ArticlePLoS computational biology2014
The free energy landscape of dimerization of a membrane protein, NanC.
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 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Single-molecule tweezers decode hidden dimerization patterns of membrane proteins within lipid bilayers.Nature communications · 2025Article
- The Role of Cholesterol in M2 Clustering and Viral Budding Explained.Journal of chemical theory and computation · 2025Article
- Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.Biochemistry · 2024Article
- Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.bioRxiv : the preprint server for biology · 2024Article
- The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT.International journal of molecular sciences · 2022Article
- Dawn of a New Era for Membrane Protein Design.Biodesign research · 2022Review
- Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model.Journal of chemical theory and computation · 2021Article
- Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-BasedJournal of medicinal chemistry · 2020Article
- Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis.PLoS computational biology · 2020Article
- Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force.Biophysical journal · 2020Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins.Nature communications · 2018Article
- Fast Calculation of Protein-Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model.Journal of chemical theory and computation · 2018Article
- Article
- Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach.PloS one · 2017Article
- Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.Current opinion in structural biology · 2016Review
- Membrane stiffness is modified by integral membrane proteins.Soft matter · 2016Article
- In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality.International journal of molecular sciences · 2016Article
- Organization and Dynamics of Receptor Proteins in a Plasma Membrane.Journal of the American Chemical Society · 2015Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Membrane proteins are frequently present in crowded environments, which favour lateral association and, on occasions, two-dimensional crystallization. To better understand the non-specific lateral association of a membrane protein we have characterized the free energy landscape for the dimerization of a bacterial outer membrane protein, NanC, in a phospholipid bilayer membrane. NanC is a member of the KdgM-family of bacterial outer membrane proteins and is responsible for sialic acid transport in E. coli. Umbrella sampling and coarse-grained molecular dynamics were employed to calculate the potentials of mean force (PMF) for a variety of restrained relative orientations of two NanC proteins as the separation of their centres of mass was varied. We found the free energy of dimerization for NanC to be in the range of -66 kJ mol(-1) to -45 kJ mol(-1). Differences in the depths of the PMFs for the various orientations are related to the shape of the proteins. This was quantified by calculating the lipid-inaccessible buried surface area of the proteins in the region around the minimum of each PMF. The depth of the potential well of the PMF was shown to depend approximately linearly on the buried surface area. We were able to resolve local minima in the restrained PMFs that would not be revealed using conventional umbrella sampling. In particular, these features reflected the local organization of the intervening lipids between the two interacting proteins. Through a comparison with the distribution of lipids around a single freely-diffusing NanC, we were able to predict the location of these restrained local minima for the orientational configuration in which they were most pronounced. Our ability to make this prediction highlights the important role that lipid organization plays in the association of two NanCs in a bilayer.
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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.