scholarly journals The Conformational Plasticity Vista of PDZ Domains

Life ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 123 ◽  
Author(s):  
Javier Murciano-Calles
Keyword(s):  
Pdz Domain ◽  
Adaptor Proteins ◽  
Pdz Domains ◽  
Post Translational Modifications ◽  
Multiple Partners ◽  
Conformational Plasticity ◽  
Modular Domain ◽  
Intrinsic Plasticity ◽  
Family Based ◽  
Living Organisms

The PDZ domain (PSD95-Discs large-ZO1) is a widespread modular domain present in the living organisms. A prevalent function in the PDZ family is to serve as scaffolding and adaptor proteins connecting multiple partners in signaling pathways. An explanation of the flexible functionality in this domain family, based just on a static perspective of the structure–activity relationship, might fall short. More dynamic and conformational aspects in the protein fold can be the reasons for such functionality. Folding studies indeed showed an ample and malleable folding landscape for PDZ domains where multiple intermediate states were experimentally detected. Allosteric phenomena that resemble energetic coupling between residues have also been found in PDZ domains. Additionally, several PDZ domains are modulated by post-translational modifications, which introduce conformational switches that affect binding. Altogether, the ability to connect diverse partners might arise from the intrinsic plasticity of the PDZ fold.

scholarly journals Interactomic affinity profiling by holdup assay: Acetylation and distal residues impact the PDZome-binding specificity of PTEN phosphatase

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244613
Author(s):  
Pau Jané ◽  
Gergő Gógl ◽  
Camille Kostmann ◽  
Goran Bich ◽  
Virginie Girault ◽  
...  
Keyword(s):  
Consensus Sequence ◽  
Pdz Domain ◽  
Pi3k Pathway ◽  
Binding Motif ◽  
Pdz Domains ◽  
Post Translational Modifications ◽  
Binding Profile ◽  
Protein Motifs ◽  
C Terminus ◽  
The Impact

Protein domains often recognize short linear protein motifs composed of a core conserved consensus sequence surrounded by less critical, modulatory positions. PTEN, a lipid phosphatase involved in phosphatidylinositol 3-kinase (PI3K) pathway, contains such a short motif located at the extreme C-terminus capable to recognize PDZ domains. It has been shown that the acetylation of this motif could modulate the interaction with several PDZ domains. Here we used an accurate experimental approach combining high-throughput holdup chromatographic assay and competitive fluorescence polarization technique to measure quantitative binding affinity profiles of the PDZ domain-binding motif (PBM) of PTEN. We substantially extended the previous knowledge towards the 266 known human PDZ domains, generating the full PDZome-binding profile of the PTEN PBM. We confirmed that inclusion of N-terminal flanking residues, acetylation or mutation of a lysine at a modulatory position significantly altered the PDZome-binding profile. A numerical specificity index is also introduced as an attempt to quantify the specificity of a given PBM over the complete PDZome. Our results highlight the impact of modulatory residues and post-translational modifications on PBM interactomes and their specificity.

scholarly journals Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF

2015 ◽  
Vol 112 (48) ◽  
pp. 14852-14857 ◽  
Author(s):  
Heath G. Pascoe ◽  
Stephen Gutowski ◽  
Hua Chen ◽  
Chad A. Brautigam ◽  
Zhe Chen ◽  
...  
Keyword(s):  
Pdz Domain ◽  
Specific Interaction ◽  
Cell Formation ◽  
General Mechanism ◽  
Nucleotide Exchange ◽  
Pdz Domains ◽  
Vast Number ◽  
C Terminus ◽  
Class B ◽  
Modular Domain

PDZ domains are abundant protein interaction modules and typically recognize a short motif at the C terminus of their ligands, with a few residues in the motif endowing the binding specificity. The sequence-based rules, however, cannot fully account for the specificity between the vast number of PDZ domains and ligands in the cell. Plexins are transmembrane receptors that regulate processes such as axon guidance and angiogenesis. Two related guanine nucleotide exchange factors (GEFs), PDZ–RhoGEF and leukemia-associated RhoGEF (LARG), use their PDZ domains to bind class B plexins and play critical roles in signaling. Here, we present the crystal structure of the full-length cytoplasmic region of PlexinB2 in complex with the PDZ domain of PDZ–RhoGEF. The structure reveals that, in addition to the canonical C-terminal motif/PDZ interaction, the 3D domain of PlexinB2 forms a secondary interface with the PDZ domain. Our biophysical and cell-based assays show that the secondary interface contributes to the specific interaction between plexin and PDZ–RhoGEF and to signaling by plexin in the cell. Formation of secondary interfaces may be a general mechanism for increasing affinity and specificity of modular domain-mediated interactions.

scholarly journals Interactomic affinity profiling by holdup assay: acetylation and distal residues impact the PDZome-binding specificity of PTEN phosphatase

