scholarly journals Electronegativity and intrinsic disorder of preeclampsia-related proteins

2016 ◽  
Vol 64 (1) ◽  
Author(s):  
Carlos Polanco ◽  
Jorge Alberto Castañón-González ◽  
Vladimir N. Uversky ◽  
Thomas Buhse ◽  
José Lino Samaniego Mendoza ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Maternal Death ◽  
Computational Study ◽  
Intrinsic Disorder ◽  
Functional Disorder ◽  
Index Method ◽  
Underdeveloped Countries ◽  
Polarity Index ◽  
Intrinsically Disorder ◽  
Related Proteins

Preeclampsia, hemorrhage, and infection are the leading causes of maternal death in underdeveloped countries. Since several proteins associated with preeclampsia are known, we conducted a computational study in which evaluated the commonness and potential functionality of intrinsic disorder in these proteins and also made an attempt to characterize their origin. To this end, we used a several supervised techniques, as a Polarity Index Method (PIM), which evaluates the electronegativity of proteins from their sequence alone. Peculiarities of resulting polar profile of the group of preeclampsia-related proteins were then compared with profiles of a group of lipoproteins, antimicrobial peptides, angiogenesis-related proteins, and the intrinsically disorder proteins. Our results showed a high graphical correlation between preeclampsia proteins, lipoproteins, and the angiogenesis proteins. These results lead us to strongly assume that the preeclampsia proteins are lipoproteins. We also show that several preeclampsia-related proteins contain significant amounts of functional disorder.

scholarly journals Detection of selective antibacterial peptides by the Polarity Profile method.

2013 ◽  
Vol 60 (2) ◽  
Author(s):  
Carlos Polanco ◽  
Thomas Buhse ◽  
José Lino Samaniego ◽  
Jorge Alberto Castañón-González
Keyword(s):  
Antimicrobial Peptides ◽  
Mammalian Cells ◽  
False Negative ◽  
Antibacterial Peptides ◽  
Index Method ◽  
Profile Method ◽  
Bacterial Membranes ◽  
Polarity Index ◽  
Polarity Profile ◽  
Almost All

Antimicrobial peptides occupy a prominent place in the production of pharmaceuticals, because of their effective contribution to the protection of the immune system against almost all types of pathogens. These peptides are thoroughly studied by computational methods designed to shed light on their main functions. In this paper, we propose a computational approach, named the Polarity Profile method that represents an improvement to the former Polarity Index method. The Polarity Profile method is very effective in detecting the subgroup of antibacterial peptides called selective cationic amphipathic antibacterial peptides (SCAAP) that show high toxicity towards bacterial membranes and exhibit almost zero toxicity towards mammalian cells. Our study was restricted to the peptides listed in the antimicrobial peptides database (APD2) of December 19, 2012. Performance of the Polarity Profile method is demonstrated through a comparison to the former Polarity Index method by using the same sets of peptides. The efficiency of the Polarity Profile method exceeds 85% taking into account the false positive and/or false negative peptides.

Bioinformatics-based characterization of proteins related to SARS-CoV-2 using the Polarity Index Method® (PIM®) and Intrinsic Disorder Predisposition

2021 ◽  
Vol 18 ◽  
Author(s):  
Carlos Polanco ◽  
Vladimir N. Uversky ◽  
Guy W. Dayhoff II ◽  
Alberto Huberman ◽  
Thomas Buhse ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Intrinsic Disorder ◽  
Cell Penetrating Peptides ◽  
Disordered Proteins ◽  
Structural Proteins ◽  
Public Health Issue ◽  
Index Method ◽  
Current Time ◽  
Intrinsically Disordered ◽  
Polarity Index

