scholarly journals Phosphorylation-induced changes in the PDZ domain of Dishevelled 3

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miroslav Jurásek ◽  
Jitender Kumar ◽  
Petra Paclíková ◽  
Alka Kumari ◽  
Konstantinos Tripsianes ◽  
...  
Keyword(s):  
Pdz Domain ◽  
Phosphorylation Sites ◽  
Pdz Domains ◽  
Recognition Motif ◽  
Regulation Mechanisms ◽  
Binding Groove ◽  
Dynamics Simulations ◽  
Induced Changes ◽  
Insight Into

AbstractThe PDZ domain of Dishevelled 3 protein belongs to a highly abundant protein recognition motif which typically binds short C-terminal peptides. The affinity of the PDZ towards the peptides could be fine-tuned by a variety of post-translation modifications including phosphorylation. However, how phosphorylations affect the PDZ structure and its interactions with ligands remains elusive. Combining molecular dynamics simulations, NMR titration, and biological experiments, we explored the role of previously reported phosphorylation sites and their mimetics in the Dishevelled PDZ domain. Our observations suggest three major roles for phosphorylations: (1) acting as an on/off PDZ binding switch, (2) allosterically affecting the binding groove, and (3) influencing the secondary binding site. Our simulations indicated that mimetics had similar but weaker effects, and the effects of distinct sites were non-additive. This study provides insight into the Dishevelled regulation by PDZ phosphorylation. Furthermore, the observed effects could be used to elucidate the regulation mechanisms in other PDZ domains.

scholarly journals Role of the PDZ Domains in Escherichia coli DegP Protein

2007 ◽  
Vol 189 (8) ◽  
pp. 3176-3186 ◽  
Author(s):  
Jack Iwanczyk ◽  
Daniela Damjanovic ◽  
Joel Kooistra ◽  
Vivian Leong ◽  
Ahmad Jomaa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protease Activity ◽  
Pdz Domain ◽  
Structural Features ◽  
Periplasmic Protein ◽  
Pdz Domains ◽  
Protease Domain ◽  
Interaction Domains ◽  
And Function

ABSTRACT PDZ domains are modular protein interaction domains that are present in metazoans and bacteria. These domains possess unique structural features that allow them to interact with the C-terminal residues of their ligands. The Escherichia coli essential periplasmic protein DegP contains two PDZ domains attached to the C-terminal end of the protease domain. In this study we examined the role of each PDZ domain in the protease and chaperone activities of this protein. Specifically, DegP mutants with either one or both PDZ domains deleted were generated and tested to determine their protease and chaperone activities, as well as their abilities to sequester unfolded substrates. We found that the PDZ domains in DegP have different roles; the PDZ1 domain is essential for protease activity and is responsible for recognizing and sequestering unfolded substrates through C-terminal tags, whereas the PDZ2 domain is mostly involved in maintaining the hexameric cage of DegP. Interestingly, neither of the PDZ domains was required for the chaperone activity of DegP. In addition, we found that the loops connecting the protease domain to PDZ1 and connecting PDZ1 to PDZ2 are also essential for the protease activity of the hexameric DegP protein. New insights into the roles of the PDZ domains in the structure and function of DegP are provided. These results imply that DegP recognizes substrate molecules targeted for degradation and substrate molecules targeted for refolding in different manners and suggest that the substrate recognition mechanisms may play a role in the protease-chaperone switch, dictating whether the substrate is degraded or refolded.

scholarly journals Insight into the Role of Water on the Methylation of Hexamethylbenzene in H‐SAPO‐34 from First Principle Molecular Dynamics Simulations

ChemCatChem ◽  
2019 ◽  
Vol 11 (16) ◽  
pp. 3993-4010 ◽  
Author(s):  
Simon Bailleul ◽  
Sven M. J. Rogge ◽  
Louis Vanduyfhuys ◽  
Veronique Van Speybroeck
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
First Principle ◽  
Dynamics Simulations ◽  
Insight Into

scholarly journals Structural basis of internal peptide recognition by PDZ domains using molecular dynamics simulations

