4.6 Article

Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor

Ying Wang et al.

Summary: This study investigates the activation mechanism of a class B GPCR, human glucagon receptor-GCGR, using molecular dynamics simulations and Markov state models. The study reveals the conformational dynamics and activation process of GCGR and highlights the role of Gs in stabilizing the glucagon binding site and achieving full activation of the receptor.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)

Article Cell Biology

Neurophysiological functions and pharmacological tools of acidic and non-acidic Ca2+ stores

Lora L. Martucci et al.

Summary: Ca2+ signaling plays a crucial role in various cell functions in the brain. Acidic Ca2+ stores in different regions of neurons provide local sources of Ca2+ to regulate synaptic transmission and other functions. This review discusses the recruitment mechanism of acidic Ca2+ stores and focuses on the role of endolysosomal two-pore channels (TPCs) and their physiological agonist, as well as their interaction with other receptors. Additionally, this review introduces new pharmacological tools and animal mutant models for studying acidic Ca2+ stores in brain function and dysfunction.

CELL CALCIUM (2022)

Review Pharmacology & Pharmacy

Computational elucidation of allosteric communication in proteins for allosteric drug design

Duan Ni et al.

Summary: This review comprehensively reviews bioinformatic methods for elucidating allosteric communication and discusses their successful applications in allosteric drug design. Current challenges and future perspectives are also discussed.

DRUG DISCOVERY TODAY (2022)

Review Cell Biology

Calcium Channels in the Heart: Disease States and Drugs

Kajol Shah et al.

Summary: Calcium ions are crucial for cell signaling and participate in various physiological functions. Mutations and dysfunctions of calcium channels in the heart can cause diseases and disorders. Drugs targeting calcium channels are used for the treatment of cardiac disorders.
Article Biochemistry & Molecular Biology

Understanding the P-Loop Conformation in the Determination of Inhibitor Selectivity Toward the Hepatocellular Carcinoma-Associated Dark Kinase STK17B

Chang Liu et al.

Summary: This study revealed the conformational dynamics of the phosphate-binding loop (P-loop) in different states of STK17B through molecular dynamics simulation. The interactions between the P-loop and inhibitors were found to contribute to inhibitor selectivity profile. These findings advance our understanding of kinase inhibitor selectivity and have implications for the design of selective inhibitors for other protein kinases.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Article Biochemistry & Molecular Biology

Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading

Minyu Li et al.

Summary: Allosteric regulation plays a crucial role in protein function, but understanding long-range allosteric regulation remains challenging. This study investigates the allosteric regulation of KRAS by SPRED1, providing mechanistic insights and shedding light on long-range allosteric regulation in complex macromolecular systems.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Mechanistic Insights into the Mechanism of Inhibitor Selectivity toward the Dark Kinase STK17B against Its High Homology STK17A

Chang Liu et al.

Summary: This study investigates the molecular mechanism of the binding selectivity of PKIS43 towards STK17B. The findings suggest that the difference in protein-ligand electrostatic interactions and the energy contribution from Arg41 in the phosphate-binding loop of STK17B are crucial for the binding specificity of PKIS43.

MOLECULES (2022)

Review Microbiology

Calcium Ions Signaling: Targets for Attack and Utilization by Viruses

Yang Qu et al.

Summary: This review discusses cellular calcium signaling and channels, the interaction of calcium-associated proteins with viruses, and the role of calcium in cell death and antiviral response during viral infection.

FRONTIERS IN MICROBIOLOGY (2022)

Article Oncology

Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C

Haiming Zhuang et al.

Summary: The Y96D mutation in KRAS(G12C) causes resistance to the drug AMG510 by impairing the direct interaction between the drug and residue 96, resulting in the opening and loosening of the drug binding pocket.

FRONTIERS IN ONCOLOGY (2022)

Article Biochemistry & Molecular Biology

The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor

Yuxin Shi et al.