Background: The global outbreak of the 2019 novel Coronavirus Disease (COVID-19) caused by the infection with the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which appeared in China at the end of 2019, signifies a major public health issue at the current time. Objective: The objective of the present study is to characterize the physicochemical properties of the SARS-CoV-2 proteins at a residues level, and to generate a “bioinformatics fingerprint” in the form of a “PIM® profile” created for each sequence utilizing the Polarity Index Method® (PIM®), suitable for the identification of these proteins. Methods: Two different bioinformatics approaches were used to analyze sequence characteristics of these proteins at the residues level, an in-house bioinformatics system PIM®, and a set of the commonly used algorithms for the predic-tion of protein intrinsic disorder predisposition, such as PONDR® VLXT, PONDR® VL3, PONDR® VSL2, PONDR® FIT, IUPred_short and IUPred_long. The PIM® profile was generated for four SARS-CoV-2 structural proteins and compared with the corresponding profiles of the SARS-CoV-2 non-structural proteins, SARS-CoV-2 putative proteins, SARS-CoV proteins, MERS-CoV proteins, sets of bacterial, fungal, and viral proteins, cell-penetrating peptides, and a set of intrinsically disordered proteins. We also searched for the UniProt proteins with PIM® profiles similar to those of SARS-CoV-2 structural, non-structural, and putative proteins. Results: We show that SARS-CoV-2 structural, non-structural, and putative proteins are characterized by a unique PIM® profile. A total of 1736 proteins were identified from the 562,253 “reviewed” proteins from the UniProt database, whose PIM® profile was similar to that of the SARS-CoV-2 structural, non-structural, and putative proteins. Conclusion: The PIM® profile represents an important characteristic that might be useful for the identification of proteins similar to SARS-CoV-2 proteins.

Identification of antimicrobial peptides by using eigenvectors

2016 ◽  
Vol 63 (3) ◽  
Author(s):  
Carlos Polanco
Keyword(s):  
Antimicrobial Peptides ◽  
Cancer Cells ◽  
Potential Application ◽  
Mammalian Cells ◽  
Computational Method ◽  
Antibacterial Peptides ◽  
Index Method ◽  
Vector Method ◽  
Polarity Index ◽  
Wide Range

Antibacterial peptides are subject to broad research due to their potential application and the benefit they can provide for a wide range of diseases. In this work, a mathematical-computational method, called the Polarity Vector Method, is introduced that has a high discriminative level (>70%) to identify peptides associated with Gram (-) bacteria, Gram (+) bacteria, cancer cells, fungi, insects, mammalian cells, parasites, and viruses, taken from the Antimicrobial Peptides Database. This supervised method uses only eigenvectors from the incident polar matrix of the group studied. It was verified with a comparative study with another extensively verified method developed previously by our team, the Polarity Index Method. The number of positive hits of both methods was up to 98% in all the tests conducted.

Bioinformatics-based identification of proteins expressed by arthropod-borne viruses transmitted by Aedes aegypti mosquito

2020 ◽  
Vol 17 ◽  
Author(s):  
Carlos Polanco ◽  
Vladimir N. Uversky ◽  
Alberto Huberman ◽  
Leire Andrés ◽  
Thomas Buhse ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Intrinsically Disordered Proteins ◽  
Intrinsic Disorder ◽  
Cell Penetrating Peptides ◽  
Disordered Proteins ◽  
Index Method ◽  
Intrinsically Disordered ◽  
Polarity Index ◽  
Uniprot Database ◽  
Prophylactic Measures

