ArticleProteins2009
Effective approach for calculations of absolute stability of proteins using focused dielectric constants.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2.Frontiers in molecular biosciences · 2023Article
- Simulating the directional translocation of a substrate by the AAA+ motor in the 26S proteasome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.Biophysical reviews · 2017Review
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- On the energy components governing molecular recognition in the framework of continuum approaches.Frontiers in molecular biosciences · 2015Review
- Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).Angewandte Chemie (International ed. in English) · 2014Article
- An effective coarse-grained model for biological simulations: recent refinements and validations.Proteins · 2014Article
- On the nature of the apparent free energy of inserting amino acids into membrane through the translocon.The journal of physical chemistry. B · 2013Article
- On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi.Journal of chemical theory and computation · 2013Article
- Computational protein engineering: bridging the gap between rational design and laboratory evolution.International journal of molecular sciences · 2012Review
- Coarse grained model for exploring voltage dependent ion channels.Biochimica et biophysica acta · 2012Article
- The linear interaction energy method for the prediction of protein stability changes upon mutation.Proteins · 2012Article
- Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.Biochemistry · 2011Article
- On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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3 authors.
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Abstract
The ability to predict the absolute stability of proteins based on their corresponding sequence and structure is a problem of great fundamental and practical importance. In this work, we report an extensive, refinement and validation of our recent approach (Roca et al., FEBS Lett 2007;581:2065-2071) for predicting absolute values of protein stability DeltaG(fold). This approach employs the semimacroscopic protein dipole Langevin dipole method in its linear response approximation version (PDLD/S-LRA) while using the best fitted values of the dielectric constants epsilon'(p) and epsilon'(eff) for the self energy and charge-charge interactions, respectively. The method is validated on a diverse set of 45 proteins. It is found that the best fitted values of both dielectric constants are around 40. However, the self energy of internal residues and the charge-charge interactions of Lys have to be treated with care, using a somewhat lower values of epsilon'(p) and epsilon'(eff). The predictions of DeltaG(fold) reported here, have an average error of only 1.8 kcal/mole compared to the observed values, making our method very promising for estimating protein stability. It also provides valuable insight into the complex electrostatic phenomena taking place in folded proteins.
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