William F Porto

IIT Kharagpur, Kharagpur, Bengal, India

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Publications (21)46 Total impact

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    ABSTRACT: The CSαβ defensins are one of the most ancient antimicrobial peptide classes and are distributed in plants, invertebrates, and fungi. In the insect immunity, the defensins play a crucial role in protection against pathogens. The discovery of novel insect defensins could be a vital tool in developing novel antimicrobial agents, which are urgently needed because of growing resistance in pathogenic bacteria and the resulting reduction in the effectiveness of conventional antibiotics over the years. In this context, novel insect defensins could be identified from the potential resource of model insects. Here, a novel defensin, MdesDEF-2, was identified from the model insect Mayetiola destructor, the most destructive insect pest of wheat worldwide. The in silico identification of MdesDEF-2 was done through searching by regular expression in M. destructor's protein sequences available at NCBI. MdesDEF-2 has 36 amino acid residues and its model was composed of two β-strands and one α-helix showing three disulfide bridges. According to the classification of CSαβ defensins, MdesDEF-2 belongs to the group of ancient insect-type defensins. The molecular dynamics simulation revealed that MdesDEF-2 has a very flexible N-terminal loop. Moreover, phylogenetic analysis together with functional predictions indicated that MdesDEF-2 could have antibacterial activity without causing membrane disruption. However, while the actual activity of MdesDEF-2 is still unclear, it is evident that its role in the biology of M. destructor is similar to that of its paralogue, MdesDEF-1, protecting the insect against microbial invasion.
    Journal of Molecular Modeling 07/2014; 20(7):2339. · 1.98 Impact Factor
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    ABSTRACT: Pharmaceutical industries have renewed interest in screening multifunctional bioactive peptides as a marketable product in health care applications. In this context, several animal and plant peptides with potential bioactivity have been reported. Milk proteins and peptides have received much attention as a source of health-enhancing components to be incorporated into nutraceuticals and functional foods. By using this source, 24 peptides have been fractionated and purified from human milk using RP-HPLC. Multifunctional roles including antimicrobial, antioxidant and growth stimulating activity have been evaluated in all 24 fractions. Nevertheless, only four fractions show multiple combined activities among them. Using a proteomic approach, two of these four peptides have been identified as lactoferrin derived peptide and kappa casein short chain peptide. Lactoferrin derived peptide (f8) is arginine-rich and kappa casein derived (f12) peptide is proline-rich. Both peptides (f8 and f12) showed antimicrobial activity against both Gram-positive and Gram-negative bacteria. Fraction 8 (f8) exhibits growth stimulating activity in 3T3 cell line and f12 shows higher free radical scavenging activity in comparison to other fractions. Finally, both peptides were in silico evaluated and some insights into their mechanism of action were provided. Thus, results indicate that these identified peptides have multiple biological activities which are valuable for the quick development of the neonate and may be considered as potential biotechnological products for nutraceutical industry.
    Peptides 04/2014; · 2.52 Impact Factor
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    ABSTRACT: Pharmaceutical industries have renewed interest in screening multifunctional bioactive peptides as a marketable product in health care applications. In this context, several animal and plant peptides with potential bioactivity have been reported. Milk proteins and peptides have received much attention as a source of health-enhancing components to be incorporated into nutraceuticals and functional foods. By using this source, 24 peptides have been fractionated and purified from human milk using RP-HPLC. Multifunctional roles including antimicrobial, antioxidant and growth stimulating activity have been evaluated in all 24 fractions. Nevertheless, only 4 fractions show multiple combined activities among them. Using a proteomic approach, two of these four peptides have been identified as lactoferrin derived peptide and kappa casein short chain peptide. Lactoferrin derived peptide (f8) is arginine-rich and kappa casein derived (f12) peptide is proline-rich. Both peptides (f8 and f12) showed antimicrobial activity against both Gram-positive and Gram-negative bacteria. Fraction 8 (f8) exhibits growth stimulating activity in 3T3 cell line and f12 shows higher free radical scavenging activity in comparison to other fractions. Finally, both peptides were in silico evaluated and some insights into their mechanism of action were provided. Thus, results indicate that these identified peptides have multiple biological activities which are valuable for the quick development of the neonate and may be considered as potential biotechnological products for for nutraceutical industry.
