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
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.
Article
Multidisciplinary Sciences
Kulkarni Madhurima, Bodhisatwa Nandi, Sneha Munshi, Athi N. Naganathan, Ashok Sekhar
Summary: The structure of a thermally accessible excited state in equilibrium with the native ensemble of a bacterial transcriptional regulator CytR has been determined using multinuclear CEST NMR. Evidence from double resonance CEST experiments suggests that the excited state, which resembles the DNA-bound form of CytR, recognizes DNA through a folding-before-binding conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR operates through a dynamical variant of the lock-and-key mechanism.
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
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
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
Biochemistry & Molecular Biology
Joris Van Lindt, Tamas Lazar, Donya Pakravan, Manon Demulder, Attila Meszaros, Ludo Van den Bosch, Dominique Maes, Peter Tompa
Summary: The LCD of hnRNPA2 interacts with RNA through the F/YGG motif, which can bind both structured and disordered RNAs. The hnRNPA2 LCD can form dense droplets through LLPS. The F/YGG motif is a general nucleic acid-interaction motif.
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)
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)
Review
Biochemistry & Molecular Biology
Katrine Bugge, Lasse Staby, Edoardo Salladini, Rasmus G. Falbe-Hansen, Birthe B. Kragelund, Karen Skriver
Summary: Hub proteins are essential in protein-protein interaction networks, with alpha alpha-hubs being a newly defined group of folded hub domains. They play a crucial role in organizing disordered transcriptional regulators and membrane scaffolds, showcasing multifaceted protein-protein interaction properties facilitated by the alpha alpha-hub fold.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Pablo Herrera-Nieto, Adria Perez, Gianni De Fabritiis
Summary: Intrinsically disordered proteins participate in biological processes by folding upon binding to other proteins. However, the process of coupled folding and binding is still poorly understood. This study used a new approach to reconstruct the binding and folding process between disordered protein c-Myb and CREB-binding protein. The long-term dynamic process revealed that a short stretch of amino acids on c-Myb forms a folded α-helix during binding, and initial native contacts formed by leucine residues, especially Leu298-Leu302, facilitate the binding and folding of the rest of the peptide.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Biochemistry & Molecular Biology
John J. Ferrie, Jonathan P. Karr, Robert Tjian, Xavier Darzacq
Summary: There are differences in structure and function between bacterial and eukaryotic transcription factors, and the intrinsically disordered regions in eukaryotic transcription factors play a crucial role in their interactions with other proteins and chromatin. Understanding the role of disordered regions is essential for a deep understanding of the regulatory mechanisms of eukaryotic transcription factors.
Article
Chemistry, Medicinal
Cecilia Chavez-Garcia, Jerome Henin, Mikko Karttunen
Summary: This research characterizes the structure and dynamics of MeCP2 protein and provides a computational model that is compatible with experimental data. The study reveals two main conformations of MeCP2 and compares the model with experimental observations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Elin Karlsson, Carl Ottoson, Weihua Ye, Eva Andersson, Per Jemth
Summary: Interactions between proteins often rely on a folded domain in one protein binding to a disordered region in the other. Recent studies suggest that nonspecific contacts by flanking regions may enhance the affinity. This study analyzed the interaction between NCOA3 and CBP across different species and found that flanking regions increased affinity 2-9 fold. The conservation of this effect suggests that flanking regions may have a functional role in promoting protein-protein interactions.