Article
Chemistry, Multidisciplinary
Tao Li, Ruipei Xie, Wei Chen, Andrew B. Schofield, Paul S. Clegg
Summary: This research presents a general strategy for creating complex HIPEs that can form interfacial films at liquid interfaces, achieving double HIPEs and Janus HIPEs for the first time. These materials exhibit unique properties and have the potential for wide application in biological processes.
Review
Chemistry, Inorganic & Nuclear
Andrew R. Jupp
Summary: Frustrated Lewis Pairs (FLPs), combinations of bulky Lewis acids and bases, have the ability to activate and catalyze small molecules. The formation of an encounter complex, where the acid and base are pre-associated, is supported by various experimental techniques. These studies provide a foundation for the exciting transformations that can be promoted by FLPs.
DALTON TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Antonella Di Savino, Johannes M. Foerster, G. Matthias Ullmann, Marcellus Ubbink
Summary: Optimal charge distribution is important for efficient formation of protein complexes, as electrostatic interactions guide encounter complex formation. However, introducing extra charged patches on a protein surface does not necessarily reduce productive encounters. A complex with a high population of encounter complex may be more affected by suboptimal charge distribution, as demonstrated in interactions between cytochrome c mutants and wild-type or variant cytochrome c peroxidases.
Article
Engineering, Mechanical
A. M. Awad, S. S. Askar, A. A. Elsadany
Summary: This paper proposes an economic competition between two firms aiming to maximize the weighted average social welfare and own profits. The competition is described by a nonlinear discrete dynamic map, and its complex dynamic characteristics such as global dynamic behavior, multistability, and synchronization are investigated. The results show that the Nash equilibrium point of the competition can be destabilized through flip bifurcation.
NONLINEAR DYNAMICS
(2022)
Article
Automation & Control Systems
Shuaibing Zhu, Jin Zhou, Jun-An Lu
Summary: In this article, the authors estimate the region of attraction on controlled complex networks with time-varying delay. A delay-independent estimation method is derived that can handle general delay but may result in conservatism. To reduce conservatism, a delay-dependent estimation method is established for networks with small delay using a new technique. Numerical simulations are provided to verify the results.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2023)
Article
Biotechnology & Applied Microbiology
Meliawati Meliawati, Tobias May, Jeanette Eckerlin, Daniel Heinrich, Andrea Herold, Jochen Schmid
Summary: Limited knowledge is available on how complex cellular behaviors are regulated in P. polymyxa. In this study, the roles of several regulatory proteins in governing different physiological traits were investigated. Precise targeted point mutations were introduced using a CRISPR-Cas9-based system. Characterization of the engineered strains revealed similarities and differences in the regulation of cellular behaviors compared to the model bacterium Bacillus subtilis. This study provides novel insights into the complex regulatory system of P. polymyxa and its potential applications in biotechnology.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Faiz Rasul, Fan Zheng, Fenfen Dong, Jiajia He, Ling Liu, Wenyue Liu, Javairia Yousuf Cheema, Wenfan Wei, Chuanhai Fu
Summary: This study reveals the crucial role of the previously uncharacterized mitochondrial membrane protein Emr1 in regulating the number of ERMES foci, with its absence significantly decreasing the foci number, affecting mitochondrial morphology and segregation. Emr1 interacts with the ERMES core component Mdm12 and is essential for ERMES functions, shedding light on the dynamic regulation of endoplasmic reticulum-mitochondria communication.
NATURE COMMUNICATIONS
(2021)
Article
Mathematics, Applied
A. P. Farajzadeh, P. Zanganehmehr, E. Hasanoglu
Summary: The paper aims to extend Kakutani's fixed point theorem, present sufficient conditions for nonempty intersection of sets, provide an existence theorem for set-valued mapping, and give an application of an existence result for a solution to a quasi-equilibrium problem.
