Systems Biology Approach to Screen and Identify Algae-Based …
433
algal AP helps to detect least quantities of toxic heavy metals in nature. Hence,
the current study focuses to tabulate novel putative algal APs through phylogenetic
analysis and to predict heavy metals (i.e. cadmium and mercury) affinity on algal
APs.
2 Experimental
In this current study, diverse ranges of algal APs (known and putative) protein sequences including EC 3.1.3.1 have been retrieved from
KEGG, Uniprot protein databases including following unique protein Ids, i.e.,
Vca_Pho (Volvox carteri): XP_002958226.1; Cre_Pho (Chlamydomonas reinhardtii): XP_001702318.1; Lyn_Pho (Lyngbya sp. PCC 8106): ZP_01623784.1;
Scy_Pho (Synechocystis sp.PCC 6803): BAA16956.1; Sco_Pho (Synechococcus
sp.PCC 7942): AAA27331.1; Nos_Pho (Nostos sp.PCC 7120): BAB76990.1;
SynWH5_Pho (Synechococcus sp.WH5701): EAQ75607.1; SynWH8_Pho (Synechococcus sp. WH8120): NP_898480.1; Sel_Pho (Synechococcus elongatus PCC
6301): YP_170873.1; Cya_Pho (Cyanothece sp.ATCC 51142): B1WW62; Gci_Pho
(Gloeothece citriformis PCC 7424): B7KHT5; Pma_Pho (Prochlorococcus marinus
NATL1A): ABM75708; Cpa_Pho (Calothrix parietina): A0A0T7BMF5; Ava_Pho
(Anabaena variabilis ATCC 29413): Q3M5K7; AhaA2_Pho (Aphanothece halophytica A2): F5HRA6; Aha_Pho (Aphanothece halophytica): F5HRA4. Retrieved
protein sequences have been undergone multiple sequence alignment and phylogenetic studies using ClustalW and Molecular Evolutionary Genetics Analysis (MEGA
4.0) software considering NJ algorithm (Tamura et al. 2007). Putative protein 3D
homology models have been generated using SWISS Model online server (Waterhouse et al. 2018) considering the most similar protein model in protein PDB
database. Putative protein model qualities have been evaluated through Ramachandran plot, Global Model Quality Estimation (GMQE), MolProbity Score (Waterhouse et al. 2018). Afterward, transmembrane helices in protein sequences have been
predicted to make sure which enzymes are secretory in nature (Krogh et al. 2001).
Finally, putative protein models have been docked with two selected heavy metals,
i.e., cadmium and mercury to predict the metal affinity and amino acid residues
involvement in these interactions using MIB webserver (Lin et al. 2016).
3 Results and Discussion
Homology modeling using SWISS Model server has shown that most of algal
AP models exist in the favored region in Ramachandran plot (average value
of 82.5%) and MolProbity value around 2 having average sequence similarity
433
algal AP helps to detect least quantities of toxic heavy metals in nature. Hence,
the current study focuses to tabulate novel putative algal APs through phylogenetic
analysis and to predict heavy metals (i.e. cadmium and mercury) affinity on algal
APs.
2 Experimental
In this current study, diverse ranges of algal APs (known and putative) protein sequences including EC 3.1.3.1 have been retrieved from
KEGG, Uniprot protein databases including following unique protein Ids, i.e.,
Vca_Pho (Volvox carteri): XP_002958226.1; Cre_Pho (Chlamydomonas reinhardtii): XP_001702318.1; Lyn_Pho (Lyngbya sp. PCC 8106): ZP_01623784.1;
Scy_Pho (Synechocystis sp.PCC 6803): BAA16956.1; Sco_Pho (Synechococcus
sp.PCC 7942): AAA27331.1; Nos_Pho (Nostos sp.PCC 7120): BAB76990.1;
SynWH5_Pho (Synechococcus sp.WH5701): EAQ75607.1; SynWH8_Pho (Synechococcus sp. WH8120): NP_898480.1; Sel_Pho (Synechococcus elongatus PCC
6301): YP_170873.1; Cya_Pho (Cyanothece sp.ATCC 51142): B1WW62; Gci_Pho
(Gloeothece citriformis PCC 7424): B7KHT5; Pma_Pho (Prochlorococcus marinus
NATL1A): ABM75708; Cpa_Pho (Calothrix parietina): A0A0T7BMF5; Ava_Pho
(Anabaena variabilis ATCC 29413): Q3M5K7; AhaA2_Pho (Aphanothece halophytica A2): F5HRA6; Aha_Pho (Aphanothece halophytica): F5HRA4. Retrieved
protein sequences have been undergone multiple sequence alignment and phylogenetic studies using ClustalW and Molecular Evolutionary Genetics Analysis (MEGA
4.0) software considering NJ algorithm (Tamura et al. 2007). Putative protein 3D
homology models have been generated using SWISS Model online server (Waterhouse et al. 2018) considering the most similar protein model in protein PDB
database. Putative protein model qualities have been evaluated through Ramachandran plot, Global Model Quality Estimation (GMQE), MolProbity Score (Waterhouse et al. 2018). Afterward, transmembrane helices in protein sequences have been
predicted to make sure which enzymes are secretory in nature (Krogh et al. 2001).
Finally, putative protein models have been docked with two selected heavy metals,
i.e., cadmium and mercury to predict the metal affinity and amino acid residues
involvement in these interactions using MIB webserver (Lin et al. 2016).
3 Results and Discussion
Homology modeling using SWISS Model server has shown that most of algal
AP models exist in the favored region in Ramachandran plot (average value
of 82.5%) and MolProbity value around 2 having average sequence similarity