Article
Mathematics
Keyou Shi, Xiaoping Wu, Yurong Tian, Xiaotian Xie
Summary: A new model of prestress loss of anchor cable was established, taking into account the effect of the frame beam, showing higher accuracy and the ability to predict the time when the prestress of anchor cable reaches stability. It was found that re-tensioning the anchor cable after 20 days of construction completion can achieve optimal prestress compensation, with greater loss of original prestress leading to more obvious compensation effects during re-tensioning.
Article
Biochemistry & Molecular Biology
Sevan Habeshian, Ganesh A. Sable, Mischa Schuettel, Manuel L. Merz, Christian Heinis
Summary: Here, we have developed a strategy that allows for the synthesis and screening of hundreds of cyclic peptides without the need for purification. This method is applicable for facile synthesis in 96-well plates and yields disulfide-cyclized peptides.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Anil Balajirao Dapkekar, Gedu Satyanarayana
Summary: We report a metal, oxidant, and base-free electrochemical approach for the synthesis of 3-selenylindoles through an oxidative cyclization reaction. This environmentally friendly method demonstrated a wide substrate scope under mild reaction conditions in an electrochemical undivided cell setup.
CHEMICAL COMMUNICATIONS
(2023)
Article
Engineering, Mechanical
Alexandre Kawano, Antonino Morassi, Ramon Zaera
Summary: In this paper, a constructive procedure is proposed to determine the radial pretension in an axially-symmetric orb-web based on one eigenfrequency and its corresponding vibration mode. The method can be applied to both axisymmetric modes and non-axisymmetric modes, and regularization technique and filtering process are proposed to improve the reconstruction of the pretension field.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2022)
Review
Polymer Science
Aidas Jokubaitis, Juozas Valivonis
Summary: This paper provides a detailed analysis of the transfer lengths of different types of FRPs based on experimental results, proposing corrections and new coefficients for engineering design codes, and filling research gaps in the field.
Article
Chemistry, Medicinal
Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor
Summary: Allosteric pathways in proteins involve networks of amino acid residues that transmit signals between distant sites. This study uses molecular dynamics simulations and suboptimal path analysis to discover new allosteric networks in steroid receptors, focusing on evolutionarily conserved pathways. The researchers identify a conserved network connecting a predicted allosteric site between helices 9 and 10 of the ligand-binding domain to the activation function surface 2 (AF-2). The study suggests the evolutionary importance of this site in steroid receptors and provides an approach to discover previously unknown allosteric sites in proteins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor
Summary: Allosteric pathways in proteins allow for the transmission of signals between distant sites through inter-residue interactions. This study utilizes molecular dynamics simulations and suboptimal path analysis to identify new allosteric networks in steroid receptors, focusing on evolutionarily conserved pathways. The investigation reveals a conserved network connecting a predicted allosteric site located between helices 9 and 10 of the ligand-binding domain to the activation function surface 2 (AF-2). The importance of this site is highlighted by its presence in a region characterized by conserved inter-residue contacts.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Ajay Sharma, Ajay Kant Gola, Satyendra Kumar Pandey
Summary: Efficient and metal-free strategies for synthesizing α-thiocyanoketones and thiazoles from β-ketosulfoxonium ylides and ammonium thiocyanate are described in this article. These methods offer simplicity, benign reaction conditions, excellent chemoselectivity, and high yield, making them a unique approach for divergent synthesis. The potential value of these methods is demonstrated through large-scale reactions and the synthesis of the anti-inflammatory drug Fanetizole.
CHEMICAL COMMUNICATIONS
(2023)
Article
Pharmacology & Pharmacy
Yue Zeng, Yueming Zheng, Tongtong Zhang, Fei Ye, Li Zhan, Zengwei Kou, Shujia Zhu, Zhaobing Gao
Summary: This study developed an efficient method to discover modulators of GluN3-containing NMDARs and identified WZB117 as a novel allosteric inhibitor of GluN1/GluN3 receptors.
FRONTIERS IN PHARMACOLOGY
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Ruoxi Zhang, Rui Kang, Daolin Tang
Summary: The balance of oxidants and antioxidants, known as redox homeostasis, is crucial for cell function. Disruption of redox homeostasis is linked to the development and treatment of various diseases, including cancer. Recent studies have shown that both oxidative and reductive stress can trigger regulated cell death, such as disulfidptosis and pyroptosis, in cancer and immune cells. Exploring the relationship between oxidative and reductive cell death could lead to novel disease treatments.