2019 ◽  
Author(s):  
Neetu Sain ◽  
Debasisa Mohanty
Keyword(s):  
Pdz Domain ◽  
Md Simulations ◽  
Open Loop ◽  
Structural Basis ◽  
Pdz Domains ◽  
Peptide Recognition ◽  
Interaction Partners ◽  
Internal Peptide ◽  
Dynamics Simulations ◽  
Loop Conformation

AbstractPDZ domains are important peptide recognition modules which usually recognize short C-terminal stretches of their interaction partners, but certain PDZ domains can also recognize internal peptides in the interacting proteins. Due to the scarcity of data on internal peptide recognition and lack of understanding of the mechanistic details of internal peptide recognition, identification of PDZ domains capable of recognizing internal peptides has been a difficult task. Since Par-6 PDZ domain can recognize both C-terminal and internal peptides, we have carried out multiple explicit solvent MD simulations of 1 μs duration on free and peptide bound Par-6 PDZ to decipher mechanistic details of internal peptide recognition. These simulations have been analyzed to identify residues which play a crucial role in internal peptide recognition by PDZ domains. Based on the conservation profile of the identified residues, we have predicted 47 human PDZ domains to be capable of recognizing internal peptides in human. We have also investigated how binding of CDC42 to the CRIB domain adjacent to the Par6 PDZ allosterically modulate the peptide recognition by Par6 PDZ. Our MD simulations on CRIB-Par6_PDZ di-domain in isolation as well as in complex with CDC42, indicate that in absence of CDC42 the adjacent CRIB domain induces open loop conformation of PDZ facilitating internal peptide recognition. On the other hand, upon binding of CDC42 to the CRIB domain, Par6 PDZ adopts closed loop conformation required for recognition of C-terminus peptides. These results provide atomistic details of how binding of interaction partners onto adjacent domains can allosterically regulate substrate binding to PDZ domains. In summary, MD simulations provide novel insights into the modulation of substrate recognition preference of PDZ by specific peptides, adjacent domains and binding of interaction partners at allosteric sites.

scholarly journals Myeloid Fbxw7 Prevents Pulmonary Fibrosis by Suppressing TGF-β Production

2022 ◽  
Vol 12 ◽  
Author(s):  
Jia He ◽  
Yue Du ◽  
Gaopeng Li ◽  
Peng Xiao ◽  
Xingzheng Sun ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Mononuclear Cells ◽  
Transforming Growth Factor ◽  
Treatment Options ◽  
Myeloid Cell ◽  
Transforming Growth Factor Β ◽  
Peripheral Blood Mononuclear ◽  
Regulation Mechanisms ◽  
Insight Into

Idiopathic pulmonary fibrosis (IPF) is a group of chronic interstitial pulmonary diseases characterized by an inexorable decline in lung function with limited treatment options. The abnormal expression of transforming growth factor-β (TGF-β) in profibrotic macrophages is linked to severe pulmonary fibrosis, but the regulation mechanisms of TGF-β expression are incompletely understood. We found that decreased expression of E3 ubiquitin ligase Fbxw7 in peripheral blood mononuclear cells (PBMCs) was significantly related to the severity of pulmonary fibrosis in IPF patients. Fbxw7 is identified to be a crucial suppressing factor for pulmonary fibrosis development and progression in a mouse model induced by intratracheal bleomycin treatment. Myeloid cell-specific Fbxw7 deletion increases pulmonary monocyte-macrophages accumulation in lung tissue, and eventually promotes bleomycin-induced collagen deposition and progressive pulmonary fibrosis. Notably, the expression of TGF-β in profibrotic macrophages was significantly upregulated in myeloid cell-specific Fbxw7 deletion mice after bleomycin treatment. C-Jun has long been regarded as a critical transcription factor of Tgfb1, we clarified that Fbxw7 inhibits the expression of TGF-β in profibrotic macrophages by interacting with c-Jun and mediating its K48-linked ubiquitination and degradation. These findings provide insight into the role of Fbxw7 in the regulation of macrophages during the pathogenesis of pulmonary fibrosis.