    Peptides 04/2014; · 2.52 Impact Factor
  • William F. Porto, Diego O. Nolasco, Octavio L. Franco
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    ABSTRACT: Glycine-rich proteins (GRPs) derived from plants compose a family of proteins and peptides that share a glycine repeat domain and can perform diverse functions. Two structural conformations have been proposed for GRPs: glycine loops arranged as a Velcro and an anti-parallel β-sheet with several β-strands. The antimicrobial peptide Pg-AMP1 is the only plant GRP with antibacterial activity reported so far and its structure remains unclear. Recently, its recombinant expression was reported, where the recombinant peptide had an additional methionine residue at the N-terminal and a histidine tag at the C-terminal (His6-tag). These changes seem to change the peptide's activity, generating a broader spectrum of antibacterial activity. In this report, through ab initio molecular modelling and molecular dynamics, it was observed that both peptide structures were composed of an N-terminal α-helix and a dynamic loop that represents two-thirds of the protein. In contrast to previous reports, it was observed that there is a tendency to adopt a globular fold instead of an extended one, which could be in both, glycine loops or anti-parallel β-sheet conformation. The recombinant peptide showed a slightly higher solvated potential energy compared to the native form, which could be related to the His6-tag exposition. In fact, the His6-tag could be mainly responsible for the broader spectrum of activity, but it does not seem to cause great structural changes. However, novel studies are needed for a better characterization of its pharmacological properties so that in the future novel drugs may be produced based on this peptide.
    Peptides 01/2014; · 2.52 Impact Factor
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    ABSTRACT: Zantedeschia aethiopica is an evergreen perennial plant cultivated worldwide and commonly used for ornamental and medicinal purposes including the treatment of bacterial infections. However, the current understanding of molecular and physiological mechanisms in this plant is limited, in comparison to other non-model plants. In order to improve understanding of the biology of this botanical species, RNA-Seq technology was used for transcriptome assembly and characterization. Following Z. aethiopica spathe tissue RNA extraction, high-throughput RNA sequencing was performed with the aim of obtaining both abundant and rare transcript data. Functional profiling based on KEGG Orthology (KO) analysis highlighted contigs that were involved predominantly in genetic information (37%) and metabolism (34%) processes. Predicted proteins involved in the plant circadian system, hormone signal transduction, secondary metabolism and basal immunity are described here. In silico screening of the transcriptome data set for antimicrobial peptide (AMP) -encoding sequences was also carried out and three lipid transfer proteins (LTP) were identified as potential AMPs involved in plant defense. Spathe predicted protein maps were drawn, and suggested that major plant efforts are expended in guaranteeing the maintenance of cell homeostasis, characterized by high investment in carbohydrate, amino acid and energy metabolism as well as in genetic information.
    PLoS ONE 01/2014; 9(3):e90487. · 3.73 Impact Factor
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    ABSTRACT: Plants produce a variety of proteins and peptides which are involved in their defense against pathogens. Serine protease inhibitors are a well-established class of inhibitors correlated with plant defense. Increased levels of protease inhibitors delay cell damage and expand the cell's life-span. Recently, the rapid emergence of antibiotic-resistant microbial pathogens has prompted immense interest in purifying novel antimicrobial proteins or peptides from plant sources. Usually, the purification of protease inhibitors is accomplished by salt-extraction, ultrafiltration and affinity chromatography. Here, we developed a novel approach based on iron oxide nanoparticles conjugated to dextran functionalized with trypsin beads that accelerate the quick screening and purification of antimicrobial peptides with serine protease inhibitor activity. The method described here also works for screening other inhibitors using particular protein kinases, and it is therefore a novel tool for use as the leading method in the development of novel antimicrobial agents with protease inhibitory activity. Finally, and no less important, molecular modelling and dynamics studies of a homologous inhibitor studied here with Escherichia coli trypsin and chymotrypsin are provided in order to shed some light on inhibitor-enzyme interactions.
