Decoding signatures for an unfolded protein

posted Sep 16, 2015, 2:40 AM by Vinod Scaria   [ updated Sep 19, 2015, 8:47 PM by SRamachandran Igib ]
Suhani Nagpal, Research Scholar, CSIR-IGIB.....

Proteins are workhorses of a cell and they achieve their correct function through a well-defined fold also known as native state. The consequence of improper fold or unfolding leads to toxic effects, which could lead to diseases such as Alzheimer’s, Huntington’s etc. Most proteins require assistance of molecular chaperones for proper folding. These chaperones are helper proteins, which provide an environment for the proteins to accurately fold into their native structure. So far the focus has been to study structural changes of chaperone. However, little is known about the non-native states.

We investigated DapA (Dihydrodipicolinate synthase), which essentially requires to fold on a GroEL chaperone. We used molecular dynamics simulations to examine time-dependent properties of DapA. Analysis of these large-scale atomistic simulations revealed unique intermediate structures of DapA. Interestingly, they possess distinct secondary structural features compared to the native state and significant increase in surface exposed hydrophobicity. The predicted data from simulations were validated with experimental data, including Circular Dichroism, 1-anilinonaphthalene-8-sulphonic acid, and previously reported HDX-MS measurements. We also constructed networks of these proteins to provide insights into stable hubs (or important residues) underlying diverse states of an unfolded protein. In summary, our work provides insights into molecular states of a partially unfolded protein substrate that is en route to chaperone binding, and we propose that it has distinct properties that acts as a driving force for its interaction with GroEL chaperone.

Nagpal S, Tiwari S, Mapa K*, Thukral L* (2015). Decoding structural properties of a partially unfolded protein substrate: en route to chaperone binding. PLoS Computational Biology. In Press

Abbreviations: DapA: Dihydrodipicolinate synthase, CD: Circular dichroism, ANS- 1-anilinonaphthalene-8-sulphonic acid, HDX-MS- hydrogen-deuterium exchange coupled to mass spectrometry

Suhani Nagpal thanks Sachin Kukreja, Shrey Singh for help in generating the 3D graphical image

The Free Energy landscape of DapA. At the bottom most level is the 'native' ensemble. The physical interactions of the amino acid residues of this ensemble is displayed in the network graphs. Dark purple nodes represent highly interacting amino acid residues whereas light coloured nodes represent sparsely interacting residues. The partially unfolded ensembles appear at the top 2 levels. It is evident that in these ensembles, the interactions are reduced compared to the 'native' state, which is densely connected.