Understanding the molecular basis of substrate binding specificity of PTB domains

Sain, Neetu; Tiwari, Garima; Mohanty, Debasisa

doi:10.1038/srep31418

Cited by 7 publications

(6 citation statements)

References 35 publications

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“…terminus, in contrast with previous reports [6,46]. Our data conclude that nsSNPs in Core1 did not disrupt Core2 and vice versa, indicating that both binding pockets have independent functional roles in their interactions with NPXY motifs, and dysfunction of either binding pocket is sufficient to initiate pathogenesis of CCMs.…”

Section: Discussioncontrasting

confidence: 99%

“…The two in-frame deletions are the exception to this observance. Both in-frame N-terminal deletions resulted in alteration of Core1 and Core2, strongly suggesting that the β1 strand/α2 helix at the N terminus may be equally essential for maintaining structure stability of the entire PTB domain as the C terminus, in contrast with previous reports [6,46]. Our data conclude that nsSNPs in Core1 did not disrupt Core2 and vice versa, indicating that both binding pockets have independent functional roles in their interactions with NPXY motifs, and dysfunction of either binding pocket is sufficient to initiate pathogenesis of CCMs.…”

Section: Discussioncontrasting

confidence: 85%

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In silico Analysis of Nonsynonymous Genomic Variants within CCM2 Gene Reaffirm the Existence of Dual Cores within Typical PTB Domain

Padarti

Belkin

Abou‐Fadel

et al. 2021

Preprint

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PurposeThe objective of this study is to validate the existence of dual cores within the typical phosphotyrosine binding (PTB) domain and to identify potentially damaging and pathogenic nonsynonymous coding single nuclear polymorphisms (nsSNPs) in the canonical PTB domain of the CCM2 gene that causes cerebral cavernous malformations (CCMs).MethodsThe nsSNPs within the coding sequence for PTB domain of human CCM2 gene, retrieved from exclusive database search, were analyzed for their functional and structural impact using a series of bioinformatic tools. The effects of the mutations on tertiary structure of the PTB domain in human CCM2 protein were predicted to examine the effect of the nsSNPs on tertiary structure on PTB Cores.ResultsOur mutation analysis, through alignment of protein structures between wildtype CCM2 and mutant, indicated that the structural impacts of pathogenic nsSNPs is biophysically limited to only the spatially adjacent substituted amino acid site with minimal structural influence on the adjacent core of the PTB domain, suggesting both cores are independently functional and essential for proper CCM2 function.ConclusionUtilizing a combination of protein conservation and structure-based analysis, we analyzed the structural effects of inherited pathogenic mutations within the CCM2 PTB domain. Our results indicated that the pathogenic amino acid substitutions lead to only subtle changes locally confined to the surrounding tertiary structure of the PTB core within which it resides, while no structural disturbance to the neighboring PTB core was observed, reaffirming the presence of dual functional cores in the PTB domain.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussioncontrasting

confidence: 85%

In silico Analysis of Nonsynonymous Genomic Variants within CCM2 Gene Reaffirm the Existence of Dual Cores within Typical PTB Domain

Padarti

Belkin

Abou‐Fadel

et al. 2021

Preprint

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“…As the first to test this approach on ENM PC predictions, this work establishes a baseline of AUC performance for future predictive models. To provide a comparative metric for a problem of similar complexity, protein-protein binding predictions, Sain et al 35 report an AUROC score of 0.7, which is typically considered strong for problems of this complexity. Related, the Youden index defines the threshold in the ROC curve that gives the best performance (Figure 2b).…”

Section: Model Validationmentioning

confidence: 99%

Machine learning provides predictive analysis into silver nanoparticle protein corona formation from physicochemical properties

Findlay

Freitas

Mobed-Miremadi

et al. 2018

Environ. Sci.: Nano

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Proteins encountered in biological and environmental systems bind to engineered nanomaterials (ENMs) to form a protein corona (PC) that alters the surface chemistry, reactivity, and fate of the ENMs. Complexities such as the diversity of the PC and variation with ENM properties and reaction conditions make the PC population difficult to predict. Here, we support the development of predictive models for PC populations by relating biophysicochemical characteristics of proteins, ENMs, and solution conditions to PC formation using random forest classification. The resulting model offers a predictive analysis into the population of PC proteins in Ag ENM systems of various ENM size and surface coatings. With an area under the receiver operating characteristic curve of 0.83 and F1-score of 0.81, a model with strong performance has been constructed based upon experimental data. The weighted contribution of each variable provides recommendations for mechanistic models based upon protein enrichment classification results. Protein biophysical properties such as pI and weight are weighted heavily. Yet, ENM size, surface charge, and solution ionic strength also proved essential to an accurate model. The model can be readily modified and applied to other ENM PC populations. The model presented here represents the first step toward robust predictions of PC fingerprints.

