Article
Biochemistry & Molecular Biology
Katarzyna Taylor, Agnieszka Piasecka, Arkadiusz Kajdasz, Aleksandra Brzek, Micaela Polay Espinoza, Cyril F. Bourgeois, Artur Jankowski, Malgorzata Borowiak, Katarzyna D. Raczynska, Lukasz J. Sznajder, Krzysztof Sobczak
Summary: This study aims to elucidate the mechanism of muscleblind-like splicing regulators (MBNLs) in alternative splicing (AS) processes. The findings indicate that DEAD-box (DDX) RNA helicases DDX5 and DDX17 play an important role in MBNL-dependent AS regulation. The helicases modulate MBNL splicing activity through changes in the ratio of MBNL splicing isoforms and accessibility of MBNL-binding sites. These findings contribute to a deeper understanding of the interdependencies between RNA-binding proteins and their implications in developmental homeostasis and pathological states.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Physiology
Joanna Xiuzhu Xu, Nicholas C. Fitzkee
Summary: The spontaneous formation of a protein corona on a nanoparticle surface plays a crucial role in the success or failure of synthetic nanoparticles as drug carriers or imaging agents in vivo. Understanding protein-nanoparticle interactions quantitatively is essential for the development of nanoparticle-based therapeutics. Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for monitoring protein competitive binding in complex serum media, providing insights into binding thermodynamics and kinetics in the nanoparticle corona.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Emma-Lucille Blayney, Milna Chennath, Charles G. Cranfield, Ronald J. Clarke
Summary: The Na+, K+-ATPase is an integral membrane protein that uses ATP hydrolysis to transport Na+ and K+ ions across the plasma membrane. It has essential roles in various physiological processes and is regulated through phosphorylation by protein kinase C (PKC) and Src kinase families. The study used the mirror tree method to analyze the coevolution between these kinases and Na+, K+-ATPase. The results suggested that the theta and eta isoforms of PKC and Src kinase are the most likely to interact with Na+, K+-ATPase. These findings will guide future experimental studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Caterina Nardella, Livia Pagano, Valeria Pennacchietti, Mariana Di Felice, Sara Di Matteo, Awa Diop, Francesca Malagrino, Lucia Marcocci, Paola Pietrangeli, Stefano Gianni, Angelo Toto
Summary: We studied the molecular determinants of ligand recognition in the C-terminal SH2 domain of the SHP2 protein by conducting mutagenesis and binding experiments. The data revealed the involvement of residues distant from the binding pocket in peptide recognition. We also identified a sparse energetic network regulating the interaction with Gab2 through double mutant cycle analysis. Our results highlight non-optimized residues governing the binding with Gab2, which may explain the ability of the SH2 domain to interact with different partners. Additionally, an analysis of kinetic and thermodynamic parameters revealed the role of a specific residue in the early and late events of the binding reaction.
Review
Biochemistry & Molecular Biology
Jayne Aiken, Erika L. F. Holzbaur
Summary: The development and proper function of the brain require the intricate formation of neuronal circuitry through synaptic connections between neurons, which must be maintained over a lifetime. Accurate trafficking of presynaptic and postsynaptic components, as well as readily accessible energy stores from localized mitochondria, are crucial for synapse-specific delivery and plasticity. Recent research has shed light on the importance of local regulation of cytoskeletal dynamics and organelle trafficking in establishing and maintaining neuronal circuitry.
Article
Multidisciplinary Sciences
Takefumi Morizumi, Kyumhyuk Kim, Hai Li, Elena G. Govorunova, Oleg A. Sineshchekov, Yumei Wang, Lei Zheng, Eva Bertalan, Ana-Nicoleta Bondar, Azam Askari, Leonid S. Brown, John L. Spudich, Oliver P. Ernst
Summary: In this study, the atomic structures of potassium channelrhodopsin 1 (HcKCR1) and a highly homologous cation channelrhodopsin (HcCCR) from Hyphochytrium catenoides were determined using cryo-electron microscopy, revealing the structural foundations of their dramatically different cation selectivity. The selectivity between potassium and sodium ions is determined at two distinct sites on the ion conduction pathway, including a patch of critical residues in the intracellular segment and a cluster of aromatic residues in the extracellular segment. This study is important for understanding the structure and cation selectivity of potassium channelrhodopsins.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Dennis Wicke, Janek Meissner, Robert Warneke, Christoph Elfmann, Joerg Stuelke
Summary: Model organisms like Bacillus subtilis have been extensively studied, but a significant number of proteins in these organisms still have unknown functions. The Understudied Proteins Initiative aims to address this issue. Highly expressed proteins that are poorly studied are likely to play important roles in cellular processes and should be a priority for further research.
