Mechanism Underlying Conformational Effects of a Disease-Associated Hydrophobic-to-Hydrophobic Substitution on an Intrinsically Disordered Region

Abstract

Disease-associated Single Nucleotide Polymorphisms (SNPs) are common in the disordered regions of proteins (21.7 % of SNPs are found in the disordered region). Most mutational studies of IDP's consider loss or gain of a charged residue. In this study, we explore the local and global effect of a charge-neutral mutation between two hydrophobic residues, with known effects on function: the Val66Met SNP in the 100-residue disordered prodomain of Brain Derived Neurotropic Factor (BDNF). Val66Met is the most frequently found SNP in the BDNF disordered domain, and is associated with various neurological and psychiatric disorders such as bipolar disorder and Alzheimer's disease. Previously, NMR studies demonstrated that the prodomain is disordered with different secondary structure preferences for Val and Met at 275K (Anastasia et al 2013). We attempt to elucidate this phenomenon at the microscopic level using large-scale, fully atomistic temperature replica exchange calculations of both the Val and Met forms of the BDNF prodomain. MD simulations indicate high propensity of secondary structure in regions similar to those identified in NMR studies. Interestingly, we observe reversed temperature dependence of the secondary structure around the SNP between Val and Met from 300K to 420K. With increasing temperature, Val66 is less likely to assume helical secondary structure, while Met66 is more likely, which is consistent with previous observations that entropy of the valine side-chain is significantly reduced upon helix formation. This cost likely offsets the entropic gain of nearby water molecules upon helix formation, associated with the hydrophobic effect and common to Val66 and Met66 helices. At room temperature, we also observe an increase in the radius of gyration of the Met66 prodomain relative to the Val66 prodomain, which can be reliably attributed to differential hydrogen bonding preferences of residues near in sequence to the SNP, affecting their likelihood of forming beta-bridges with distant residues. This is consistent with an experimentally observed higher hydrodynamic radius for the Met66 proregion than for Val66 proregion. These results indicate the seemingly subtle substitution may exert its effects by critically adjusting entropic cost of local secondary-structure elements, which, in turn, affects the conformational ensemble via differential long-range beta bridging patterns. Furthermore, although the SNP is neutral, it alters the exposure of charged residues around the SNP, which can potentially affect the binding characteristics of the prodomain to its highly charged receptor, SORCS2.