Structure and function relationships of proteins based on polar profile: a review.

Abstract

Proteins in the post-genome era impose diverse research challenges, the main are the understanding of their structure-function mechanism, and the growing need for new pharmaceutical drugs, particularly antibiotics that help clinicians treat the ever- increasing number of Multidrug-Resistant Organisms (MDROs). Although, there is a wide range of mathematical-computational algorithms to satisfy the demand, among them the Quantitative Structure-Activity Relationship algorithms that have shown better performance using a characteristic training data of the property searched; their performance has stagnated regardless of the number of metrics they evaluate and their complexity. This article reviews the characteristics of these metrics, and the need to reconsider the mathematical structure that expresses them, directing their design to a more comprehensive algebraic structure. It also shows how the main function of a protein can be determined by measuring the polarity of its linear sequence, with a high level of accuracy, and how such exhaustive metric stands as a "fingerprint" that can be applied to scan the protein regions to obtain new pharmaceutical drugs, and thus to establish how the singularities led to the specialization of the protein groups known today.

On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains

“…This may hence be linked to the physical aspect of polarity. Accordingly, as we have shown in previous studies [7], the concept of the amino acid polarities also serves to establish and predict prebiotic scenarios of peptide formation.…”

“…Such proteins fold as a set of α-helices, β-strand structures, or irregular regions assembled in motifs which, in turn, agglomerate into functional domains. Understanding the interaction of these functional domains can help to set a structure-function relationship [7] and this knowledge can be applied to the design of pharmaceutical drugs to combat disease [66]. Proteins involved in the entry of the virus into the cell are of particular interest because they are firstchoice therapeutic targets and they facilitate an early diagnosis.…”

“…In this work, we have used a supervised learning program called Polarity Index Method (PIM) [6] that has proved its effectiveness in the identification of different protein functional groups. Its metric only uses the polar profile [7] of the protein amino acid sequence to look for the regularities in the proteins associated with Ebola virus disease and their functional domains [8] that have been experimentally identified. To achieve this objective, a comprehensive bioinformatics study was conducted looking at the polar profiles of two protein groups associated with Ebola virus disease paying attention to their structural disorder propensity [9].…”

Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops

“…Several reports gave a comprehensive review on structure-function relationship in proteins (Hegyi and Gerstein, 1999 ; Orengo et al, 1999 ; Lee et al, 2007 ; Redfern et al, 2008 ; Sadowski and Jones, 2009 ; Fang et al, 2010 ; Uversky and Dunker, 2010 ; Polanco et al, 2016 ). Also, studies on particular proteins have been reported (Mills et al, 1995 ; Mulakala and Reilly, 2002 ; Albenne et al, 2009 ; Feng et al, 2009 ; Payne et al, 2011 ; Scavuzzo-Duggan et al, 2015 ), and quite a few approaches have been even proposed for function prediction or for structure-function relationship studies (Guerrucci and Bell, 1995 ; Lavery and Sacquin-Mora, 2007 ; Xie et al, 2007 ; Atkinson et al, 2009 ; Wu et al, 2010 ; Osadchy and Kolodny, 2011 ; Micheletti, 2013 ; Cohn, 2016 ; Mudgal et al, 2017 ).…”

Comprehensive Interactions of ACE Inhibitors With Their Receptor by a Support Vector Machine Model and Molecular Docking

“…QSAR is a ligand‐based method that has been popularly applied for predicting biological activity . Both 2D QSAR and 3D QSAR are widely used for modeling.…”