ArticleProtein science : a publication of the Protein Society2004
Quantification of helix-helix binding affinities in micelles and lipid bilayers.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.Journal of chemical theory and computation · 2023Article
- How physical forces drive the process of helical membrane protein folding.EMBO reports · 2022Review
- Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane).Bioinformatics (Oxford, England) · 2014Article
- Life at the border: adaptation of proteins to anisotropic membrane environment.Protein science : a publication of the Protein Society · 2014Review
- Structural adaptations of proteins to different biological membranes.Biochimica et biophysica acta · 2013Article
- Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes.Journal of chemical information and modeling · 2011Article
- Transmembrane helix association affinity can be modulated by flanking and noninterfacial residues.Biophysical journal · 2009Article
- Association energetics of membrane spanning alpha-helices.Current opinion in structural biology · 2008Review
- Molecular simulations of lipid-mediated protein-protein interactions.Biophysical journal · 2008Article
- Insight into the recognition patterns of the ErbB receptor family transmembrane domains: heterodimerization models through molecular dynamics search.European biophysics journal : EBJ · 2008Article
- The role of hydrophobic interactions in positioning of peripheral proteins in membranes.BMC structural biology · 2007Article
- An unfolding story of helical transmembrane proteins.Biochemistry · 2006Review
- Asn- and Asp-mediated interactions between transmembrane helices during translocon-mediated membrane protein assembly.EMBO reports · 2006Article
- Calculating the free energy of association of transmembrane helices.Biophysical journal · 2006Article
- Positioning of proteins in membranes: a computational approach.Protein science : a publication of the Protein Society · 2006Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
A theoretical approach for estimating association free energies of alpha-helices in nonpolar media has been developed. The parameters of energy functions have been derived from DeltaDeltaG values of mutants in water-soluble proteins and partitioning of organic solutes between water and nonpolar solvents. The proposed approach was verified successfully against three sets of published data: (1) dissociation constants of alpha-helical oligomers formed by 27 hydrophobic peptides; (2) stabilities of 22 bacteriorhodopsin mutants, and (3) protein-ligand binding affinities in aqueous solution. It has been found that coalescence of helices is driven exclusively by van der Waals interactions and H-bonds, whereas the principal destabilizing contributions are represented by side-chain conformational entropy and transfer energy of atoms from a detergent or lipid to the protein interior. Electrostatic interactions of alpha-helices were relatively weak but important for reproducing the experimental data. Immobilization free energy, which originates from restricting rotational and translational rigid-body movements of molecules during their association, was found to be less than 1 kcal/mole. The energetics of amino acid substitutions in bacteriorhodopsin was complicated by specific binding of lipid and water molecules to cavities created in certain mutants.
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