scholarly journals ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9066 ◽  
Author(s):  
Binghui Liu ◽  
Ling Leng ◽  
Xuer Sun ◽  
Yunfang Wang ◽  
Jie Ma ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Large Scale ◽  
Protein Identification ◽  
Protein Domain ◽  
Matrix Proteins ◽  
Reference Database ◽  
Hybrid Features ◽  
Ecm Proteins ◽  
Machine Learning Model ◽  
Multicellular Organisms

Extracellular matrix (ECM) proteins play an essential role in various biological processes in multicellular organisms, and their abnormal regulation can lead to many diseases. For large-scale ECM protein identification, especially through proteomic-based techniques, a theoretical reference database of ECM proteins is required. In this study, based on the experimentally verified ECM datasets and by the integration of protein domain features and a machine learning model, we developed ECMPride, a flexible and scalable tool for predicting ECM proteins. ECMPride achieved excellent performance in predicting ECM proteins, with appropriate balanced accuracy and sensitivity, and the performance of ECMPride was shown to be superior to the previously developed tool. A new theoretical dataset of human ECM components was also established by applying ECMPride to all human entries in the SwissProt database, containing a significant number of putative ECM proteins as well as the abundant biological annotations. This dataset might serve as a valuable reference resource for ECM protein identification.

scholarly journals Regulation of cellular functions by extracellular matrix.

1992 ◽  
Vol 2 (10) ◽  
pp. S83 ◽  
Author(s):  
A Teti
Keyword(s):  
Extracellular Matrix ◽  
Growth Factor Receptor ◽  
Matrix Proteins ◽  
Intercellular Spaces ◽  
Cellular Functions ◽  
Proliferation And Differentiation ◽  
Alpha Beta ◽  
Covalently Linked ◽  
Multicellular Organisms ◽  
Specific Ligand

Multicellular organisms are formed by specialized cells assembled in tissues. Individual cells contact and interact with other cells and with the extracellular matrix--a network of secreted proteins and carbohydrates that fills the intercellular spaces. The extracellular matrix helps cells to bind together and regulates a number of cellular functions, such as adhesion, migration, proliferation, and differentiation. It is formed by macromolecules, locally secreted by resident cells. The two main classes of macromolecules are polysaccharide glycosaminoglycans, usually covalently linked to proteins in the form of proteoglycans, and fibrous proteins of two functional types, structural (collagen, elastin) and adhesive (fibronectin, laminin, vitronectin, etc.). Receptors for extracellular matrix macromolecules are present in virtually all of the cells studied. They belong to the superfamily of integrins, alpha beta heterodimers, which, in most cases, recognize the Arg-Gly-Asp sequence of extracellular matrix proteins. On the exterior side of the cell, integrins link an extracellular matrix macromolecule, whereas in the cytosol, they bind the cytoskeleton, thereby forming a membrane bridge between extracellular and intracellular fibers. This structure enables the cell to adhere to the substratum. Similar to hormone- or growth factor-receptor binding, the interaction of the integrin with its specific ligand induces immediate signal transduction and influences cellular activities.

scholarly journals The Role of Structural Extracellular Matrix Proteins in Urothelial Bladder Cancer (Review)

2007 ◽  
Vol 2 ◽  
pp. BMI.S294 ◽  
Author(s):  
Andrea Brunner ◽  
Alexandar Tzankov
Keyword(s):  
Extracellular Matrix ◽  
Cancer Cells ◽  
Cell Invasion ◽  
Matrix Proteins ◽  
Urothelial Bladder Cancer ◽  
Ecm Proteins ◽  
Cancer Review ◽  
Urothelial Bladder ◽  
Carcinoma Of The Bladder

The extracellular matrix (ECM) plays a key role in the modulation of cancer cell invasion. In urothelial carcinoma of the bladder (UC) the role of ECM proteins has been widely studied. The mechanisms, which are involved in the development of invasion, progression and generalization, are complex, depending on the interaction of ECM proteins with each other as well as with cancer cells. The following review will focus on the pathogenetic role and prognostic value of structural proteins, such as laminins, collagens, fibronectin (FN), tenascin (Tn-C) and thrombospondin 1 (TSP1) in UC. In addition the role of integrins mediating the interaction of ECM molecules and cancer cells will be addressed, since integrin-mediated FN, Tn-C and TSP1 interactions seem to play an important role during tumor cell invasion and angiogenesis.

