Article
Biochemistry & Molecular Biology
Hui Xiao, Lan Duo, James Zhen, Hongsu Wang, Zhefeng Guo
Summary: This study used site-directed spin labeling and EPR spectroscopy to investigate the structure and dynamics of Aβ40 fibrils. The results suggest that the strength of spin exchange interaction in Aβ40 fibrils is primarily determined by static disorder. The entire Aβ40 sequence, except residue D1, is highly ordered, with the hydrophobic regions showing the lowest static disorder. Dynamic disorder is relatively constant across all residues, with residues 22 and 23 having the highest dynamic disorder. Aβ40 fibrils exhibit overall more ordered packing interactions compared to Aβ42 fibrils, and the C-terminal residue is ordered in Aβ40 fibrils but has high static disorder in Aβ42 fibrils. The higher static disorder in Aβ42 fibrils may contribute to increased aggregation through secondary nucleation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Andrius Sakalauskas, Tomas Sneideris, Vytautas Smirnovas
Summary: Protein aggregation into amyloid fibrils is associated with various disorders, but the mechanisms behind the conversion of non-harmful proteins into such aggregates are not fully understood. Recent studies suggest that multiple types of protein aggregates may co-exist in tissues of patients with amyloid-related disorders, potentially influencing each other.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Mantas Ziaunys, Kamile Mikalauskaite, Andrius Sakalauskas, Vytautas Smirnovas
Summary: The aggregation of amyloidogenic proteins is related to various diseases, with limited treatment options currently available. The challenge in the discovery of potential anti-amyloid molecules lies in identifying the actual inhibitors from complex mixtures. This study successfully scavenged potential aggregation-inhibiting molecules from different compounds and effectively separated them from the aggregates.
BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Anna Sulatskaya, Anastasiia O. Kosolapova, Alexander G. Bobylev, Mikhail Belousov, Kirill S. Antonets, Maksim Sulatsky, Irina M. Kuznetsova, Konstantin K. Turoverov, Olesya Stepanenko, Anton A. Nizhnikov
Summary: Both amyloids and beta-barrel proteins have beta-sheet-rich structures, with the latter being able to form functional amyloids in vivo. These beta-barrel amyloid proteins can interact with each other and form toxic oligomers, potentially contributing to the development of amyloidoses. Rapidly growing discoveries suggest that the number and diversity of functions of amyloid-forming beta-barrel proteins are significantly greater than currently understood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Alexander G. Bobylev, Roman S. Fadeev, Liya G. Bobyleva, Margarita I. Kobyakova, Yuri M. Shlyapnikov, Daniil V. Popov, Ivan M. Vikhlyantsev
Summary: The study found that amyloid aggregates of smooth-muscle titin can impair cell adhesion and lead to cell death. The surface roughness may be a key factor contributing to the highly antiadhesive properties. The negative impact of amyloid aggregates on cell adhesion is likely intrinsic to other amyloid proteins with similar structure and properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Evelyn Rose Kamski-Hennekam, Jinfeng Huang, Rashik Ahmed, Giuseppe Melacini
Summary: The ability of ATP to modulate protein solubility is critical in understanding proteinopathies like Parkinson's disease. ATP levels decline with age, which is the most significant risk factor for Parkinson's. This study shows that ATP affects multiple stages of alpha-synuclein aggregation, and the disruption of ATP's function may play a role in Parkinson's etiology.
Review
Neurosciences
Hai-Shan Jiao, Peng Yuan, Jin-Tai Yu
Summary: Mutations in the TMEM106B gene are risk factors for various neurodegenerative diseases. Previous understanding of the underlying mechanism focused on the impairment of lysosome biogenesis caused by TMEM106B loss-of-function. However, mutations in TMEM106B increase its expression level, thus the molecular process linking these mutations to the apparent disruption in TMEM106B function remains mysterious.
MOLECULAR NEURODEGENERATION
(2023)
Article
Clinical Neurology
Dexter N. Dean, Jennifer C. Lee
Summary: Parkinson's disease and melanoma have a complex relationship, with evidence showing mutual susceptibility between patients despite their different pathologies. The protein α-syn plays a crucial role in both diseases, interacting with melanin synthesis and Pmel17. Further investigations are needed to fully understand these connections and potential treatment implications.
