Article
Biochemistry & Molecular Biology
Shintaro Nagaoka, Noriko Sugiyama, Rie Yatsunami, Satoshi Nakamura
Summary: This study characterized recombinant IPMDH from the extremely halophilic archaeon Haloarcula japonica TR-1, showing that KCl concentration significantly affects its activity and conformation. The results provide new insights into the properties of haloarchaeal IPMDH.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Hisham M. Dokainish, Yuji Sugita
Summary: The study proposes a new approach, gREST_SSCR, for exploring open-closed conformational changes in multidomain proteins. By using this method, a wider conformational space is reached compared to conventional MD, while maintaining the stability of protein domains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Raine E. S. Thomson, Saskya E. Carrera-Pacheco, Elizabeth M. J. Gillam
Summary: The engineering of proteins to improve stability is important for various applications. Structural information is needed for rational design approaches, while bioinspired methods based on phylogenetic analyses show promise when structures are unavailable. This review provides an overview of factors important for successful inference of thermostable proteins using ancestral sequence reconstruction.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Robotics
Akinori Sakaguchi, Kaoru Yamamoto
Summary: This paper presents a novel quadrotor with a 3-axis deformable frame. By adding servo motors, it can achieve different frame configurations in roll-pitch deformation mode and yaw deformation mode. Experimental results demonstrate its stable flight in deformed states and showcase its versatility in applications.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2022)
Article
Engineering, Mechanical
Anshul Jain, Hemant Jawale
Summary: This paper compares two 3-Degree of Freedom Spatial Parallel Manipulators (3-RRS and 3-RPS) belonging to the 3-[PP]S-Y family. Their performance is compared by considering the effects of link tolerance and parasitic motions on the same task space and End-Effector positions.
PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART C-JOURNAL OF MECHANICAL ENGINEERING SCIENCE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Ateek Shah, Yamini Mathur, Amrita B. Hazra
Summary: The diverse organisms inhabiting various environmental niches on our planet are engaging in an active exchange of biomolecules for survival. This commentary describes how plant-associated bacterial pathogens synthesize and deploy hormones to manipulate host plant physiology, using the example of the AldA enzyme from Pseudomonas syringae. The study highlights the importance of understanding the dynamics of NAD(H) in ALDH-catalyzed reactions for potential applications in engineering novel enzymes.
BIOSCIENCE REPORTS
(2021)
Article
Multidisciplinary Sciences
Martina Audagnotto, Werngard Czechtizky, Leonardo De Maria, Helena Kack, Garegin Papoian, Lars Tornberg, Christian Tyrchan, Johan Ulander
Summary: Proteins can exist in different conformations, and recent findings have shown that co-evolutionary analysis combined with machine-learning techniques can improve distance predictions between residue pairs. In this study, deep learning approaches and mechanistic modeling were used to investigate protein conformational ensembles. The predicted models were compared to experimental structures, and a potential correlation between experimental dynamics and predicted models was found, highlighting the areas of improvement in protein folding and dynamics prediction.
SCIENTIFIC REPORTS
(2022)
Article
Mathematics, Applied
Xin Nie, Andrea Seppi
Summary: In this study, we generalize the notion of domains of dependence in the Minkowski space and define and study regular domains in the affine space with respect to a proper convex cone. In three dimensions, we prove that every proper regular domain can be uniquely foliated by specific surfaces with constant affine Gaussian curvature. This result is based on the analysis of a Monge-Ampere equation with extended real-valued lower semicontinuous boundary condition.
Article
Hematology
Aaron Issaian, Ariel Hay, Monika Dzieciatkowska, Domenico Roberti, Silverio Perrotta, Zsuzsanna Darula, Jasmina Redzic, Micheal P. Busch, Grier P. Page, Stephen C. Rogers, Allan Doctor, Kirk C. Hansen, Elan Z. Eisenmesser, James C. Zimring, Angelo D'Alessandro
Summary: AE1 plays a crucial role in regulating erythrocyte metabolism and storage quality, impacting red blood cell aging and storage. Dysfunction of AE1 results in oxidative imbalance, affecting blood quality and transfusion efficacy in donors.
