ArticleProceedings of the National Academy of Sciences of the United States of America2008
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 55 citations in OpenAlex.
- Addressing the Challenges of Solid-State Nanopores: Strategies for Performance Enhancement.International journal of molecular sciences · 2026Review
- Nanopore-based massively parallel sensing for peptide profiling and protein identification.Nature communications · 2026Article
- Quantification of Conformational Changes of Kinase Regulators, Kinases, and Regulator-Kinase Complexes Using the TSR Algorithm.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Methane Hydrate-in-Oil Systems in the Presence of Natural Amino Acid-Equilibrium Phase Condition Measurements.ACS omega · 2024Article
- Blobs form during the single-file transport of proteins across nanopores.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Solid-State Nanopores for Biomolecular Analysis and Detection.Advances in biochemical engineering/biotechnology · 2024Review
- The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering.Chemical science · 2021Article
- Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL.Biochemistry · 2021Article
- Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization.eLife · 2020Article
- Real-Time Conformational Changes and Controlled Orientation of Native Proteins Inside a Protein Nanoreactor.Journal of the American Chemical Society · 2017Article
- Single Molecule Nanopore Spectrometry for Peptide Detection.ACS sensors · 2017Article
- Smoothing of the GB1 hairpin folding landscape by interfacial confinement.Biophysical journal · 2012Article
- Role of water in protein aggregation and amyloid polymorphism.Accounts of chemical research · 2012Article
- Interactions between ionizable amino acid side chains at a lipid bilayer-water interface.The journal of physical chemistry. B · 2011Article
- Models of macromolecular crowding effects and the need for quantitative comparisons with experiment.Current opinion in structural biology · 2010Review
- Mesoporous silica chips for selective enrichment and stabilization of low molecular weight proteome.Proteomics · 2010Article
- Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.Journal of chemical theory and computation · 2010Article
- Reconciling theories of chaperonin accelerated folding with experimental evidence.Cellular and molecular life sciences : CMLS · 2010Review
- Ligand migration through the internal hydrophobic cavities in human neuroglobin.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.Protein engineering, design & selection : PEDS · 2009Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Confinement effects on protein stability are relevant in a number of biological applications ranging from encapsulation in the cylindrical cavity of a chaperonin, translocation through pores, and structure formation in the exit tunnel of the ribosome. Consequently, free energies of interaction between amino acid side chains in restricted spaces can provide insights into factors that control protein stability in nanopores. Using all-atom molecular dynamics simulations, we show that 3 pair interactions between side chains--hydrophobic (Ala-Phe), polar (Ser-Asn) and charged (Lys-Glu)--are substantially altered in hydrophobic, water-filled nanopores, relative to bulk water. When the pore holds water at bulk density, the hydrophobic pair is strongly destabilized and is driven to large separations corresponding to the width and the length of the cylindrical pore. As the water density is reduced, the preference of Ala and Phe to be at the boundary decreases, and the contact pair is preferred. A model that accounts for the volume accessible to Phe and Ala in the solvent-depleted region near the pore boundary explains the simulation results. In the pore, the hydrogen-bonded interactions between Ser and Asn have an enhanced dependence on their relative orientations, as compared with bulk water. When the side chains of Lys and Glu are restrained to be side by side, parallel to each other, then salt bridge formation is promoted in the nanopore. Based on these results, we argue and demonstrate that for a generic amphiphilic sequence, cylindrical confinement is likely to enhance thermodynamic stability relative to the bulk.
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