MOVEMENT DISORDERS
(2021)
Article
Engineering, Biomedical
Yabin Zhou, Jin Hua, Dan Ding, Youhong Tang
Summary: Research has identified approximately 50 proteins that can form amyloid fibrils and cause neurodegenerative diseases, but the mechanism of amyloid fibril formation remains unclear. Molecular fluorescence probes such as AIE play an important role in amyloid studies, with the advantage of overcoming the drawbacks of traditional fluorescence probes.
Article
Chemistry, Multidisciplinary
Ranit Pariary, Sandip Dolui, Gourav Shome, Sk Abdul Mohid, Achintya Saha, Bhisma N. Ratha, Amaravadhi Harikishore, Kuladip Jana, Atin K. Mandal, Anirban Bhunia, Nakul C. Maiti
Summary: Our studies demonstrate that Coomassie Brilliant Blue G-250 shows promise as a chemical chaperone for stabilising the alpha-helical native human insulin conformers, preventing their aggregation and increasing insulin secretion. This multipolar effect, along with its non-toxic nature, could be valuable for the development of highly bioactive, targeted, and biostable therapeutic insulin.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Zeyaul Islam, Mohamed H. Ali, Anton Popelka, Raghvendra Mall, Ehsan Ullah, Janarthanan Ponraj, Prasanna R. Kolatkar
Summary: Amyloid fibrillation, related to various neurological disorders, was studied by examining lysozyme fibrillation using nano-infrared spectroscopy (nanoIR). The study showed that lysozyme transformed into mainly parallel beta-sheets in its fibrillar structure, and nanoIR can complement other biophysical studies in analyzing the aggregation process for potential therapeutic design against amyloid disorders.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Ivan Sanchis, Roque Spinelli, Alvaro Siano
Summary: Alzheimer's disease is characterized by the presence of toxic beta-amyloid peptide aggregates. Recent discovery shows that Aβ(1-42) fibrils have catalytic activity on acetylcholine hydrolysis. This study examines the catalytic activity of Aβ(1-40) fibrils and finds that they display moderate enzymatic activity, suggesting a potential role of natural peptide aggregates as biocatalysts in neurological disorders.
Article
Chemistry, Multidisciplinary
Han-Wen Chang, Ho- Ma, Yi-Shan Wu, Ming-Che Lee, Eric Chung-Yueh Yuan, Shing-Jong Huang, Yu-Sheng Cheng, Meng-Hsin Wu, Ling-Hsien Tu, Jerry Chun Chung Chan
Summary: This study successfully prepared high molecular-weight oligomeric aggregates of A beta with uniform size and monomorphic structure by incubating A beta peptides in reverse micelles. The A beta Os-40 adopted the structural motif of beta-loop-beta and the A beta Os-42 accelerated the fibrillization of A beta(40) monomers. Cross-seeding experiments showed that A beta Os-42 had an impact on the chemical states of certain residues in A beta Os-40.
Article
Biochemistry & Molecular Biology
Elisabete Ferreira, Zaida L. Almeida, Pedro F. Cruz, Marta Sousa, Paula Verissimo, Rui M. M. Brito
Summary: Several degenerative amyloid diseases have no effective treatment and are associated with the formation of protein aggregates and insoluble amyloid fibrils. Developing a reliable and economic screening protocol to identify potential fibril disruptors is important for finding new therapeutic strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
D. Santorelli, S. Rocchio, F. Fata, I Silvestri, F. Angelucci, F. Imperi, D. Marasco, C. Diaferia, L. Gigli, N. Demitri, L. Federici, A. Di Matteo, C. Travaglini-Allocatelli
Summary: The study found that ribosome-binding factor A folds via a 3-state mechanism in vitro and can form fibrils with a cross-beta structure. Additionally, the research suggests that the folding intermediate of PaRbfA may expose amyloidogenic regions, potentially acting as aggregation nuclei in fibril formation.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Chemistry, Multidisciplinary
Olav Schiemann, Caspar A. Heubach, Dinar Abdullin, Katrin Ackermann, Mykhailo Azarkh, Elena G. Bagryanskaya, Malte Drescher, Burkhard Endeward, Jack H. Freed, Laura Galazzo, Daniella Goldfarb, Tobias Hett, Laura Esteban Hofer, Luis Fabregas Ibanez, Eric J. Hustedt, Svetlana Kucher, Ilya Kuprov, Janet Eleanor Lovett, Andreas Meyer, Sharon Ruthstein, Sunil Saxena, Stefan Stoll, Christiane R. Timmel, Marilena Di Valentin, Hassane S. Mchaourab, Thomas F. Prisner, Bela Ernest Bode, Enrica Bordignon, Marina Bennati, Gunnar Jeschke
Summary: Distance distribution information obtained by pulsed dipolar EPR spectroscopy plays a crucial role in structural biology research, providing unique constraints for integrative structural modeling. Quality standards for sample preparation, measurements, data conversion, interpretation, and reporting have been defined to ensure the reliability of structural models and biological conclusions, with support from a multi-laboratory benchmark study and analysis of data sets with known distance distribution ground truth. The guidelines mainly focus on proteins labeled with nitroxides and double electron-electron resonance measurements, while also offering suggestions for similar cases.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Joshua Casto, Alysia Mandato, Lukas Hofmann, Idan Yakobov, Shreya Ghosh, Sharon Ruthstein, Sunil Saxena
Summary: Understanding the structural and mechanistic details of protein-DNA interactions can lead to new ways of combating the virulence of pathogenic bacteria. The study on the Copper Efflux Regulator (CueR) protein reveals that it can bend DNA at high protein concentrations, and this bending enables the coordination with RNA polymerase.
