Article
Nutrition & Dietetics
Veronica Segura, Angela Ruiz-Carnicer, Irati Mendia, Marta Garzon-Benavides, Angeles E. Pizarro, Isabel Comino, Carolina Sousa
Summary: A gluten-free diet is the only treatment for celiac disease, but adherence can be challenging due to the presence of gluten in many foods. This study proposes the development of an automatable ELISA to monitor adherence to the diet by quantifying urine gluten immunogenic peptides. The assay was validated and found to be stable, and it showed that after 12 months on the diet, only 27% of patients had detectable u-GIP compared to 100% at diagnosis. Therefore, this highly sensitive immunoassay could be used in clinical laboratories to analyze u-GIP from a large number of samples.
Review
Chemistry, Physical
Izabella Brand
Summary: Proteins in the cytoplasm bind selectively and sensitively to DNA, leading to structural changes in both biomolecules. Detection of these changes requires sophisticated analytical methods, with electrochemical detection being particularly suitable. This has laid the foundations for the development of biosensors.
CURRENT OPINION IN ELECTROCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Takatsugu Kosugi, Masahito Ohue
Summary: The study developed a quantitative estimation index QEPPI specifically for early screening of compounds targeting protein-protein interactions, which showed better performance compared to the commonly used method QED.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Hitoshi Iuchi, Junna Kawasaki, Kento Kubo, Tsukasa Fukunaga, Koki Hokao, Gentaro Yokoyama, Akiko Ichinose, Kanta Suga, Michiaki Hamada
Summary: The COVID-19 pandemic has revealed the limitations of medical and research institutions in managing emerging infectious diseases. Predicting virus-host interactions through host range prediction and protein-protein interaction prediction can enhance our understanding of infectious diseases. Although multiple algorithms have been developed for this purpose, there are still challenges that need to be addressed. Despite the difficulties, bioinformatics can play a significant role in advancing research on infectious diseases and human health.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Xiaodi Yang, Xianyi Lian, Chen Fu, Stefan Wuchty, Shiping Yang, Ziding Zhang
Summary: The study introduces a database called HVIDB that provides comprehensive annotated data on human-virus protein-protein interactions and integrates online PPI prediction tools. Users can easily access reliable information on various human virus PPIs and conduct in-depth analysis through this database.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Huajun Zhang, Shuyan Dai, Xujun Liang, Jun Li, Yongheng Chen
Summary: This study demonstrates that FOXM1 prefers binding tandem DNA sites, and this binding preference may be driven by intermolecular protein-protein interactions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Angelita Rebollo, Louise Fliedel, Pierre Tuffery
Summary: PEPscan can be used to identify candidate interfering peptides (IPs) that disrupt target protein-protein interactions, but the information it provides about the binding site is ambiguous and may include false positives. The protocol could be optimized to reduce non-specific binding. PEPscan also shows promise in investigating interactions between proteins and other molecules, such as polysaccharides and labeled peptides.
Review
Oncology
Mehdi Sharifi Tabar, Habib Francis, Dannel Yeo, Charles G. Bailey, John E. J. Rasko
Summary: Normal protein-protein interactions (normPPIs) play a crucial role in regulating physiological processes, but in cancer, this organized network is disrupted, leading to oncogenic protein-protein interactions (oncoPPIs). Recent advancements in mass spectrometry (MS), structural biology, and drug discovery have allowed scientists to identify and characterize oncoPPIs. However, the construction of a reference oncoPPI map for different types of cancers is still lacking due to technical challenges. Therefore, there is an urgent need to develop experimental workflows to overcome these challenges and create comprehensive reference maps.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Review
Cardiac & Cardiovascular Systems
Jared S. Kushner, Guoxia Liu, Robyn J. Eisert, Gary A. Bradshaw, Geoffrey S. Pitt, J. Travis Hinson, Marian Kalocsay, Steven O. Marx
Summary: This review outlines the application of proximity proteomics in cardiovascular research, discussing its principles, concepts, and potential for future research.
