1
|
Falomir-Lockhart AH, Villegas-Castagnaso EE, Giovambattista G, Rogberg-Muñoz A. Computational prediction of nsSNPs effects on protein function and structure, a prioritization approach for further in vitro studies applied to bovine GSTP1. Free Radic Biol Med 2018; 129:486-491. [PMID: 30315934 DOI: 10.1016/j.freeradbiomed.2018.10.403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/20/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022]
Abstract
The development of high-throughput technologies in the last decade produced an exponential increase in the amount of biological data available. The case of redox biology and apoptosis is not an exception, and nowadays there is a need to integrate information from multiple "omics" studies. Therefore, validation of proposed discoveries is essential. However, the study in biological systems of the effect of the massive amounts of sequence variation data generated with next-generation sequencing (NGS) technologies can be a very difficult and expensive process. In this context, the present study aimed to demonstrate the advantages of a computational methodology to systematically analyze the structural and functional effects of protein variants, in order to prioritize further studies. This approach stands out for its easy implementation, low costs and low time consumed. First, the possible impact of mutations on protein structure and function was tested by a combination of tools based on evolutionary and structural information. Next, homology modeling was performed to predict and compare the 3D protein structures of unresolved amino acid sequences obtained from genomic resequencing. This analysis applied to the bovine GSTP1 allowed to determine that some of amino acid substitutions may generate important changes in protein structure and function. Moreover, the haplotype analysis highlighted three structure variants worthwhile studying through in vitro or in vivo experiments.
Collapse
Affiliation(s)
- A H Falomir-Lockhart
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - E E Villegas-Castagnaso
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - A Rogberg-Muñoz
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (UNLP-CONICET La Plata), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina; Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| |
Collapse
|
2
|
Lima AN, Philot EA, Trossini GHG, Scott LPB, Maltarollo VG, Honorio KM. Use of machine learning approaches for novel drug discovery. Expert Opin Drug Discov 2016; 11:225-39. [PMID: 26814169 DOI: 10.1517/17460441.2016.1146250] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The use of computational tools in the early stages of drug development has increased in recent decades. Machine learning (ML) approaches have been of special interest, since they can be applied in several steps of the drug discovery methodology, such as prediction of target structure, prediction of biological activity of new ligands through model construction, discovery or optimization of hits, and construction of models that predict the pharmacokinetic and toxicological (ADMET) profile of compounds. AREAS COVERED This article presents an overview on some applications of ML techniques in drug design. These techniques can be employed in ligand-based drug design (LBDD) and structure-based drug design (SBDD) studies, such as similarity searches, construction of classification and/or prediction models of biological activity, prediction of secondary structures and binding sites docking and virtual screening. EXPERT OPINION Successful cases have been reported in the literature, demonstrating the efficiency of ML techniques combined with traditional approaches to study medicinal chemistry problems. Some ML techniques used in drug design are: support vector machine, random forest, decision trees and artificial neural networks. Currently, an important application of ML techniques is related to the calculation of scoring functions used in docking and virtual screening assays from a consensus, combining traditional and ML techniques in order to improve the prediction of binding sites and docking solutions.
Collapse
Affiliation(s)
- Angélica Nakagawa Lima
- a Centro de Ciências Naturais e Humanas , Universidade Federal do ABC , São Paulo , Brazil
| | - Eric Allison Philot
- a Centro de Ciências Naturais e Humanas , Universidade Federal do ABC , São Paulo , Brazil
| | | | - Luis Paulo Barbour Scott
- c Centro de Matemática, Computação e Cognição , Universidade Federal do ABC , São Paulo , Brazil
| | | | - Kathia Maria Honorio
- a Centro de Ciências Naturais e Humanas , Universidade Federal do ABC , São Paulo , Brazil.,d Escola de Artes, Ciências e Humanidades , Universidade de São Paulo , São Paulo , Brazil
| |
Collapse
|
3
|
Scian M, Le Trong I, Mazari AMA, Mannervik B, Atkins WM, Stenkamp RE. Comparison of epsilon- and delta-class glutathione S-transferases: the crystal structures of the glutathione S-transferases DmGSTE6 and DmGSTE7 from Drosophila melanogaster. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2089-98. [PMID: 26457432 PMCID: PMC4601370 DOI: 10.1107/s1399004715013929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 12/30/2022]
Abstract
Cytosolic glutathione transferases (GSTs) comprise a large family of enzymes with canonical structures that diverge functionally and structurally among mammals, invertebrates and plants. Whereas mammalian GSTs have been characterized extensively with regard to their structure and function, invertebrate GSTs remain relatively unstudied. The invertebrate GSTs do, however, represent potentially important drug targets for infectious diseases and agricultural applications. In addition, it is essential to fully understand the structure and function of invertebrate GSTs, which play important roles in basic biological processes. Invertebrates harbor delta- and epsilon-class GSTs, which are not found in other organisms. Drosophila melanogaster GSTs (DmGSTs) are likely to contribute to detoxication or antioxidative stress during development, but they have not been fully characterized. Here, the structures of two epsilon-class GSTs from Drosophila, DmGSTE6 and DmGSTE7, are reported at 2.1 and 1.5 Å resolution, respectively, and are compared with other GSTs to identify structural features that might correlate with their biological functions. The structures of DmGSTE6 and DmGSTE7 are remarkably similar; the structures do not reveal obvious sources of the minor functional differences that have been observed. The main structural difference between the epsilon- and delta-class GSTs is the longer helix (A8) at the C-termini of the epsilon-class enzymes.