APPLIED AND COMPUTATIONAL MATHEMATICS
(2021)
Article
Mathematics, Interdisciplinary Applications
Sumati Kumari Panda, A. M. Nagy, Velusamy Vijayakumar, Bipan Hazarika
Summary: This study investigates the stability of complex-valued neural networks with fractional order in the context of complex-valued rectangular b-metric spaces. The suitable condition for uniform stability of fractionally ordered CVNNs is addressed using the generalized contraction principle, and the existence and uniqueness of the equilibrium point are established. Numerical results are presented to demonstrate the feasibility and correctness of the proposed results.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Chemistry, Multidisciplinary
Yanping Liu, Yingchao Wang, Hongyu Zhang, Yuewen Wu, Shuo Zhao, Qian Li, Chunguang Shao, Zhen Wang
Summary: Rapid pressurization induced crystallization of polybutene-1 results in improved mechanical properties with higher melting points and fracture strains, providing new possibilities for adjusting material properties.
Article
Computer Science, Artificial Intelligence
Shiqin Ou, Zhenyuan Guo, Jingxuan Ci, Shuqing Gong, Shiping Wen
Summary: This paper focuses on the multistability problems of switched complex-valued neural networks with state-dependent switching rules. Several sufficient conditions are derived using differential inclusions theory and fixed point theorem, which show the existence of 25n equilibria, 9n of which are locally stable for n-neuron switched complex-valued neural networks. The number of stable equilibria in n-neuron switched complex-valued neural networks significantly increases from 4n to 9n compared to conventional complex-valued neural networks. Finally, four numerical examples are provided to support the theoretical results.
Article
Chemistry, Applied
Junmeng Lu, Weiyi Zhang, Xue Zhao, Xinglian Xu
Summary: This study evaluated the improvement of emulsion properties of PSE-like chicken breast protein through pH-shifting and found that pH-shifting promoted the exposure of hydrophobic groups, changed secondary structures, and resulted in more stable emulsion interfaces with increased protein interactions.
Article
Chemistry, Inorganic & Nuclear
Qi Yang, Tingting Liu, Jiwen Tan, Liyang Zhu, Qian Liu, Suliang Yang, Guoxin Tian
Summary: The complexation of uranium(VI) with dipicolinic acid and the presence of a protonated complex in aqueous solutions were investigated in this study. The stability constants of known complexes were reevaluated considering the missing protonated species. While a crystal of a solid compound with a specific coordination mode was successfully grown, the corresponding complex species in solution could not be clearly identified.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Sharan K. Bagal, Clare Gregson, Daniel H. O' Donovan, Kurt G. Pike, Andrew Bloecher, Peter Barton, Alexandra Borodovsky, Erin Code, Shaun M. Fillery, Jessie Hao-Ru Hsu, Sameer P. Kawatkar, Chengzhi Li, David Longmire, Youfeng Nai, Samuel C. Nash, Andrew Pike, James Robinson, Jon A. Read, Phillip B. Rawlins, Minhui Shen, Jia Tang, Peng Wang, Haley Woods, Beth Williamson
Summary: This study identifies potent and orally bioavailable EED ligands with good solubilities, which exhibit in vivo efficacy in EZH2-driven tumors through optimization of design strategies.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Gregory G. Theophall, Lisa M. S. Ramirez, Aaron Premo, Sergey Reverdatto, Michaele B. Manigrasso, Gautham Yepuri, David S. Burz, Ravichandran Ramasamy, Ann Marie Schmidt, Alexander Shekhtman
Summary: The diaphanous-related formin, Diaphanous 1 (DIAPH1), is essential for the assembly of Filamentous (F)-actin structures and plays a significant role in RAGE signaling. Mutations in DIAPH1, including the RRKR motif, are associated with hearing loss, macrothrombocytopenia, and cardiovascular diseases. The study demonstrates the importance of the RRKR interactions with DID in the formation of productive encounter complexes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Antonella Di Savino, Johannes M. Foerster, G. Matthias Ullmann, Marcellus Ubbink
Summary: Optimal charge distribution is important for efficient formation of protein complexes, as electrostatic interactions guide encounter complex formation. However, introducing extra charged patches on a protein surface does not necessarily reduce productive encounters. A complex with a high population of encounter complex may be more affected by suboptimal charge distribution, as demonstrated in interactions between cytochrome c mutants and wild-type or variant cytochrome c peroxidases.
