Article
Biochemistry & Molecular Biology
Manjeet Kumar, Sarah L. Teakel, Crystall Swarbrick, Intifar S. Chowdhury, David C. Thorn, Margaret Sunde, John A. Carver, Jade K. Forwood
Summary: Acot enzymes play important roles in cell signaling, lipid metabolism, inflammation, and ion channel opening. Acot7 can spontaneously form amyloid fibrils under physiological conditions. The aggregation mechanism of Acot7 involves conformational rearrangement and the formation of enhanced beta-sheet structures in the initial phase, followed by the formation of amyloid fibrils.
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Andrius Sakalauskas, Kamile Mikalauskaite, Ruta Snieckute, Vytautas Smirnovas
Summary: Prion protein aggregation into amyloid fibrils is linked to prion diseases, but the polymorphism of these aggregates complicates the search for anti-amyloid compounds. Research shows that prion protein fibrils can form multiple types under different temperature conditions, depending on the initial state of the protein molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Moritz Lemke, Jens Reiners, Sander H. J. Smits, Nils Lakomek, Georg Groth
Summary: This study successfully reconstitutes recombinant full-length ETR1 protein into lipid nanodiscs, allowing the study of the purified plant receptor for the first time in a detergent-free membrane-like environment.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Kamile Mikalauskaite, Lukas Krasauskas, Vytautas Smirnovas
Summary: Protein aggregation into amyloid fibrils plays a role in neurodegenerative diseases such as Alzheimer's and Parkinson's. Despite significant research, the process remains poorly understood, hindering the development of treatments. Recent reports of cross-interactions between amyloidogenic proteins, including Tau and prion, have further complicated the process. This study observed a conformation-specific association between Tau and prion fibrils, increasing their aggregate formation and amyloid binding capacity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Robertas Ursache, Cristovao De Jesus Vieira Teixeira, Valerie Denervaud Tendon, Kay Gully, Damien De Bellis, Emanuel Schmid-Siegert, Tonni Grube Andersen, Vinay Shekhar, Sandra Calderon, Sylvain Pradervand, Christiane Nawrath, Niko Geldner, Joop E. M. Vermeer
Summary: Suberin, a complex hydrophobic biopolymer, is crucial for plant root adaptative responses. Two sets of auxin-regulated enzymes were identified to mediate suberin biosynthesis and remodelling in differentiated root cells, providing insights into the mechanisms of plant root plasticity.
Article
Multidisciplinary Sciences
Gonzalo J. Beitia, Trevor J. Rutherford, Stefan M. Freund, Hugh R. Pelham, Mariann Bienz, Melissa Gammons
Summary: The study reveals that intermolecular contacts in the DEP dimer of Dishevelled protein play a crucial role in its stability and function in relaying canonical Wnt signals, and these contacts are mediated by a phosphorylation site that can regulate the protein's activity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Linh H. Tran, Anna Urbanowicz, Michal Jasinski, Mariusz Jaskolski, Milosz Ruszkowski
Summary: Cytokinins play a vital role in regulating biological processes in plants, with the main cytokinin receptor CRE1 involving a complex signaling pathway that includes cytokinin binding, autophosphorylation, phosphorelay, and interactions with other proteins such as HPt and RR. The crystal structures of the REC domain of CRE1 reveal insights into its dimerization and potential conformational changes that may be necessary for signal transduction.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Physics, Multidisciplinary
Hyeon-Jong Park, Hye-Won Ko, Gyungchoon Go, Jung Hyun Oh, Kyoung-Whan Kim, Kyung-Jin Lee
Summary: In this study, we theoretically demonstrate the spin swapping effect in centrosymmetric ferromagnets, which is mediated by an orbital degree of freedom and does not require inversion asymmetry or impurity spin-orbit scattering. Our research emphasizes the important role of the orbital degree of freedom in describing spin-orbit-coupled transport in centrosymmetric materials.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Christopher W. Akey, Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M. Varberg, Zulin Yu, Fei Fang, Yi Shi, Junjie Wang, Daniel Salzberg, Kangkang Song, Chen Xu, James C. Gumbart, Sergey Suslov, Jay Unruh, Sue L. Jaspersen, Brian T. Chait, Andrej Sali, Javier Fernandez-Martinez, Steven J. Ludtke, Elizabeth Villa, Michael P. Rout
Summary: This study provides a structure of the isolated yeast NPC and reveals how flexible connectors tie together different structural and functional layers. It also suggests an evolutionary and mechanistic link between assembly and transport. Additionally, the study identifies three major NPC variants that may signify functional specializations at the nuclear periphery.
Article
Biochemistry & Molecular Biology
Pramod Aryal, Shankar Raj Devkota, Devadharshini Jeevarajah, Ruby Law, Richard J. Payne, Ram Prasad Bhusal, Martin J. Stone
Summary: Class A tick evasins are natural chemokine-binding proteins that inhibit leukocyte recruitment and inflammation by blocking signaling of CC subfamily chemokines. The N-terminal region of evasins is critical for chemokine recognition, influencing binding affinity and selectivity. Engineering the N termini of evasins can lead to unique chemokine recognition profiles.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Prabir Khatua, Asis K. Jana, Ulrich H. E. Hansmann
Summary: The study shows that the presence of fatty acids, such as lauric acid, stabilizes both ring-like and barrel-shaped oligomer models, with a stronger effect on barrel-shaped models.
