Computational Studies of Membrane Proteins Based on NMR Observables

University Of Kansas Center For Research Inc, Lawrence KS

Investigators

Abstract

Membrane proteins play important roles in many vital cellular processes, such as transmembrane (TM) signaling, transport of ions and small molecules, energy transduction, and cell-cell recognition. This project seeks to acquire novel insights into membrane proteins, dynamics and interactions with lipids, which are important determinants of their functions. Despite impressive successes of X-ray crystallography in structure determination of membrane proteins with multiple TM helices, it is still challenging to obtain the structural information of membrane proteins with one or a few TM helices. These membrane proteins are abundant and often involved in important TM-induced signaling and regulation through formation of hetero-/homo-oligomers. Although difficulties exist in obtaining inter-helix distance information by measuring long-range NOEs for these membrane proteins, their structures are determinable by measuring various orientational NMR observables, such as chemical shift anisotropy (CSA) and dipolar coupling (DC) in solid-state NMR (ssNMR), and residual dipolar coupling (RDC) in solution NMR experiments. However, the present NMR structure determination methods for membrane proteins are not able to extract important dynamics and interaction information that possibly are embedded in time- and ensemble-averaged NMR observables. This project will fill the knowledge gap by utilizing the orientational NMR restraint potentials to use the available experimental observables with additional benefits from the realistic molecular dynamics simulation of membrane systems. The ssNMR ensemble dynamics technique recently developed in the investigator's research group will make it possible to extract the intrinsic dynamics and/or distinct configurations of different domains. Comparisons of the free energy calculation results along key TM helix motions with NMR observable-based structure refinement and ensemble dynamics results will offer cross-validation of membrane proteins, structures and dynamics from different approaches. This research with selected complex membrane protein models will enhance our understanding of structure, dynamics, and function of membrane proteins with one or a few TM helices and their oligomers. This project also seeks to foster synergistic scientific research and education by providing reliable and general computational methods to students and researchers in the membrane protein NMR field and other disciplines through the CHARMM-GUI website (www.charmm-gui.org), which has been developed in the investigator's research group. In addition to graduate student training, undergraduate students will be involved in the proposed research to promote their interests in computational biophysics. In addition, this project will raise the scientific literacy of the public through the publication of research results and workshop participation. Finally, this project will help further development of our summer program called "Summer Research Program for HIgh School Students (SURPHISS) in Molecular Modeling and Simulations" by supporting graduate and undergraduate students interested in the education of high school students.