scholarly journals Long Polar Fimbriae of Enterohemorrhagic Escherichia coli O157:H7 Bind to Extracellular Matrix Proteins

2011 ◽  
Vol 79 (9) ◽  
pp. 3744-3750 ◽  
Author(s):  
Mauricio J. Farfan ◽  
Lidia Cantero ◽  
Roberto Vidal ◽  
Douglas J. Botkin ◽  
Alfredo G. Torres
Keyword(s):  
Escherichia Coli ◽  
Extracellular Matrix ◽  
Enterohemorrhagic Escherichia Coli ◽  
Matrix Proteins ◽  
Intestinal Cells ◽  
T84 Cells ◽  
Content Type ◽  
Fimbrial Subunit ◽  
Ecm Proteins

ABSTRACTAdherence to intestinal cells is a key process in infection caused by enterohemorrhagicEscherichia coli(EHEC). Several adhesion factors that mediate the binding of EHEC to intestinal cells have been described, but the receptors involved in their recognition are not fully characterized. Extracellular matrix (ECM) proteins might act as receptors involved in the recognition of enteric pathogens, including EHEC. In this study, we sought to characterize the binding of EHEC O157:H7 to ECM proteins commonly present in the intestine. We found that EHEC prototype strains as well as other clinical isolates adhered more abundantly to surfaces coated with fibronectin, laminin, and collagen IV. Further characterization of this phenotype, by using antiserum raised against the LpfA1 putative major fimbrial subunit and by addition of mannose, showed that a reduced binding of EHEC to ECM proteins was observed in a long polar fimbria (lpf) mutant. We also found that the two regulators, H-NS and Ler, had an effect in EHEC Lpf-mediated binding to ECM, supporting the roles of these tightly regulated fimbriae as adherence factors. Purified Lpf major subunit bound to all of the ECM proteins tested. Finally, increased bacterial adherence was observed when T84 cells, preincubated with ECM proteins, were infected with EHEC. Taken together, these findings suggest that the interaction of Lpf and ECM proteins contributes to the EHEC colonization of the gastrointestinal tract.

Domain organizations of extracellular matrix proteins and their evolution

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 35-42
Author(s):  
Jürgen Engel ◽  
Vladimir P. Efimov ◽  
Patrik Maurer
Keyword(s):  
Extracellular Matrix ◽  
Cell Signalling ◽  
Coiled Coil ◽  
Structure And Function ◽  
Matrix Proteins ◽  
Cell Binding ◽  
Ecm Proteins ◽  
Triple Helices ◽  
And Function ◽  
Polypeptide Chains

The astonishing diversity in structure and function of extracellular matrix (ECM) proteins originates from different combinations of domains. These are defined as autonomously folding units. Many domains are similar in sequence and structure indicating common ancestry. Evolutionarily homologous domains are, however, often functionally very different, which renders function prediction from sequence difficult. Related and different domains are frequently repeated in the same or in different polypeptide chains. Common assembly domains include α-helical coiled-coil domains and collagen triple helices. Other domains have been shown to be involved in assembly to other ECM proteins or in cell binding and cell signalling. The function of most of the domains, however, remains to be elucidated. ECM proteins are rather recent `inventions', and most occur either in plants or mammals but not in both. Their creation by domain shuffling involved a number of different mechanisms at the DNA level in which introns played an important role.

scholarly journals Prediction of Extracellular Matrix Proteins by Fusing Multiple Feature Information, Elastic Net, and Random Forest Algorithm

Mathematics ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 169 ◽  
Author(s):  
Minghui Wang ◽  
Lingling Yue ◽  
Xiaowen Cui ◽  
Cheng Chen ◽  
Hongyan Zhou ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Random Forest ◽  
Class Imbalance ◽  
Extracellular Matrix Proteins ◽  
Elastic Net ◽  
Matrix Proteins ◽  
Local Descriptor ◽  
Ecm Proteins ◽  
Multiple Feature ◽  
Leave One Out

