scholarly journals Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1

2019 ◽  
Author(s):  
Wen Xiong ◽  
Tuo-Xian Tang ◽  
Evan Littleton ◽  
Arba Karcini ◽  
Iulia M. Lazar ◽  
...  
Keyword(s):  
Domain Structure ◽  
Isothermal Calorimetry ◽  
Shigella Flexneri ◽  
Protein Domain ◽  
Bacterial Survival ◽  
Phosphate Binding ◽  
Reducing Conditions ◽  
Relevant Role ◽  
Vhs Domain ◽  
And Function

AbstractTom1 transports endosomal ubiquitinated proteins that are targeted for degradation in the lysosomal pathway. Infection of eukaryotic cells by Shigella flexneri boosts oxygen consumption and promotes the synthesis of phosphatidylinositol-5-phosphate [PtdIns5P], which triggers Tom1 translocation to signaling endosomes. Removing Tom1 from its cargo trafficking function hinders protein degradation in the host and, simultaneously, enables bacterial survival. Tom1 preferentially binds PtdIns5P via its VHS domain, but the effects of a reducing environment as well as PtdIns5P on the domain structure and function are unknown. Thermal denaturation studies demonstrate that, under reducing conditions, the monomeric Tom1 VHS domain switches from a three-state to a two-state transition behavior. PtdIns5P reduced thermostability, interhelical contacts, and conformational compaction of Tom1 VHS, suggesting that the phosphoinositide destabilizes the protein domain. Destabilization of Tom1 VHS structure was also observed with other phospholipids. Isothermal calorimetry data analysis indicates that, unlike ubiquitin, Tom1 VHS endothermically binds to PtdIns5P through two noncooperative binding sites, with its acyl chains playing a relevant role in the interaction. Altogether, these findings provide mechanistic insights about the recognition of PtdIns5P by the VHS domain that may explain how Tom1, when in a different VHS domain conformational state, interacts with downstream effectors under S. flexneri infection.

scholarly journals dom2vec: Capturing domain structure and function using self-supervision on protein domain architectures

2020 ◽  
Author(s):  
Damianos P. Melidis ◽  
Brandon Malone ◽  
Wolfgang Nejdl
Keyword(s):  
Domain Structure ◽  
Language Processing ◽  
Performance Comparison ◽  
Structure And Function ◽  
Protein Domain ◽  
Linguistic Features ◽  
Enzymatic Function ◽  
Protein Prediction ◽  
And Function

Abstract Background: Word embedding approaches have revolutionized natural language processing (NLP) research. These approaches aim to map words to a low-dimensional vector space, in which words with similar linguistic features cluster together. Embedding-based methods have also been developed for proteins, where words are amino acids and sentences are proteins. The learned embeddings have been evaluated qualitatively, via visual inspection of the embedding space and extrinsically, via performance comparison on downstream protein prediction tasks. However, these sequence embeddings have the caveat that biological metadata do not exist for each amino acid, in order to measure the quality of each unique learned embedding vector. Results: Here, we present dom2vec, an approach for learning protein domain embeddings using word2vec on InterPro annotations. In contrast to sequence embeddings, biological metadata do exist for protein domains, related to each domain separately. Therefore, we present four intrinsic evaluation strategies to quantitatively assess the quality of the learned embedding space. To perform a reliable evaluation in terms of biology knowledge, we selected the metadata related to the most distinctive biological characteristics of domains. These are the structure, enzymatic and molecular function of a given domain. Notably, dom2vec obtains adequate level of performance in the intrinsic assessment, therefore we can draw an analogy between the local linguistic features in natural languages and the domain structure and function information in domain architectures. Moreover, we demonstrate the dom2vec applicability on protein prediction tasks, by comparing it with state-of-the-art sequence embeddings in three downstream tasks. We show that dom2vec outperform sequence embeddings for toxin and enzymatic function prediction and is comparable with sequence embeddings in cellular location prediction. Conclusions: We report that the application of word2vec on InterPro annotations produces domain embeddings with two significant advantages over sequence embeddings. First, each unique dom2vec vector can be quantitatively evaluated towards its available structure and function metadata. Second, the produced embeddings can outperform the sequence embeddings for a subset of downstream tasks. Overall, dom2vec embeddings are able to capture the most important biological properties of domains and surpass sequence embeddings for a subset of prediction tasks.

scholarly journals Capturing Protein Domain Structure and Function Using Self-Supervision on Domain Architectures