CIRCULATION RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Lukas Gerstweiler, Jingxiu Bi, Anton Peter Jacob Middelberg
Summary: Expression of viral capsomeres in bacterial systems and their subsequent assembly into virus-like particles can be a cost-effective option for future vaccines. However, purification is challenging due to poor binding to chromatography media. This study shows that protein-DNA interactions in bacterial lysates can lead to the formation of complexes that hinder proper purification, but can be modulated by controlling ionic strength to enhance bind-elute behavior on salt-tolerant chromatography media. DNA-protein interactions negatively impact in vitro assembly, forming worm-like structures instead of virus-like particles. Controlling DNA-protein interactions is crucial for downstream viral vaccine process development.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Review
Cell Biology
Mario Gonzalez-Garcia, Giuliana Fusco, Alfonso De Simone
Summary: The conversion of soluble proteins into insoluble amyloid aggregates is linked to various neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. The small prefibrillar oligomers formed during protein aggregation are identified as the most harmful species. Interactions with biological membranes play a crucial role in the onset of cellular toxicity. Further research is needed to understand the transient interactions involving heterogeneous protein aggregates for developing effective therapeutic strategies against protein misfolding diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
S. Behera, Pragyan P. Dash, Ajit K. Bishoyi, K. Dash, P. Mohanty, Chita R. Sahoo, Rabindra N. Padhy, M. Mishra, B. N. Ghosh, H. Sahoo, B. R. Jali
Summary: Resistance to antibiotics and antifungal drugs has become a common public health threat, leading to the need for alternative, non-toxic agents. This study designed and synthesized two novel antibiotic molecules, which showed significant inhibitory activity against bacterial strains and fungal strains. Molecular docking studies revealed their potential targets, and binding interaction with a serum protein was also observed. Furthermore, the toxicity analysis indicated their non-cytotoxic nature.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Pharmacology & Pharmacy
Hwankyu Lee
Summary: Molecular dynamics simulations have revealed the impact of protein corona on nanoparticles, showing the competitive adsorption and desorption mechanism of proteins on nanoparticle surfaces, as well as the interactions between protein-coated nanoparticles and cell membranes. These simulations provide insights into the Vroman effect and offer predictions consistent with experimental observations on a molecular scale.
Article
Biotechnology & Applied Microbiology
Ismail S. Mohiuddin, Sung-Jen Wei, In-Hyoung Yang, Gloria M. Martinez, Shengping Yang, Eun J. Cho, Kevin N. Dalby, Min H. Kang
Summary: A novel cell-based luminescence assay was developed to identify inhibitors targeting c-MYC transcriptional activation, leading to the discovery of five potential lead compounds with significant ability to kill cancer cells. Two candidate compounds from the DNA-PKcs assay and three from the MK2 assay were identified through a two-step validation method.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Review
Biochemical Research Methods
Lun Hu, Xiaojuan Wang, Yu-An Huang, Pengwei Hu, Zhu-Hong You
Summary: This paper reviews recent efforts towards developing effective computational models for predicting protein-protein interactions (PPIs). It introduces algorithms for learning computational models for PPI prediction and classifies these models into different categories. Different validation schemes and metrics for evaluating prediction performance are discussed, as well as the use of biological databases in extensive experiments to compare different prediction models. Finally, open issues in PPI prediction for future work are presented, discussing how tackling these issues can lead to improved performance.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Andreas Hecker, Luise H. Brand, Sebastien Peter, Nathalie Simoncello, Joachim Kilian, Klaus Harter, Valerie Gaudin, Dierk Wanke
Article
Plant Sciences
Carly M. Shanks, Andreas Hecker, Chia-Yi Cheng, Luise Brand, Silvio Collani, Markus Schmid, G. Eric Schaller, Dierk Wanke, Klaus Harter, Joseph J. Kieber
Article
Biochemistry & Molecular Biology
Sebastian Soyk, Klara Simkova, Evelyne Zuercher, Leonie Luginbuehl, Luise H. Brand, Cara K. Vaughan, Dierk Wanke, Samuel C. Zeeman
Article
Multidisciplinary Sciences
Dirk Goerdes, Grit Koch, Kerstin Thurow, Uener Kolukisaoglu
Article
Plant Sciences
Marius L. Theune, Ulrich Bloss, Luise H. Brand, Friederike Ladwig, Dierk Wanke
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Plant Sciences
Anne Mohrholz, Hequan Sun, Nina Gloeckner, Sabine Hummel, Uener Kolukisaoglu, Korbinian Schneeberger, Klaus Harter
Review
Biochemistry & Molecular Biology
Uener Kolukisaoglu
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Plant Sciences
Tomas M. Tessi, Sabine Brumm, Eva Winklbauer, Benjamin Schumacher, Georgina Pettinari, Ignacio Lescano, Claudio A. Gonzalez, Dierk Wanke, Veronica G. Maurino, Klaus Harter, Marcelo Desimone
Summary: AZG2 is a cytokinin transporter regulated by auxins, playing a role in root system architecture determination.
