A reduced mechanical model for cAMP-modulated gating in HCN channels

Stephanie Weißgraeber,Kay Hamacher,Gerhard Thiel,Andrea Saponaro

doi:10.1038/srep40168

Abstract

We developed an in silico mechanical model to analyze the process of cAMP-induced conformational modulations in hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which conduct cations across the membrane of mammalian heart and brain cells. The structural analysis reveals a quaternary twist in the cytosolic parts of the four subunits in the channel tetramer. This motion augments the intrinsic dynamics of the very same protein structure. The pronounced differences between the cAMP bound and unbound form include a mutual interaction between the C-linker of the cyclic nucleotide binding domain (CNBD) and the linker between the S4 and S5 transmembrane domain of the channel. This allows a mechanistic annotation of the twisting motion in relation to the allosteric modulation of voltage-dependent gating of this channel by cAMP.

Highlights

Typical for these channels is the characteristic architecture with six transmembrane domains (TMDs) of which the 4th TMD contains the voltage sensor and the last two TMDs the pore[3]
We created a structural model of the hyperpolarization-activated cyclic nucleotide-gated (HCN) channel and simulated cAMP removal from the binding pocket using a coarse-grained approach to reveal the dynamics of the allosteric change upon nucleotide
Details on the homology model, which is based on joining the crystal structures of the cyclic nucleotide binding domain (CNBD) of HCN4 with the transmembrane part of the Kv1.2 channel as well as other details and quality assurance steps are shown in the supplementary material

Summary

Introduction

Typical for these channels is the characteristic architecture with six transmembrane domains (TMDs) of which the 4th TMD contains the voltage sensor and the last two TMDs the pore[3] At their cytosolic carboxyl termini, HCN channels have a canonical cyclic nucleotide-binding domain (CNBD), which is structurally similar to regulatory domains in different forms of life ranging from bacteria to humans[4]. The comparative analysis implies that cAMP binding generates large rigid body movements of the helical domains together with a stabilization of several of the helices In contrast to this detailed knowledge of the cytosolic domain, the structure and dynamics of the transmembrane region of HCN channels remain unknown up to now. We created a structural model of the HCN channel and simulated cAMP removal from the binding pocket using a coarse-grained approach to reveal the dynamics of the allosteric change upon nucleotide www.nature.com/scientificreports/

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Conclusion