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
Materials Science, Multidisciplinary
Boris Apter, Nadezda Lapshina, Igor Lapsker, Amir Handelman, Antonella Accardo, Carlo Diaferia, Giancarlo Morelli, Gil Rosenman
Summary: This study investigates a fold-sensitive fluorescence phenomenon observed in biological and bioinspired amyloid samples, demonstrating different properties compared to classical fluorescence. This phenomenon exhibits a wideband spectrum with high quantum yield and tunable wavelength, paving the way for advanced fluorescence optical nanomaterials and new methods of bioimaging and diagnostics.
ADVANCED OPTICAL MATERIALS
(2021)
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
Chemistry, Physical
Priscila Baltazar Goncalves, Fernando L. Palhano, Yraima Cordeiro, Ana Carolina Renno Sodero
Summary: The misfolding and aggregation of α-synuclein is a pathological hallmark of Parkinson's disease. Epigallocatechin-3-gallate (EGCG) can prevent the formation of toxic aggregates and remodel existing toxic fibrils into non-toxic aggregates. Through molecular docking and dynamics simulations, the study investigates the interactions of oxidized EGCG and Thioflavin T with mature α-syn fibrils.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Applied
Zejian Xu, Xiaoshuai Wang, Yue Gao, Yan Zhang, Lianzhou Jiang, Xiaonan Sui
Summary: In this study, the influence of protein concentration on the amyloid fibrillation of soy protein was systematically investigated. The results showed that soy protein-derived amyloid fibrils exhibited rich and diverse polymorphism, with at least five distinct types of longrigid fibrils. The behavior of polypeptide hydrolysis and the ratio of parallel to antiparallel beta-sheets were found to be dependent on protein concentration. These findings contribute to a deeper understanding of the formation mechanism of soy protein-derived amyloid fibrils and lay the foundation for their potential use as functional ingredients in the food industry.
FOOD HYDROCOLLOIDS
(2023)
Review
Biochemistry & Molecular Biology
Torsten John, Lisandra L. L. Martin, Bernd Abel
Summary: This review discusses the impact of surface interfaces on the structure and aggregation mechanisms of peptides and proteins, particularly their association with amyloid fibril formation and neurodegenerative diseases. Research findings demonstrate that surface interfaces can both accelerate and inhibit peptide self-assembly, with adsorption typically promoting aggregation. The review introduces experimental and theoretical models for better understanding peptide self-assembly at hard and soft matter interfaces, and proposes relationships between biological interfaces and amyloid fibril formation.
MACROMOLECULAR BIOSCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Romualdo Troisi, Nicole Balasco, Ida Autiero, Luigi Vitagliano, Filomena Sica
Summary: In this paper, the structural aspects of protein-aptamer recognition process were reviewed by surveying the content of the Protein Data Bank. The study identified a significant increase in the number of determined structures of protein-aptamer complexes in the last two years. The complex architectures and the molecular mechanism of the binding process were also analyzed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Daniel Kachkin, Kirill V. Volkov, Julia Sopova, Alexander G. Bobylev, Sergei A. Fedotov, Sergei G. Inge-Vechtomov, Oxana Galzitskaya, Yury O. Chernoff, Aleksandr A. Rubel, Anna Y. Aksenova
Summary: This study assessed the amyloid properties of RAD51 protein in vitro and in a bacterial system. The purified human RAD51 protein formed amyloid-like aggregates with a cross-beta fibrillar structure, and were stained with amyloid-specific dyes. Cytoplasmic aggregates of RAD51 were also observed in cell cultures overexpressing RAD51.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
A. A. Shaldzhyan, Y. A. Zabrodskaya, I. L. Baranovskaya, M. Sergeeva, A. N. Gorshkov, I. I. Savin, S. M. Shishlyannikov, E. S. Ramsay, A. Protasov, A. P. Kukhareva, V. V. Egorov
Summary: The influenza NS1 protein can form amyloid-like fibrils in vitro, with significant structural changes occurring during fibril formation. A protein fragment capable of inducing fibrillogenesis was also discovered, suggesting a potential relationship between influenza A infection and modulation of the immune response.
