Protein folding, stability and recognition

Abstract: Proteins make up for most of the dry mass of a cell and they are highly involved in virtually all cellular processes. The importance of the proteins is reflected by frequent association between dysfunctional proteins and diseases. Proteins have also wide applications in industries. The function of a protein is closely related to its marginally stable structure, which is encoded in its primary amino acid sequence. In order to understand protein functions and design proteins for new applications, we need to understand the stability and the folding process of a protein. Further proteins often assert their functions by interacting with other molecules and ions. The capability of recognizing and binding other molecules and ions is the key to many vital functions. Although the protein stability and recognition may appear to be different problems, they share the same basic physiochemical principle. In this thesis, the issues of protein stability and folding and the recognition of specific DNA sequences are examined for a number of different systems. In the first study, molecular dynamics simulations have been conducted to examine the homeodomain-DNA recognition. It was found that residue 50 interacts more favourably through a number of interaction modes (hydrogen bonds, water mediated hydrogen bonds and van der Waals interactions) with its consensus DNA sequence thus plays a considerable role in DNA recognition. Further high mobility water molecules were found in the protein-DNA interface and they may have nanosecond scale residence time. In the second study, the influence of Zn ion on DNA binding and stability of the transcriptional factor p53 DNA binding domain is probed by molecular dynamics simulations. The Zn ion had an attractive force on the DNA backbone phosphates; further Zn ion appeared to coordinate motions among different structural elements. Possible aggregation initiation site on p53 DNA binding domain without Zn ion was proposed. In the third paper, we examined the thermal unfolding pathways of the p53 tetramerization domain, a small tetramer. The transition state was studied by phi value analysis. In the initial stage the native hydrophobic contacts were lost followed by simultaneous unfolding of the tertiary and secondary structures. The unfolding followed tetramer to dimer to monomer pathway and the transition state was not a well-defined structure but an ensemble of different structures. In the last study the stability and function of hypoxanthine phosphoribosyl transferase were inspected and related to the mutational spectrum and evolutionary conservation. The results show that there are a number of residues where no substitution was found despite several of them are vitally important to the protein. This suggests that these areas could be protected from mutations at the DNA level and/or enjoy more sufficient DNA repair mechanism.