Article
Biochemistry & Molecular Biology
Hans Koss, Barry Honig, Lawrence Shapiro, Arthur G. Palmer
Summary: NMR spectroscopy was used to elucidate the roles of Trp2 and Trp4 in Cadherin-11 dimerization, revealing that the dimerization mechanism of type II cadherins involves coupled folding and strand swapping.
Article
Multidisciplinary Sciences
Yang Lu, Ruoyu Wang, Yuzhang Zhu, Zhenyi Wang, Wangxi Fang, Shihong Lin, Jian Jin
Summary: The study shows that the formation of NaCl crystal dendrites in TFC-PA nanofiltration membranes significantly increases water flux without compromising solute rejection, due to the reduced physical binding between the active layer and the support layer caused by the formation of crystal dendrites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Ta-Chou Huang, Wolfgang B. Fischer
Summary: A novel algorithm is proposed for assembling bitopic transmembrane domains of membrane proteins. The algorithm is tested with viral channel forming proteins and shows promising results in generating structures based on a 7-dimensional space. The assembly of TMDs can be achieved through simultaneous or sequential docking, and scoring is obtained using estimated binding energies. The algorithm improves data when using polypeptides with adapted amino acid coordinates.
Article
Biochemistry & Molecular Biology
Melina Daniilidis, Matthias J. Brandl, Franz Hagn
Summary: Membrane mimetics play a crucial role in studying the structure and function of membrane proteins. In this study, the authors compared the biophysical properties of circularized and linear nanodiscs and found that circularized nanodiscs have improved membrane fluidity and size stability, making them advantageous for high-resolution NMR studies at elevated temperatures.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Ewelina Lipiec, Janina Kaderli, Jan Kobierski, Roland Riek, Katarzyna Skirlinska-Nosek, Kamila Sofinska, Marek Szymonski, Renato Zenobi
Summary: Abnormal aggregation of amyloid-beta is a complex and heterogeneous process, and a new approach using TERS has provided detailed molecular structure information of single amyloid-beta aggregates, revealing a beta-sheet rearrangement. This study will contribute to a better understanding of the etiology of Alzheimer's disease.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Witek Kwiatkowski, Radoslaw Bomba, Pavel Afanasyev, Daniel Boehringer, Roland Riek, Jason Greenwald
Summary: Chemical gradients in simple mixtures can lead to the formation of amyloid-like peptide fibrils inside a proto-cellular compartment. The synergy between fatty acids or lipid vesicles as a filter and barrier results in an increase in molecular complexity and spatial order, providing a potential route for the early molecular evolution towards a living cell.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Correction
Chemistry, Physical
Carolin Seuring, Joeri Verasdonck, Philippe Ringler, Riccardo Cadalbert, Henning Stahlberg, Anja Bockmann, Beat H. Meier, Roland Riek
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Anna Olerinyova, Adar Sonn-Segev, Joseph Gault, Cedric Eichmann, Johannes Schimpf, Adrian H. Kopf, Lucas S. P. Rudden, Dzmitry Ashkinadze, Radoslaw Bomba, Lukas Frey, Jason Greenwald, Matteo T. Degiacomi, Ralf Steinhilper, J. Antoinette Killian, Thorsten Friedrich, Roland Riek, Weston B. Struwe, Philipp Kukura
Summary: This study explores the application of mass photometry (MP) to Integral membrane proteins (IMPs) and membrane-mimetic systems at the single-particle level. By applying MP to amphipathic vehicles and lipid nanodiscs, the research characterizes particle size, sample purity, and heterogeneity, enabling high-resolution studies of membrane-protein structure and interactions. Evidence suggests that using native styrenemaleic acid nanodiscs could reveal new insights into the structure of membrane proteins compared to conventional detergent purification methods.
Article
Multidisciplinary Sciences
Pratibha Kumari, Dhiman Ghosh, Agathe Vanas, Yanick Fleischmann, Thomas Wiegand, Gunnar Jeschke, Roland Riek, Cedric Eichmann
Summary: This study investigated the interaction between monomeric alpha-Syn and its fibrillar form using NMR and electron paramagnetic resonance spectroscopy, revealing that intermolecular interactions reduce intramolecular contacts in monomeric alpha-Syn, leading to further unfolding of its intrinsically disordered states and critically contributing to the aggregation kinetics of alpha-Syn during secondary nucleation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Ajay Singh Sawner, Soumik Ray, Preeti Yadav, Semanti Mukherjee, Rajlaxmi Panigrahi, Manisha Poudyal, Komal Patel, Dhiman Ghosh, Eric Kummerant, Ashutosh Kumar, Roland Riek, Samir K. Maji
Summary: Studies have shown that the liquid-liquid phase separation of alpha-synuclein (alpha-Syn) strongly depends on the presence of salts in vitro, promoting hydrophobic interactions by neutralizing charges. The process can either occur spontaneously or be delayed depending on specific conditions.