Algorithms ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 28
Author(s):  
Damianos P. Melidis ◽  
Wolfgang Nejdl
Keyword(s):  
Amino Acid ◽  
Domain Structure ◽  
Biological Properties ◽  
Structure And Function ◽  
Protein Domain ◽  
Biological Information ◽  
Natural Languages ◽  
Enzymatic Function ◽  
Current Sequence ◽  
And Function

Predicting biological properties of unseen proteins is shown to be improved by the use of protein sequence embeddings. However, these sequence embeddings have the caveat that biological metadata do not exist for each amino acid, in order to measure the quality of each unique learned embedding vector separately. Therefore, current sequence embedding cannot be intrinsically evaluated on the degree of their captured biological information in a quantitative manner. We address this drawback by our approach, dom2vec, by learning vector representation for protein domains and not for each amino acid base, as biological metadata do exist for each domain separately. To perform a reliable quantitative intrinsic evaluation in terms of biology knowledge, we selected the metadata related to the most distinctive biological characteristics of a domain, which are its structure, enzymatic, and molecular function. Notably, dom2vec obtains an adequate level of performance in the intrinsic assessment—therefore, we can draw an analogy between the local linguistic features in natural languages and the domain structure and function information in domain architectures. Moreover, we demonstrate the dom2vec applicability on protein prediction tasks, by comparing it with state-of-the-art sequence embeddings in three downstream tasks. We show that dom2vec outperforms sequence embeddings for toxin and enzymatic function prediction and is comparable with sequence embeddings in cellular location prediction.

scholarly journals Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Wen Xiong ◽  
Tuo-Xian Tang ◽  
Evan Littleton ◽  
Arba Karcini ◽  
Iulia M. Lazar ◽  
...  
Keyword(s):  
Domain Structure ◽  
Phosphate Binding ◽  
Vhs Domain

scholarly journals Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence

2020 ◽  
Author(s):  
Ravi Vattepu ◽  
Rachel A. Klausmeyer ◽  
Allan Ayella ◽  
Rahul Yadav ◽  
Joseph T. Dille ◽  
...  
Keyword(s):  
Cell Line ◽  
Domain Structure ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Actin Binding ◽  
Structure Stability ◽  
Hydrophobic Core ◽  
Tyrosine Fluorescence ◽  
And Function ◽  
Ig Domain

ABSTRACTImmunoglobulin (Ig) domains are the most prevalent protein domain structure and share a highly conserved folding pattern; however, this structural family of proteins is also the most diverse in terms of biological roles and tissue expression. Ig domains vary significantly in amino acid sequence but share a highly conserved tryptophan in the hydrophobic core of this beta-stranded protein. Palladin is an actin binding and bundling protein that has five Ig domains and plays an important role in normal cell adhesion and motility. Mutation of the core tryptophan in one Ig domain of palladin has been identified in a pancreatic cancer cell line, suggesting a crucial role for this sole tryptophan in palladin Ig domain structure, stability, and function. We found that actin binding and bundling was not completely abolished with removal of this tryptophan despite a partially unfolded structure and significantly reduced stability of the mutant Ig domain as shown by circular dichroism investigations. In addition, this mutant palladin domain displays a tryptophan-like fluorescence attributed to an anomalous tyrosine emission at 345 nm. Our results indicate that this emission originates from a tyrosinate that may be formed in the excited ground state by proton transfer to a nearby glutamyl residue. Furthermore, this study emphasizes the importance of tryptophan in protein structural stability and illustrates how tyrosinate emission contributions may be overlooked during the interpretation of the fluorescence properties of proteins.SHORT ABSTRACTThis study explores the functional and structural consequences of a point mutation in palladin, an Ig domain protein first identified in a pancreatic tumor cancer cell line. While exploring the consequences of mutating this conserved tryptophan in the hydrophobic core of the most prevalent domain structure found in proteins, an anomalous tyrosine fluorescence phenomenon was exposed.

The Effect of NaCl on Survival of Shigella flexneri in Broth as Affected by Temperature and pH†‡

2002 ◽  
Vol 65 (5) ◽  
pp. 774-779 ◽  
Author(s):  
LAURA L. ZAIKA
Keyword(s):  
Shigella Flexneri ◽  
Foodborne Pathogen ◽  
Brain Heart Infusion ◽  
Major Effect ◽  
Plate Count ◽  
Bacterial Survival ◽  
Two Phase ◽  
Bacterial Populations ◽  
Lag Times ◽  
D Values

