ArticleBMC structural biology2007
Energetics of the protein-DNA-water interaction.
Article in BMC structural biology, 2007. 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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Who cites it
19 citing papers in PubMed.
- Interfacial water confers transcription factors with dinucleotide specificity.Nature structural & molecular biology · 2025Article
- A Combined Molecular Dynamics and Hydropathic INTeraction (HINT) Approach to Investigate Protein Flexibility: The PPARγ Case Study.Molecules (Basel, Switzerland) · 2024Article
- HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham.Frontiers in molecular biosciences · 2023Review
- The role of zinc finger linkers in zinc finger protein binding to DNA.Journal of computer-aided molecular design · 2021Article
- The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition.The journal of physical chemistry. B · 2021Article
- Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection ofSensors (Basel, Switzerland) · 2020Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- From protein structure to function via single crystal optical spectroscopy.Frontiers in molecular biosciences · 2015Review
- Predicting the molecular interactions of CRIP1a-cannabinoid 1 receptor with integrated molecular modeling approaches.Bioorganic & medicinal chemistry letters · 2014Article
- DNA adsorption to and elution from silica surfaces: influence of amino acid buffers.The journal of physical chemistry. B · 2013Article
- Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Solvated protein-DNA docking using HADDOCK.Journal of biomolecular NMR · 2013Article
- Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target.PloS one · 2013Article
- Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif.PloS one · 2011Article
- Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.Nucleic acids research · 2010Article
- Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies.Molecular immunology · 2009Article
- Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT.Journal of computer-aided molecular design · 2009Article
- Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach.Chemical research in toxicology · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundTo understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species.
resultsAn initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r2 of 0.21 and standard error of +/- 1.71 kcal mol-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r2 of 0.56 and standard error of +/- 1.28 kcal mol-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts.
conclusionThis study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel.
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