Pathway and endpoint free energy calculations for cyclic nucleotide binding in HCN channel
Lei Zhou 1 and Steven A. Siegelbaum 2*
1 Columbia University
2 Columbia University, HHMI
* To whom correspondence should be addressed. E-mail: sas8{at}columbia.edu.
Submitted on February 11, 2008
Revised on March 19, 2008
Accepted on 21 March 2008
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Abstract |
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Both cAMP and cGMP are important intracellular second messengers that differentially bind to and regulate a variety of proteins, including cyclic nucleotide-gated channels (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) channels. Previous site directed mutagenesis studies have isolated two conserved residues that are critical for enabling certain channels to selectively bind cGMP relative to cAMP. However, no definitive mechanism has been identified that explains the preferential activation of other channels by cAMP. Here we apply computational binding free energy methods, including thermodynamic integration (TI), linear interaction energy (LIE), and continuum electrostatic calculations, to gain insights into the mechanisms of cyclic nucleotide selectivity. Consistent with experimental observations, computational results for the cAMP-selective HCN channels show that the binding free energy of cAMP is lower (more favorable) than that of cGMP. Surprisingly, cAMP selectivity is not due to its preferential contacts with protein, but rather reflect the greater hydration energy of cGMP relative to cAMP, resulting in a greater energetic cost for cGMP binding to the channel.
Key Words:
HCN channel, binding free energy, cyclic nucleotide