    The Analyst 12/2013; · 4.23 Impact Factor
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    ABSTRACT: Phytopathogens cause economic losses in agribusiness. Plant-derived compounds have been proposed to overcome this problem, including the antimicrobial peptides (AMPs). This paper reports the identification of Ps-AFP1, a novel AMP isolated from the Pisum sativum radicle. Ps-AFP1 was purified and evaluated against phytopathogenic fungi, showing clear effectiveness. In silico analyses were performed, suggesting an unusual fold and disulfide bond pattern. A novel fold and a novel AMP class were here proposed, the αβ-trumpet fold and αβ-trumpet peptides, respectively. The name αβ-trumpet was created due to the peptide's fold, which resembles the musical instrument. The Ps-AFP1 mechanism of action was also proposed. Microscopic analyses revealed that Ps-AFP1 could affect the fungus during the hyphal elongation from spore germination. Furthermore, confocal microscopy performed with Ps-AFP1 labeled with FITC shows that the peptide was localized at high concentration along the fungal cell surface. Due to low cellular disruption rates, it seems that the main target is the fungal cell wall. The binding thermogram and isothermal titration, molecular dynamics and docking analyses were also performed, showing that Ps-AFP1 could bind to chitin producing a stable complex. Data here reported provided novel structural-functional insights into the αβ-trumpet peptide fold.
    Biochimie 07/2013; · 3.14 Impact Factor
  • William F Porto, Octavio L Franco
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    ABSTRACT: Among the main classes of cysteine-stabilized antimicrobial peptides, the snakin/GASA family has not yet had any structural characterization. Through the combination of ab initio and comparative modeling with a disulfide bond predictor, the three-dimensional structure prediction of snakin-1 is here reported. The structure was composed of two long α-helices with a disulfide pattern of Cys(I)-Cys(IX), Cys(II)-Cys(VII), Cys(III)-Cys(IV), Cys(V)-Cys(XI), Cys(VI)-Cys(XII) and Cys(VIII)-Cys(X). The overall structure was maintained throughout molecular dynamics simulation. Snakin-1 showed a small degree of structural similarity with thionins and α-helical hairpins. This is the first report of snakin-1 structural characterization, shedding some light on the snakin/GASA family.
    Peptides 04/2013; · 2.52 Impact Factor
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    02/2013: pages 1-13;
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    ABSTRACT: Keratitis treatment has become more complicated due to the emergence of bacterial or fungal pathogens with enhanced antibiotic resistance. The pharmaceutical applications of N-heterocyclic carbene complexes have received remarkable attention due to their antimicrobial properties. In this paper, the new precursor, 3,3'-(p-phenylenedimethylene) bis{1-(2- methyl-allyl)imidazolium} bromide (1a) and its analogous PF6 salt (1b) were synthesized. Furthermore, silver(I) and gold(I) -N-heterocyclic carbene (NHC) complexes [Ag2LBr2/Au2LBr2; 2a/3a], [(Ag2L2)(PF6)2/(Au2L2)(PF6)2; 2b/3b] were developed from their corresponding ligands. All compounds were screened for their antimicrobial activities against multiple keratitis-associated human eye pathogens, including bacteria and fungi. Complexes 2a and 3a showed highest activity, and the effectiveness of 3a was also studied, focusing eradication of pathogen biofilm. Furthermore, the structures of 1a, 2a and 3b were determined using single crystal X-ray analysis, 2b and 3a were optimized theoretically. The mechanism of action of 3a was evaluated by scanning electron microscopy and docking experiments, suggesting that its target is the cell membrane. In summary, 3a may be helpful in developing antimicrobial therapies in patients suffering from keratitis-associated eye infections caused by multidrug-resistant pathogens.
