ArticlePloS one2012
Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 50 citations in OpenAlex.
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- An In Silico Study Investigating Camptothecin-Analog Interaction with Human Protein Tyrosine Phosphatase, SHP2 (PTPN11).Pharmaceuticals (Basel, Switzerland) · 2023Article
- A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis.Scientific reports · 2022Article
- APE1/Ref-1 Role in Inflammation and Immune Response.Frontiers in immunology · 2022Review
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- Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA.Metabolic brain disease · 2019Article
- Prediction and Structural Comparison of Deleterious Coding Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) in Human LEP Gene Associated with Obesity.BioMed research international · 2019Article
- "Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations.Scientific reports · 2018Article
- Exploiting the Ref-1-APE1 node in cancer signaling and other diseases: from bench to clinic.NPJ precision oncology · 2017Article
- Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach.PloS one · 2017Article
- Localized structural frustration for evaluating the impact of sequence variants.Nucleic acids research · 2016Article
- Distribution of single-nucleotide variants on protein-protein interaction sites and its relationship with minor allele frequency.Protein science : a publication of the Protein Society · 2016Article
- Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins.Biophysics and physicobiology · 2016Article
- Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins.Current opinion in structural biology · 2015Review
- On human disease-causing amino acid variants: statistical study of sequence and structural patterns.Human mutation · 2015Article
- Free energy simulations of amylin I26P mutation in a lipid bilayer.European biophysics journal : EBJ · 2015Article
- Modeling and docking studies on novel mutants (K71L and T204V) of the ATPase domain of human heat shock 70 kDa protein 1.International journal of molecular sciences · 2014Article
- Structure-function studies on non-synonymous SNPs of chemokine receptor gene implicated in cardiovascular disease: a computational approach.The protein journal · 2013Article
- Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundElucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mutations in APE1 protein modify the physicochemical property of amino acids that affect the protein stability and dynamic behavior. Further, these mutations disrupt the binding sites and prohibit the protein to form complexes with its interacting DNA. PRINCIPAL
findingsIn this study, we developed a rapid and cost-effective method to analyze variants in APE1 gene that are associated with disease susceptibility and evaluated their impacts on APE1-DNA complex dynamic behavior. Initially, two different in silico approaches were used to identify deleterious variants in APE1 gene. Deleterious scores that overlap in these approaches were taken in concern and based on it, two nsSNPs with IDs rs61730854 (I64T) and rs1803120 (P311S) were taken further for structural analysis. SIGNIFICANCE: Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions. This study addresses such new methods for validating functional polymorphisms of human APE1 which is critically involved in causing deficit in repair capacity, which in turn leads to genetic instability and carcinogenesis.
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