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Updated: Aug 26, 2025
Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit
Published on: June 28, 2013
In silico structural modeling and quality assessment of Plasmodium knowlesi apical membrane antigen 1 using
F N Haron1, A Azazi1, K H Chua2
1Faculty of Health Sciences, Universiti Sultan Zainal Abidin, 21300 Kuala Nerus, Terengganu, Malaysia.
Abstract:
Plasmodium knowlesi is the most common zoonotic parasite associated with human malaria infection in Malaysia. Apical membrane antigen 1 (AMA1) protein in the parasite plays a critical role in parasite invasion into host cells. To date, there is no complete three-dimensional ectodomain structure of P. knowlesi AMA1 (PkAMA1) protein. The knowledge of a protein structure is important to understand the protein molecular functions. Three in silico servers with respective structure prediction methods were used in this study, i.e., SWISS-MODEL for homology modeling and Phyre2 for protein threading, which are template-based modeling, while I-TASSER for template-free ab initio modeling. Two query sequences were used in the study, i.e., native ectodomain of PkAMA1 strain H protein designated as PkAMA1-H and a modified PkAMA1 (mPkAMA1) protein sequence in adaptation for Pichia pastoris expression. The quality of each model was assessed by ProSA-web, QMEAN and SAVES v6.0 (ERRAT, Verify3D and Ramachandran plot) servers. Generated models were then superimposed with two models of Plasmodium AMA1 deposited in Protein Data Bank (PDB), i.e., PkAMA1 (4UV6.B) and Plasmodium vivax AMA1 (PvAMA1, 1W81) protein structures for similarity assessment, quantified by root-meansquare deviation (RMSD) value. SWISS-MODEL, Phyre2 and I-TASSER server generated two, one and five models, respectively. All models are of good quality according to ProSA-web assessment. Based on the average values of model quality assessment and superimposition, the models that recorded highest values for most parameters were selected as best predicted models, i.e., model 2 for both PkAMA1-H and mPkAMA1 from SWISS-MODEL as well as model 1 of PkAMA1-H and model 3 of mPkAMA1 from I-TASSER. Template-based method is useful if known template is available, but template-free method is more suitable if there is no known available template. Generated models can be used as guidance in further protein study that requires protein structural data, i.e., protein-protein interaction study.
Insights
This study computationally predicts the 3D structure of Plasmodium knowlesi AMA1 protein, crucial for malaria parasite invasion. The findings provide valuable structural data for future research on this significant zoonotic pathogen.
Area of Science:
- Parasitology
- Structural Biology
- Bioinformatics
Background:
- Plasmodium knowlesi is a common zoonotic cause of malaria in Malaysia.
- The Apical Membrane Antigen 1 (AMA1) protein is vital for malaria parasite invasion into host cells.
- The three-dimensional structure of P. knowlesi AMA1 (PkAMA1) ectodomain is currently unknown.
Purpose of the Study:
- To predict the three-dimensional ectodomain structure of P. knowlesi AMA1 (PkAMA1) using in silico methods.
- To evaluate and compare different protein structure prediction servers and methods.
- To generate high-quality PkAMA1 models for future structural and functional studies.
Main Methods:
- Utilized three in silico servers: SWISS-MODEL (homology modeling), Phyre2 (protein threading), and I-TASSER (template-free ab initio modeling).
- Employed two query sequences: native PkAMA1-H and modified mPkAMA1 for Pichia pastoris expression.
- Assessed model quality using ProSA-web, QMEAN, and SAVES v6.0 (ERRAT, Verify3D, Ramachandran plot), and compared with existing PDB structures (4UV6.B, 1W81).
Main Results:
- SWISS-MODEL, Phyre2, and I-TASSER generated a total of eight models (two, one, and five, respectively).
- All generated models demonstrated good quality based on ProSA-web assessment.
- Selected best models included SWISS-MODEL's model 2 (PkAMA1-H and mPkAMA1) and I-TASSER's model 1 (PkAMA1-H) and model 3 (mPkAMA1) based on comprehensive quality and similarity assessments.
Conclusions:
- Both template-based (SWISS-MODEL, Phyre2) and template-free (I-TASSER) methods can predict PkAMA1 structures.
- Template-free methods are advantageous when no suitable templates are available.
- The generated PkAMA1 models provide essential structural data for future protein-protein interaction studies and drug development targeting malaria.
