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1 Supplementary material for: CHOLESTEROL SENSITIVITY OF KIR2.1 IS CONTROLLED BY A BELT OF RESIDUES AROUND THE CYTOSOLIC PORE Avia Rosenhouse-Dantsker 1, Diomedes E. Logothetis 2 and Irena Levitan 1 1 Department of Medicine, Pulmonary Section, University of Illinois at Chicago, Chicago, IL 612; 2 Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
2 G-loop residues: Backbone/sidechain atom Average distance (Å) Standard Deviation (Å) G(Cα-Cα) M1(Cα-Cα) M1(Cβ-Cβ) V2(Cα-Cα) V2(Cβ-Cβ) E3(Cα-Cα) E3(Cβ-Cβ) A4(Cα-Cα) A4(Cβ-Cβ) T5(Cα-Cα) T5(Cβ-Cβ) A6(Cα-Cα) M7(Cα-Cα) M7(Cβ-Cβ) T8(Cα-Cα) T8(Cβ-Cβ) T9(Cα-Cα) T9(Cβ-Cβ) Q3(Cα-Cα) Q3(Cβ-Cβ) Supplementary Table S1: Average distance between the backbone Cα or the side-chain Cβ of G-loop residues in two opposite facing subunits. The standard deviation is an indication of the flexibility of the G-loop at the different residues. Distances that exhibit significant variations are highlighted gray.
3 G-loop gating D51(Cα-Cα)/ D51(Cβ-Cβ)/ H53(Cα-Cα)/ H53(Cβ-Cβ)/ E191(Cα-Cα)/ E191(Cβ-Cβ)/ V194(Cα-Cα)/ V194(Cβ-Cβ)/ elements N N K / Q / R K / Q / R Q Q L / M L / M R P R P R P R P R P R P R P R P E3(Cα-Cα) < -4 E3(Cβ-Cβ) * -4 E3(Oε 1/2 -Oε 1/2 ) A4(Cα-Cα) A4(Cβ-Cβ) T5(Cα-Cα) T5(Cβ-Cβ) T5(Oγ 1 -Oγ 1 ) A6(Cα-Cα) M7(Cα-Cα) M7(Cβ-Cβ) M7(Sδ-Sδ) Supplementary Table S2: Correlations and their significance between the G-loop gating elements of the channel and the cholesterol sensitivity belt residues of the N-terminus and the link between the C-terminus and the inner TM helix. R is the correlation, and P is the significance. Significant correlations are highlighted gray (P.5).
4 G-loop gating N216(Cα-Cα)/ N216(Cβ-Cβ)/ K219(Cα-Cα)/ K219(Cβ-Cβ)/ L222(Cα-Cα)/ L222(Cβ-Cβ)/ C311(Cα-Cα)/ C311(Cβ-Cβ)/ elements D D N N I / M I / M A A R P R P R P R P R P R P R P R P E3(Cα-Cα) E3(Cβ-Cβ) E3(Oε 1/2 -Oε 1/2 ) A4(Cα-Cα) A4(Cβ-Cβ) * T5(Cα-Cα) T5(Cβ-Cβ) T5(Oγ 1 -Oγ 1 ) A6(Cα-Cα) M7(Cα-Cα) M7(Cβ-Cβ) M7(Sδ-Sδ) Supplementary Table S3: Correlations and their significance between the G-loop gating elements of the channel and the cholesterol sensitivity belt residues of the CD- and G- loops. R is the correlation, and P is the significance. Significant correlations are highlighted gray (P.5).