Article
Biochemistry & Molecular Biology
Florian J. Gisdon, Christian G. Feiler, Oxana Kempf, Johannes M. Foerster, Jonathan Haiss, Wulf Blankenfeldt, G. Matthias Ullmann, Elisa Bombarda
Summary: In this study, the catalytic mechanism of the PCS-like enzyme from the cyanobacterium Nostoc sp. (NsPCS) was investigated. By combining structural, spectroscopic, thermodynamic, and theoretical techniques, several crystal structures of NsPCS were obtained, capturing different states of the catalyzed chemical reaction. NsPCS was found to be a relatively slow enzyme, whose activity is sensitive to the redox state of the substrate. The study also suggests that NsPCS may function as part of a redox sensing system.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Florian J. Gisdon, Elisa Bombarda, G. Matthias Ullmann
Summary: The catalytic mechanisms of serine and cysteine peptidases are similar, but they differ in an important aspect. Our research demonstrates that serine peptidases use a concerted mechanism facilitated by a negative electrostatic potential and a compact active site geometry, representing an oxygen-insensitive alternative to cysteine peptidases.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Simon Ernst, Alexander N. Volkov, Melina Stark, Lea Hoelscher, Katharina Steinert, Susanne Fetzner, Ulrich Hennecke, Steffen Lorenz Drees
Summary: Quorum sensing regulates the synthesis of azetidine-derived natural products in the opportunistic pathogen Pseudomonas aeruginosa. In this study, the researchers engineered P. aeruginosa to express the biosynthetic azegene cluster, leading to the discovery of two new products. Further investigation revealed the importance of these products in biological activity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Julien Olivet, Sibusiso B. Maseko, Alexander N. Volkov, Kourosh Salehi-Ashtiani, Kalyan Das, Michael A. Calderwood, Jean-Claude Twizere, Christoph Gorgulla
Article
Multidisciplinary Sciences
Sagar Bhattacharya, Eleonora G. Margheritis, Katsuya Takahashi, Alona Kulesha, Areetha D'Souza, Inhye Kim, Jennifer H. Yoon, Jeremy R. H. Tame, Alexander N. Volkov, Olga V. Makhlynets, Ivan V. Korendovych
Summary: Directed evolution is a powerful tool for improving protein properties and functionality. However, the vast number of possible amino acid sequences limits its potential. Current predictive methods rely on structural and bioinformatics information, which may not be available for all proteins, and they have limited ability to identify beneficial mutations outside of the active site. Machine learning methods show promise but require large training datasets. This study demonstrates the use of NMR spectroscopy to identify mutagenic hot spots in enzymes, providing a simple and a priori knowledge-free approach for directed enzyme evolution.
Article
Chemistry, Medicinal
Marie Haufroid, Alexander N. Volkov, Johan Wouters
Summary: Tuberculosis remains as a major cause of death caused by a treatable pathogen. The increasing resistance to common antibiotics necessitates the development of new drugs with new therapeutic targets. The enzyme MtSerB2, which allows immune evasion of Mycobacterium tuberculosis, is a potential target for drug design. This study presents a new approach based on virtual screening for selecting harmine-derived compounds to inhibit MtSerB2. The affinity of these compounds for MtSerB2 is characterized through screening methods, providing structural information and the development of pharmacophore models for more complex inhibitors. This research may lead to the development of antimycobacterial molecules targeting MtSerB2 and inhibiting the growth of the pathogen.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Sebastian Weigert, Pablo Perez-Garcia, Florian J. Gisdon, Andreas Gagsteiger, Kristine Schweinshaut, G. Matthias Ullmann, Jennifer Chow, Wolfgang R. Streit, Birte Hoecker
Summary: The handling of plastic waste and microplastic has become one of the greatest challenges of our time. Recent studies on plastic degrading enzymes have provided new prospects for biological decomposition and recycling. In this study, the candidate PET6 enzyme from Vibrio gazogenes was chosen for further investigation. The characterization of PET6 revealed its widespread occurrence in various Vibrio strains and its superior ability to degrade polyethylene terephthalate under high salt concentrations. Mutations from other PET degrading enzymes were introduced to PET6 to enhance its activity, demonstrating the evolutionary potential of the enzyme. The crystal structure and molecular dynamics simulations of PET6 provided insights into its adaptation to saline environments. The findings suggest that Vibrio and the PET6 enzyme are worthy subjects for studying PET degradation in marine environments.