Shigella, a major foodborne pathogen, survives well in salt-containing environments. However, systematic data are scarce. We studied the behavior of Shigella flexneri 5348 in brain heart infusion broth (pH 4 to 6) containing 0.5 to 8% NaCl. Stationary-phase cells were inoculated into sterile media at initial concentrations of 6 to 7 log10 CFU/ml and incubated at 12 to 37°C. Bacterial population sizes were determined periodically by plate counts. Survivor curves were derived from plate count data by using a two-phase linear model to determine lag times and slopes of the curves, from which decimal reduction times (D-values) and times to a 4-log10 inactivation (T4D) were calculated. In media of pH 6, the bacteria grew in the presence of ≤6% NaCl at 19 and 37°C and in the presence of ≤7% NaCl at 28°C. In media of pH 5, growth was observed in the presence of ≤2, ≤4, ≤4, and 0.5% NaCl at 37, 28, 19, and 12°C, respectively. Growth did not occur and bacterial populations gradually declined in media of pH 4. While NaCl had a major effect on growth, bacterial survival was affected to a lesser extent. Lag times decreased with increasing NaCl levels; however, the effect on D-values and T4D values was less pronounced. The average T4D values for media of pH 4 containing 0.5 to 6% NaCl were 4, 13, 23, and 61 days at 37, 28, 19, and 12°C, respectively. These results show that S. flexneri is salt tolerant and suggest that salty foods may serve as vehicles for infection with this bacterium.

scholarly journals Structure and function of an ectopic Polycomb chromatin domain

2019 ◽  
Vol 5 (1) ◽  
pp. eaau9739 ◽  
Author(s):  
Sandip De ◽  
Yuzhong Cheng ◽  
Ming-an Sun ◽  
Natalie D. Gehred ◽  
Judith A. Kassis
Keyword(s):  
Domain Structure ◽  
Regulatory Elements ◽  
Structure And Function ◽  
Polycomb Group ◽  
Chromatin Domain ◽  
Repressive Mark ◽  
Group Response ◽  
Dna Elements ◽  
And Function

Polycomb group proteins (PcGs) drive target gene repression and form large chromatin domains. InDrosophila, DNA elements known as Polycomb group response elements (PREs) recruit PcGs to the DNA. We have shown that, within theinvected-engrailed(inv-en) Polycomb domain, strong, constitutive PREs are dispensable for Polycomb domain structure and function. We suggest that the endogenous chromosomal location imparts stability to this Polycomb domain. To test this possibility, a 79-kbentransgene was inserted into other chromosomal locations. This transgene is functional and forms a Polycomb domain. The spreading of the H3K27me3 repressive mark, characteristic of PcG domains, varies depending on the chromatin context of the transgene. Unlike at the endogenous locus, deletion of the strong, constitutive PREs from the transgene leads to both loss- and gain-of function phenotypes, demonstrating the important role of these regulatory elements. Our data show that chromatin context plays an important role in Polycomb domain structure and function.

scholarly journals Inositol Pyrophosphate Pathways and Mechanisms: What Can We Learn from Plants?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2789 ◽  
Author(s):  
Caitlin Cridland ◽  
Glenda Gillaspy
Keyword(s):  
Inositol Phosphate ◽  
Specific Protein ◽  
Protein Domain ◽  
Growth And Survival ◽  
Inositol Pyrophosphate ◽  
Protein Partners ◽  
Inositol Pyrophosphates ◽  
Energy Sensing ◽  
And Function ◽  
Complex Signaling

The ability of an organism to maintain homeostasis in changing conditions is crucial for growth and survival. Eukaryotes have developed complex signaling pathways to adapt to a readily changing environment, including the inositol phosphate (InsP) signaling pathway. In plants and humans the pyrophosphorylated inositol molecules, inositol pyrophosphates (PP-InsPs), have been implicated in phosphate and energy sensing. PP-InsPs are synthesized from the phosphorylation of InsP6, the most abundant InsP. The plant PP-InsP synthesis pathway is similar but distinct from that of the human, which may reflect differences in how molecules such as Ins(1,4,5)P3 and InsP6 function in plants vs. animals. In addition, PP-InsPs can potentially interact with several major signaling proteins in plants, suggesting PP-InsPs play unique signaling roles via binding to protein partners. In this review, we will compare the biosynthesis and role of PP-InsPs in animals and plants, focusing on three central themes: InsP6 synthesis pathways, synthesis and regulation of the PP-InsPs, and function of a specific protein domain called the Syg1, Pho1, Xpr1 (SPX ) domain in binding PP-InsPs and regulating inorganic phosphate (Pi) sensing. This review will provide novel insights into the biosynthetic pathway and bioactivity of these key signaling molecules in plant and human systems.

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