Review
Biochemistry & Molecular Biology
Goro Kato
Summary: This review discusses the structural and functional aspects of Src protein and its regulatory mechanism. By reviewing nuclear magnetic resonance analyses and recent studies, the authors explore new characteristics and regulatory roles of Src protein. Finally, the new regulatory roles are integrated with the canonical model to elucidate the functions of full-length Src.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Feng Yuan, Christopher T. Lee, Arjun Sangani, Justin R. Houser, Liping Wang, Eileen M. Lafer, Padmini Rangamani, Jeanne C. Stachowiak
Summary: Membrane curvature is crucial for cellular functions and recent studies have revealed the role of intrinsically disordered proteins in driving membrane bending. Repulsive interactions among disordered domains lead to convex curvature, while attractive interactions result in concave curvature, forming membrane-bound liquid-like condensates. This study investigates the effects of disordered domains containing both repulsive and attractive interactions on curvature. The findings show that the position of the attractive or repulsive domain relative to the membrane determines the curvature, with increasing ionic strength altering the transition from convex to concave. These results provide design rules for membrane bending by disordered proteins.
Article
Cell Biology
Guanlan Fan, Fan Wang, Yurou Chen, Qian Zheng, Jie Xiong, Qiongying Lv, Kejia Wu, Jiaqiang Xiong, Lei Wei, Dongqing Li, Jiachen Zhang, Wei Zhang, Feng Li
Summary: In this study, OTUD1 is identified as an Akt-associated protein and is downregulated upon Akt activation. Ectopic OTUD1 inhibits Akt phosphorylation, and a short peptide (OUN-36) located in the OTUD1 N-terminal intrinsically disordered region strongly binds to the Akt PH domain. OUN-36-based therapy efficiently abrogates Akt feedback reactivation and sensitizes cancer cells to chemotherapy and immunotherapy.
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
Cell Biology
Katarzyna Soltys, Andrzej Ozyhar
Summary: RXR beta is a subtype of human retinoid X receptor (RXR) that is expressed in almost all tissues. It has a unique and longest N-terminal sequence called the AB region, which exhibits ligand-independent activation function. The molecular properties of the AB region of RXR beta (AB_hRXRB) have been characterized through biochemical and biophysical analysis, along with in silico examinations. AB_hRXRB displays characteristics of a coil-like intrinsically disordered region and can undergo liquid-liquid phase separation (LLPS), similar to another subtype of RXR - RXR gamma (AB_hRXRG).
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Biochemistry & Molecular Biology
Tobias Gruber, Marc Lewitzky, Lisa Machner, Ulrich Weininger, Stephan M. Feller, Jochen Balbach
Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure elements and play important roles in cellular processes. This study focuses on the C-terminal region of Gab1, an IDP, and investigates its induced structure and binding properties under both non-crowding and crowding conditions. The results show that under crowding conditions, pre-structured motifs are formed in certain regions of Gab1, which are also the binding regions for the protein SHP2. Phosphorylation has no impact on the dynamics and disordered nature of Gab1. Therefore, biological crowders can enhance the binding capacity of SHP2 to Gab1, even in the absence of phosphorylation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Samuel Naudi-Fabra, Martin Blackledge, Sigrid Milles
Summary: Single molecule fluorescence and nuclear magnetic resonance spectroscopy are powerful techniques for analyzing intrinsically disordered proteins. They provide complementary views to decipher the complex properties and interactions of IDPs, and have made significant contributions to our understanding of their molecular characteristics.
Article
Biochemistry & Molecular Biology
Katarzyna Soltys, Krzysztof Wycisk, Andrzej Ozyhar
Summary: The study focused on the liquid-liquid phase separation properties of the AB region of human RXR gamma receptor, highlighting the importance of hydrophobic interactions in the formation of liquid condensates.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Multidisciplinary
Dan Wang, Shaowen Wu, Dongdong Wang, Xingyu Song, Maohua Yang, Wolun Zhang, Shaohui Huang, Jingwei Weng, Zhijun Liu, Wenning Wang
Summary: This study investigates the interaction mechanism between protein 4.1G-CTD and NuMA using experimental and computational methods. The results demonstrate the importance of the compact disordered state of 4.1G-CTD for its binding to NuMA. This work sheds light on the molecular recognition mechanism of intrinsically disordered proteins/regions (IDPs/IDRs) and expands the conventional structure-function paradigm in protein biochemistry.
Article
Chemistry, Physical
Samuel Wohl, Matthew Jakubowski, Wenwei Zheng
Summary: The study introduced a new model to explain the influence of salt on protein structure, revealing the significant role of salting-out effect in IDP sequences, especially those with moderately charged residues. This model also shows general applicability in conformation studies of other proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Olivia A. Fraser, Sophia M. Dewing, Emery T. Usher, Christy George, Scott A. Showalter
Summary: Intrinsically disordered proteins are frequently regulated through post-translational modification, but the mechanistic understanding of lysine N-epsilon-acetylation is lagging behind proteomic discoveries. Here, we present a non-perturbing NMR method to monitor N-epsilon-lysine acetylation, which allows detection without the need for exogenous tags. This method has broad applications in studying various systems including intrinsically disordered proteins and lysine deacetylase enzyme assays.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Cell Biology
Meghan T. Harris, Michael T. Marr II
Summary: Cells activate stress response pathways to survive adverse conditions by inhibiting global translation and utilizing alternative methods of translation initiation, such as IRES. Cellular IRESs have been identified in many stress response transcripts. eIF5B promotes IRES activity through its N-terminal region via a non-canonical mechanism.
Article
Chemistry, Multidisciplinary
Yang Lu, Bhargy Sharma, Wei Long Soon, Xiangyan Shi, Tianyun Zhao, Yan Ting Lim, Radoslaw M. Sobota, Shawn Hoon, Giovanni Pilloni, Adam Usadi, Konstantin Pervushin, Ali Miserez
Summary: By combining transcriptomic and proteomic studies, this research obtained the complete primary sequences of slime proteins in velvet worms and identified key features for slime self-assembly. The study revealed that slime proteins contain cysteine residues that mediate the formation of multi-protein complexes via disulfide bonding. It also found that low complexity domains in the N-termini have a propensity for liquid-liquid phase separation. Moreover, the rigid and flexible domains of the slime proteins were mapped using solid-state nuclear magnetic resonance.
Article
Biochemistry & Molecular Biology
Carlos Gil-Duran, Romina Sepulveda, Maximiliano Rojas, Victor Castro-Fernandez, Victoria Guixe, Inmaculada Vaca, Gloria Levican, Fernando D. Gonzalez-Nilo, Maria-Cristina Ravanal, Renato Chavez
Summary: This study analyzed the molecular mechanisms of the GH10 endoxylanase XynA. By eliminating a portion of the enzyme, new activities emerged and were found to be related to changes in secondary structure and dynamics. Molecular dynamics simulations revealed a previously unseen hinge-bending motion that further facilitated the emergence of the new activity.
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
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)