2020 ◽  
Author(s):  
Pau Jané ◽  
Gergő Gógl ◽  
Camille Kostmann ◽  
Goran Bich ◽  
Virginie Girault ◽  
...  
Keyword(s):  
High Throughput ◽  
Experimental Approach ◽  
Consensus Sequence ◽  
Pdz Domain ◽  
Binding Motif ◽  
Pdz Domains ◽  
Post Translational Modifications ◽  
Binding Profile ◽  
Protein Motifs ◽  
The Impact

AbstractProtein domains often recognize short linear protein motifs composed of a core conserved consensus sequence surrounded by less critical, modulatory positions. Here we used an accurate experimental approach combining high-throughput holdup chromatographic assay and fluorescence polarization to measure quantitative binding affinity profiles of the PDZ domain-binding motif (PBM) of PTEN phosphatase towards the 266 known human PDZ domains. Inclusion of N-terminal flanking residues, acetylation or mutation of a lysine at a modulatory position significantly altered the PDZome-binding profile of the PTEN PBM. A specificity index is also introduced to quantify the specificity of a given PBM over the complete PDZome. Our results highlight the impact of modulatory residues and post-translational modifications on PBM interactomes and their specificity.

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 Redox-Mediated Post-Translational Modifications of Proteolytic Enzymes and Their Role in Protease Functioning

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 650
Author(s):  
Anastasiia I. Petushkova ◽  
Andrey A. Zamyatnin
Keyword(s):  
Redox Regulation ◽  
Proteolytic Enzymes ◽  
Post Translational Modifications ◽  
Regulated Cell Death ◽  
Age Related ◽  
Living Organisms ◽  
Dose Dependent ◽  
Hydrolysis Of ◽  
Flexible Dose ◽  
Dependent Mechanism

Proteolytic enzymes play a crucial role in metabolic processes, providing the cell with amino acids through the hydrolysis of multiple endogenous and exogenous proteins. In addition to this function, proteases are involved in numerous protein cascades to maintain cellular and extracellular homeostasis. The redox regulation of proteolysis provides a flexible dose-dependent mechanism for proteolytic activity control. The excessive reactive oxygen species (ROS) and reactive nitrogen species (RNS) in living organisms indicate pathological conditions, so redox-sensitive proteases can swiftly induce pro-survival responses or regulated cell death (RCD). At the same time, severe protein oxidation can lead to the dysregulation of proteolysis, which induces either protein aggregation or superfluous protein hydrolysis. Therefore, oxidative stress contributes to the onset of age-related dysfunction. In the present review, we consider the post-translational modifications (PTMs) of proteolytic enzymes and their impact on homeostasis.

Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95

2019 ◽  
Vol 75 (4) ◽  
pp. 381-391 ◽  
Author(s):  
Ana Camara-Artigas ◽  
Javier Murciano-Calles ◽  
Jose C. Martínez
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Pdz Domain ◽  
Postsynaptic Density ◽  
Crystal Form ◽  
Space Groups ◽  
The Third ◽  
Conformational Plasticity ◽  
Α Helix ◽  
Postsynaptic Density Protein

PDZ domains are protein–protein recognition modules that interact with other proteins through short sequences at the carboxyl terminus. These domains are structurally characterized by a conserved fold composed of six β-strands and two α-helices. The third PDZ domain of the neuronal postsynaptic density protein 95 has an additional α-helix (α3), the role of which is not well known. In previous structures, a succinimide was identified in the β2–β3 loop instead of Asp332. The presence of this modified residue results in conformational changes in α3. In this work, crystallographic structures of the following have been solved: a truncated form of the third PDZ domain of the neuronal postsynaptic density protein 95 from which α3 has been removed, D332P and D332G variants of the protein, and a new crystal form of this domain showing the binding of Asp332 to the carboxylate-binding site of a symmetry-related molecule. Crystals of the wild type and variants were obtained in different space groups, which reflects the conformational plasticity of the domain. Indeed, the overall analysis of these structures suggests that the conformation of the β2–β3 loop is correlated with the fold acquired by α3. The alternate conformation of the β2–β3 loop affects the electrostatics of the carboxylate-binding site and might modulate the binding of different PDZ-binding motifs.

scholarly journals Correlation Analysis for Protein Evolutionary Family Based on Amino Acid Position Mutations and Application in PDZ Domain

PLoS ONE ◽  
2010 ◽  
Vol 5 (10) ◽  
pp. e13207 ◽  
Author(s):  
Qi-Shi Du ◽  
Cheng-Hua Wang ◽  
Si-Ming Liao ◽  
Ri-Bo Huang
Keyword(s):  
Amino Acid ◽  
Correlation Analysis ◽  
Pdz Domain ◽  
Amino Acid Position ◽  
Family Based

Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97This paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Caroline A. Ewens ◽  
Patrik Kloppsteck ◽  
Andreas Förster ◽  
Xiaodong Zhang ◽  
Paul S. Freemont
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Adaptor Proteins ◽  
Post Translational Modifications ◽  
Aaa Atpase ◽  
Cellular Processes ◽  
Transcription Factor Activation ◽  
Functional Implications ◽  
Aaa Protein ◽  
Selection Of

p97, also known as VCP (valosin-containing protein), is a hexameric AAA+ ATPase that participates in a variety of cellular processes. It is believed that p97 mediates these processes through the binding of various adaptor proteins. Many factors govern adaptor binding and the regulatory mechanisms are not yet well understood. Sites of phosphorylation and acetylation on p97 have been identified and such post-translational modifications may be involved in regulating p97 function. Phosphorylation and, to a lesser extent, acetylation of p97 have been shown to modify its properties — for example, by modulating adaptor binding and directing subcellular localization. These modifications have been implicated in a number of p97-mediated processes, including misfolded protein degradation, membrane fusion, and transcription factor activation. This review describes the known phosphorylation and acetylation sites on p97 and discusses their possible structural and functional implications.

