobrega de Oliveira Moritz, Arthur Moraes Franco da Rocha, Paulo Roberto Dores-Silva, Noeli Soares Melo da Silva, Ana Rita de Araujo Nogueira, Lisandra Marques Gava, Thiago Vagas Seraphim, Julio Cesar Borges
Summary: J-domain proteins form a large molecular chaperone family involved in proteostasis processes, with hDjC20 playing a vital role in mitochondria and being heavily influenced by the presence of Zn+2.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Meiling Zhang, Jiaxiang Zhang, Yan Liang, Shicheng Tian, Shuyang Xie, Tong Zhou, Qin Wang
Summary: This study determined the crystal structures of RGLG2 VWA domain in Arabidopsis thaliana, revealing that Ca2+ ions act as regulators and affect the conformational change of RGLG2-VWA domain.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Bork, Sander H. J. Smits, Lutz Schmitt
Summary: This study reveals the structure and calcium ion binding properties of CBL1 protein, and proposes a binding model of CBL1 for Ca2+. Additionally, it provides preliminary insights into the formation of the dimer interface of CBL1.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Evgeniia V. Leisi, Andrey V. Moiseenko, Sofia S. Kudryavtseva, Denis V. Pozdyshev, Vladimir I. Muronetz, Lidia P. Kurochkina
Summary: The pathogenesis of prion diseases involves the transformation of prion protein into an insoluble form. This study found that two phage chaperonins can promote the fibrillation of prion protein in an ATP-dependent manner, resulting in the formation of less toxic large clusters. These fibrils differ in morphology and properties from those formed spontaneously in acidic pH with denaturants.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak
Summary: Magnesium is an important divalent cation for regulating enzyme activity. The binding of Mg2+ through the PAS domain inhibits phosphoglycerate kinase (PGK) activity in LmPAS-PGK at neutral pH, but PGK activity is derepressed at acidic pH. Mutation studies revealed that the Asp-4 residue is crucial for Mg2+ binding at neutral pH.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Shima Ghaedizadeh, Majid Zeinali, Bahareh Dabirmanesh, Behnam Rasekh, Khosrow Khajeh, Ali Mohammad Banaei-Moghaddam
Summary: Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies can increase the rate of CO2 absorption from industrial flue gases. This study successfully improved the thermostability of a known hyperthermostable carbonic anhydrase through rational engineering of a single-point mutation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Khaled A. Elnahriry, Dorothy C. C. Wai, Lauren M. Ashwood, Muhammad Umair Naseem, Tibor G. Szanto, Shaodong Guo, Gyorgy Panyi, Peter J. Prentis, Raymond S. Norton
Summary: Sea anemone venom contains a peptide called Tst2, which shows sequence similarity to peptides that interact with various ion channels. Recombinant Tst2 was successfully produced and its structure and function were studied. The results showed that Tst2 is an inhibitor of the TRPV1 channel.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
