Article
Cell Biology
Filomena Broeskamp, Elizabeth S. M. Edrich, Oskar Knittelfelder, Lisa Neuhaus, Thorsten Meyer, Jonas Heyden, Lukas Habernig, Florian Kreppel, Campbell W. Gourlay, Patrick Rockenfeller
Summary: This study investigated the impact of mitochondrial outer membrane protein Por1 on yeast autophagy, showing that POR1 deficiency reduces autophagic capacity and alters organelle and lipid homeostasis. It was found that the reduced autophagy caused by POR1 deficiency could be circumvented by overexpression of Psd1, suggesting a role for Por1 in Psd1-mediated autophagy regulation.
Article
Multidisciplinary Sciences
Bing Zhang, Sensen Zhang, Maya M. Polovitskaya, Jingbo Yi, Binglu Ye, Ruochong Li, Xueying Huang, Jian Yin, Sebastian Neuens, Tom Balfroid, Julie Soblet, Daphne Vens, Alec Aeby, Xiaoling Li, Jinjin Cai, Yingcai Song, Yuanxi Li, Marco Tartaglia, Yang Li, Thomas J. Jentsch, Maojun Yang, Zhiqiang Liu
Summary: The study reveals that ClC-6 is an ion exchanger protein expressed in the nervous system and associated with severe neurological diseases. The researchers used cryo-EM structures and functional studies to uncover the structure, function, and regulation of ClC-6, as well as identifying hotspots for disease-causing mutations.
Article
Biochemistry & Molecular Biology
Nicolas Tricaud, Benoit Gautier, Jade Berthelot, Sergio Gonzalez, Gerben Van Hameren
Summary: This study found that after nerve injury, there are changes in the pH, motility, and calcium content of Schwann cell mitochondria, leading to demyelination. Calcium release through VDAC channels plays a crucial role in this process. The altered kinetics of mitochondrial calcium release in diabetic mice suggest a potential mechanism for the development of peripheral neuropathy. Blocking VDAC could be a promising target for developing drugs to treat diabetic peripheral neuropathy.
Article
Biochemical Research Methods
Ali Punjani, David J. J. Fleet
Summary: 3DFlex is a motion-based neural network model that can determine high-resolution 3D density from 2D image data and provide a motion model for flexible protein conformational changes.
Article
Chemistry, Physical
Aisha Ahsan, Luiza Buimaga-Iarinca, Thomas Nijs, Sylwia Nowakowska, Sk Rejaul, S. Fatemeh Mousavi, Mehdi Heydari, Meike Stoehr, Sameena S. Zaman, Cristian Morari, Lutz H. Gade, Thomas A. Jung
Summary: Host-guest architectures provide ideal systems for investigating site-specific physical and chemical effects. In this study, we found that the symmetry, registry, lateral packing, and adsorption height of small clusters formed upon condensation are modified by the presence of cycloalkanes in confined spaces. While cyclopentane and cycloheptane show cooperativity upon filling, cyclooctane and to a lesser degree cyclohexane redistribute to more favorable adsorption sites. This site-specific modification of interaction and behavior is crucial for applications of porous materials in gas storage or catalysis.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Tianyu Hu, Michael J. Morten, Steven W. Magennis
Summary: The study investigates the dynamics of DNA three-way junctions containing slip-outs composed of CAG or CTG repeats using single-molecule Forster resonance energy transfer. Two-state behavior is observed in 3WJs with only repeats in the slip-out, while additional dynamics are observed when the triplet repeats extend into the adjacent duplex, likely involving interconversion of positional isomers. This research suggests a branchpoint migration model that may have implications for how repeat slip-outs are processed by cellular machinery and disease progression.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Pradeep R. Nair
Summary: This article predicts the possibility of trap emission-limited logarithmic and power-law transients in perovskite materials, which is validated by numerical simulations and experimental reports. The findings indicate the need to revisit existing methods for estimating recombination parameters in pump-probe spectroscopy and suggest appropriate methodologies for back extracting trap distribution parameters.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Review
Mathematics, Applied
Arindam Mishra, Subrata Ghosh, Syamal Kumar Dana, Tomasz Kapitaniak, Chittaranjan Hens
Summary: Researchers have observed similarities between the spiking and bursting behaviors of superconducting Josephson junctions with that of neurons. Recent studies have also shown similar neuronal functional behavior in superconducting nanowires. The history of this research highlights the origins and dynamic interpretations of these phenomena.
