Access Type

Open Access Dissertation

Date of Award

January 2014

Degree Type


Degree Name



Biomedical Engineering

First Advisor

Dr. Yeshitila Gebremichael


Neurofilaments (NFs) are class IV intermediate filaments, abundantly found in the large myelinated axons. They are the key determinants of axonal diameter and consequently the nerve conduction properties. On the other hand, abnormal NF accumulation has been the hallmark of debilitating neurodegenerative disorders. NF compaction is also one of the pathological manifestations of traumatic axonal Injury. However, the exact relation between the disorganized NFs and the etiology of the neurodegenerative disorders is yet to be fully understood. NFs are assembled from three subunits: Low (NFL), Medium (NFM) and Heavy (NFH). These subunits are characterized by a common alpha helical rod domain and carboxyl terminal domains of different lengths specific to each subunit. The tails project from the core of the filament and contain a number of KSP repeat motifs that belongs to the sites for phosphorylation. Especially, the C-terminal tails of NFM and NFH that have relatively longer lengths and higher number of KSP repeats were found to be the key participants of the sidearm-mediated interfilament interactions that regulate the axonal diameter. Though it has been established that the NFs play a central role in determining the axonal caliber, there are several unresolved questions about the structure and functions of NFs.

The overarching goal of our research has been to understand the structural biophysical basis of NF organization. Multi-scale computational models that incorporate electro-physiological characteristics of NFs have been instrumental in revealing these behaviors. The primary objective of my research was to investigate the conformational properties of interacting neurofilaments sidearms using sequence based coarse grained model. This study provided insights into the nature of sidearm mediated NF-NF interaction which regulates the axonal caliber. The second objective was to study the structure of an isolated NF model under the influence of hydrophobic interactions and the presence of divalent ions like Ca2+. The results enhanced the current understanding of the equilibrium structural properties of the single neurofilament brush system and the effect of cellular changes including ionic strength and presence of divalent ions. The final part objective of our study was to investigate the structural transitions in the NF medium (NFM) subunit at an atomistic level, under the influence of varying physiological parameters. Though conclusive evidence about the key molecular changes underlying the sidearm expansion could not be gathered, the structures exhibit minimal difference with respect to phosphorylation. Overall, the studies provide insightful details of NF architecture up to molecular level, which is essential to elucidate their behavior observed in certain pathological conditions leading to their accumulation and neurodegeneration.