Transition Structures and the Evolution of Protein Folds

North Carolina State University, Raleigh NC

Investigators

Abstract

Protein structures cluster into families of folds that act as evolutionary templates, where the backbone structures are recycled to create proteins with different functions. Theoretical models of protein evolution propose the existence of a "neutral network" in sequence space that interconnects the different sequences encoding the same fold. In such networks, continuous paths of point mutations or small insertion/deletion changes connect all component sequences. These networks can be quite large, since many different sequences can encode the same fold. A fundamental question in protein evolution is how and how often exchanges between different neutral networks occur, leading to evolution from one fold to another. During evolution, the induction of new phenotypic traits by a small number of mutations has to be balanced against the deleterious effects on vital functions that mutations can cause. There is evidence that molecular evolution may be steered by the ability of biomolecules to take on numerous conformations as a bridge between different folds. Under this scenario, an evolving protein can initially attain increased fitness for a new function without losing its original function. Bridge states allow proteins to explore new structures and functions while part of the structural ensemble retains the initial conformation and function as insurance. Of particular interest are rare bridge or transition sequences that fold with different probabilities into distinct non-overlapping structures. Protein stability is generally viewed in terms of a two-state transition between a unique native state and an ensemble of unfolded ones. However, design and mutagenesis experiments suggest that the difference in free energy of alternative folds may be much smaller than typically envisioned, leading to evolutionary rates that are sensitive to the free energy differences between alternative conformations. This research centers on how protein folds change over time, on how the existence of alternative folds affects the rates of protein evolution, and on how new protein functionality can evolve from an already existing protein. Emphasis is given to the characterization of the conformational space, evolutionary pathways, connections, and properties of select protein sequences that, in principle, can stably adopt two different folds, or exist in one fold but are 1 to 3 mutations away from a different fold. Specific protein systems that show a very high sequence identity but display different folds and functions will be considered, such as alternate folds based on the patterning of polar versus non-polar amino acids in the P22 Arc repressor homodimer; and engineered proteins based on the GA and GB domains of the cell wall Protein G of Streptococcus bacteria. The study of these protein systems by atomistic molecular dynamic techniques will be complemented by molecular evolution analyses of diverse protein families, especially those for which the evolutionary impact of tertiary structure has previously been investigated without regard to the potential role of alternative protein folds on evolutionary rates. A novel evolutionary inference procedure that can quantitatively assesses the evolutionary influence of alternative folds will facilitate these investigations. The most interesting of putative ancestral proteins that are identified by the inference procedure will then be studied in more detail with atomistic modeling techniques that will examine all relevant structural characteristics. This project will foster interaction between the molecular simulation and evolution research communities, which have traditionally been largely isolated from each other. This is primarily a student/postdoc based research project, which will foster educational ties between NC State Bioinformatics and Physics. The larger computational biomolecular community will benefit through the continued development of freely available software for the AMBER package, as well as through the development of new evolutionary inference software. In addition, The PI will develop new graduate courses, foster the retention and recruitment of minority students, develop the Biophysics option at NC State, provide international research experience to students (mainly via a collaboration in Japan), and provide for a well-rounded and rich environment for students and research partners at all educational levels.