Article
Engineering, Multidisciplinary
Flavio Galliana, Roberto Cerri, Davide Corona
Summary: The precision resistive divider at INRIM is made up of bulk metal foil resistors in various values to achieve decade ratios. It can be automatically calibrated with a top-class calibrator and a precision multimeter to minimize load error and reduce the effect of relay emfs. The project is transferable to secondary laboratories for knowledge transfer within the framework of INRIM.
Article
Chemistry, Multidisciplinary
Amanda Arcidiacono, Davide Accomasso, Lorenzo Cupellini, Benedetta Mennucci
Summary: This study utilizes QM/MM surface hopping nonadiabatic dynamics to investigate the excited-state decay of canthaxanthin in OCP, revealing possible pathways for structural changes and photoactivation.
Article
Chemistry, Physical
Arda Yildirim, Christina Krause, Patrick Huber, Andreas Schoenhals
Summary: This study investigates the phase behavior and molecular dynamics of HATn with different alkyl chain lengths using various techniques. The results reveal the significant impact of alkyl chain length on the system properties and provide detailed discussion on the observed relaxation processes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Subhasmita Mahapatra, Nisha Amarnath Jonniya, Suman Koirala, Parimal Kar
Summary: In this study, the phosphorylation-induced conformational dynamics of FGFR1 in both apo and ATP-bound states were investigated using molecular dynamics simulations. The findings reveal that phosphorylation and ATP binding can lead to a fully active configuration of FGFR1 kinase. The formation of a 3-10 helix in the activation loop and strong salt-bridge interactions contribute to the stability and compactness of the structure.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Md Fulbabu Sk, Parimal Kar
Summary: The papain-like protease (PLpro) of the coronavirus family plays a crucial role in viral polyprotein processing and immune evasion, with deubiquitination and deISGylation activities. Molecular dynamics simulations revealed the structural and energetic basis of PLpro recognition by human ISG15, showing a stronger binding affinity between SCoV2-PLpro and hISG15. The study elucidated differential deISGylating activities of PLpro among CoVs and highlighted the specificity of SCoV2-PLpro towards hISG15.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Engineering, Electrical & Electronic
S. Demirezen, A. G. Al-Sehemi, A. Yuzer, M. Ince, A. Dere, A. A. Al-Ghamdi, F. Yakuphanoglu
Summary: In this study, symmetrical copper-phthalocyanine (CuPc) was coated on a p-Si wafer using the spin-coating method. The photoresponse and electrical properties of the Al/symmetrical CuPc/p-Si structures/diodes were investigated under different solar irradiances. The experimental results showed that the photocurrent of the diodes was influenced by the solar irradiance.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2022)
Article
Biophysics
Paul Campitelli, Jin Lu, S. Banu Ozkan
Summary: The study of the SARS-CoV-2 coronavirus has revealed differences in long-range dynamics and dynamic flexibility of the main protease (mPro) compared to SARS-CoV-1. Significant cross-chain coupling is observed between active sites and specific distal residues in CoV-2 mPro. Inhibitor binding induces different changes in flexibility in the two systems. These differences are likely the result of allosteric influence, where substitutions in CoV-2 lead to flexibility and dynamic changes elsewhere in the structure.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Friedrich Finkenwirth, Michael Sippach, Sinah N. Pecina, Mario Gaede, Julia Ruta, Adrian Ricke, Elena Bondarenko, Johann P. Klare, Maximilian Zinke, Sascha Lange, Adam Lange, Heinz-Jurgen Steinhoff, Thomas Eitinger
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2020)
Article
Chemistry, Multidisciplinary
Jonas Schaefer, Jessica Nehls, Markus Schoen, Ingo Mey, Claudia Steinem
Article
Chemistry, Multidisciplinary
Jutta Hoffmann, Julia Ruta, Chaowei Shi, Kitty Hendriks, Veniamin Chevelkov, W. Trent Franks, Hartmut Oschkinat, Karin Giller, Stefan Becker, Adam Lange
MAGNETIC RESONANCE IN CHEMISTRY
(2020)
Article
Biophysics
Peter Muehlenbrock, Kira Herwig, Loan Vuong, Ingo Mey, Claudia Steinem
BIOPHYSICAL JOURNAL
(2020)
Article
Multidisciplinary Sciences
Thomas Schubert, Taras Sych, Josef Madl, Maokai Xu, Ramin Omidvar, Lukas J. Patalag, Annika Ries, Katharina Kettelhoit, Annette Brandel, Yves Mely, Claudia Steinem, Daniel B. Werz, Roland Thuenauer, Winfried Roemer
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Kitty Hendriks, Carl Oester, Chaowei Shi, Han Sun, Adam Lange
Summary: The study demonstrates that K+-selective mutants lose selectivity filter stability under Na+ conditions without collapsing into a defined structure, and structural changes occur.