Article
Chemistry, Multidisciplinary
Saroj K. Rout, David Rhyner, Roland Riek, Jason Greenwald
Summary: This study demonstrates that the products of an amino acid condensation reaction, based on the templating nature of amyloids, can undergo self-replication to enhance yield and stereoselectivity. This finding further supports the potential role of amyloids in prebiotic molecular evolution.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Patrick Vagenknecht, Artur Luzgin, Maiko Ono, Bin Ji, Makoto Higuchi, Daniela Noain, Cinzia A. Maschio, Jens Sobek, Zhenyue Chen, Uwe Konietzko, Juan A. Gerez, Roland Riek, Daniel Razansky, Jan Klohs, Roger M. Nitsch, Xose Luis Dean-Ben, Ruiqing Ni
Summary: This study demonstrated high-resolution imaging of tau protein in the whole brain of mice using non-invasive imaging technique. The results showed that the tau-targeted probe PBB5 specifically bound to tau protein and exhibited similar binding ability in diseased brain tissue.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2022)
Article
Biochemistry & Molecular Biology
M. Ross, A. Obolensky, E. Averbukh, M. Desrosiers, R. Ezra-Elia, H. Honig, E. Yamin, A. Rosov, H. Dvir, E. Gootwine, E. Banin, D. Dalkara, R. Ofri
Summary: Sheep carrying a mutated CNGA3 gene can serve as a natural large animal model of achromatopsia, and subretinal injection of a vector carrying the CNGA3 transgene can result in long-term recovery of cone function and photopic vision. Current research aims to develop more efficacious vectors for safer transgene delivery, while avoiding potential drawbacks of subretinal injections.
Article
Biochemistry & Molecular Biology
Dzmitry Ashkinadze, Piotr Klukowski, Harindranath Kadavath, Roland Riek, Peter Gu
Summary: This article presents an automated and unbiased method called PDBCor for detecting and analyzing correlated motions in experimental protein structures. The correlations extracted with PDBcor can be useful for subsequent experiments and validation.
Article
Biochemistry & Molecular Biology
Dzmitry Ashkinadze, Harindranath Kadavath, Roland Riek, Peter Guntert
Summary: Recent advances in liquid-state NMR allow the determination of multi-state protein conformations, providing insights into protein dynamics. The structural correlation measure, PDBcor, is introduced as a tool for multi-state protein structure analysis, enabling a comprehensive assessment of protein conformation clustering.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Biochemical Research Methods
Rakesh Krishnan, Srivastav Ranganathan, Samir K. Maji, Ranjith Padinhateeri
Summary: Phase separation of biomolecules can be mediated by both specific and non-specific interactions, which play important roles in polymer systems. The interplay between specific and non-specific interaction strengths affects the phase separation of polymers and the formation of mature aggregates. We find that weaker non-specific interactions promote phase separation, while stronger non-specific interactions prevent the transition to a mature state. Additionally, the degree of participation of non-core regions in attractive interactions also significantly influences the self-assembled states of polymers.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Cell Biology
Ambuja Navalkar, Ajoy Paul, Arunima Sakunthala, Satyaprakash Pandey, Amit Kumar Dey, Sandhini Saha, Sarthak Sahoo, Mohit Kumar Jolly, Tushar K. Maiti, Samir K. Maji
Summary: This study reveals that p53 can form amyloids, which disrupt the normal functions of the protein and contribute to cancer development. Targeting key molecules affected by p53 amyloid formation can reverse the oncogenic phenotype and induce apoptosis in cells.
JOURNAL OF CELL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Piotr Klukowski, Roland Riek, Peter Guentert
Summary: Nuclear Magnetic Resonance (NMR) spectroscopy is a widely used technique in structural biology but is limited by the tedious data analysis process. A team of researchers has developed a machine learning-based method called ARTINA, which can automatically analyze protein NMR data, providing signal positions, resonance assignments, and structures using only NMR spectra and protein sequences as input. Tested on a benchmark dataset, ARTINA demonstrated high accuracy in solving protein structures and assigning resonances, making the NMR analysis process more accessible to non-experts.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Pradeep Kadu, Laxmikant Gadhe, Ambuja Navalkar, Komal Patel, Rakesh Kumar, Murali Sastry, Samir K. Maji
Summary: Biomolecules interact with metals, producing nanostructured hybrid materials. However, the relationship between the physical properties of biomolecules and the resulting nanomaterial morphologies is not well understood. Through the study of amyloidogenic proteins/peptides and their pH conditions, we establish principles for the growth of gold nanocrystals and predict their morphology. We also investigate the nucleation and crystal growth mechanism of gold nanostructures and demonstrate the effective isolation of intact nanostructures from amyloid templates using protein digestion.