Review
Biochemistry & Molecular Biology
Marcos Gil-Garcia, Valentin Iglesias, Irantzu Pallares, Salvador Ventura
Summary: Computational tools have been developed to identify prion-like proteins in different species, showing that the prion phenomenon is well conserved. These proteins are not only linked to the formation of protein-nucleic acid coacervates, but also associated with human diseases.
Review
Biochemistry & Molecular Biology
Neva Caliskan, Chris H. Hill
Summary: This review summarizes the research findings on cardiovirus 2A protein, highlighting its importance and mechanisms in translation, and aims to explore other gene expression strategies mediated by RNA viruses.
BIOSCIENCE REPORTS
(2022)
Article
Oncology
Xi Li, Yiming Li, Guodong Liu, Wei Wu
Summary: The AXIN2 polymorphisms rs11079571, rs1133683, and rs35285779 are significantly associated with overall cancer risk. Additionally, combinations of other polymorphisms such as rs7210356 and rs9915936, rs9915936 and rs7224837, rs7224837 and rs7210356, rs35435678 and rs35285779 also show significant correlations with cancer susceptibility in different populations.
Article
Biochemistry & Molecular Biology
Yasushi Kondo, Joseph W. Paul, Sriram Subramaniam, John Kuriyan
Summary: BRAF is a crucial protein kinase that regulates cell fate in animal cells. Recent studies have shown how active and inactive forms of BRAF interact with the protein 14-3-3, revealing new insights into its regulatory mechanisms. Changes in the phosphorylation state of BRAF alter its complex composition, stabilizing the active dimeric form of the kinase.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Anas Khawaja, Miriam Cipullo, Annika Krueger, Joanna Rorbach
Summary: This review summarizes the biogenesis of mitochondrial ribosomal subunits, mtSSU and mtLSU, based on structural findings, and discusses potential crosstalk between mtSSU and mtLSU assembly pathways as well as coordination between mitoribosome biogenesis and other processes involved in mitochondrial gene expression.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Materials Science, Multidisciplinary
Timo Schillmoeller, Regine Herbst-Irmer, Dietmar Stalke
Summary: This study investigates the dependency of the photophysical properties of simple thiophosphoranyl anthracene excimers on their solid-state arrangement, and modulates resulting intermolecular interactions through crystallization. Novel insights into excimer formation factors and the dependence of photophysical properties on intermolecular interactions are obtained. The research will aid in developing and controlling the photophysical properties of solid-state luminescent materials.
ADVANCED OPTICAL MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Darryl Aucoin, Yongjie Xia, Theint Theint, Philippe S. Nadaud, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
JOURNAL OF STRUCTURAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Hai Wang, Zan Gao, Xuanyou Liu, Pranay Agarwal, Shuting Zhao, Daniel W. Conroy, Guang Ji, Jianhua Yu, Christopher P. Jaroniec, Zhenguo Liu, Xiongbin Lu, Xiaodong Li, Xiaoming He
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Physical
Matthew D. Shannon, Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, Christopher P. Jaroniec
Article
Biochemical Research Methods
Dwaipayan Mukhopadhyay, Chitral Gupta, Theint Theint, Christopher P. Jaroniec
JOURNAL OF MAGNETIC RESONANCE
(2018)
Article
Chemistry, Multidisciplinary
Alberto Perez, Kari Gaalswyk, Christopher P. Jaroniec, Justin L. MacCallum
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Biochemical Research Methods
Christopher P. Jaroniec
JOURNAL OF MAGNETIC RESONANCE
(2019)
Article
Biochemical Research Methods
Alia Hassan, Caitlin M. Quinn, Jochem Struppe, Ivan V. Sergeyev, Chunting Zhang, Changmiao Guo, Brent Runge, Theint Theint, Hanh H. Dao, Christopher P. Jaroniec, Melanie Berbon, Alons Lends, Birgit Habenstein, Antoine Loquet, Rainer Kuemmerle, Barbara Perrone, Angela M. Gronenborn, Tatyana Polenova
JOURNAL OF MAGNETIC RESONANCE
(2020)
Article
Chemistry, Multidisciplinary
Sevastyan O. Rabdano, Matthew D. Shannon, Sergei A. Izmailov, Nicole Gonzalez Salguero, Mohamad Zandian, Rudra N. Purusottam, Michael G. Poirier, Nikolai R. Skrynnikov, Christopher P. Jaroniec