    PLoS ONE 01/2013; 8(3):e58346. · 3.73 Impact Factor
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    ABSTRACT: Lectins are proteins with ability to bind reversibly and non-enzymatically to a specific carbohydrate. They are involved in numerous biological processes and show enormous biotechnological potential. Among plant lectins, the hevein domain is extremely common, being observed in several kinds of lectins. Moreover, this domain is also observed in an important class of antimicrobial peptides named hevein-like peptides. Due to higher cysteine residues conservation, hevein-like peptides could be mined among the sequence databases. By using the pattern CX(4,5)CC[GS]X(2)GXCGX[GST]X(2,3)[FWY]C[GS]X[AGS] novel hevein-like peptide precursors were found from three different plants: Oryza sativa, Vitis vinifera and Selaginella moellendorffii. In addition, an hevein-like peptide precursor from the phytopathogenic fungus Phaeosphaeria nodorum was also identified. The molecular models indicate that they have the same scaffold as others, composed of an antiparallel β-sheet and short helices. Nonetheless, the fungal hevein-like peptide probably has a different disulfide bond pattern. Despite this difference, the complexes between peptide and N,N,N-triacetylglucosamine are stable, according to molecular dynamics simulations. This is the first report of an hevein-like peptide from an organism outside the plant kingdom. The exact role of an hevein-like peptide in the fungal biology must be clarified, while in plants they are clearly involved in plant defense. In summary, data here reported clear shows that an in silico strategy could lead to the identification of novel hevein-like peptides that could be used as biotechnological tools in the fields of health and agribusiness.
    Peptides 09/2012; 38(1):127-136. · 2.52 Impact Factor
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    ABSTRACT: Antimicrobial peptides (AMPs) are compounds that act in a wide range of physiological defensive mechanisms developed to counteract bacteria, fungi, parasites and viruses. These molecules have become increasingly important as a consequence of remarkable microorganism resistance to common antibiotics. This report shows Escherichia coli expressing the recombinant antimicrobial peptide Pg-AMP1 previously isolated from Psidium guajava seeds. The deduced Pg-AMP1 open reading frame consists in a 168bp long plus methionine also containing a His6 tag, encoding a predicted 62 amino acid residue peptide with related molecular mass calculated to be 6.98kDa as a monomer and 13.96kDa at the dimer form. The recombinant Pg-AMP1 peptide showed inhibitory activity against multiple Gram-negative (E. coli, Klebsiella pneumonia and Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus and Staphylococcus epidermides) bacteria. Moreover, theoretical structure analyses were performed in order to understand the functional differences between natural and recombinant Pg-AMP1 forms. Data here reported suggest that Pg-AMP1 is a promising peptide to be used as a biotechnological tool for control of human infectious diseases.
    Peptides 07/2012; 37(2):294-300. · 2.52 Impact Factor
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    ABSTRACT: Antimicrobial resistance is an ever-increasing problem throughout the world and has already reached severe proportions. Bacteria can develop ways to render traditional antibiotics ineffective, raising a crucial need to find new antimicrobials with novel mode of action. We demonstrate here a novel class of pyrazine functionalized Ag(I) and Au(I)-NHC complexes as antibacterial agents against human pathogens that are resistant to several antibiotics. Complete synthetic and structural studies of Au(I) and Ag(I) complexes of 2-(1- methylimidazolium) pyrimidinechloride (L-1), 2,6-bis(1-methylimidazol)pyrazinechloride (L-2) and 2,6-bis(1-methyl imidazol) pyrazinehexa-fluorophosphate (L-3) are reported herein. Chloro[2,6-bis(1-methyl imidazol)pyrazine]gold(I), 2b and chloro [2,6-bis(1- methyl imidazol)pyrazine]silver(I), 2a complexes are found to have more potent antimicrobial activity than other synthesized compounds and several conventionally used antibiotics. Complexes 2b and 2a also inhibit the biofilm formation by Gram-positive bacteria, Streptococcus mutans and Gram-negative bacteria, Escherichia coli, causing drastic damage to the bacterial cell wall and increasing membrane permeability. Complexes 2b and 2a strongly binds to both Lys and Dap-Type peptidoglycan layers, which may be the reason for damage to the bacterial cell wall. Theoretical studies of all the complexes reveal that 2b and 2a are more reactive than other complexes, and this may be the cause of differences in antibacterial activity. These findings will pave the way towards developing a new class of antibiotics against different groups of conventional antibiotic-resistant bacteria.
