Characterization of the NADH dehydrogenase subunit I
of the Fasciola gigantica using Computational tools
Fasciola gigantica, a parasitic worm belonging to class Trematoda
(Phylum: Platyhelminthes).This parasite causes fascioliasis in cattle,
buffalo, goats, sheep, donkeys and human. The infection of ruminants
with the parasite Fasciola gigantica is a cause of important economic
loss throughout Asia and Africa. Infected ruminants showed weight loss,
reduced productivity and poor milk production. It is regarded as one of
the prominent platyhelminth infections of ruminants in Asia and Africa
. Human Fascioliasis (HF) has now been found in almost all
governorates of the Delta region, in the city of Alex, in some
governorates of Upper Egypt, and in the reclaimed desert land. The
population at risk in Egypt is considered to be 27 million .
The flowchart shown below reveals the different stages of F.gigantica
life cycle. It has been reported that the most important intermediate
hosts of F. gigantica are L. auricularia; however, L. rufescens and
L. acuminata are the host snails in the Indian Subcontinent .
Infection strategy across globe:
Human Fascioliasis is increasingly recognized as causing significant
human disease, with 2.4 million people infected across the globe 
.Being endemic in 61 countries, the infection prevalence is estimated
to be high in the areas where extensive sheep and cattle raising occurs
and where dietary practices include the consumption of raw aquatic
Figure 1: Flowchart depicting the different stages in the life-cycle of
Selecting NADH dehydrogenase subunit 1 for Computational studies:
The recent studies made in inferring the taxonomic relationship between
Parasitic helminthes (includes, Fasciola sp.) and Facultative Anaerobic
Eukaryotes based on Multiple Lineages of the Mitochondrial Gene
NADH dehydrogenase subunit 1 (ND1) by Lynne van Herwerden, David
Blair and Takeshi Agatsuma .This study invoked us to employ
computational aspects of Bioinformatics to characterize the protein
NADH dehydrogenase subunit 1.
Extracting informations from the Protein sequence:
The protein sequence for NADH dehydrogenase subunit 1 was retrieved
from the NCBI (National Centre for Biotechnological Informations)
The identification of motif from the protein sequence is computationally
possible but in many cases, it will lead to random matches which will be
biologically insignificant. Hence, we proceeded the scanning of motif
from multiple approaches such as PeroxiBase profiles, PROSITE
patterns, PROSITE profiles, Pfam HMMs (both local and global models)
through the program MotifScan .
Figure 2: Result of MotifScan program.
Table 1: The list of motifs generated by MotifScan program for the
F.gigantica NADH dehydrogenase subunit1 protein sequence.
Motif No Residue Residue Types of Motif Computational
position position Method
1 71 74 N-glycosylation site freq_pat
2 53 56 Casein kinase II freq_pat
3 49 54 N-myristoylation freq_pat
3 99 104 N-myristoylation freq_pat
3 163 168 N-myristoylation freq_pat
4 1 5 Big-1 (bacterial Ig– prf
like domain 1)
5 1 25 Phenylalanine rich prf
pfam_fs 6 63 NADH pfam_fs
6 84 106 CD47 pfam_fs
pfam_ls 6 177 NADH pfam_ls
Many motifs were identified and we had safely ignored the matches
produced by different methods to make our proceedings sensible relying
on the fact that it belongs to the NADH dehydrogenase family of
proteins and we had concentrated on NADH dehydrogenase motif.
Pair wise Comparisons:
To study the phylogenetical analysis of this protein, we compared the
NADH dehydrogenase subunit 1 of Fasciola gigantica with that of
Fasciola hepatica and the results showed that they are found to be
Orthologous proteins because these two proteins perform the same
We used the program EMBOSS (European Molecular Biology Open-
Software) Suite hosted by EBI-EMBL (European Bioinformatics
Institute-European Molecular Biology Laboratory).Blosum 62 amino acid
substitution matrix was utilized to facilitate global sequence alignment
using Needleman-Wunsch Algorithm and the parameters are briefly
Open Gap penalty 10.0
Extension Gap penalty 0.5
Table 2: Parameters used in the EMBOSS program
Figure 3: Pair wise sequence comparison of F.hepatica and F.gigantica
Identity: 91.5 % (162/177)
Similarity: 93.2 % (165/177)
Gaps: 0.0 % (0/177)
(This result shows that this pair wise alignment is significant.)
Prediction of the 3 Dimensional Structures:
We searched through all the template structural databases to identify a
potential template for our protein sequence to build a 3-D model using
Homology modeling as our protein doesn’t have a structure(s) in any of
the Primary databases like PDB, MMDB, SCOP and CATH. No
template(s) was identified by programs like Geno3D,SWISS-MODEL
and EsyPred .
Secondary Structure Prediction:
Figure 4: Secondary Structure Prediction using QuickPhyre server.
(Helices and Coils were identified using Consensus).
Therefore, we decided to perform secondary structure prediction and to
build a 3-D model using folds from different families. This fold
represents different protein families and it is accomplished by
QuickPhyre Server, Imperial College, London .
Fold Recognition (continued ):
Figure 5: Fold recognized from different protein families using
These individual folds helped us to build a 3-D model irrespective of its
protein families, but by the sequence comparison of our protein
sequence with that of each individual fold.
Modeling of 3-D Protein Structure:
Due to the absence of template for building a model, we utilized the
above folds to conceptually build a protein model using QuickPhyre
We compared the secondary structure prediction analysis results
(Figure 4) with that of our modeled protein. Helices and coils shown in
the consensus are typically true because the NADH dehydrogenase
complex (of human) contains 60 trans-membrane helices and some
coils if we hope that this protein is conserved for its functions through
generations and maintained its structure.
Predicted 3-D model of the NADH dehydrogenase subunit1 :
Figure 6: The picture depicts the coiled region (red) of the protein NADH
Results & Discussions:
Our procedure to model a protein is based on the fold recognition from
different families. The drawback of our procedure is that helical regions
were not built as the bond between hydrogen is far apart or fewer and
due to the lack of structural template to assist the hydrogen bonding.
The potential identification is the Coils which can play a vital role in
protein complex formation as well as other functions like translocation of
protons in the respiratory chain. How far the F.gigantica NADH
dehydrogenase is similar in function to human? With the identification of
known redox centers and NADH binding site in human enzyme, the
ability of complex formation and other unidentified information can help
us to study this particular protein, its affinity for binding proteins and to
prepare a more effective drug than Triclabendazole in future.
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Kelley LA & Sternberg MJE Nature Protocols. 4, 363 - 371 (2009)