Summary: The positively charged N-terminal histone tails interact with nucleosomal DNA, influencing their susceptibility to modifications and recognition by chromatin-binding proteins. The NMR data reveals that H4 tails are dynamically disordered in nucleosomes, showing a reduced conformational flexibility compared to free peptides. The findings suggest a fuzzy interaction between histone H4 tails and nucleosomal DNA, characterized by variable salt bridges and hydrogen bonds.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Mohamad Zandian, Nicole Gonzalez Salguero, Matthew D. Shannon, Rudra N. Purusottam, Theint Theint, Michael G. Poirier, Christopher P. Jaroniec
Summary: In this study, high-resolution NMR measurements were used to investigate the dynamics and interactions of H3 tails in nucleosome arrays with different lengths of linker DNA. The H3 tail dynamics in nucleosome arrays were found to be significantly attenuated compared to nucleosomes with or without linker DNA, but were not modulated by the specific linker DNA length investigated.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Zhe Qi, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
Summary: In this study, the influence of the dynamic domain on the structure of the amyloid core region of huPrP23-144 was systematically evaluated. It was found that deleting a large portion of the N-terminal tail can result in amyloid fibrils with native-like core structure, while deleting additional flexible residues outside the core structure causes perturbation to the fibril structure.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Daniel W. Conroy, Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N. Purusottam, Matthew D. Shannon, Hashim M. Al-Hashimi, Christopher P. Jaroniec
Summary: The majority of base pairs in DNA follow the canonical Watson-Crick geometry, but they can also adopt alternative Hoogsteen conformations which are important for biological function and mechanism. This study demonstrates that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can be used as a spectroscopic tool to observe and distinguish between Watson-Crick and Hoogsteen base pairs in various DNA systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Qiuye Li, Christopher P. Jaroniec, Witold K. Surewicz
Summary: This study presents a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with the Y145Stop mutation associated with familial prion disease. The findings not only explain previous biochemical observations but also provide direct support for the conformational adaptability model of prion propagation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sean T. Smrt, Nicole Gonzalez Salguero, Justin K. Thomas, Mohamad Zandian, Michael G. Poirier, Christopher P. Jaroniec
Summary: Chromatin, a dynamic protein-DNA complex that regulates eukaryotic genome accessibility and essential functions. Solid-state NMR techniques were used to investigate the conformational dynamics of histone H3 tails in nucleosome arrays with different DNA linker lengths. The chemical shifts and line broadening of certain residues at the H3-nucleosomal DNA interface varied in arrays with short DNA linkers compared to arrays with longer linkers, indicating increased nucleosome packing heterogeneity and structural strain.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Wenjun Sun, Olga O. Lebedenko, Nicole Gonzalez Salguero, Matthew D. Shannon, Mohamad Zandian, Michael G. Poirier, Nikolai R. Skrynnikov, Christopher P. Jaroniec
Summary: The nucleosome, the fundamental repeat unit of chromatin, consists of DNA and a histone protein octamer. The histone tails play important roles in chromatin compaction and regulation. This study investigates the conformation and interactions of histone H4 tails in nucleosomes using experimental results and molecular dynamics simulations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biophysics
Hanh H. Dao, May Z. Hlaing, Yixuan Ma, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
Summary: Solid-state NMR was used to establish the chemical shift assignments for amyloid fibrils formed by the A117V and M129V mutants of human PrP23-144, providing insights into the amyloid core regions and secondary protein structures. These mutants are associated with the development of Gerstmann-Straussler-Scheinker disease in the context of full-length PrP in vivo.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)