    Current Medicinal Chemistry 06/2012; 19(24):4184-93. · 3.72 Impact Factor
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    William F. Porto, Osmar N. Silva, Oct�vio L. Franco
    04/2012; , ISBN: 978-953-51-0555-8
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    William F. Porto, Osmar N. Silva, Octávio L. Franco
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    ABSTRACT: In recent decades the activity of conventional antibiotics against pathogenic bacteria has decreased due to the development of resistance. This phenomenon has generated the socalled ‘superbugs’, which are multi-resistant bacteria. In this context, antimicrobial peptides (AMP) appear as an alternative to control them. AMPs have been found in several sources, including animals, plants and fungi, constituting the first line of host defence against pathogens. However, the use of AMPs as therapeutic agents has some limitations, such as stability, cytotoxicity and mainly their amino acid length, since amino acids are expensive building blocks. Despite these limitations they have compensatory properties, including secondary activities such as immunomodulation or antitumor ones. Several methods have been applied since the 1990s for rational AMPs design, in order to generate analogues with improved activity, looking to reduce limitations and increase advantages. Computer-aided identification and design of AMPs play a crucial role in this area. The discovery of AMP properties, through the first rational design studies, will allow the development of methods for prediction of AMPs, which in turn, should lead to identification prior to synthesis of novel analogues. Thus, this chapter will be dedicated to describing important techniques in prediction and rational design of AMPs and their applications for drug development.
    04/2012: pages 20; , ISBN: William F. Porto, Osmar N. Silva and Octávio L. Franco (2012). Prediction and Rational Design of Antimicrobial Peptides, Protein Structure, Dr. Eshel Faraggi (Ed.), ISBN: 978-953-51-0555-8, InTech, Available from: http://www.intechopen.com/books/protein-s
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    ABSTRACT: Healthcare-associated infections (HAIs) are causes of mortality and morbidity worldwide. The prevalence of bacterial resistance to common antibiotics has increased in recent years, highlighting the need to develop novel alternatives for controlling these pathogens. Pitviper venoms are composed of a multifaceted mixture of peptides, proteins and inorganic components. L-amino oxidase (LAO) is a multifunctional enzyme that is able to develop different activities including antibacterial activity. In this study a novel LAO from Bothrops mattogrosensis (BmLAO) was isolated and biochemically characterized. Partial enzyme sequence showed full identity to Bothrops pauloensis LAO. Moreover, LAO here isolated showed remarkable antibacterial activity against Gram-positive and -negative bacteria, clearly suggesting a secondary protective function. Otherwise, no cytotoxic activities against macrophages and erythrocytes were observed. Finally, some LAO fragments (BmLAO-f1, BmLAO-f2 and BmLAO-f3) were synthesized and further evaluated, also showing enhanced antimicrobial activity. Peptide fragments, which are the key residues involved in antimicrobial activity, were also structurally studied by using theoretical models. The fragments reported here may be promising candidates in the rational design of new antibiotics that could be used to control resistant microorganisms.
    PLoS ONE 01/2012; 7(3):e33639. · 3.73 Impact Factor
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    William F Porto, Allan S Pires, Octavio L Franco
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    ABSTRACT: The antimicrobial peptides (AMP) have been proposed as an alternative to control resistant pathogens. However, due to multifunctional properties of several AMP classes, until now there has been no way to perform efficient AMP identification, except through in vitro and in vivo tests. Nevertheless, an indication of activity can be provided by prediction methods. In order to contribute to the AMP prediction field, the CS-AMPPred (Cysteine-Stabilized Antimicrobial Peptides Predictor) is presented here, consisting of an updated version of the Support Vector Machine (SVM) model for antimicrobial activity prediction in cysteine-stabilized peptides. The CS-AMPPred is based on five sequence descriptors: indexes of (i) α-helix and (ii) loop formation; and averages of (iii) net charge, (iv) hydrophobicity and (v) flexibility. CS-AMPPred was based on 310 cysteine-stabilized AMPs and 310 sequences extracted from PDB. The polynomial kernel achieves the best accuracy on 5-fold cross validation (85.81%), while the radial and linear kernels achieve 84.19%. Testing in a blind data set, the polynomial and radial kernels achieve an accuracy of 90.00%, while the linear model achieves 89.33%. The three models reach higher accuracies than previously described methods. A standalone version of CS-AMPPred is available for download at <http://sourceforge.net/projects/csamppred/> and runs on any Linux machine.
