Studies of the structure of potassium channel KcsA in the open conformation and the effect of anionic lipids on channel inactivation Dongyu (Allison) Zhang Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Dongyu Zhang All rights reserved Abstract Studies of the structure of potassium channel KcsA in the open conformation and the effect of anionic lipids on channel inactivation Dongyu Zhang Membrane proteins play a vital role in cellular processes. In this thesis, we use KcsA, a prokaryotic potassium channel, as a model to investigate the gating mechanism of ion channels and the effect of anionic lipids on the channel activity using solid-state NMR spectroscopy. KcsA activity is known to be highly dependent on the presence of negatively charged lipids. Multiple crystal structures combined with biochemistry assays suggest that KcsA is co-purified with anionic lipids with phosphatidylglycerol headgroup. Here, we identified this specifically bound, isotopically labeled lipid in the protein 13C-13C correlation spectra. Our results reveal that the lipid cross peaks show stronger intensity when the channel is in the inactivated state compared to the activated state, which indicates a stronger protein-lipid interaction when KcsA is inactivated. In addition, our data shows that including anionic lipids into proteoliposomes leads to a weaker potassium ion affinity at the selectivity filter. Considering ion loss as a model of inactivation, our results suggest anionic lipids promote channel inactivation. However, the surface charge is not the only physical parameter that regulates channel gating or conformational preference. We found that the channel adapted to different conformations when reconstituted into liposome either made of DOPC or DOPE, two zwitterionic lipids. Also, we were able to stabilize the open-conformation of KcsA in 3:1 DOPE/DOPG liposome at pH 4.0 and acquired several multi-dimensional solid-state NMR experiments for site-specific resonance assignments. This is the first time that we obtain wild-type full-length KcsA structural information on the transient state. The structure is not only important for understanding channel gating, but can also serve as a homology model for investigating drug binding with more complicated potassium channels such as human voltage gated channel (hERG). Table of Contents List of Figures ................................................................................................................................ iv 1. Introduction ............................................................................................................................. 1 1.1 Cell membrane and membrane proteins ......................................................................... 1 1.2 Potassium channel ........................................................................................................... 3 1.2.1 Pore-forming domain and selectivity ...................................................................... 3 1.2.2 Gating and inactivation ........................................................................................... 4 1.2.3 KcsA as a model ..................................................................................................... 5 1.3 Solid-state NMR studies of membrane proteins ............................................................. 6 1.3.1 Overview of structural biology techniques ............................................................. 6 1.3.2 SSNMR methodologies for membrane proteins ..................................................... 7 1.4 Contribution of this thesis ............................................................................................... 9 1.5 Reference ...................................................................................................................... 11 2. Site-specific Solid-state Resonance Assignments of KcsA in the open conformation ......... 13 2.1 Abstract ......................................................................................................................... 13 2.2 Introduction ................................................................................................................... 13 2.2.1 What is chemical shift and resonance assignments? ............................................. 13 2.2.2 The importance of the open conformation of KcsA ............................................. 16 2.3 Methods......................................................................................................................... 18 2.3.1 KcsA purification .................................................................................................. 18 2.3.2 NMR Spectroscopy ............................................................................................... 20 i 2.3.3 Data processing ..................................................................................................... 21 2.3.4 Assignment ........................................................................................................... 21 2.4 Results and Discussions ................................................................................................ 22 2.4.1 Assignment overview ............................................................................................ 22 2.4.2 Challenges in assignment ...................................................................................... 27 2.4.3 Comparison of SSNMR assigment of KcsA in open and deactivated state ........ 27 2.4.4 How do we know this open conformation is the open-conductive state? ............. 28 2.5 Reference ...................................................................................................................... 39 3. The effect of anionic lipids on the structure and function of KcsA ...................................... 41 3.1 Abstract ......................................................................................................................... 41 3.2 Introduction ................................................................................................................... 41 3.2.1 Effect of phospholipids on potassium channel KcsA ........................................... 41 3.3 Results ........................................................................................................................... 45 3.3.1 Observation of the specific binding lipid with PG headgroup .............................. 45 3.3.2 Lipids affect the conformational preferences of the gates in KcsA and the open conformation is stable in the absence of added anionic lipids .............................................. 48 3.3.3 Loss of ion affinity upon reconstitution in liposome with anionic head groups at acidic pH 53 3.4 Discussion ..................................................................................................................... 55 3.5 Material and Method ..................................................................................................... 57 3.5.1 Protein overexpression and purification ............................................................... 57 3.5.2 NMR spectroscopy ................................................................................................ 58 ii 3.6 Reference ...................................................................................................................... 59 4. TmDOTP : An NMR- based Thermometer for Magic Angle Spinning NMR Experiments 62 4.1 Abstract ......................................................................................................................... 62 4.2 Introduction ................................................................................................................... 63 4.2.1 NMR sample preparation ...................................................................................... 65 4.2.2 NMR Spectroscopy ............................................................................................... 65 4.3 Results and Discussion ................................................................................................. 67 1 4.3.1 H NMR signals of H2O and TmDOTP provide precise temperature measurements ........................................................................................................................ 67 4.3.2 Sample heating due to spinning is proportional to the rotor frequency squared .. 68 4.3.3 The influence of TmDOTP on hydrated proteoliposome samples ....................... 69 4.3.4 RF heating is linear with pulse power, pulse length and duty cycle ..................... 70 4.3.5 Inequivalent RF heating on pellet vs. supernatant ................................................ 71 4.3.6 Application and significance ................................................................................. 73 4.4 Conclusion .................................................................................................................... 73 4.5 Reference ...................................................................................................................... 75 Appendix 1 .................................................................................................................................... 77 A1.1 Working with SMALPs KcsA ......................................................................................... 82 Reference .................................................................................................................................