Article
Biology
Masahiro Noji, Tatsushi Samejima, Keiichi Yamaguchi, Masatomo So, Keisuke Yuzu, Eri Chatani, Yoko Akazawa-Ogawa, Yoshihisa Hagihara, Yasushi Kawata, Kensuke Ikenaka, Hideki Mochizuki, Jozsef Kardos, Daniel E. Otzen, Vittorio Bellotti, Johannes Buchner, Yuji Goto
Summary: Noji et al. test the link between protein folding and misfolding upon heating and agitation, showing that folding and amyloid formation are separated by the supersaturation barrier of a protein, breakdown of which shifts the protein to the amyloid pathway. This study is valuable for understanding protein folding versus self-assembly and amyloidogenesis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Immunology
Reka A. Kovacs, Henrietta Vadaszi, Eva Bulyaki, Gyorgy Torok, Vilmos Toth, Dominik Matyas, Judit Kun, Eva Hunyadi-Gulyas, Flora Zsofia Fedor, Adam Csincsi, Katalin Medzihradszky, Laszlo Homolya, Gabor Juhasz, Katalin A. Kekesi, Mihaly Jozsi, Balazs A. Gyorffy, Jozsef Kardos
Summary: Elements of the immune system, particularly components of innate immunity, play important roles not only in host defense but also in the nervous system, such as complement-mediated synaptic pruning and the involvement of neuronal pentraxins in synapse formation and plasticity. The study reveals that NPs play a regulatory role in C1q's synaptic function, and further investigation is needed to determine if this role is intensified in pathological conditions like Alzheimer's disease.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Elek Telek, Kristof Karadi, Jozsef Kardos, Andras Kengyel, Zsuzsanna Fekete, Henriett Halasz, Miklos Nyitrai, Beata Bugyi, Andras Lukacs
Summary: The Myo16Tail protein region plays a crucial role in neuronal functioning, cell cycle regulation, and phosphoinositide 3-kinase signaling. It interacts with the N-terminal ankyrin domain of myosin 16, demonstrating high structural flexibility and intrinsic disorder. These features suggest that Myo16Tail may act as a flexible display site crucial in post-translational modifications and regulatory functions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Nikoletta Murvai, Lajos Kalmar, Beata Szabo, Eva Schad, Andras Micsonai, Jozsef Kardos, Laszlo Buday, Kyou-Hoon Han, Peter Tompa, Agnes Tantos
Summary: Disordered plant chaperones are crucial for plants to survive in harsh conditions, with dehydrins being one of the largest groups of disordered chaperones expressed under various abiotic stress conditions. Despite their importance, the exact role and relevance of the conserved regions in dehydrins have not been formally addressed. Research on the intrinsically disordered stress protein ERD14 in A. thaliana shows that different conserved segments, whether directly involved in partner binding or not, are equally necessary for proper function, highlighting the importance of balanced interplay between different regions for cellular protection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zoltan Szabolcsi, Amanda Demeter, Peter Kiraly, Andrea Balogh, Melissa L. Wilson, Jennifer R. King, Szabolcs Hetey, Zsolt Gelencser, Koji Matsuo, Beata Hargitai, Paulette Mhawech-Fauceglia, Petronella Hupuczi, Andras Szilagyi, Zoltan Papp, Lynda D. Roman, Victoria K. Cortessis, Nandor Gabor Than
Summary: Through analysis of DNA methylation and transcriptome data in gestational trophoblastic diseases (GTDs), it was found that DNA methylation levels increase with disease severity in GTDs. Differentially expressed genes exhibit upregulation in complete moles and downregulation in choriocarcinoma cells. DNA methylation mainly influences gene expression and pathways related to trophoblast differentiation in moles and choriocarcinoma cells.
Article
Biology
Eva Bulyaki, Judit Kun, Tamas Molnar, Alexandra Papp, Andras Micsonai, Henrietta Vadaszi, Borbala Marialigeti, Attila Istvan Kovacs, Gabriella Gellen, Keiichi Yamaguchi, Yuxi Lin, Masatomo So, Mihaly Jozsi, Gitta Schlosser, Young-Ho Lee, Karoly Liliom, Yuji Goto, Jozsef Kardos
Summary: The exceptional amyloidogenicity of the pathogenic D76N beta 2m variant is realized by the deleterious synergy of diverse effects of destabilized native structure, higher sensitivity to negatively charged amphiphilic molecules (e.g., lipids) and polyphosphate, more effective fibril nucleation, higher conformational stability of fibrils, and elevated affinity for extracellular components, including extracellular matrix proteins, relative to WT beta 2m.
