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. Author manuscript; available in PMC: 2020 Jul 24.
Published in final edited form as: Science. 2019 Mar 29;363(6434):1418–1423. doi: 10.1126/science.aav7541

Fig. 2. All-atom MD simulation of PLN, a pentameric TM α-helical bundle, illuminates critical apolar packing interactions.

Fig. 2.

(A) Final simulation frame for full-length PLN in a POPC bilayer. Water molecules are hidden. (B) The TM domains of published NMR structures of PLN (PDB IDs: 1ZLL, red; 2KYV, blue) compared with our MD simulation. RMSF of backbone atoms versus the simulation medoid is displayed as ribbon color. (C) Snapshot showing the water-filled central cavity and rapidly fluctuating polar side-chain interactions at the splayed N-terminal third of the TM-spanning α helices. (D) Central cavity size within each helical bundle versus membrane depth. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.