title: The hydrophobic temperature dependence of amino acids directly calculated from protein structures.
abstract: The hydrophobic effect is the main driving force in protein folding. One can estimate the relative strength of this hydrophobic effect for each amino acid by mining a large set of experimentally determined protein structures. However, the hydrophobic force is known to be strongly temperature dependent. This temperature dependence is thought to explain the denaturation of proteins at low temperatures. Here we investigate if it is possible to extract this temperature dependence directly from a large set of protein structures determined at different temperatures. Using NMR structures filtered for sequence identity, we were able to extract hydrophobicity propensities for all amino acids at five different temperature ranges (spanning 265-340 K). These propensities show that the hydrophobicity becomes weaker at lower temperatures, in line with current theory. Alternatively, one can conclude that the temperature dependence of the hydrophobic effect has a measurable influence on protein structures. Moreover, this work provides a method for probing the individual temperature dependence of the different amino acid types, which is difficult to obtain by direct experiment.
authors.affiliation: Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: van Dijk
authors.affiliation: Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands.
authors.forename: Arlo
authors.initials: A
authors.lastname: Hoogeveen
authors.affiliation: Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands.
authors.forename: Sanne
authors.initials: S
authors.lastname: Abeln
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D009682:Magnetic Resonance Spectroscopy; D015233:Models, Statistical; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents; D014867:Water