title: Structural, functional and molecular docking study to characterize GMI1 from Arabidopsis thaliana.
abstract: γ-irradiation and Mitomycin C Induced 1 (GMI1), is a member of the SMC-hinge domain-containing protein family that takes part in double stranded break repair mechanism in eukaryotic cells. In this study we hypothesize a small molecule-Adenosine Tri Phosphate (ATP) binding region of novel SMC like GM1 protein in model organism Arabidopsis thaliana using in silico modeling. Initially, analyzing sequence information for the protein indicated presence of motifs - 'Walker A nucleotide-binding domain' that are required to interact with nucleotides along with 'Walker B' motif and ABC signature sequences. This was further proven through GMI1-ATP docking experiment and results were verified by comparing the values with controls. In negative control, no binding was seen in the same binding region of GMI1 structure for small molecules randomly selected form PubChem database, whereas in positive control binding affinity of other known proteins with ATP binding potential resembled GMI1-ATP binding affinity of -5.4 kcal/mol. Furthermore we also docked small molecules that shares structural similarity with ATP to GMI1 and found that Purine Mononucleotide bound the region with the best affinity, which implies that the compound may bind the protein with strong binding and can work as a potential agonist/antagonist to GMI1. We believe that the study would shed more light into the GM1 mechanism of action. Although the computational predictions made here are based on concrete confidence, it should be mentioned that in vitro experimentation does not fall into the scopes of this study and thus the results found here have to be further validated in vitro.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh. rezaul.nayeem@gmail.com
authors.forename: Md Rezaul
authors.initials: MR
authors.lastname: Islam
authors.forename: Md Ismail
authors.initials: MI
authors.lastname: Hosen
authors.forename: Aubhishek
authors.initials: A
authors.lastname: Zaman
authors.forename: Md Ohedul
authors.initials: MO
authors.lastname: Islam
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics*; D019295:Computational Biology; D004260:DNA Repair / Q000235:genetics*; D008958:Models, Molecular; D057054:Molecular Imaging; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship; D016415:Sequence Alignment; D017385:Sequence Homology
chemical_list: D029681:Arabidopsis Proteins; D002868:Chromosomal Proteins, Non-Histone; C584333:GMI1 protein, Arabidopsis; D000255:Adenosine Triphosphate