Mechanism and role of PDZ domains in signaling complex assembly

2001 ◽  
Vol 114 (18) ◽  
pp. 3219-3231 ◽  
Author(s):  
Baruch Z. Harris ◽  
Wendell A. Lim
Keyword(s):  
Cell Signaling ◽  
Pdz Domain ◽  
Photoreceptor Cells ◽  
Protein Recognition ◽  
Pdz Domains ◽  
Peptide Motifs ◽  
Signaling Complex ◽  
Multicellular Organisms ◽  
Drosophila Photoreceptor

PDZ domains are protein-protein recognition modules that play a central role in organizing diverse cell signaling assemblies. These domains specifically recognize short C-terminal peptide motifs, but can also recognize internal sequences that structurally mimic a terminus. PDZ domains can therefore be used in combination to bind an array of target proteins or to oligomerize into branched networks. Several PDZ-domain-containing proteins play an important role in the transport, localization and assembly of supramolecular signaling complexes. Examples of such PDZ-mediated assemblies exist in Drosophila photoreceptor cells and at mammalian synapses. The predominance of PDZ domains in metazoans indicates that this highly specialized scaffolding module probably evolved in response to the increased signaling needs of multicellular organisms.

Chloride-dependent conformational changes in the GlyT1 glycine transporter

2020 ◽  
Author(s):  
Yuan-Wei Zhang ◽  
Stacy Uchendu ◽  
Vanessa Leone ◽  
Richard T. Bradshaw ◽  
Ntumba Sangwa ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Ion Pair ◽  
Cysteine Residues ◽  
Glycine Transporter ◽  
Open Conformation ◽  
Transporter Family ◽  
Transport Cycle ◽  
Dynamics Simulations ◽  
Insight Into

AbstractThe human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl- exerts its influence is unknown. To examine the role that Cl- plays in the transport cycle, we measured the effect of Cl- on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1000-fold by Cl-. We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl- independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine and Cl- stabilized an inward-open conformation of GlyT1b. We then examined whether Cl- acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homologue indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl-, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide novel and unexpected insight into the role of Cl- in this family of transporters.

scholarly journals Role of intracellular poroelasticity on freezing-induced deformation of cells in engineered tissues

2016 ◽  
Vol 13 (123) ◽  
pp. 20160480
Author(s):  
Soham Ghosh ◽  
Altug Ozcelikkale ◽  
J. Craig Dutton ◽  
Bumsoo Han
Keyword(s):  
Water Transport ◽  
Biomedical Applications ◽  
Biological Tissues ◽  
Cell Dehydration ◽  
Spatio Temporal ◽  
Cellular Water ◽  
Induced Changes ◽  
Cellular Water Transport ◽  
Insight Into

Freezing of biomaterials is important in a wide variety of biomedical applications, including cryopreservation and cryosurgeries. For the success of these applications to various biomaterials, biophysical mechanisms, which determine freezing-induced changes in cells and tissues, need to be well understood. Specifically, the significance of the intracellular mechanics during freezing is not well understood. Thus, we hypothesize that cells interact during freezing with the surroundings such as suspension media and the extracellular matrix (ECM) via two distinct but related mechanisms—water transport and cytoskeletal mechanics. The underlying rationale is that the cytoplasm of the cells has poroelastic nature, which can regulate both cellular water transport and cytoskeletal mechanics. A poroelasticity-based cell dehydration model is developed and confirmed to provide insight into the effects of the hydraulic conductivity and stiffness of the cytoplasm on the dehydration of cells in suspension during freezing. We further investigated the effect of the cytoskeletal structures on the cryoresponse of cells embedded in the ECM by measuring the spatio-temporal intracellular deformation with dermal equivalent as a model tissue. The freezing-induced change in cell, nucleus and cytoplasm volume was quantified, and the possible mechanism of the volumetric change was proposed. The results are discussed considering the hierarchical poroelasticity of biological tissues.