Background: The female Aedes aegypti mosquito is a vector of several arthropodborne viruses, such as Mayaro, Dengue, Chikungunya, Yellow Fever, and Zika. These viruses cause the death of at least 600000 people a year and temporarily disable several millions more around the world. Up to date, there are no effective prophylactic measures that would prevent the contact and bite of this arthropod and, therefore, its consequential contagion. Objective: The objective of the present study was to search for the regularities of the proteins expressed by these five viruses, at residues level, and obtain a "bioinformatic fingerprint" to select them. Methods: We used two bioinformatic systems, our in-house bioinformatic system named Polarity Index Method® (PIM®) supported at residues level, and the commonly used algorithm for the prediction of intrinsic disorder predisposition, PONDR® FIT. We applied both programs to the 29 proteins that express the five groups of arboviruses studied, and we calculated for each of them their Polarity Index Method® profile and their intrinsic disorder predisposition. This information was then compared with analogous information for other protein groups, such as proteins from bacteria, fungi, viruses, and cell penetrating peptides from the UniProt database, and a set of intrinsically disordered proteins. Once the "fingerprint" of each group of arboviruses was obtained, these "fingerprints" were searched among the 559228 "reviewed" proteins from the UniProt database. Results: In total, 1736 proteins were identified from the 559228 “reviewed” proteins from UniProt database, with similar "PIM® profile" to the 29 mutated proteins that express the five groups of arboviruses. Conclusion: We propose that the “PIM® profile” of characterization of proteins might be useful for the identification of proteins expressed by arthropod-borne viruses transmitted by Aedes aegypti mosquito.

Bioinformatics-based identification of Selective Cationic Amphipatic Antibacterial Peptides: Aurein 1.2 variants case

2020 ◽  
Vol 17 ◽  
Author(s):  
Carlos Polanco ◽  
Alberto Huberman ◽  
Vladimir N. Uversky ◽  
Leire Andrés ◽  
Thomas Buhse ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Intrinsically Disordered Proteins ◽  
Intrinsic Disorder ◽  
Cell Penetrating Peptides ◽  
Disordered Proteins ◽  
Antibacterial Peptides ◽  
Index Method ◽  
Intrinsically Disordered ◽  
Polarity Index ◽  
Uniprot Database

Background: Selective Cationic Amphipathic Antibacterial Peptides (SCAAPs) occupy a prominent place in the production of new drugs on account of their high toxicity towards bacteria and low toxicity towards mammalian cells, low hemolytic activity, and contribution to the protection of the human immune system. Introduction: Their number in nature is very low and experimental tests are very protracted and costly. Therefore, it would be useful to have bioinformatics tools that would identify them in the existing databases and also propose new synthetic SCAAPs. Method: In order to reduce the costs of identification and/or chemical synthesis. To know the physicochemical characteristics of SCAAPs at a residues level and to obtain a “bioiformatics fingerprint” suitable for their selection, we have modified the Polarity Index Method® (PIM®) to include the α-helical configuration of each sequence to determine their individual “PIM® profile”. We have also used a set of computer program to determine their “Intrinsic Disorder Predisposition”. This information was then compared with other protein groups such as bacteria, fungi, virus and cell penetrating peptides (CPP) from the UniProt database and a set of intrinsically disordered proteins. Once the “fingerprint” of SCAAPs was obtained, it was used for searching among the 559228 “reviewed” proteins from the UniProt database and a set of synthetic SCAAPs characterized by the predefined “PIM® profile” selected. Results: Our results showed that the metric named “PIM® profile” can identify, with a high level of accuracy, a group of bacterial SCAAPs. This bioinformatics study was supported at residues level, using the in-house bioinformatics system Polarity Index Method the commonly used algorithm for the prediction of intrinsic disorder predisposition, PONDR® FIT. Conclusions: The Polarity Index Method seems highly efficient identifying SCAAP candidates.

scholarly journals Attacins: A Promising Class of Insect Antimicrobial Peptides

Antibiotics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 212
Author(s):  
Francesco Buonocore ◽  
Anna Maria Fausto ◽  
Giulia Della Pelle ◽  
Tomislav Roncevic ◽  
Marco Gerdol ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Antimicrobial Effect ◽  
Short Review ◽  
Microbial Pathogens ◽  
Special Focus ◽  
Gram Negative Bacteria ◽  
Physiological Importance ◽  
Related Proteins ◽  
Large Repertoire