MOLECULAR MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Emi Hibino, Natsuko Goda, Misaki Hisada, Takeshi Tenno, Hidekazu Hiroaki
Summary: In this study, the researchers investigated the molecular mechanisms of how glycyrrhizin (GL) modifies tight junction (TJ) integrity. They found that GL binds to the first PDZ domain of zonula occludens-1 (ZO-1(PDZ1)) and identified the relevant interactions between GL and ZO-1(PDZ1). The researchers also examined the interaction of ZO-1(PDZ1) with glycyrrhetinic acid and with GA-3-monoglucuronide, and found a lower affinity compared to GL. The study also confirmed that high-dose GL prolonged the TJ-opening process mediated by sodium deoxycholate.
Article
Biochemical Research Methods
Leo A. Baumgart, Ji Eun Lee, Asaf Salamov, David J. Dilworth, Hyunsoo Na, Matthew Mingay, Matthew J. Blow, Yu Zhang, Yuko Yoshinaga, Chris G. Daum, Ronan C. O'Malley
Summary: This study presents a high-throughput method for characterizing TF-target gene interactions across species, revealing themes of ancient conservation and rapid evolution of regulatory modules, as well as identifying new TF DNA binding motifs.
Article
Nanoscience & Nanotechnology
Wenchao Bi, Xiaodi Jiang, Chao Li, Yuan Liu, Guohua Gao, Guangming Wu, Muhammad Atif, Mohamad AlSalhi, Guozhong Cao
Summary: This study focuses on the preparation and investigation of nanomaterials tailored for supercapacitors. It is found that Na+ ions exhibit faster diffusion in the nanomaterials, leading to better charge storage capability and stability.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Review
Biochemistry & Molecular Biology
Janin Riedelsberger, Julia K. Miller, Braulio Valdebenito-Maturana, Miguel A. Pineros, Wendy Gonzalez, Ingo Dreyer
Summary: HKT channels are a plant protein family responsible for sodium and potassium uptake, as well as Na+-K+ homeostasis. They are divided into two classes based on sequence polymorphisms and play diverse roles in salt tolerance and potassium shortage responses in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Meiqi Wang, Yu-Chen Wang, Zhou-Lan Bai, Yang Sui, Detao Yin, Hua Yin
Summary: This study investigated the interaction between silica particles and thyroxine binding protein (TBG), and found that silica particles can affect the structure and function of TBG, leading to disruptions in the transport of thyroid hormones.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Geng Chen, Jun Xu, Asuka Inoue, Maximilian F. Schmidt, Chen Bai, Qiuyuan Lu, Peter Gmeiner, Zheng Liu, Yang Du
Summary: This study reports two structures of the human GPR88-Gi complex, revealing an allosteric ligand involved in the interaction between the receptor and G-protein, and a potential endogenous ligand of GPR88.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Martin Zacharias
Summary: The rational design of protein-protein binding interfaces is crucial in generating protein assemblies with desired functions. The Match_Motif method simplifies the initial effort for designing a putative binding interface between two proteins and proposes improvements based on known protein-protein complex structures.
Article
Chemistry, Analytical
Sadia Fida Ullah, Geisianny Moreira, Shoumen Palit Austin Datta, Eric McLamore, Diana Vanegas
Summary: BLI is a crucial laboratory technique used in studying biomolecular interactions and this paper introduces a framework connecting BLI research outputs with key performance indicators in biosensor design, serving as guidance for the development of point-of-need biosensors.