scholarly journals Quantitative Phosphoproteomics Reveals System-Wide Phosphorylation Network Altered by Spry in Mouse Mammary Stromal Fibroblasts

2019 ◽  
Vol 20 (21) ◽  
pp. 5400 ◽  
Author(s):  
Tiezhu Shi ◽  
Linli Yao ◽  
Ying Han ◽  
Piliang Hao ◽  
Pengfei Lu
Keyword(s):  
Cancer Progression ◽  
Receptor Tyrosine Kinase ◽  
Normal Development ◽  
Underlying Mechanism ◽  
Phosphorylation Sites ◽  
Additional Insight ◽  
Stromal Fibroblasts ◽  
Rtk Signaling ◽  
Insight Into

Understanding the fundamental role of the stroma in normal development and cancer progression has been an emerging focus in recent years. The receptor tyrosine kinase (RTK) signaling pathway has been reported playing critical roles in regulating the normal and cancer microenvironment, but the underlying mechanism is still not very clear. By applying the quantitative phosphoproteomic analysis of Sprouty proteins (SPRYs), generic modulators of RTK signaling and deleted mouse mammary fibroblasts, we quantified a total of 11,215 unique phosphorylation sites. By contrast, 554 phosphorylation sites on 425 proteins had SPRY-responsive perturbations. Of these, 554 phosphosites, 362 sites on 277 proteins, were significantly increased, whereas 192 sites on 167 proteins were decreased. Among the regulated proteins, we identified 31 kinases, 7 phosphatases, and one phosphatase inhibitor that were not systematically characterized before. Furthermore, we reconstructed a phosphorylation network centered on RTK signaling regulated by SPRY. Collectively, this study uncovered a system-wide phosphorylation network regulated by SPRY, providing an additional insight into the complicated RTK signaling pathways involved in the mammary gland microenvironment.

scholarly journals The electrostatic allostery could be the trigger for the changes in dynamics for the PDZ domain of PICK1

2020 ◽  
Author(s):  
Amy O. Stevens ◽  
Yi He
Keyword(s):  
Surface Membrane ◽  
Pdz Domain ◽  
Binding Pocket ◽  
Pdz Domains ◽  
Interaction Domain ◽  
Bar Domain ◽  
Protein Protein Interaction ◽  
Loop Region ◽  
Key Factor ◽  
Dynamics Simulations

ABSTRACTThe PDZ domain is a highly abundant protein-protein interaction domain that exists in many signaling proteins, such as PICK1. Despite the highly conserved structure of the PDZ family, the PDZ family has an extremely low sequence identity, making each PDZ domain unique. PICK1 is the only protein in the human genome that is comprised of a PDZ domain and a BAR domain. PICK1 regulates surface membrane proteins and has been identified as an integral player in drug addiction. Like many PDZ-containing proteins, PICK1 is positively regulated by its PDZ domain and has thus drawn attention to be a potential drug target to curb the effects of substance abuse. The goal of this study is to use all-atom molecular dynamics simulations and the electrostatic analysis program, DelPhi, to better understand the unique interactions and dynamic changes in the PICK1 PDZ domain upon complex formation. Our results demonstrated that the PICK1 PDZ domain shares similar canonical PDZ-ligand hydrogen bonding networks and fluctuations of the carboxylate-binding loop to other PDZ domains. Furthermore, our results are unique to the PICK1 PDZ domain as we reveal that the binding of ligand opens up the binding pocket and, at the same time, reduces the fluctuations of both the central part of the binding pocket and the short loop region between the αA-helix and βC-strand. More importantly, the binding of ligand resulted in charge redistribution at the binding pocket region as well as the N- and C-termini of the PDZ domain that are not a part of the binding pocket. These results suggest that the electrostatic allostery resulted from ligand binding could be the key factor leading to the changes in dynamics which may be associated with the activation of PICK1. Based on these results, an effective drug to target PDZ domain must not only stably bind to the PICK1 PDZ domain but also prevent the electrostatic allostery of the PDZ domain.

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