Article
Multidisciplinary Sciences
Vasyl Bondarenko, Marta M. Wells, Qiang Chen, Tommy S. Tillman, Kevin Singewald, Matthew J. Lawless, Joel Caporoso, Nicole Brandon, Jonathan A. Coleman, Sunil Saxena, Erik Lindahl, Yan Xu, Pei Tang
Summary: In this study, using a combination of experiments and computational methods, the full-length intracellular domain (ICD) structure of the human alpha 7 nicotinic acetylcholine receptor in a resting state was determined. It was found that a significant portion of the ICD residues are located in highly flexible regions, with a large loop (loop L) contributing to its stability by anchoring onto the MA helix. Known motifs for cytoplasmic binding, regulation, and signaling were observed in both helices and disordered flexible regions, highlighting the important role of ICD conformational plasticity in orchestrating various biological processes.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Idan Yakobov, Alysia Mandato, Lukas Hofmann, Kevin Singewald, Yulia Shenberger, Lada Gevorkyan-Airapetov, Sunil Saxena, Sharon Ruthstein
Summary: In this study, the dynamical changes of Escherichia coli CueR as a function of copper and DNA binding are measured using EPR spectroscopy. The results show that copper controls the activation of the transcription processes by initiating a series of dynamical changes over the protein.
Article
Biochemistry & Molecular Biology
Kevin Singewald, James A. Wilkinson, Zikri Hasanbasri, Sunil Saxena
Summary: The dynamics of site-specific proteins play a crucial role in protein function. This study utilized EPR spectroscopy to measure the dynamics of specific sites on a protein surface, and validated the results using molecular dynamics simulations. Additionally, small variations were observed at different sites, potentially due to local geometry and electrostatics. This work expands the utility of Cu(II)NTA-based EPR measurements.
Article
Chemistry, Multidisciplinary
Manasseh Kusi Osei, Saber Mirzaei, Xiaowei Bogetti, Edison Castro, Mohammad Azizur Rahman, Sunil Saxena, Raul Hernandez Sanchez
Summary: Template-assisted synthesis of [M-4] clusters was achieved using a tetraamine scaffold L-R(NH2)(4) to direct the formation of C-4-symmetric L-R(NH)(4)Cu-4 clusters. The study showed the importance of metal-metal direct interactions in cluster formation. Computational and experimental analysis indicated the presence of a delocalized electronic structure in the clusters.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biophysics
L. Hofmann, A. Mandato, S. Saxena, S. Ruthstein
Summary: Electron paramagnetic resonance (EPR) spectroscopy is a promising structural biology tool to unravel complex and dynamic biological mechanisms. In this article, the advantages of continuous wave (CW) and pulsed EPR distance measurements in resolving transcription processes and protein-DNA interaction are discussed.
BIOPHYSICAL REVIEWS
(2022)
Article
Biochemical Research Methods
Joshua Casto, Xiaowei Bogetti, Hannah R. Hunter, Zikri Hasanbasri, Sunil Saxena
Summary: The narrow excitation bandwidth of monochromic pulses limits the sensitivity of pulsed dipolar spectroscopy on Cu(II)-based measurements. To overcome this limitation, frequency-swept pulses with large excitation bandwidths have been used. In this study, we demonstrate the effectiveness of chirp pulses on commercial instrumentation for Cu(II) distance measurements, and discuss the sensitivity considerations for robust distance measurements using Cu(II) labels in proteins. We show that a sweeping bandwidth chirp pulse can significantly improve the sensitivity of long-range distance measurements, while the sensitivity of short-range distances only slightly increases due to specific considerations for the chirp pulse duration.