CANCER GENE THERAPY
(2023)
Article
Chemistry, Physical
Zhaolin Wu, Yuhang Guo, MingZhi Qin, Chaoyou Liao, Xiufen Wang, Liqun Zhang
Summary: Most ionic electrical components are made from non-recyclable or degradable petroleum-based materials, calling for a green fabrication solution. In this study, a liquid-free dynamic polymer network was prepared using a biobased monomer. The synthetic ionic conductive elastomer exhibited high transparency, good extensibility, and ideal conductivity, making it suitable for strain sensors. It also showed self-healing ability, recyclability, and degradability. This research offers a new perspective and method for coordinating the synthetic efficiency and overall performance of smart materials for soft electronic devices.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Engineering, Mechanical
Xuguang Dong, Zheng Li, Zizhi Cui, Canming Zhou
Summary: This paper investigates the stability of the pile-prestressed anchor composite structure in retain engineering. A stability analysis model considering both prestress and pile body is established, and a dynamic search algorithm is proposed. The effectiveness of the model is confirmed through comparisons with existing methods. The study finds that the safety coefficient of the composite structure is influenced by the prestress, pile length, pile diameter, and pile spacing. Additionally, the safety coefficient increases initially and then decreases with the increase of slip line depth. Increasing the prestress of the anchor in the middle and lower part of the slope has a significant effect on improving the safety coefficient. The proposed model and algorithm can consider multiple failure modes and provide a safety coefficient, making it highly valuable in assessing the stability of the pile-prestressed anchor composite structure retaining slope.
ENGINEERING FAILURE ANALYSIS
(2022)
Article
Pharmacology & Pharmacy
Lu Jin, Xiaoyu Han, Xinlei Zhang, Zhimin Zhao, Judith Ulrich, Tatiana Syrovets, Thomas Simmet
Summary: This study demonstrates that oleanolic acid may function as an allosteric agonist inducing clustering of alpha(M) on macrophages by shifting the balance from the closed to the extended-open conformation. The molecular target identified in this study holds potential for a purposeful use of oleanolic acid to modulate chronic inflammatory responses.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jacopo Sgrignani, Andrea Cavalli
Summary: The inhibitors camostat, nafamostat, and bromhexine target the transmembrane serine protease TMPRSS2 to prevent viral infections. Computational simulations reveal that binding of Ile256 induces a conformational change in the catalytic site of TMPRSS2, providing a rationale for enzyme activation. Furthermore, bromhexine competes with Ile256 for the binding site, suggesting its potential as an allosteric inhibitor of TMPRSS2.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Engineering, Civil
Pablo M. Paez, Beradi Sensale-Cozzano
Summary: This paper proposes an equation to estimate the prestress loss in continuous unbonded prestressed concrete beams, and develops a numerical model for time-dependent analysis. The equation accounts for concrete creep and shrinkage, relaxation of prestressing steel, presence of non-prestressed steel reinforcement, and friction between tendons and ducts. Experimental and numerical results validate the equation and finite element approach for modelling the behavior of this type of prestressed concrete member over time.
ENGINEERING STRUCTURES
(2021)
Article
Chemistry, Physical
Benedikt Rennekamp, Fabian Kutzki, Agnieszka Obarska-Kosinska, Christopher Zapp, Frauke Graeter
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Review
Biochemistry & Molecular Biology
Florian Franz, Csaba Daday, Frauke Graeter
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Chemistry, Physical
Eduardo R. Cruz-Chu, Gonzalo J. Villegas-Rodriguez, Tobias Jager, Luca Valentini, Nicola M. Pugno, Konstantinos Gkagkas, Frauke Grater
NPJ COMPUTATIONAL MATERIALS
(2020)
Article
Biochemical Research Methods
Fan Jin, Frauke Grater
Summary: The study found that multi-site phosphorylation causes V-shaped changes in collapse propensity of all proteins based on their initial net charge, expanding neutral or overall negatively charged IDPs and shrinking positively charged IDPs. In two of the IDPs, only two biologically relevant phosphorylation sites are enough to significantly expose the adjacent negatively charged active site, increasing the likelihood of interaction with other binding partners.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Claudia L. Gomez-Flores, Denis Maag, Mayukh Kansari, Van-Quan Vuong, Stephan Irle, Frauke Graeter, Tomas Kubar, Marcus Elstner
Summary: This paper investigates the generation of free energy surfaces in complex reactions using the semiempirical method DFTB and improves its accuracy by developing a specific reaction parametrization (SRP). Through the implementation of an artificial neural network (ANN), the authors successfully generate highly accurate free energy surfaces for thiol-disulfide exchange in two molecular complexes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Niccolo Banterle, Adrian P. Nievergelt, Svenja de Buhr, Georgios N. Hatzopoulos, Charlene Brillard, Santiago Andany, Tania Huebscher, Frieda A. Sorgenfrei, Ulrich S. Schwarz, Frauke Graeter, Georg E. Fantner, Pierre Goenczy