Article
Biochemistry & Molecular Biology
Ilona van Alen, Aleksandra Chikunova, Danny B. van Zanten, Amber A. de Block, Monika Timmer, Steffen Brunle, Marcellus Ubbink
Summary: Conserved residues are usually essential for protein function, but mutations in highly conserved residues of BlaC did not significantly affect the enzyme. One mutation, D179N, even increased ceftazidime resistance while maintaining good activity against penicillins. Crystal structures of BlaC D179N revealed minor structural changes compared to wild-type BlaC, and introducing this mutation in other beta-lactamases resulted in decreased antibiotic resistance. The importance of the interaction with Arg164 explains why Asp179 is not essential in BlaC.
Article
Chemistry, Inorganic & Nuclear
Qing Miao, Rene Dekkers, Karthick Babu Sai Sankar Gupta, Mark Overhand, Rubin Dasgupta, Marcellus Ubbink
Summary: A hydrophilic rigid macrocyclic ligand was designed and synthesized for investigating the conformational dynamics of its complex with europium using NMR spectroscopy. The results showed that the complex exists in two conformers, with the twisted square antiprismatic one being favored. This ligand is suitable for developing rigid probes for paramagnetic NMR of proteins and is less likely to cause protein precipitation due to its hydrophilic nature.
INORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Mike Sleutel, Brajabandhu Pradhan, Alexander N. Volkov, Han Remaut
Summary: Two decades after the discovery of functional amyloids, the authors propose an atomic model of curli protofibrils and their higher modes of organization using AlphaFold2 modeling and cryo-electron microscopy. They uncover the structural diversity of curli building blocks and fibril architectures, providing insights into the physicochemical robustness of curli and inter-species promiscuity. This study facilitates further engineering efforts to expand the repertoire of curli-based functional materials.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Carola S. Seelmann, Simona G. Huwiler, Martin Culka, Marc J. F. Strampraad, Till Biskup, Stefan Weber, G. Matthias Ullmann, Volker Schunemann, Peter-Leon Hagedoorn, Antonio J. Pierik, Matthias Boll
Summary: In anaerobic aromatic compound degrading microbes, class II benzoyl-coenzyme A (CoA) reductases (BCRs) reduce benzoyl-CoA to cyclohexa-1,5-diene-1-carboxyl-CoA (1,5-dienoyl-CoA) through a tungsten-bis-metallopterin (MPT) cofactor. This study provides experimental evidence for the Birch-like reduction mechanism via W(V)/radical intermediates and reveals the unique tetrahydro state of MPT cofactors essential for the reversibility of enzymatic Birch reduction.
Article
Biochemical Research Methods
Marusa Prolic-Kalinsek, Alexander N. Volkov, San Hadzi, Jeroen Van Dyck, Indra Bervoets, Daniel Charlier, Remy Loris
Summary: YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. It recognizes a specific DNA sequence and forms a tetramer. The POU domain in YdaT has flexibility in the free state but becomes fixed upon DNA binding.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anna Caccamo, Felix Vega de Luna, Khadija Wahni, Alexander N. Volkov, Jonathan Przybyla-Toscano, Antonello Amelii, Alexandre Kriznik, Nicolas Rouhier, Joris Messens, Claire Remacle
Summary: Recent studies have identified a novel class of ascorbate peroxidases called APX-R, with a focus on APX2 from Chlamydomonas reinhardtii in this study. Experimental results indicate that APX2 exhibits peroxidase activity with guaiacol as an electron donor, along with the ability to bind copper and heme. Evidence suggests a potential interaction between APX2 and plastocyanin, highlighting the role of APX2 in regulating copper transfer to plastocyanin.
Article
Chemistry, Physical
Rajeev Ranjan Roy, G. Matthias Ullmann
Summary: This article introduces a method called the Virtual Model Compound Approach (VMCA) to extrapolate the redox potential of a model compound based on the known redox potentials of proteins. The authors carefully selected high-resolution structures for analysis, dividing them into fitting and independent test sets. By re-refining certain structures, they were able to reduce the standard deviation of the model redox potential and obtain a more reliable result.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)