9629047 Gunner Protein structures are determined by the protein's environment as well as its primary sequence. Protein function often demands protein movement. This can involve small, delocalized changes or may require several distinct, low energy protein states. The relative energy of separable protein states is often determined by the concentration of ligand. Binding the ligand can induce a change in binding affinity (e.g. hemoglobin (( O2), catalysis rate (e.g. cell surface receptors ( bound ligand), inter-protein association (e.g. calmodulin ( Ca+2), or proton binding (photosynthetic reaction centers ( electron transfer). The objective of the research is to determine how binding of ligand or ion can modify the free energy of different structures, focusing on the binding of charged effectors such as phosphate, calcium, protons, and electrons. The goal will then be to analyze the mechanism that controls vectorial proton transfer in three proteins whose structures have been solved to atomic resolution: the cytochrome oxidase, the bc1 complex, and the proton ATPase. Proteins are the group of biological molecules that carry out chemical reactions to transform our food to useful energy. This energy is then used by different proteins in the organism to carry out work, such as building new molecules for cell growth. The shape of the protein determines what it can do. By changing the shape, a process can be turned on or off. While proteins are far too complex to be analyzed completely with the basic laws of physics, computer modeling of proteins can be used to ask what forces in nature are the most important for making the structure that is seen. In many proteins, when a small group is bound, it's structure changes between two distinct shapes. The goal of this work is to explore how binding a charged group changes the structure.
