Mapping sticky regions in proteins to aid the design of aggregation inhibitors for neurodegenerative diseases

01 Aug 2018

Mapping sticky regions in proteins to aid the design of aggregation inhibitors for neurodegenerative diseases


By Dr. R Mahalakshmi, Intermediate Fellow

IISER Bhopal

Membrane proteins make up one-third of the total number of proteins of any cell. As gatekeepers of the cell, they play many important roles such as transporting material (another protein, small molecules, nutrients, ions etc.) in and out of the cell, relaying signals between cell's internal and external environments. For this reason, they are the targets of more than 50 % of medicinal drugs available in the market today. 

Membrane protein, as the name indicates, resides in the membrane, and requires a membrane environment to fold, retain structure and stability, and carry out its function. The membrane itself is amphipathic – it has water-soluble and water-insoluble regions. Hence, the membrane protein also contains two distinct regions to match the organization of the membrane – water-solvated and lipid-solvated regions. The lipid-solvated part of membrane protein stays occluded from water, as it is enriched with hydrophobic (water-repelling) residues. Under conditions of cellular stress, if the membrane protein exits its native environment, the hydrophobic region is exposed to the aqueous milieu of the cell. This event can drive protein aggregation, and under extreme cases, causes amyloid-like structures leading to neurodegenerative diseases including Alzheimer’s, and Parkinson’s. One effective approach to ameliorate membrane protein aggregation and delay the onset of neurodegeneration is to inhibit this aggregation process. The successful design of aggregation inhibitors requires a molecular understanding of the regions of a membrane protein that are susceptible to aggregation.

Interestingly, not all lipid-solvated regions of a membrane protein are prone to aggregation. Hence, an accurate method is required that will experimentally provide molecular details of aggregation-prone regions of a membrane protein. In this study, we have developed a simple, and cost-effective, yet highly accurate method to map the aggregation hotspots of a membrane protein. We use the human voltage-dependent anion channel (VDAC) as our model system. VDACs are abundant in mitochondria – the powerhouse of the cell. They are found specifically in the mitochondrial outer membrane, and are essential for bidirectional transport of metabolites, nutrient molecules, and ions across the mitochondrial membrane. VDACs are also implicated in the formation and propagation of neurodegenerative aggregates, and therefore, in various neurodegenerative diseases. Hence, VDACs can be excellent targets for aggregation inhibitors that can ameliorate disease conditions. We developed a simple method, which we call “Peptide-Based Reverse Mapping” to accurately map the aggregation-prone zones of all three human VDACs.

We use a bottom-up approach, wherein we experimentally examine the aggregation propensity of short segments of the full-length protein. This provides us with molecular information on the precise regions of the VDAC protein that are prone to aggregation. Through our work, we not only identify the intrinsic aggregation hotspots of human VDACs, but also demonstrate that our method and approach is simple and cost-effective, which can be adapted by any laboratory worldwide to accurately determine the aggregation zones of any protein.


Direct Structural Annotation of Membrane Protein Aggregation Loci using Peptide-Based Reverse Mapping. Lella, M and Mahalakshmi, R*. Journal of Physical Chemistry Letters. May 2018.

Banner image credit: VardaShoshan-Barmatz et al. Image shows dimerization of human VDAC1