Markov entropy backbone electrostatic descriptors for predicting proteins biological activity

• Published in: Bioorganic & medicinal chemistry letters Vol. 14; no. 18; pp. 4691 - 4695
• Main Authors: González-Dı́az, Humberto, Molina, Reinaldo, Uriarte, Eugenio
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 20.09.2004; Elsevier
• Subjects: 3D-QSAR; Alcohol Dehydrogenase - chemistry; Alcohol Dehydrogenase - pharmacology; Analytical biochemistry: general aspects, technics, instrumentation; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Electrostatic field; Fundamental and applied biological sciences. Psychology; Linear Models; Markov chain; Markov Chains; Medical sciences; Miscellaneous; Muramidase - chemistry; Muramidase - pharmacology; Pharmacology. Drug treatments; Probability; Protein electrostatics; Proteins - chemistry; Proteins - pharmacology; Quantitative Structure-Activity Relationship; Static Electricity; Tetrahydrofolate Dehydrogenase - chemistry; Tetrahydrofolate Dehydrogenase - pharmacology; Markov chain; 3D-QSAR; Electrostatic field; Protein electrostatics; Discriminant analysis; Enzyme; Electrostatic interaction; Prediction; Lipophily; Partition coefficient; Entropy; Cross validation; Alcohol dehydrogenase; Physicochemical properties activity relationship; Modeling; Protein; Structure activity relation; Glycosidases; Classification; Hydrolases; Oxidoreductases; Dihydrofolate reductase; Thermodynamic properties; O-Glycosidases; Lysozyme
• ISSN: 0960-894X; 1464-3405
• DOI: 10.1016/j.bmcl.2004.06.100

[Display omitted] The spherical truncation of electrostatic interactions between aminoacids makes it possible to break down long-range spatial electrostatic interactions, resulting in short-range interactions. As a result, a Markov Chain model may be used to calculate the probabilities with which the effect of a given interaction reaches aminoacids at different distances within the backbone. The entropies of a Markov Chain model of this type may then be used to codify information about the spatial distribution of charges in the protein used in this study exploring the structure–activity relationship. In this paper, a linear discriminant analysis is reported, which correctly classified 92.3% of 26 under investigation in training and leave-one-out cross validation, purely for illustrative purposes. Classification was carried out for three possible activities: lysozymes, dihydrofolate reductases, and alcohol dehydrogenases. The discriminant analysis equations were contracted into two canonical roots. These simple canonical roots have high regression coefficients ( R c1 = 0.903 and R c2 = 0.70). Root1 explains the biological activity of alcohol dehydrogenases while Root2 discriminates between lysozymes and dihydrofolate reductases. It was possible to profile the effect of core, middle, and surface aminoacids on biological activity. In contrast, a model considering classic physicochemical parameters such as: polarizability, refractivity, and partition coefficient classify correctly only the 80.8% of the proteins.