ArticlePLoS computational biology2014
Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 57 citations in OpenAlex.
- Dynamics and thermal stability of the bypass polymerase, DinB homolog (Dbh).Frontiers in molecular biosciences · 2024Article
- Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems.Journal of biological physics · 2022Review
- Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.JACS Au · 2022Article
- Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch.International journal of molecular sciences · 2022Article
- Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics.PLoS computational biology · 2021Article
- Photo-activatable Ub-PCNA probes reveal new structural features of the Saccharomyces cerevisiae Polη/PCNA complex.Nucleic acids research · 2021Article
- The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition.The journal of physical chemistry. B · 2021Article
- Article
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 2020Article
- Conformational state switching and pathways of chromosome dynamics in cell cycle.Applied physics reviews · 2020Article
- Binding-Induced Conformational Changes Involved in Sliding Clamp PCNA and DNA Polymerase DPO4.iScience · 2020Article
- Investigations of the underlying mechanisms of HIF-1α and CITED2 binding to TAZ1.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins.Journal of chemical information and modeling · 2020Article
- Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase.Journal of chemical theory and computation · 2020Article
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- A conserved loop-wedge motif moderates reaction site search and recognition by FEN1.Nucleic acids research · 2018Article
- Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition.ACS central science · 2018Article
- Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.Molecules (Basel, Switzerland) · 2018Article
- Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2017Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-DNA recognition is a central biological process that governs the life of cells. A protein will often undergo a conformational transition to form the functional complex with its target DNA. The protein conformational dynamics are expected to contribute to the stability and specificity of DNA recognition and therefore may control the functional activity of the protein-DNA complex. Understanding how the conformational dynamics influences the protein-DNA recognition is still challenging. Here, we developed a two-basin structure-based model to explore functional dynamics in Sulfolobus solfataricus DNA Y-family polymerase IV (DPO4) during its binding to DNA. With explicit consideration of non-specific and specific interactions between DPO4 and DNA, we found that DPO4-DNA recognition is comprised of first 3D diffusion, then a short-range adjustment sliding on DNA and finally specific binding. Interestingly, we found that DPO4 is under a conformational equilibrium between multiple states during the binding process and the distributions of the conformations vary at different binding stages. By modulating the strength of the electrostatic interactions, the flexibility of the linker, and the conformational dynamics in DPO4, we drew a clear picture on how DPO4 dynamically regulates the DNA recognition. We argue that the unique features of flexibility and conformational dynamics in DPO4-DNA recognition have direct implications for low-fidelity translesion DNA synthesis, most of which is found to be accomplished by the Y-family DNA polymerases. Our results help complete the description of the DNA synthesis process for the Y-family polymerases. Furthermore, the methods developed here can be widely applied for future investigations on how various proteins recognize and bind specific DNA substrates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.