Article
Biochemistry & Molecular Biology
Andras Micsonai, Eva Moussong, Frank Wien, Eszter Boros, Henrietta Vadaszi, Nikoletta Murvai, Young-Ho Lee, Tamas Molnar, Matthieu Refregiers, Yuji Goto, Agnes Tantos, Jozsef Kardos
Summary: The BeStSel method is a powerful tool for analyzing protein secondary structure composition, providing accurate information and predicting protein folding down to the topology/homology level. It also helps distinguish intrinsically disordered proteins and assists in experimental verification and in silico modeling using CD spectroscopy.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Andras Micsonai, Eva Moussong, Nikoletta Murvai, Agnes Tantos, Orsolya Toke, Matthieu Refregiers, Frank Wien, Jozsef Kardos
Summary: This article proposes a method for classifying disorder and order based on the analysis of far-UV CD spectroscopy data. The method only requires CD data at three wavelength points, making it useful for experimental verification of proteins without a stable tertiary structure.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Vilmos Toth, Henrietta Vadaszi, Lilla Ravasz, Daniel Mittli, Dominik Matyas, Tamas Molnar, Andras Micsonai, Tamas Szaniszlo, Reka A. Kovacs, Tunde Juhasz, Tamas Beke-Somfai, Gabor Juhasz, Balazs Andras Gyorffy, Katalin A. Kekesi, Jozsef Kardos, Peter Lorincz
Summary: This study found that neuronal-specific septin-3 is associated with synaptic/neuronal autophagy, can bind autophagy protein Atg8, and localize to autophagic membranes. The elevated levels of septin-3 may indicate enhanced or impeded autophagy in neurons.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Henrietta Vadaszi, Bence Kiss, Andras Micsonai, Gitta Schlosser, Tamas Szaniszlo, Reka A. Kovacs, Balazs A. Gyoerffy, Katalin A. Kekesi, Yuji Goto, Barbara Uzonyi, Karoly Liliom, Jozsef Kardos
Summary: C1q, a complement component, plays a role in synapse elimination in the central nervous system. However, the molecular mechanism of C1q-associated synapse phagocytosis is still unclear. This study designed single-chain proteins that can inhibit the function of C1q and validated their structure and binding capabilities. These findings can contribute to understanding the localization and functions of C1q in neurons and developing inhibitors for therapeutic purposes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Obstetrics & Gynecology
Nandor Gabor Than, Roberto Romero, Daniel Gyorffy, Mate Posta, Gaurav Bhatti, Bogdan Done, Piya Chaemsaithong, Eunjung Jung, Manaphat Suksai, Francesca Gotsch, Dahiana M. Gallo, Mariachiara Bosco, Bomi Kim, Yeon Mee Kim, Tinnakorn Chaiworapongsa, Simona W. Rossi, Andras Szilagyi, Offer Erez, Adi L. Tarca, Zoltan Papp
Summary: This study identified different molecular subclasses of preeclampsia through longitudinal proteomic profiling, laying the foundation for the development of new diagnostic and personalized tools for prevention.
JOURNAL OF PERINATAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Tamas Szaniszlo, Mate Fulop, Matyas Pajkos, Gabor Erdos, Reka Agnes Kovacs, Henrietta Vadaszi, Jozsef Kardos, Zsuzsanna Dosztanyi
Summary: The study characterized the interaction between Dynein light chain LC8 and centrosomal protein LCA5, revealing that LC8 acts as an oligomerization engine in the formation of oligomers of LCA5.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Istvan Hajdu, Barbara M. Vegh, Andras Szilagyi, Peter Zavodszky
Summary: The amyloidogenic processing of APP depends on its phosphorylation by ROCK2 and the phosphorylation of BACE1. The binding mechanisms and structural details of the interactions between APP-ROCK2 and BACE1-ROCK2 are unknown. In this study, it was found that BACE1 weakly binds to ROCK2, inducing an allosteric conformational change, and APP strongly binds to the ROCK2-BACE1 complex. The results suggest that there are two binding sites involved in the ROCK2-APP interaction: the substrate-binding groove and the allosteric binding site.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Meeting Abstract
Immunology
Mate Posta, Daniel Gyorffy, Peter Kiraly, Beata Hargitai, Orsolya Oravecz, Agnes Zvara, Laszlo Puskas, Andras Szilagyi, Petronella Hupuczi, Nandor Acs, Zoltan Papp, Nandor G. Than
JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2023)
Meeting Abstract
Biophysics
Elek Telek, Kristof Karadi, Jozsef Kardos, Andras Kengyel, Zsuzsanna Fekete, Henriett Halasz, Miklos Nyitrai, Beata Bugyi, Andras Lukacs
BIOPHYSICAL JOURNAL
(2022)