A Bioinformatics Approach for Homology Modeling Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7

Abstract

Malaria is a major public health concern, and malarial parasites have developed resistance against the commonly available drugs. So now a days it is a major concern to find out a new target for drug therapy. Plasmodium falciparum 3D7, one of the strains of plasmodium species also lacks in a functional tricarboxylic acid cycle and solely dependent on glycolysis for its energy supply like other plasmodium species. Although enzymes of malarial parasite have been considered as potential antimalarial drug targets, a little is known about their structural biology. The tertiary structure of triose phosphate isomerase of P. falciparum 3D7 was determined by means of homology modeling through multiple alignment followed by intensive optimization and validation. The modeling was done by Swiss-Model Workspace. The obtained model was verified with the structure validation programs such as, PROCHECK, Verify3D, and QMEAN for reliability. The verify3D value of 0.69 indicates that the environment profile of the model is good. A self-optimized prediction method with alignment or SOPMA is employed for calculation of the secondary structural features of triose phosphate isomerase. The secondary structure indicates that the predicted 3D structure of triosephosphate isomerase of P. falciparum 3D7 contains 48.37% α-helix, 29.27% random coil, and 16.67% extended strand. Active site determination through CASTp suggests that this protein can be utilized as a potential drug target. However, these will further be tested by wet lab studies for a targeted vaccine design against P. falciparum 3D7.

The potentials of Calotropis procera against filarial elephantiasis: an in-silico approach

“…ERRAT plots show a quality factor of 93.9547 which shows that the model has a good quality (Messaoudi et al 2013). 96.14% of the residues had passed the average 3D-1D score >= 0.2 when validated by Verify3D (Ullah et al 2012). In the Ramachandran plot, 0 % residues were found in the disallowed region inferring that the model has a good secondary structure (Waghmare et al 2016) Glutathione-s-transferase was taken as the target and phytocompounds structures from the plant Calotropis procera were taken as ligands for docking studies.…”

In silico approach to develop structure and functional analysis of response receiver regulator protein of the strain pseaudomonas fulva 12x

“…In this study, Model build up is done using different program which suggest that the proteins contains alpha helix, beta strand and loop. The program CPH model 3.o server was used to save query sequence as PDB file, then submit to another web based software ,name swiss -prot workspace that reduce the problem of downloading and installising wide range of program packages and databases [40]. PROCHEK program check the Stereo chemical quality and perfection of the developed models that shows amino acid percentage in the favorable region was 93.5% and in the disallowed region was 0.0%.…”

Immunoinformatics Based Vaccine Design for Zea M 1 Pollen Allergen

“…8 In SDAP allergen database, 9 FAO/WHO Allergenicity Rules based on sequence homology for full FASTA alignment for fasta sequence of 2HCZ showed 50 sequences of allergens with an E score higher than 0.01. Alignment was made with FAST 3.45.…”

“…From SDAP allergen database, 9 50 homologous allergens are identified using amino acid sequence of pollen allergen Zea m 1 as shown in Table 1, since sequences with E values < 0.01 are almost always homologous in nature. All 50 protein sequences are retrieved from SwissProt 11 and aligned to identify conserved sequences with varying length using Muscle tool 3.8.31 12 in Table 2.…”