    PLoS ONE 01/2012; 7(12):e51444. · 3.73 Impact Factor
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    ABSTRACT: In recent years, a number of peptides containing a cyclic structural fold have been described. Among them, the cyclotides family was widely reported in different plant tissues, being composed of small cyclic peptides containing 6 conserved cysteine residues connected by disulfide bonds and forming a cysteine-binding cyclic structure known as a cyclic cysteine knot. This structural scaffold is responsible for an enhanced structural stability against chemical, thermal, and proteolytic degradation. Because of the observed stability and multifunctionality, including insecticidal, antimicrobial, and anti-HIV (human immunodeficiency virus) action, much effort has gone into trying to elucidate the structural-function relations of cyclotide compounds. This review focuses on the novelties involving gene structure, precursor formation and processing, and protein folding of the cyclotide family, shedding some light on molecular mechanisms of cyclotide production. Because cyclotides are clear targets for drug development and also biotechnology applications, their chemical synthesis, heterologous systems production, and protein grafting are also addressed.
    Journal of Evidence-Based Complementary & Alternative Medicine. 01/2012; 17(1).
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    ABSTRACT: The antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as components of the innate immune system. Recently, it was demonstrated that a single AMP can perform various functions; this ability is known as "peptide promiscuity." However, little is known about promiscuity in plant AMPs without disulfide bonds. This study was carried out to evaluate the promiscuity of Cn-AMP1: a promising disulfide-free plant peptide with reduced size and cationic and hydrophobic properties. Its activity against human pathogenic bacteria and fungal pathogens, as well as its in vitro immunostimulatory activity and effects on cancerous and healthy mammalian cell proliferation were studied here. Cn-AMP1 exerts antimicrobial effects against Gram-positive bacteria, Gram-negative bacteria, and fungi. Moreover, tumor cell viability activity in Caco-2 cells, as well as immunostimulatory activity by evaluating upregulated inflammatory-cytokine secretion by monocytes was also positively observed. Cn-AMP1 does not exhibit a well-defined conformation in aqueous solution and probably undergoes a 3(10)-helix transition in hydrophobic environments. The experimental results support the promiscuous activity of Cn-AMP1, presenting a wide range of activities, including antibacterial, antifungal, and immunostimulatory activity. In the future, Cn-AMP1 should be used in the development of novel biopharmaceuticals, mainly due to its reduced size and broad spectrum of activity.
    Biopolymers 01/2012; 98(4):322-31. · 2.88 Impact Factor
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    ABSTRACT: The cysteine knot motifs are widely spread in several classes of peptides including those with antimicrobial functions. These motifs offer a major stability to the protein structure. Nevertheless, the antimicrobial activity is modulated by physicochemical properties. In this paper, we create a model of support vector machine to predict antimicrobial activity from sequences with similar motifs, based on physicochemical properties: net charge, ratio between hydrophobic and charged residues, average hydrophobicity and hydrophobic moment. The support vector machine model was trained with 146 antimicrobial peptides with six cysteines from the antimicrobial peptides database and an equal number of random sequences predicted as transmembrane proteins. The polynomial kernel shows the best accuracy (77.4%) on 10-fold cross validation. Testing in a blind dataset, we observe an accuracy of 83.02%. Through this model, proteins of varied size with a cysteine knot motif can be predicted with good reliability.
    Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings; 01/2010

Publication Stats

74 Citations
46.00 Total Impact Points

Institutions

  • 2013
    • IIT Kharagpur
      • Department of Biotechnology
      Kharagpur, Bengal, India
  • 2012
    • Universidade Católica de Brasília
      • Centro de Análises Proteômicas e Bioquímicas - CAPB
      Brasília, Federal District, Brazil