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Chemistry, Physical
Alysia Mandato, Zikri Hasanbasri, Sunil Saxena
Summary: There have been significant improvements in pulsed ESR sensitivity, making it more applicable for the measurement of biological distance constraints at physiological concentrations and in complex systems. This work demonstrates the power of double quantum coherence (DQC) experiments at Q-band frequencies, enabling rapid and reliable measurements of spin distances at nanomolar concentrations. These nanomolar concentration measurements can lead to further advancements in the use of ESR, especially in cellular contexts.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Xiaowei Bogetti, Anthony Bogetti, Joshua Casto, Gordon Rule, Lillian Chong, Sunil Saxena
Summary: The catalytic activity of hGSTA1-1 depends on the conformational dynamics of its C-terminal helix a9. The structure of the ligand-free state of the hGSTA1-1 homodimer was determined using EPR distance measurements and WE simulations. Negative cooperativity between the monomers of hGSTA1-1 was observed in the simulations, which suggests its importance in interacting with various toxic substrates.
Review
Chemistry, Multidisciplinary
Xiaowei Bogetti, Sunil Saxena
Summary: This Review discusses computational modeling techniques that enhance the interpretation of Electron Paramagnetic Resonance (EPR) measurements of biomolecules. Molecular dynamics simulations and enhanced sampling strategies are utilized to predict EPR spectra and sample stable conformations of biomolecules and their spin labels. The integration of de novo predictions, EPR measurements, and MD simulations is proposed for efficient sampling of alternate protein conformations. The importance of coupling EPR with modeling tools to investigate protein dynamics and structure is highlighted.
Article
Chemistry, Physical
Zikri Hasanbasri, Nicholas A. Moriglioni, Sunil Saxena
Summary: Combining rigid Cu(ii) labels and pulsed-EPR techniques allows for precise investigation of protein structure and dynamics through distance constraint measurements. The unknown relative orientation of spins in a bilabeled protein poses a challenge due to the orientational selectivity effect. This study dissects the orientational selectivity phenomenon using in silico samples to optimize acquisition schemes and demonstrates the efficiency of rectangular pulses in double electron-electron resonance experiments.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Chemistry, Analytical
Kevin Singewald, Hannah Hunter, Timothy F. Cunningham, Sharon Ruthstein, Sunil Saxena
Summary: This review focuses on the use of Electron Paramagnetic Resonance (EPR) to measure residue-specific dynamics in proteins, with a specific emphasis on Cu(II)-based spin labels. It discusses the limitations of nitroxide-based spin labels and showcases the use of new Cu(II)-based protein labels, which improve rigidity and expand the spin-labeling toolkit. The review also describes how EPR measurements of the Cu(II) label reflect protein backbone motion and fluctuations, and provides insights into the measurement of site-specific dynamics at both alpha-helices and beta-sheets using the dHis motif. The review concludes by outlining the limitations of the dHis method and suggesting future developments.
ANALYSIS & SENSING
(2023)
Article
Chemistry, Physical
Xiaowei Bogetti, Zikri Hasanbasri, Hannah R. Hunter, Sunil Saxena
Summary: Recent advances in site-directed Cu2+ labeling of proteins and nucleic acids have provided a new methodology for measuring the structure-function relationship in biomolecules. However, accessing the higher sensitivity of Q-band DEER has been challenging for Cu2+ labels designed for proteins. In this study, the orientational effects of the label are analyzed through simulations, and it is shown that three strategically selected magnetic field DEER measurements are generally sufficient for obtaining an orientational-averaged DEER time trace at Q-band.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biology
Kevin Singewald, James A. Wilkinson, Sunil Saxena
Summary: Site-directed spin labeling with EPR allows for measuring residue-specific dynamics and distance distributions in biomolecules. Labeling proteins with a Cu(II)-NTA complex utilizing strategically placed histidine residues (dHis motif) overcomes limitations of typical spin labels. This approach provides unique structural constraints for integrative structural biophysics, complementing traditional techniques like NMR and crystallography.