Several adaptor proteins promote intracellular localisation of the transporter MRP4/ABCC4 in platelets and haematopoietic cells

2017 ◽  
Vol 117 (01) ◽  
pp. 105-115 ◽  
Author(s):  
Yvonne Schaletzki ◽  
Marie-Luise Kromrey ◽  
Susanne Bröderdorf ◽  
Elke Hammer ◽  
Markus Grube ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Protein Interactions ◽  
Pdz Domain ◽  
Adaptor Protein ◽  
Adaptor Proteins ◽  
Apical Plasma Membrane ◽  
Dense Granules ◽  
Haematopoietic Cells ◽  
And Function

SummaryThe multidrug resistance protein 4 (MRP4/ABCC4) has been identified as an important transporter for signalling molecules including cyclic nucleotides and several lipid mediators in platelets and may thus represent a novel target to interfere with platelet function. Besides its localisation in the plasma membrane, MRP4 has been also detected in the membrane of dense granules in resting platelets. In polarised cells it is localised at the basolateral or apical plasma membrane. To date, the mechanism of MRP4 trafficking has not been elucidated; protein interactions may regulate both the localisation and function of this transporter. We approached this issue by searching for interacting proteins by in vitro binding assays, followed by immunoblotting and mass spectrometry, and by visualising their co-localisation in platelets and haematopoietic cells. We identified the PDZ domain containing scaffold proteins ezrin-binding protein 50 (EBP50/NHERF1), postsynaptic density protein 95 (PSD95), and sorting nexin 27 (SNX27), but also the adaptor protein complex 3 subunit β3A (AP3B1) and the heat shock protein HSP90 as putative interaction partners of MRP4. The knockdown of SNX27, PSD95, and AP3B1 by siRNA in megakaryoblastic leuk aemia cells led to a redistribution of MRP4 from intracellular structures to the plasma membrane. Inhibition of HSP90 led to a diminished expression and retention of MRP4 in the endoplasmic reticulum. These results indicate that MRP4 localisation and function are regulated by multiple protein interactions. Changes in the adaptor proteins can hence lead to altered localisation and function of the transporter.Supplementary Material to this article is available at www.thrombosis-online.com.

scholarly journals Structures of a Human Papillomavirus (HPV) E6 Polypeptide Bound to MAGUK Proteins: Mechanisms of Targeting Tumor Suppressors by a High-Risk HPV Oncoprotein

2007 ◽  
Vol 81 (7) ◽  
pp. 3618-3626 ◽  
Author(s):  
Yi Zhang ◽  
Jhimli Dasgupta ◽  
Runlin Z. Ma ◽  
Lawrence Banks ◽  
Miranda Thomas ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
High Risk ◽  
Crystal Structures ◽  
Tumor Suppressors ◽  
Specific Binding ◽  
Pdz Domain ◽  
Pdz Domains ◽  
Hpv E6 ◽  
C Terminus ◽  
High Risk Hpv

ABSTRACT Human papillomavirus (HPV) E6 oncoprotein targets certain tumor suppressors such as MAGI-1 and SAP97/hDlg for degradation. A short peptide at the C terminus of E6 interacts specifically with the PDZ domains of these tumor suppressors, which is a property unique to high-risk HPVs that are associated with cervical cancer. The detailed recognition mechanisms between HPV E6 and PDZ proteins are unclear. To understand the specific binding of cellular PDZ substrates by HPV E6, we have solved the crystal structures of the complexes containing a peptide from HPV18 E6 bound to three PDZ domains from MAGI-1 and SAP97/Dlg. The complex crystal structures reveal novel features of PDZ peptide recognition that explain why high-risk HPV E6 can specifically target these cellular tumor suppressors for destruction. Moreover, a new peptide-binding loop on these PDZs is identified as interacting with the E6 peptide. Furthermore, we have identified an arginine residue, unique to high-risk HPV E6 but outside the canonical core PDZ recognition motif, that plays an important role in the binding of the PDZs of both MAGI-I and SAP97/Dlg, the mutation of which abolishes E6's ability to degrade the two proteins. Finally, we have identified a dimer form of MAGI-1 PDZ domain 1 in the cocrystal structure with E6 peptide, which may have functional relevance for MAGI-1 activity. In addition to its novel insights into the biochemistry of PDZ interactions, this study is important for understanding HPV-induced oncogenesis; this could provide a basis for developing antiviral and anticancer compounds.

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