Review
Biochemistry & Molecular Biology
Sylvie Ricard-Blum, John R. Couchman
Summary: Syndecans are transmembrane heparan sulfate proteoglycans that play potential roles in development and disease, including vascular diseases, inflammation, and various cancers. The recent structural data provides insights into their complex functions, including both intrinsic signaling and cooperative mechanisms with other receptors. The interaction with glycanation and partner proteins impacts the conformation and function of syndecan. Genetic models suggest that syndecans act as mechanosensors and influence actin cytoskeleton organization. The clustering of syndecan with other cell surface receptors has implications in tissue differentiation and disease. The understanding of structure/function relationships in mammalian syndecans is important due to their diagnostic and therapeutic potential in cancer.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Nanoscience & Nanotechnology
Noriyuki Kodera, Daisuke Noshiro, Sujit K. Dora, Tetsuya Mori, Johnny Habchi, David Blocquel, Antoine Gruet, Marion Dosnon, Edoardo Salladini, Christophe Bignon, Yuko Fujioka, Takashi Oda, Nobuo N. Noda, Mamoru Sato, Marina Lotti, Mineyuki Mizuguchi, Sonia Longhi, Toshio Ando
Summary: High-speed atomic force microscopy imaging can provide a semiquantitative, realistic description of the dynamic structure of intrinsically disordered proteins, which dynamically sample a multitude of conformational states, making their structural analysis difficult.
NATURE NANOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Ushasi Pramanik, Atanu Nandy, Laxmikanta Khamari, Saptarshi Mukherjee
Summary: Intrinsically disordered proteins (IDPs) possess unique dynamic characteristics that are difficult to study using traditional methods. Single-molecule measurements provide a better understanding of the conformational transitions of IDPs. These approaches are important for revealing the structural transitions of IDPs and future research directions.
Review
Chemistry, Multidisciplinary
Enrico Falcone, Christelle Hureau
Summary: This study reports on a concept that explains the formation of reactive oxygen species by copper ions bound to the amyloid-β peptide involved in Alzheimer's disease. The concept is based on a refined and extended in-between state mechanism that was first described a decade ago for pure electron transfer.
CHEMICAL SOCIETY REVIEWS
(2023)
Review
Chemistry, Multidisciplinary
Enrico Falcone, Christelle Hureau
Summary: This article reports on the refinement and extension of a decade-old concept for pure electron transfer to explain the formation of reactive oxygen species by copper ions bound to the Aβ peptide in Alzheimer's disease. The coordination of copper in intrinsically disordered peptides is versatile, and instead of direct electron transfer, an in-between state (IBS) mechanism is proposed. The IBS in copper-bound intrinsically disordered proteins (IDPs) is accessible due to the flexibility of IDPs and fast exchange between coordination sites, and it accounts for the formation of reactive oxygen species (ROS).
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Multidisciplinary Sciences
Jingyao Li, Bojing Jiang, Xinyuan Chang, Han Yu, Yichao Han, Fuzhong Zhang
Summary: The authors have developed a method to enhance the strength of low molecular-weight protein materials by fusing intrinsically-disordered mussel foot protein fragments. This approach can be applied to a wide range of protein-based materials and has the potential to achieve high yields.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Summary: This review discusses different aspects of disordered proteins and protein regions, as well as the experimental and computational methods used to characterize them. Additionally, the role of disordered proteins in diseases and their potential as drug targets are explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Qilin Xie, Kota Kasahara, Junichi Higo, Takuya Takahashi
Summary: This study investigated the effects of phosphorylation on the function of PC4 using enhanced molecular dynamics simulation. The results showed that phosphorylation significantly weakened the interaction between PC4 and VP16ad, leading to the formation of a compact structure in the IDR. This study is important for computational elucidation of the functional modulation of PC4.
Article
Biochemistry & Molecular Biology
Christopher M. Furman, Ting-Yi Wang, Qiuye Zhao, Kumar Yugandhar, Haiyuan Yu, Eric Alani
Summary: This study demonstrated that dynamic and coordinated rearrangements of the MLH IDRs regulate the function of the MLH complex positively and negatively in MMR.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Emilie Aponte, Marie Lafitte, Audrey Sirvent, Valerie Simon, Maud Barbery, Elise Fourgous, Mariano Maffei, Florence Armand, Romain Hamelin, Julie Pannequin, Philippe Fort, Miquel Pons, Serge Roche, Yvan Boublik
Summary: This study reveals the important role of the unique domain ULBR in Src tyrosine kinase in malignant cell transformation. The ULBR is involved in membrane anchoring, MAPK signaling, and phosphorylation of specific membrane-localized tyrosine kinases needed for Src oncogenic signaling.
Article
Multidisciplinary Sciences
Thinh D. N. Luong, Suhani Nagpal, Mourad Sadqi, Victor Munoz
Summary: This article introduces a method called "Molecular LEGO" that allows for the dissection of conformational landscapes of unbound intrinsically disordered proteins (IDPs) and provides insights into the functional mechanisms of these proteins. The method was applied to the protein NCBD and revealed specific energetic biases and conformational rheostatic behavior in NCBD's folding landscape, which are likely crucial for its function as a transcriptional coactivator.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Guy Jacoby, Merav Segal Asher, Tamara Ehm, Inbal Abutbul Ionita, Hila Shinar, Salome Azoulay-Ginsburg, Ido Zemach, Gil Koren, Dganit Danino, Michael M. Kozlov, Roey J. Amir, Roy Beck
Summary: This study introduces a new type of peptide amphiphiles, intrinsically disordered peptide amphiphiles (IDPA), that exhibit a sharp pH-induced micellar phase-transition. The shape transition can serve as a mechanism for the design of cargo hold-and-release applications, demonstrating the potential of tailoring interactions between disordered peptides for various stimuli-responsive biomedical applications.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Akihito Nishiyama, Masahiro Shimizu, Tomoyuki Narita, Noriyuki Kodera, Yuriko Ozeki, Akira Yokoyama, Kouta Mayanagi, Takehiro Yamaguchi, Mariko Hakamata, Amina Kaboso Shaban, Yoshitaka Tateishi, Kosuke Ito, Sohkichi Matsumoto
Summary: The DNA-binding protein 1 (MDP1) of mycobacteria induces dormancy phenotypes by compacting DNA through reversible cross-linking of adjacent DNA strands using the intrinsically disordered region (IDR). This IDR-mediated DNA compaction model helps in understanding the molecular mechanism of MDP1 suppression of genomic function in non-replicating dormant mycobacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Damiano Piovesan, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, Andras Hatos, Ivan Micetic, Federica Quaglia, Lisanna Paladin, Pathmanaban Ramasamy, Zsuzsanna Dosztanyi, Wim F. Vranken, Norman E. Davey, Gustavo Parisi, Monika Fuxreiter, Silvio C. E. Tosatto
Summary: The latest version of MobiDB database provides more flexibility and visualization tools, allowing users to search and download large datasets more quickly.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Kiersten M. Ruff, Rohit Pappu
Summary: Accurate predictions of protein structures using AlphaFold have made significant progress. Most protein sequences in the human proteome have been structurally annotated, with over 30% of regions being disordered.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)