Summary: In this study, molecular dynamics simulations were used to investigate the differences in efficacy induced by GR agonists. The study revealed distinct discrepancies in the conformation of the cofactor TIF2 and identified a pair of essential residues involved in ligand-induced conformational changes. The community network analysis identified essential communities and communication pathways correlated with ligand efficacy. These findings provide insights into the allosteric communication between the ligand-binding and cofactor-binding pockets.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Review Biochemistry & Molecular Biology

Essential metals in health and disease

Klaudia Jomova et al.

Summary: Twenty essential elements, half of which are metals and half are non-metals, are required for proper functioning of the human body. Metallo-regulatory mechanisms in cells help maintain homeostasis of metal-ions crucial for various cellular processes, especially in the central nervous system. Imbalances in essential metals can lead to diseases such as neurological disorders, mental health problems, cardiovascular diseases, cancer, and diabetes. A multidisciplinary approach involving bioinorganic chemists, biophysicists, and biologists is needed to further understand the role of metal ions in biological systems.

CHEMICO-BIOLOGICAL INTERACTIONS (2022)

Review Biochemistry & Molecular Biology

Molecular Mechanisms Underlying Ca2+/Calmodulin-Dependent Protein Kinase Kinase Signal Transduction

Hiroshi Tokumitsu et al.

Summary: CaMKK acts as the activating kinase for multiple downstream kinases, playing important roles in various Ca2+-dependent pathways as well as pathophysiological pathways. Its molecular mechanism and pharmacological inhibitors are areas of focus in research.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Review Neurosciences

CaMKII: a central molecular organizer of synaptic plasticity, learning and memory

Ryohei Yasuda et al.

Summary: This Review provides an overview of the synaptic regulation and function of Calcium-calmodulin-dependent protein kinase II (CaMKII), which plays a central role in synaptic plasticity, learning, and memory. Activation of CaMKII by increased calcium ion levels leads to phosphorylation of synaptic proteins, regulating their structure and function. These processes are crucial for synaptic plasticity and learning and memory.

NATURE REVIEWS NEUROSCIENCE (2022)

Article Biochemistry & Molecular Biology

Computational Dissection of the Role of Trp305 in the Regulation of the Death-Associated Protein Kinase-Calmodulin Interaction

Yu-Ping Zhu et al.

Summary: This study investigates the conformational and binding changes of the DAPK1-CaM complex in different mutation states through molecular dynamics simulations, revealing the crucial role of the Trp305 mutation in regulating DAPK1 activity mediated by CaM.

BIOMOLECULES (2022)

Article Biochemistry & Molecular Biology

Elucidation of the conformational dynamics and assembly of Argonaute-RNA complexes by distinct yet coordinated actions of the supplementary microRNA

Haiming Zhuang et al.

Summary: This study reveals that additional supplementary pairing can enhance the interaction between miRNA and target RNA, and influence the conformational dynamics and assembly of AGO protein. These findings provide guidance for the design of miRNA mimics and anti-miRNAs, and open up new possibilities for engineering AGO proteins in the field of gene regulation.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)

Review Biochemistry & Molecular Biology

Structural Aspects and Prediction of Calmodulin-Binding Proteins

Corey Andrews et al.

Summary: Calmodulin is a crucial intracellular protein that binds Ca2+ and acts as a second messenger in various biological activities through interactions with proteins and peptides. Its ability to bind targets with different structures is due to the flexible central helix separating the N- and C-terminal lobes.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Multidisciplinary Sciences

Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design

Shaoyong Lu et al.

Summary: G protein-coupled receptors (GPCRs) are a critical target for drug development, and the comprehensive characterization of the angiotensin II (AngII) type 1 receptor (AT1R) provides insights into designing allosteric GPCR modulators.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6

Xinyi Li et al.

Summary: CRISPR-Cas systems in prokaryotes serve as adaptive immunity against invading phages and plasmids. Phages have developed diverse protein inhibitors, called anti-CRISPR (Acr) proteins, to counteract this system, leading bacteria to co-evolve Cas variants as anti-anti-CRISPR systems. At the atomic level, interactions between Streptococcus thermophilus Cas9 (St1Cas9) and the anti-CRISPR protein AcrIIA6 alter the conformational dynamics and catalytic activity of St1Cas9, highlighting a potential for designing allosteric Acr peptidomimetics.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins

Yuanhao Wang et al.