Collapse
Affiliation(s)
- Michele Scian
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
| | - Isolde Le Trong
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
| | - Aslam M. A. Mazari
- Department of Neurochemistry, Arrhenius Laboratories, Stockholm University, SE-10 691 Stockholm, Sweden
| | - Bengt Mannervik
- Department of Neurochemistry, Arrhenius Laboratories, Stockholm University, SE-10 691 Stockholm, Sweden
| | - William M. Atkins
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
| | - Ronald E. Stenkamp
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
| |
Collapse
|
4
|
Kolodny R, Kosloff M. From Protein Structure to Function via Computational Tools and Approaches. Isr J Chem 2013. [DOI: 10.1002/ijch.201200078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
5
|
Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens. Funct Integr Genomics 2011; 12:157-72. [PMID: 21909786 DOI: 10.1007/s10142-011-0248-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/06/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
In the present work, we describe the characterisation of the glutathione transferase (GST) gene family from Agrobacterium tumefaciens C58. A genome survey revealed the presence of eight GST-like proteins in A. tumefaciens (AtuGSTs). Comparison by multiple sequence alignment generated a dendrogram revealing the phylogenetic relationships of AtuGSTs-like proteins. The beta and theta classes identified in other bacterial species are represented by five members in A. tumefaciens C58. In addition, there are three "orphan" sequences that do not fit into any previously recognised GST classes. The eight GST-like genes were cloned, expressed in Escherichia coli and their substrate specificity was determined towards 17 different substrates. The results showed that AtuGSTs catalyse a broad range of reactions, with different members of the family exhibiting quite varied substrate specificity. The 3D structures of AtuGSTs were predicted using molecular modelling. The use of comparative sequence and structural analysis of the AtuGST isoenzymes allowed us to identify local sequence and structural characteristics between different GST isoenzymes and classes. Gene expression profiling was conducted under normal culture conditions as well as under abiotic stress conditions (addition of xenobiotics, osmotic stress and cold and heat shock) to induce and monitor early stress-response mechanisms. The results reveal the constitutive expression of GSTs in A. tumefaciens and a modulation of GST activity after treatments, indicating that AtuGSTs presumably participate in a wide range of functions, many of which are important in counteracting stress conditions. These functions may be relevant to maintaining cellular homeostasis as well as in the direct detoxification of toxic compounds.
Collapse
|
6
|
Bhattacharya A, Sood P, Citovsky V. The roles of plant phenolics in defence and communication during Agrobacterium and Rhizobium infection. MOLECULAR PLANT PATHOLOGY 2010; 11:705-19. [PMID: 20696007 PMCID: PMC6640454 DOI: 10.1111/j.1364-3703.2010.00625.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Phenolics are aromatic benzene ring compounds with one or more hydroxyl groups produced by plants mainly for protection against stress. The functions of phenolic compounds in plant physiology and interactions with biotic and abiotic environments are difficult to overestimate. Phenolics play important roles in plant development, particularly in lignin and pigment biosynthesis. They also provide structural integrity and scaffolding support to plants. Importantly, phenolic phytoalexins, secreted by wounded or otherwise perturbed plants, repel or kill many microorganisms, and some pathogens can counteract or nullify these defences or even subvert them to their own advantage. In this review, we discuss the roles of phenolics in the interactions of plants with Agrobacterium and Rhizobium.
Collapse
Affiliation(s)
- Amita Bhattacharya
- Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | | | | |
Collapse
|
7
|
Abstract
Bacterial glutathione transferases (GSTs) are part of a superfamily of enzymes that play a key role in cellular detoxification. GSTs are widely distributed in prokaryotes and are grouped into several classes. Bacterial GSTs are implicated in a variety of distinct processes such as the biodegradation of xenobiotics, protection against chemical and oxidative stresses and antimicrobial drug resistance. In addition to their role in detoxification, bacterial GSTs are also involved in a variety of distinct metabolic processes such as the biotransformation of dichloromethane, the degradation of lignin and atrazine, and the reductive dechlorination of pentachlorophenol. This review article summarizes the current status of knowledge regarding the functional and structural properties of bacterial GSTs.
Collapse
Affiliation(s)
- Nerino Allocati
- Dipartimento di Scienze Biomediche, Università G. d'Annunzio, Chieti, Italy.
| | | | | | | |
Collapse
|
8
|
Garcia W, Travensolo RF, Rodrigues NC, Muniz JRC, Caruso CS, Lemos EGM, Araujo APU, Carrilho E. Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:85-7. [PMID: 18259055 PMCID: PMC2374177 DOI: 10.1107/s174430910706825x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 12/23/2007] [Indexed: 11/11/2022]
Abstract
Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 A, alpha = 63.45, beta = 80.66, gamma = 94.55 degrees. xfGST crystals diffracted to 2.23 A resolution on a rotating-anode X-ray source.
Collapse
Affiliation(s)
- Wanius Garcia
- Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| | - Regiane F. Travensolo
- Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| | - Nathalia C. Rodrigues
- Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| | - João R. C. Muniz
- Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| | - Célia S. Caruso
- Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| | - Eliana G. M. Lemos
- Laboratório de Bioquímica de Microrganismos e de Plantas, Departamento de Tecnologia, UNESP, Jaboticabal, Brazil
| | - Ana Paula U. Araujo
- Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| | - Emanuel Carrilho
- Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos, Brazil
| |
Collapse
|