title: Shortening a loop can increase protein native state entropy.
abstract: Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability.
authors.affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Yulian
authors.initials: Y
authors.lastname: Gavrilov
authors.affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Shlomi
authors.initials: S
authors.lastname: Dagan
authors.affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
authors.forename: Yaakov
authors.initials: Y
authors.lastname: Levy
mesh_terms: D017766:Acid Anhydride Hydrolases / Q000737:chemistry / Q000378:metabolism; D019277:Entropy; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism; D013049:Spectrin / Q000737:chemistry / Q000378:metabolism; D044763:Ubiquitin-Conjugating Enzymes / Q000737:chemistry / Q000378:metabolism; D018909:src Homology Domains; D000097024:Acylphosphatase
chemical_list: D017766:Acid Anhydride Hydrolases; D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins; D013049:Spectrin; D044763:Ubiquitin-Conjugating Enzymes; D000097024:Acylphosphatase; C077072:UBC7 protein, S cerevisiae
keywords: coarse-grained model; conformational entropy; molecular dynamics; native state dynamics; protein folding