Proteins are the molecular machines responsible for maintaining the biological self-organization in living cells. However, in order to perform their molecular functions, protein molecules themselves must fold into highly specific 3-dimensional shapes known as the native states. The information to fold to a functional native state of a protein is encoded in its one-dimensional string of amino acids, the primary sequence. However, structural conversion from the native state is a frequently observed process such as in the aggregation and fibrilization of amyloidogenic proteins, which is thought to be a critical process in the development of a variety of neurodegenerative diseases such as Alzheimer’s, Parkinson, Huntington, and prion diseases. A new class of proteins known as transformer proteins has recently emerged. The transformer proteins can undergo structural transformations that allow them to perform multiple functions, and they are re-defining the general perspective of sequence-structure-function relationship. In this talk, I will discuss the computer simulations of some model protein systems that shed light on the protein folding dynamics, including structural transitions in amyloidogenic proteins as well as the alpha helix to beta barrel structural transformation of the C-terminal domain of the transcription factor RfaH.
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