Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein.

Ruchi Lohia,Grace Brannigan,Reza Salari,Bert L De Groot

doi:10.1371/journal.pcbi.1007390

Abstract

The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica-exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary structure changes due to the Val66Met mutation, when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies “blobs” of 4-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β-bridging between V66 and V94 (on either side of the linker) with specific side-chain interactions between M66 and M95. The protein backbone in the vicinity of M95 is then free to form β-bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.

Highlights

We report on molecular dynamics simulations of a protein that is critical for neuronal health throughout adulthood
We identify a molecular mechanism in which the mutation may change the global conformations of the protein and its ability to bind to receptors
The physiological significance of intrinsically disordered proteins (IDPs), which can explore a wide range of conformational ensembles in their functional form, is well-established [1– 5]

Summary

Introduction

The physiological significance of intrinsically disordered proteins (IDPs), which can explore a wide range of conformational ensembles in their functional form, is well-established [1– 5]. More than 35% of IDPs reported in DISPROT [19] are strong polyampholytes, and their ensemble properties can be predicted using statistical theories of polyampholytes from polymer physics and global properties of the sequence, including the fraction of charged residues and the separation of oppositely charged residues (Fig 1c) [20–23]. This role is consistent with the long-range nature of electrostatic interactions, which can affect coupling between distant residues in an otherwise disordered structure

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