Article
Biochemistry & Molecular Biology
Miyuki Iwasaki, Tomoaki Kajiwara, Yukiko Yasui, Yoshihiro Yoshitake, Motoki Miyazaki, Shogo Kawamura, Noriyuki Suetsugu, Ryuichi Nishihama, Shohei Yamaoka, Dierk Wanke, Kenji Hashimoto, Kazuyuki Kuchitsu, Sean A. Montgomery, Shilpi Singh, Yasuhiro Tanizawa, Masaru Yagura, Takako Mochizuki, Mika Sakamoto, Yasukazu Nakamura, Chang Liu, Frederic Berger, Katsuyuki T. Yamato, John L. Bowman, Takayuki Kohchi
Summary: Research has shown that sex chromosomes diverged early during the evolution of haploid liverworts, with the sex determinant identified on the U chromosome of Marchantia polymorpha. The Feminizer gene encodes a plant-specific BASIC PENTACYSTEINE transcription factor, playing a role in female differentiation via regulation of other genes. Phylogenetic analyses suggest that dimorphic sex chromosomes were already established 430 million years ago in ancestral liverworts, with implications that ancestral functions can be retained after the acquisition of a sex determination mechanism.
Article
Biochemistry & Molecular Biology
Natalie Krieger, Kai-Florian Pastryk, Karl Forchhammer, Uener Kolukisaoglu
Summary: PII protein is a highly conserved regulatory protein found in both bacteria and higher plants. Studies have shown that in plants, PII protein forms foci with itself and other proteins, potentially involved in plastidic protein degradation. This discovery provides a new perspective for further elucidating the physiological functions of PII proteins in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Pascal Rath, Johanna Rapp, Klaus Brilisauer, Marvin Braun, Uener Kolukisaoglu, Karl Forchhammer, Stephanie Grond
Summary: This study establishes a powerful hybrid synthetic approach for efficiently obtaining various C-7 sugar analogues and applies them for structure-activity relationship studies. It reveals that 7dSh could serve as a valid target for herbicides and antimicrobial agents.
Article
Biochemistry & Molecular Biology
Xiaolu Xu, Sabine Hummel, Klaus Harter, Uener Kolukisaoglu, Michael Riemann, Peter Nick
Summary: The transition to terrestrial plants led to a loss of microtubule minus-end-directed dynein motors and an expansion of class-XIV kinesins. OsDLK, a class-XIV kinesin from rice, plays a role in cell elongation during development and moves into the nucleus in response to cold stress. The import of OsDLK into the nucleus might be correlated with its specific DNA binding, particularly to the Opaque2 motif, which is found in the promoter region of NtAvr9/Cf9, a transcription factor involved in cold adaptation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Xuan Tran, Erva Keskin, Paul Winkler, Marvin Braun, Uener Kolukisaoglu
Summary: Plastids in plants are believed to have originated from cyanobacteria and retain bacterial characteristics. Recent research has found that peptidoglycans, a component of bacterial cell walls, exist in the envelopes of moss chloroplasts. The question arises whether similar structures are also present in chloroplasts of angiosperms. This study visualized peptidoglycan's canonical amino acids around chloroplasts in Arabidopsis and Nicotiana, supported by additional detection of peptidoglycan-binding proteins. Experiments with D-cycloserine and AtMurE knock-out lines in Arabidopsis confirmed the central role of this pathway in plastid genesis and division, indicating that peptidoglycans are integral parts of plastids in the entire plant lineage. The biosynthesis and further functions of these organelles remain to be elucidated.