Research Projects

Protein misfolding and aggregation play an essential role in the progression of various neurodegenerative disorders, including Alzheimer’s, Parkinson’s, and Huntington’s diseases. The partially unfolded or misfolded intermediates involved are not easy to characterize experimentally due to their transient and unstable nature. These intermediates are obtained during protein folding/unfolding experiments and simulations. Our research will systematically study how proteins lose their structural rigidity during unfolding and how the intermediates in the unfolding pathways tend to form oligomers. Proteins display heterogeneity, frustration, and disorder—traits seen in glasses and amorphous solids. Though it has been shown for amorphous materials like colloids that rigidity transition is first order, studies based on rigidity percolation of proteins showed that the loss of rigidity can be both gradual (second) or sudden (first), depending on the proteins. We will investigate the exact nature of the rigidity transition in proteins during unfolding. Our preliminary data shows that at each stage of unfolding, multiple bonds in the protein are broken, which is called an avalanche. Avalanches will be used to predict the protein regions most susceptible to unfolding. We hypothesize that large avalanches lead to significant structural changes, leading to the most stable intermediates. The objectives of the project are: 1. To investigate the role of inhomogeneous strain thresholds of the non-covalent bonds and the backbone stiffness in the rigidity transition in proteins. 2. To predict which regions of proteins are more susceptible to unfolding using the avalanches and to probe our hypothesis that large avalanches give rise to stable intermediates. 3. To study the propensity of the unfolding intermediates to form oligomers using Molecular Dynamics (MD) simulations and Docking studies, and to design experimental probes to study aggregation. The methodology will involve building an ENMs with sequence-dependent spring constants with inhomogeneous strain thresholds from the crystal structure of representative proteins. Hooke's law will be used to calculate the strain in individual springs, and the springs will be broken if the thresholds are breached. The intermediates formed through avalanches will be obtained using unfolding studies of ENM, and their stability will be tested using MD simulations. A database of the intermediates of different proteins to form oligomers will be created, including the docking scores and the potential of mean force between the intermediates, the hydrophobicity of the surface, and the experimental observations. Significance: If successful, this project will provide a novel understanding of protein misfolding mechanisms. The approach may also find application in a systematic screening of proteins for aggregation propensity, identifying stabilizing mutations, and informing the design of therapeutic interventions targeting early misfolded states.