Compared to the non-selective wild-type NaK channel, the stronger link between the selectivity filter and the pore helix in K+-selective mutants reduces the ion-dependent conformational flexibility of the selectivity filter.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Maximilian Zinke, Gunnar F. Schroeder, Adam Lange
Summary: Technological advances have allowed for detailed studies of bacteriophage tail tubes using cryo-EM. These structures, which connect the DNA-containing capsid with a receptor function, consist of helical and polymerized major tail proteins. This review highlights the role of integrative structural biology approaches and discusses the limitations of high-resolution reconstructions due to the flexibility of tail tubes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Carl Oester, Kumar Tekwani Movellan, Benjamin Goold, Kitty Hendriks, Sascha Lange, Stefan Becker, Bert L. de Groot, Wojciech Kopec, Loren B. Andreas, Adam Lange
Summary: This study investigates the structure and interactions of potassium ions in ion channels using solid-state NMR. The findings reveal differences in ion binding and water molecule interactions in different selective ion channels, despite having identical amino acid sequences and crystal structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Ronja Rabea Paschke, Swantje Mohr, Sascha Lange, Adam Lange, Jacek Kozuch
Summary: Viroporins are small viral ion channels that play essential roles during viral infections. Using surface-enhanced infrared absorption spectroscopy, we track and quantify the large-scale structural changes during opening of the Influenza A viroporin, the M2 proton channel, in a model membrane. This motion is blocked by inhibition providing a clear spectroscopic strategy to explore mechanisms of viroporin function and test new antiviral drugs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Claudia Bohg, Carl Oster, Berke Turkaydin, Michael Lisurek, Pascal Sanchez-Carranza, Sascha Lange, Tillmann Utesch, Han Sun, Adam Lange
Summary: Rhomboid proteases hydrolyze substrate helices within the lipid bilayer to release soluble domains from the membrane. The lateral gate formed by TM2 and TM5 in the model rhomboid GlpG allows access of the hydrophobic substrate to the active site. The opening dynamics of the lateral gate in rhomboid proteases strongly affects their enzymatic activity.
Article
Chemistry, Physical
Veniamin Chevelkov, Sascha Lange, Henry Sawczyc, Adam Lange
Summary: Protein dynamics play a crucial role in determining protein function. Traditional static structure determination methods, such as X-ray crystallography and cryo-EM, have limitations in understanding protein motions. Molecular simulations can predict global and local protein motions, but directly measuring local dynamics at the residue level is still essential. Solid-state nuclear magnetic resonance (NMR) provides a powerful tool for studying dynamics in rigid or membrane-bound biomolecules. A novel method is presented here that eliminates errors caused by radio-frequency field inhomogeneity, allowing for direct and accurate measurement of residue-specific motion amplitudes.
ACS PHYSICAL CHEMISTRY AU
(2023)
Article
Chemistry, Multidisciplinary
Claudia Bohg, Carl Oster, Tillmann Utesch, Susanne Bischoff, Sascha Lange, Chaowei Shi, Han Sun, Adam Lange
Summary: Intramembrane proteolysis is fundamental in biological and pathological processes, but selective inhibitors for intramembrane proteases are few. This study utilized solid-state NMR spectroscopy to investigate the binding of two different inhibitors to the bacterial rhomboid protease GlpG and determined the binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations.
Article
Multidisciplinary Sciences
Maximilian Zinke, Katrin A. A. Sachowsky, Carl Oester, Sophie Zinn-Justin, Raimond Ravelli, Gunnar F. Schroeder, Michael Habeck, Adam Lange
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Physical
Jeremias Sibold, Vera E. Tewaag, Thomas Vagedes, Ingo Mey, Claudia Steinem
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Mathias Bosse, Jeremias Sibold, Holger A. Scheidt, Lukas J. Patalag, Katharina Kettelhoit, Annika Ries, Daniel B. Werz, Claudia Steinem, Daniel Huster
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)