In order to perform its biological function, a protein must fold from a linear chain of amino acids to its three dimensional native structure. Much of the current knowledge of the mechanisms involved in protein folding is the result of experimental and theoretical investigations in idealized dilute environments. Proteins however fold in the more complex cellular environment. Crowding in the cell, sequence mutations, and changes in pH and/or temperature can cause the folding process to go astray. This can lead to the formation of improperly folded entities that can in turn self-assemble to form large fibrillar aggregates enriched in beta-sheet structure. Most, if not all proteins, appear capable of aggregating, intimating that aggregation is an inherent property of polypeptide chains. A comprehensive understanding of protein folding cannot be limited to the study of a single protein, but must include an investigation of interactions between proteins. The aim of this project is to probe from a theoretical perspective the physico-chemical principles governing the assembly of both proteins and peptides into a variety of supramolecular structures. Because of the length and time scales associated with folding and aggregation, the study of these processes lends itself to a hierarchy of computational models. The PI will develop new mid-resolution coarse-grained off-lattice backbone-sidechain protein and peptide models, with explicit chirality and directional hydrogen bonding. These models will be applied to the study of folding and aggregation in the bulk and under the influence of environmental factors present in the cell (confinement, crowding and surface interactions). The coarse-grained simulations will be complemented by atomically detailed simulations geared at probing the early stages of aggregation, the structural nature of protofilaments, and the interaction of aggregation inhibiting peptides with protofilaments. The fully atomic simulations will be performed in close collaboration with the experimental groups of Professor Stephen Meredith (U of Chicago) and Professor Aphroditi Kapurniotu (U of Aachen).
A deeper understanding of the fundamental principles governing protein folding and aggregation will have impacts in a number of disciplines including the emerging field of biomaterials. The proposed research is inherently interdisciplinary, and the PI has established collaborations with two leading experimental groups. It is anticipated that results from simulations performed in the context of this project will guide new experimental studies. All computational programs developed will be made freely available to the public. The PI is actively involved in the mentoring of under-represented groups in science (both minority and women), in curricular developments and in outreach programs. The PI will adapt computational modules that she previously developed in a Computational Biochemistry course at UCSB for use in a graduate level class at a minority serving institution (Cal State LA). The PI is also co-chairing a committee for designing a physical chemistry sequence for biochemistry majors. The PI is involved in chemistry outreach activities to local Santa Barbara elementary school children and is planning on developing an outreach program in the present funding cycle targeting the involvement of young girls in science.
Intellectual Merit This proposal focused on developing computational methods to study the effects of the cellular environment on protein folding and aggregation. In vivo, proteins fold in a dense environment, rich in interfaces (ranging from membranes to surfaces created by other biomolecules) and with a host of species present that can act as crowding agents. Both crowding and surface effects can dramatically alter protein folding mechanisms as well as affect aggregation pathways and resulting aggregate morphologies. Using a combination of fully atomistic simulations and novel coarse-grained models developed in the context of this grant, the PI studied 1) how chaperonin molecules assist the folding of proteins in the crowded cellular milieu; 2) how model surfaces can influence the folding of proteins; 3) the mechanisms by which proteins self-assemble into aggregate species, both in the presence and absence of surfaces. The outcome of this work has been a deeper theoretical understanding of the mechanisms and driving forces behind folding and assembly. Broader Impacts A deeper understanding of the fundamental principles governing protein folding and aggregation impacts a number of disciplines including biotechnology and biomaterials. The results from the simulations performed in the context of this grant have guided new experimental studies. All computational models and algorithms developed in the context of this proposal were made freely available to the public. The PI is actively involved in the mentoring of under-represented groups in science (both minority and women) and in curricular developments. The PI is involved in chemistry outreach activities to local Santa Barbara elementary school children, including weekly demonstrations to fifth grade students, as well as monthly "Science Night" events.