Summary: The dual phosphorylation of K-Ras induces structural changes affecting nucleotide and catalytic sites, reducing the catalytic competence and signal delivery abilities of GAP, SOS, and Raf. Phosphorylation also disrupts the Ras/Raf interface allosteric pathway, altering the distribution of Ras-GTP sub-states and identifying potential druggable pockets. These findings highlight the impact of phosphorylation on Ras function and signal transduction, suggesting it as a target for cancer drug discovery.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

The mechanism of activation of monomeric B-Raf V600E

Ryan C. Maloney et al.

Summary: Oncogenic mutations in B-Raf, especially the V600E mutation, are common in cancer and are a major drug target. This study found that the V600E mutation destabilizes the inactive state while stabilizing the active state, providing insights for the development of new Raf inhibitors.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations

Xiaoli An et al.

Summary: This study elucidates the mechanism of conformational coupling between different sites of the protein, highlighting the crucial role of flexibility in certain regions for agonist binding and action. The results provide important structural information for the design of novel GPR40 agonists.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Chemistry, Multidisciplinary

Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy

Duan Ni et al.

Summary: Allostery is a direct and efficient method for fine-tuning protein functions, gaining recognition in drug discovery. Identifying allosteric sites is a challenge for drug design, with recent studies revealing bidirectional allosteric coupling and reversed communication between orthosteric and allosteric sites. A new framework combining computational and experimental strategies has been proposed for predicting allosteric sites, demonstrating desirable performance in identifying potential cryptic sites for allosteric drug design.

CHEMICAL SCIENCE (2021)

Article Biochemistry & Molecular Biology

Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B

Xinyi Li et al.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2020)

Article Chemistry, Medicinal

Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a

Aakash Saha et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Biochemistry & Molecular Biology

Conformational ensembles of non-peptide ω-conotoxin mimetics and Ca+2 ion binding to human voltage-gated N-type calcium channel Cav2.2

Sameera et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Biochemistry & Molecular Biology

The quaternary assembly of KRas4B with Raf-1 at the membrane

Hyunbum Jang et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Review Chemistry, Medicinal

Death-associated protein kinase (DAPK) family modulators: Current and future therapeutic outcomes

Ahmed Karam Farag et al.

MEDICINAL RESEARCH REVIEWS (2019)

Review Oncology

Calmodulin and PI3K Signaling in KRAS Cancers

Ruth Nussinov et al.

TRENDS IN CANCER (2017)

Review Biochemistry & Molecular Biology

Why Calcium? How Calcium Became the Best Communicator

Ernesto Carafoli et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2016)

Article Chemistry, Multidisciplinary

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

Giulia Palermo et al.

ACS CENTRAL SCIENCE (2016)

Article Biochemistry & Molecular Biology

Molecular mechanisms of protein kinase regulation by calcium/calmodulin

Bertrand Simon et al.

BIOORGANIC & MEDICINAL CHEMISTRY (2015)

Article Biochemistry & Molecular Biology

How calcium inhibits the magnesium-dependent kinase GSK3β: A molecular simulation study

Shao-Yong Lu et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)

Article Chemistry, Multidisciplinary

An overview of the Amber biomolecular simulation package

Romelia Salomon-Ferrer et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)

Article Multidisciplinary Sciences

Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy

Larry R. Masterson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biophysics

Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

Michal Rostkowski et al.

BMC STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy

Morgan Lawrenz et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Molecular Basis of the Death-Associated Protein Kinase-Calcium/Calmodulin Regulator Complex

Inaki de Diego et al.

SCIENCE SIGNALING (2010)

Article Multidisciplinary Sciences

Dynamical networks in tRNA: protein complexes

Anurag Sethi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Statistical analysis of structural characteristics of protein Ca2+-binding sites

Michael Kirberger et al.

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2008)

Review Chemistry, Physical

Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms

Jianyin Shao et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Review Chemistry, Multidisciplinary

Structure and regulation of calcium/calmodulin-dependent protein kinases

TR Soderling et al.

CHEMICAL REVIEWS (2001)