Pressure-Based Mapping of Protein Free Energy Landscapes

Rensselaer Polytechnic Institute, Troy NY

Investigators

Abstract

Title: Pressure Based Mapping of Protein Free Energy Landscapes Proteins are the molecules in our bodies and in all other living organisms, plants, bacteria, fish, animals, that do most of the work to maintain and reproduce life. They are chains of small chemicals, called amino acids that are linked together. The number and order of the amino acids defines the shape or structure of the protein and also its function. Proteins fold up into compact shapes, but to do their jobs like digesting food or generating the force that makes birds and insects fly, they have to change their shape. This research is aimed at understanding how the sequence of amino acids defines the folding of proteins and how they change their shapes to function. Understanding how protein sequences control their shape and function will be of great use in designing new proteins for applications in biotechnology. For example, better, more active and more stable proteins can be designed for green chemistry bioreactors to make the chemicals used in daily life without harming the environment. Proteins are nano-machines and nanomaterials that will find numerous applications in electronics, computing, biosensing and nano-fabrication. All of these technological advances will be based on the understanding of the relationship between protein sequence, stability and function. The strong international collaboration on which this research is based will provide the students with a world-view of the scientific endeavor, and help them establish international networks that will aid them as they pursue their careers. The graduate and undergraduate students who will participate in the research will be immersed in a comprehensive interdisciplinary environment, incorporating multiple experimental and computational approaches. The large NMR data sets generated by the research are shared with the NSF sponsored undergraduate educational program in the undergraduate computer science major at RPI, the Data Analytics Through-out Undergraduate Mathematics program (DATUM). Support will be provided for the undergraduate research program run by the Center for Biotechnology. The research will also involve the RPI high school internship program run by the Center for Biotechnology for Troy area high schools (with a large minority population). The objective of this project is to map experimentally the folding free energy landscapes for selected model proteins, and to identify the sequence and structural determinants of their folding cooperativity, initiation and pathways. This will be accomplished by exploiting the advantages of pressure perturbation coupled with site specific NMR, fluorescence, SAXS and other biophysical approaches. The underlying premise of the present proposal is that pressure, due to its unique mechanism of action, can provide exclusive insights into protein folding. Within the framework of the main objective, three specific questions will be addressed: How does sequence code for protein folding cooperativity. How are protein cooperative interactions linked to their volumetric thermal expansion. How do residual native interactions in pressure unfolded states affect folding mechanisms. This project will address central outstanding issues in protein folding and conformational dynamics, first by significantly and systematically increasing the experimental database of detailed protein folding energy landscapes. Secondly, it will provide experimental scenarios describing how sequence defines folding routes and cooperativity. Finally, it will reveal how sequence specifically controls access to excited states on folding landscapes. This project is jointly funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Physics of Living Systems Program in the Division of Physics in the Directorate of Mathematical and Physical Sciences.