Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA
DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> is a member of the X-family of DNA polymerases, playing a critical role in th...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-05-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/10/8988 |
| _version_ | 1797599727867396096 |
|---|---|
| author | Amit Srivastava Haitham Idriss Dirar Homouz |
| author_facet | Amit Srivastava Haitham Idriss Dirar Homouz |
| author_sort | Amit Srivastava |
| collection | DOAJ |
| description | DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> is a member of the X-family of DNA polymerases, playing a critical role in the base excision repair (BER) pathway in mammalian cells by implementing the nucleotide gap-filling step. In vitro phosphorylation of DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> with PKC on S44 causes loss in the enzyme’s DNA polymerase activity but not single-strand DNA binding. Although these studies have shown that single-stranded DNA binding is not affected by phosphorylation, the structural basis behind the mechanism underlying phosphorylation-induced activity loss remains poorly understood. Previous modeling studies suggested phosphorylation of S44 was sufficient to induce structural changes that impact the enzyme’s polymerase function. However, the S44 phosphorylated-enzyme/DNA complex has not been modeled so far. To address this knowledge gap, we conducted atomistic molecular dynamics simulations of pol <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> complexed with gapped DNA. Our simulations, which used explicit solvent and lasted for microseconds, revealed that phosphorylation at the S44 site, in the presence of Mg ions, induced significant conformational changes in the enzyme. Specifically, these changes led to the transformation of the enzyme from a closed to an open structure. Additionally, our simulations identified phosphorylation-induced allosteric coupling between the inter-domain region, suggesting the existence of a putative allosteric site. Taken together, our results provide a mechanistic understanding of the conformational transition observed due to phosphorylation in DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> interactions with gapped DNA. Our simulations shed light on the mechanisms of phosphorylation-induced activity loss in DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> and reveal potential targets for the development of novel therapeutics aimed at mitigating the effects of this post-translational modification. |
| first_indexed | 2024-03-11T03:38:23Z |
| format | Article |
| id | doaj.art-4342d41faf194d738819cd61bf3c316b |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T03:38:23Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4342d41faf194d738819cd61bf3c316b2023-11-18T01:45:27ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-05-012410898810.3390/ijms24108988Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNAAmit Srivastava0Haitham Idriss1Dirar Homouz2Department of Physics, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab EmiratesSchool of Public Health, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UKDepartment of Physics, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab EmiratesDNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> is a member of the X-family of DNA polymerases, playing a critical role in the base excision repair (BER) pathway in mammalian cells by implementing the nucleotide gap-filling step. In vitro phosphorylation of DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> with PKC on S44 causes loss in the enzyme’s DNA polymerase activity but not single-strand DNA binding. Although these studies have shown that single-stranded DNA binding is not affected by phosphorylation, the structural basis behind the mechanism underlying phosphorylation-induced activity loss remains poorly understood. Previous modeling studies suggested phosphorylation of S44 was sufficient to induce structural changes that impact the enzyme’s polymerase function. However, the S44 phosphorylated-enzyme/DNA complex has not been modeled so far. To address this knowledge gap, we conducted atomistic molecular dynamics simulations of pol <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> complexed with gapped DNA. Our simulations, which used explicit solvent and lasted for microseconds, revealed that phosphorylation at the S44 site, in the presence of Mg ions, induced significant conformational changes in the enzyme. Specifically, these changes led to the transformation of the enzyme from a closed to an open structure. Additionally, our simulations identified phosphorylation-induced allosteric coupling between the inter-domain region, suggesting the existence of a putative allosteric site. Taken together, our results provide a mechanistic understanding of the conformational transition observed due to phosphorylation in DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> interactions with gapped DNA. Our simulations shed light on the mechanisms of phosphorylation-induced activity loss in DNA polymerase <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula> and reveal potential targets for the development of novel therapeutics aimed at mitigating the effects of this post-translational modification.https://www.mdpi.com/1422-0067/24/10/8988DNA polymerase βpost-translational modificationsMD simulationsprincipal component analysis |
| spellingShingle | Amit Srivastava Haitham Idriss Dirar Homouz Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA International Journal of Molecular Sciences DNA polymerase β post-translational modifications MD simulations principal component analysis |
| title | Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA |
| title_full | Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA |
| title_fullStr | Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA |
| title_full_unstemmed | Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA |
| title_short | Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase <i>β</i> Bound to Gapped DNA |
| title_sort | structural insights into phosphorylation mediated polymerase function loss for dna polymerase i β i bound to gapped dna |
| topic | DNA polymerase β post-translational modifications MD simulations principal component analysis |
| url | https://www.mdpi.com/1422-0067/24/10/8988 |
| work_keys_str_mv | AT amitsrivastava structuralinsightsintophosphorylationmediatedpolymerasefunctionlossfordnapolymeraseibiboundtogappeddna AT haithamidriss structuralinsightsintophosphorylationmediatedpolymerasefunctionlossfordnapolymeraseibiboundtogappeddna AT dirarhomouz structuralinsightsintophosphorylationmediatedpolymerasefunctionlossfordnapolymeraseibiboundtogappeddna |