Insects produce a large repertoire of antimicrobial peptides (AMPs) as the first line of defense against bacteria, viruses, fungi or parasites. These peptides are produced from a large precursor that contains a signal domain, which is cleaved in vivo to produce the mature protein with antimicrobial activity. At present, AMPs from insects include several families which can be classified as cecropins, ponericins, defensins, lebocins, drosocin, Metchnikowin, gloverins, diptericins and attacins according to their structure and/or function. This short review is focused on attacins, a class of glycine-rich peptides/proteins that have been first discovered in the cecropia moth (Hyalophora cecropia). They are a rather heterogeneous group of immunity-related proteins that exhibit an antimicrobial effect mainly against Gram-negative bacteria. Here, we discuss different attacin and attacin-like AMPs that have been discovered so far and analyze their structure and phylogeny. Special focus is given to the physiological importance and mechanism of action of attacins against microbial pathogens together with their potential pharmacological applications, emphasizing their roles as antimicrobials.

Identification of proteins associated with amyloidosis by polarity index method

2015 ◽  
Vol 62 (1) ◽  
pp. 41-55 ◽  
Author(s):  
Carlos Polanco ◽  
José Lino Samaniego ◽  
Vladimir N. Uversky ◽  
Jorge Alberto Castañón-González ◽  
Thomas Buhse ◽  
...  
Keyword(s):  
Index Method ◽  
Polarity Index

scholarly journals A switch from constitutive chemical defence to inducible innate immune responses in the invasive ladybird Harmonia axyridis

2013 ◽  
Vol 9 (3) ◽  
pp. 20130006 ◽  
Author(s):  
Henrike Schmidtberg ◽  
Christian Röhrich ◽  
Heiko Vogel ◽  
Andreas Vilcinskas
Keyword(s):  
Immune Responses ◽  
Antimicrobial Peptides ◽  
Harmonia Axyridis ◽  
Chemical Defence ◽  
Coccinella Septempunctata ◽  
Invasion Biology ◽  
Innate Immune ◽  
Innate Immune Responses ◽  
Simultaneous Synthesis ◽  
Related Proteins

The harlequin ladybird, Harmonia axyridis , has emerged as a model species for invasion biology, reflecting its remarkable capacity to outcompete native ladybird species when introduced into new habitats. This ability may be associated with its prominent resistance to pathogens and intraguild predation. We recently showed that the constitutive antibacterial activity present in the haemolymph of H. axyridis beetles can be attributed to the chemical defence compound harmonine. Here, we demonstrate that H. axyridis differs from other insects, including the native ladybird Coccinella septempunctata, by reducing rather than increasing the antimicrobial activity of its haemolymph following the injection of bacteria. However, both species produce new or more abundant proteins in the haemolymph, indicating that bacterial challenge induces innate immune responses associated with the synthesis of immunity-related proteins. Our results suggest that H. axyridis beetles can switch from constitutive chemical defence to inducible innate immune responses, supporting hypothesis that inducible antimicrobial peptides protect host beetles against pathogens that survive constitutive defences. These alternative antimicrobial defence mechanisms may reflect a trade-off resulting from fitness-related costs associated with the simultaneous synthesis of harmonine and antimicrobial peptides/proteins.

Erythropoietin and co.: intrinsic structure and functional disorder

2017 ◽  
Vol 13 (1) ◽  
pp. 56-72 ◽  
Author(s):  
Vladimir N. Uversky ◽  
Elrashdy M. Redwan
Keyword(s):  
Growth Factor ◽  
Intrinsic Disorder ◽  
Biological Processes ◽  
Functional Disorder ◽  
Intrinsic Structure

Erythropoietin (Epo) is a glycoprotein with important roles in erythropoiesis and other biological processes by serving as a hormone, a cytokine, or a growth factor. At least in part, the Epo multifunctionality is driven by its partners. The goal of this article is to evaluate the roles of intrinsic disorder in the functions of Epo and its primary interactors, EpoR, βCR, and HIF-1α.

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