5 G-loop gating Q57(Cα-Cα)/ Q57(Cβ-Cβ)/ N1(Cα-Cα)/ N1(Cβ-Cβ)/ elements E / H E / H A A R P R P R P R P E3(Cα-Cα) E3(Cβ-Cβ) E3(Oε 1/2 -Oε 1/2 ) A4(Cα-Cα) A4(Cβ-Cβ) T5(Cα-Cα) T5(Cβ-Cβ) T5(Oγ 1 -Oγ 1 ) A6(Cα-Cα) M7(Cα-Cα) M7(Cβ-Cβ) M7(Sδ-Sδ) Supplementary Table S4: Correlations and their significance between the G-loop gating elements of the channel and Q57 and N1. R is the correlation, and P is the significance. None of the correlations (R) is significant since P>.5 for all cases. Both Q57 and N1 are just outside the cytosolic cholesterol sensitivity belt.
6 Figure Captions for Supplementary Figures Supplemental Figure S1: Alignment of sequences of the cytosolic domains of modeled Kir2.1 and Kir2.3 channels. Supplemental Figure S2: Representative traces of whole-cell basal currents recorded at mv/+mv in Xenopus oocytes showing the effect of cholesterol enrichment on Kir2.1, and the mutants D51N, H53Q, N1A, E191Q, V194L, and C311A. The waveform and the scale are shown in the bottom left corner of the figure. The black traces were obtained following application of HK solution, and the red curves were obtained when BaCl 2 is added to the HK solution (See Methods). Supplemental Figure S3: A. Plot of each of the residues in the modeled cytosolic domain of the channel and the lower TM domain and the percentage of poses in which they appeared. B. The similarity (in percentage) between each of the 135 poses obtained from the docking run and the other 134 poses. The poses are ordered based on the cluster to which they belong. Cluster 1 includes poses 1-63, cluster 2 includes poses 64-74, cluster 3 includes poses 75-87, cluster 4 includes poses , cluster 5 includes poses , and cluster 6 includes poses Each square in the figure represents a pair of poses as labeled on the x and y axes, and its color is an indication of the similarity of the poses (in percentage). As reflected in the colored matrix, the similarity of clusters 1-3 is rather high such that most of their members exhibit at least % similarity. The similarity between clusters 4 and 5 and between each of theses clusters and clusters 1-3 is significantly lower: for most pairs, the similarity is around -%. Cluster 6, on the other hand is completely different from all other clusters, exhibiting % similarity with any of them. Supplemental Figure S4: Location of the cholesterol molecule in each of the centers of the six clusters of the potential cholesterol binding sites identified by the docking analysis relative to the belt of the residues that affect cholesterol sensitivity of the channels identified by the site-directed mutagenesis. In clusters 1-5, the cholesterol molecule is located between two adjacent subunits and in cluster 6, the cholesterol molecule is located between the four subunits of the channel. The residues that participate in the binding site are colored yellow, and the residues of the cholesterol sensitivity belt are colored red. Below each model are shown the residues that appear in the binding sites defined by all members of each cluster, and the percentage of poses in the cluster in which each residue appears. Most clusters (clusters 1-5) suggest possible binding sites at the interface between the cytosolic domain and the TM domain. In clusters 1-3, 5 cholesterol is almost parallel to the pore of the channel, partially penetrating into the cytosolic domain, and in cluster 4, cholesterol is almost perpendicular to the pore, mostly interacting with the slide helix and the TM domain. Cluster 6, on the other hand, suggests a possible binding site at center of the cytosolic domain away from the TM domain.
7 Supplementary Figure S1
8 Supplementary Figure S2 Control Cholesterol enriched Control Cholesterol enriched Kir2.1 N1A D51N E191Q H53Q V194L mv mv mv µa - mv 3 msec 3 msec msec C311A
9 Supplementary Figure S3 A Appearance in poses (%) cytosolic residue lower TM or slide helix residue B Pose Pose
10 Supplemenrary Figure S4 Cluster 1 Cluster 2 Cluster 3 Appearance in Cluster 1 poses (%) Appearance in Cluster 2 poses (%) Appearance in Cluster 3 poses (%) Cluster 4 Cluster 5 Cluster 6 Appearance in Cluster 1 poses (%) Appearance in Cluster 5 poses (%) Appearance in Cluster 1 poses (%)
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