Extracellular matrix (ECM) proteins play an important role in a series of biological processes of cells. The study of ECM proteins is helpful to further comprehend their biological functions. We propose ECMP-RF (extracellular matrix proteins prediction by random forest) to predict ECM proteins. Firstly, the features of the protein sequence are extracted by combining encoding based on grouped weight, pseudo amino-acid composition, pseudo position-specific scoring matrix, a local descriptor, and an autocorrelation descriptor. Secondly, the synthetic minority oversampling technique (SMOTE) algorithm is employed to process the class imbalance data, and the elastic net (EN) is used to reduce the dimension of the feature vectors. Finally, the random forest (RF) classifier is used to predict the ECM proteins. Leave-one-out cross-validation shows that the balanced accuracy of the training and testing datasets is 97.3% and 97.9%, respectively. Compared with other state-of-the-art methods, ECMP-RF is significantly better than other predictors.

scholarly journals An Ensemble Method with Hybrid Features to Identify Extracellular Matrix Proteins

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0117804 ◽  
Author(s):  
Runtao Yang ◽  
Chengjin Zhang ◽  
Rui Gao ◽  
Lina Zhang
Keyword(s):  
Extracellular Matrix ◽  
Extracellular Matrix Proteins ◽  
Ensemble Method ◽  
Matrix Proteins ◽  
Hybrid Features

scholarly journals Engineering Extracellular Matrix Proteins to Enhance Cardiac Regeneration After Myocardial Infarction

2021 ◽  
Vol 8 ◽  
Author(s):  
Hamid Esmaeili ◽  
Chaoyang Li ◽  
Xing Fu ◽  
Jangwook P. Jung
Keyword(s):  
Myocardial Infarction ◽  
Extracellular Matrix ◽  
Cardiac Regeneration ◽  
Cardiac Cells ◽  
Matrix Proteins ◽  
Direct Integration ◽  
Compelling Evidence ◽  
Cardiomyocyte Proliferation ◽  
Myocardial Repair ◽  
Ecm Proteins

Engineering microenvironments for accelerated myocardial repair is a challenging goal. Cell therapy has evolved over a few decades to engraft therapeutic cells to replenish lost cardiomyocytes in the left ventricle. However, compelling evidence supports that tailoring specific signals to endogenous cells rather than the direct integration of therapeutic cells could be an attractive strategy for better clinical outcomes. Of many possible routes to instruct endogenous cells, we reviewed recent cases that extracellular matrix (ECM) proteins contribute to enhanced cardiomyocyte proliferation from neonates to adults. In addition, the presence of ECM proteins exerts biophysical regulation in tissue, leading to the control of microenvironments and adaptation for enhanced cardiomyocyte proliferation. Finally, we also summarized recent clinical trials exclusively using ECM proteins, further supporting the notion that engineering ECM proteins would be a critical strategy to enhance myocardial repair without taking any risks or complications of applying therapeutic cardiac cells.

Anode Glow Discharge Plasma Treatment of Titanium Plates Facilitates Adsorption of Extracellular Matrix Proteins to the Plates

2005 ◽  
Vol 84 (7) ◽  
pp. 668-671 ◽  
Author(s):  
H. Yamamoto ◽  
Y. Shibata ◽  
T. Miyazaki
Keyword(s):  
Extracellular Matrix ◽  
Cell Adhesion ◽  
Glow Discharge ◽  
Photoelectron Spectroscopy ◽  
Discharge Plasma ◽  
Matrix Proteins ◽  
Glow Discharge Plasma ◽  
Phosphate Adsorption ◽  
Ecm Proteins ◽  
Better Than

Glow discharge plasma (GDP) supplied to an anode (GDP+) promotes calcium phosphate adsorption onto titanium better than that supplied to a cathode (GDP-). However, the adsorption of extracellular matrix (ECM) proteins is crucial for cell adhesion to titanium. Since GDP+ induced both inorganic adsorption and cell adhesion, we hypothesized that the inorganic adsorption in a culture medium might affect the adsorption of the ECM proteins. In this study, ECM proteins adsorbed on titanium with and without GDP were examined by x-ray photoelectron spectroscopy. After 1 hr of incubation, increasing sodium adsorption on GDP+ specimens induced adsorption of ECM proteins as shown by NH+ and COO− signals without calcium adsorption. In contrast, since no specific adsorption of sodium on GDP-specimens was detected, GDP-did not contribute to the adsorption of ECM proteins. Thus, promotion of sodium adsorption of GDP+ was effective, at least in the initial ECM protein adsorption on a titanium surface.

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