Summary: Discovering mechanisms controlling organelle assembly is a fundamental pursuit in biology. The centriole is a conserved organelle with a 9-fold symmetrical arrangement of microtubules. Research shows that the surface can convert the inherent helical propensity of SAS-6 polymers into 9-fold rings, guiding ring stacking and imparting chiral features to centrioles and cilia.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Isabel M. Martin, Michele M. Nava, Sara A. Wickstroem, Frauke Graeter
Summary: This study investigates the mechanotransducing functions of the essential adhesion component integrin-linked kinase (ILK) using force-probe molecular-dynamics simulations. The results suggest that ATP plays a role in facilitating cellular force generation and migration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Uladzimir Barayeu, Danny Schilling, Mohammad Eid, Thamara Nishida Xavier da Silva, Lisa Schlicker, Nikolina Mitreska, Christopher Zapp, Frauke Graeter, Aubry K. Miller, Reinhard Kappl, Almut Schulze, Jose Pedro Friedmann Angeli, Tobias P. Dick
Summary: Ferroptosis is a type of cell death caused by radical-driven lipid peroxidation. Our study shows that sulfane sulfur species, particularly hydropersulfides, scavenge free radicals and suppress ferroptosis. Cysteine can support ferroptosis resistance independently of the GPX4 pathway by providing sulfur for S-0 biosynthesis.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Po-Chia Chen, Fabian Kutzki, Angelika Mojzisch, Bernd Simon, Emma-Ruoqi Xu, Camilo Aponte-Santamaria, Kai Horny, Cy Jeffries, Reinhard Schneppenheim, Matthias Wilmanns, Maria A. Brehm, Frauke Graeter, Janosch Hennig
Summary: Von Willebrand disease is a bleeding disorder associated with mutations in the VWF gene. This study investigates the structure and dynamics of the C6 domain and the G2705R variant in C6, using nuclear magnetic resonance spectroscopy, molecular dynamics simulations and aggregometry. The findings show that the G2705R mutation destabilizes VWF by promoting hinging between the subdomains of C6.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan uenal, Debora Monego, Kai Riedmiller, Ganna Gryn'ova, David M. Hudson, Frauke Graeter
Summary: The authors used scale-bridging simulations to identify breakage points in collagen and studied the mechanical and chemical impact of these ruptures on the tissue. They found that collagen has a unique failure mode that helps prevent material ageing and macroscopic failure.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Wojtek Treyde, Kai Riedmiller, Frauke Graeter
Summary: Knowledge of reliable X-H bond dissociation energies is crucial for studying the radical chemistry of proteins. By computing the X-H bond dissociation energies of model dipeptides, our work provides a highly valuable and unprecedented data set with accuracy and comprehensiveness. This dataset is likely to be useful for predicting protein biochemistry involving radicals.
Article
Chemistry, Physical
Matthias Brosz, Nicholas Michelarakis, Uwe H. F. Bunz, Camilo Aponte-Santamaria, Frauke Graeter
Summary: Poly(para-phenylene ethynylene)s (PPEs) are a class of conjugated and semi-flexible polymers with a wide range of technological applications. In this study, a coarse-grained model for PPEs was developed using the Martini 3 force field to study large-scale assemblies computationally. The model successfully reproduced key structural and thermodynamic properties of single PPE chains and mixtures. It was found that chain entanglement increased with PPE chain length, while nematic ordering decreased. The Martini 3 PPE model allows for investigation of the structural organization of PPE bulk systems at large spatio-temporal scales and is predicted to be applicable for studying out-of-equilibrium behavior under mechanical force.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Denis Maag, Marina Putzu, Claudia L. Gomez-Flores, Frauke Graeter, Marcus Elstner, Tomas Kubar
Summary: In the study, it was found that the thiol-disulfide exchange reactions were directed by electrostatic interactions, with the sulfur atoms preferring to attack Cys55 over Cys24. These interactions play a significant role in the regioselectivity of the reactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Nicholas Michelarakis, Florian Franz, Konstantinos Gkagkas, Frauke Graeter
Summary: This study used non-equilibrium Molecular Dynamics simulations to investigate the shear viscosity mechanism of Nafion solutions, revealing the presence of rod-shaped Nafion microstructures in the absence or low shear flow, with higher shear rates breaking these structures and aligning Nafion strands in the flow direction to reduce shear viscosities.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Evolutionary Biology
Gustavo Caetano-Anolles, M. Fayez Aziz, Fizza Mughal, Frauke Graeter, Ibrahim Koc, Kelsey Caetano-Anolles, Derek Caetano-Anolles
EVOLUTIONARY BIOINFORMATICS
(2019)