ArticleBiophysical journal2006
Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 81 citations in OpenAlex.
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- Functional Role of an Unusual Transmembrane Acidic Residue in the Calcium Pump Regulator Myoregulin.Biochemistry · 2023Article
- Mapping temperature-dependent conformational change in the voltage-sensing domain of an engineered heat-activated KProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations.The journal of physical chemistry. B · 2017Article
- Influence of glutamic acid residues and pH on the properties of transmembrane helices.Biochimica et biophysica acta. Biomembranes · 2017Article
- The Single Transmembrane Segment of Minimal Sensor DesK Senses Temperature via a Membrane-Thickness Caliper.Journal of bacteriology · 2016Article
- Naratriptan aggregation in lipid bilayers: perspectives from molecular dynamics simulations.Journal of molecular modeling · 2016Article
- Novel pH-Sensitive Cyclic Peptides.Scientific reports · 2016Article
- Marginally hydrophobic transmembrane α-helices shaping membrane protein folding.Protein science : a publication of the Protein Society · 2015Review
- Measurement of the membrane dipole electric field in DMPC vesicles using vibrational shifts of p-cyanophenylalanine and molecular dynamics simulations.The journal of physical chemistry. B · 2015Article
- Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach.Journal of chemical sciences (Bangalore, India) · 2015Article
- Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers.Biochimica et biophysica acta · 2014Article
- Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations.Biochimica et biophysica acta · 2014Article
- Side-chain to main-chain hydrogen bonding controls the intrinsic backbone dynamics of the amyloid precursor protein transmembrane helix.Biophysical journal · 2014Article
- Partitioning of amino acids into a model membrane: capturing the interface.The journal of physical chemistry. B · 2014Article
- Ser/Thr motifs in transmembrane proteins: conservation patterns and effects on local protein structure and dynamics.The Journal of membrane biology · 2012Article
- Outer membrane phospholipase A in phospholipid bilayers: a model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers.Biochimica et biophysica acta · 2012Article
- Determining peptide partitioning properties via computer simulation.The Journal of membrane biology · 2011Review
- Residue-specific side-chain packing determines the backbone dynamics of transmembrane model helices.Biophysical journal · 2010Article
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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
Understanding the solvation of amino acids in biomembranes is an important step to better explain membrane protein folding. Several experimental studies have shown that polar residues are both common and important in transmembrane segments, which means they have to be solvated in the hydrophobic membrane, at least until helices have aggregated to form integral proteins. In this work, we have used computer simulations to unravel these interactions on the atomic level, and classify intramembrane solvation properties of amino acids. Simulations have been performed for systematic mutations in poly-Leu helices, including not only each amino acid type, but also every z-position in a model helix. Interestingly, many polar or charged residues do not desolvate completely, but rather retain hydration by snorkeling or pulling in water/headgroups--even to the extent where many of them exist in a microscopic polar environment, with hydration levels corresponding well to experimental hydrophobicity scales. This suggests that even for polar/charged residues a large part of solvation cost is due to entropy, not enthalpy loss. Both hydration level and hydrogen bonding exhibit clear position-dependence. Basic side chains cause much less membrane distortion than acidic, since they are able to form hydrogen bonds with carbonyl groups instead of water or headgroups. This preference is supported by sequence statistics, where basic residues have increased relative occurrence at carbonyl z-coordinates. Snorkeling effects and N-/C-terminal orientation bias are directly observed, which significantly reduces the effective thickness of the hydrophobic core. Aromatic side chains intercalate efficiently with lipid chains (improving Trp/Tyr anchoring to the interface) and Ser/Thr residues are stabilized by hydroxyl groups sharing hydrogen bonds to backbone oxygens.
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