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“…The loop connecting helices B and C is the longest in our model and contains a region of conformational heterogeneity, as evidenced by high B-factors and the absence of clear electron density. Intriguingly, the B-C loop harbors an NPxY sequence, which is the canonical phosphotyrosine-binding (PTB) domain-interacting motif (86). The presence of this motif on a flexible, solvent-exposed loop in MavE may suggest a role for this protein in recruiting PTB domains, which predominantly exist on adaptor or scaffold proteins (49).…”

Section: Discussionmentioning

confidence: 99%

An Indispensable Role for the MavE Effector of Legionella pneumophila in Lysosomal Evasion

Vaughn

Voth

Price

et al. 2021

mBio

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Diversion of the Legionella pneumophila-containing vacuole (LCV) from the host endosomal-lysosomal degradation pathway is one of the main virulence features essential for manifestation of Legionnaires’ pneumonia. Many of the ∼350 Dot/Icm-injected effectors identified in L. pneumophila have been shown to interfere with various host pathways and processes, but no L. pneumophila effector has ever been identified to be indispensable for lysosomal evasion. While most single effector mutants of L. pneumophila do not exhibit a defective phenotype within macrophages, we show that the MavE effector is essential for intracellular growth of L. pneumophila in human monocyte-derived macrophages (hMDMs) and amoebae and for intrapulmonary proliferation in mice. The mavE null mutant fails to remodel the LCV with endoplasmic reticulum (ER)-derived vesicles and is trafficked to the lysosomes where it is degraded, similar to formalin-killed bacteria. During infection of hMDMs, the MavE effector localizes to the poles of the LCV membrane. The crystal structure of MavE, resolved to 1.8 Å, reveals a C-terminal transmembrane helix, three copies of tyrosine-based sorting motifs, and an NPxY eukaryotic motif, which binds phosphotyrosine-binding domains present on signaling and adaptor eukaryotic proteins. Two point mutations within the NPxY motif result in attenuation of L. pneumophila in both hMDMs and amoeba. The substitution defects of P78 and D64 are associated with failure of vacuoles harboring the mutant to be remodeled by the ER and results in fusion of the vacuole to the lysosomes leading to bacterial degradation. Therefore, the MavE effector of L. pneumophila is indispensable for phagosome biogenesis and lysosomal evasion. IMPORTANCE Intracellular proliferation of Legionella pneumophila within a vacuole in human alveolar macrophages is essential for manifestation of Legionnaires’ pneumonia. Intravacuolar growth of the pathogen is totally dependent on remodeling the L. pneumophila-containing vacuole (LCV) by the ER and on its evasion of the endosomal-lysosomal degradation pathway. The pathogen has evolved to inject ∼350 protein effectors into the host cell where they modulate various host processes, but no L. pneumophila effector has ever been identified to be indispensable for lysosomal evasion. We show that the MavE effector localizes to the poles of the LCV membrane and is essential for lysosomal evasion and intracellular growth of L. pneumophila and for intrapulmonary proliferation in mice. The crystal structure of MavE shows an NPxY eukaryotic motif essential for ER-mediated remodeling and lysosomal evasion by the LCV. Therefore, the MavE effector of L. pneumophila is indispensable for phagosome biogenesis and lysosomal evasion.

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Understanding the molecular basis of substrate binding specificity of PTB domains

Cited by 7 publications

References 35 publications

In silico Analysis of Nonsynonymous Genomic Variants within CCM2 Gene Reaffirm the Existence of Dual Cores within Typical PTB Domain

In silico Analysis of Nonsynonymous Genomic Variants within CCM2 Gene Reaffirm the Existence of Dual Cores within Typical PTB Domain

Machine learning provides predictive analysis into silver nanoparticle protein corona formation from physicochemical properties

An Indispensable Role for the MavE Effector of Legionella pneumophila in Lysosomal Evasion

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