Free Energy Essay

1078 words - 4 pages

Substantial efforts have been devoted to characterize the above interesting phenomenon in the passed several years [7, 16-20, 26, 27]. Water distribution in the crystal structure of AQP1 has suggested the unlikelihood of proton transporting through the channel [7]. Molecular dynamics (MD) simulations utilizing the multi-state empirical valence bond (MS-EVB) model[23, 24, 28-31] have explained the originality of proton blocking behavior in the AQP1 channel [18, 19]. One free energy barrier for proton permeation in wild-type AQP1 originates from a constriction region, or the selectivity filter (SF) domain located at the extracellular pore mouth, which is composed of residue Phe56, His180, Cys189 and Arg195. This domain is also referred as the ar/R region since it provides an aromatic environment with restraints to the incoming solutes inside the protein. In wild-type AQP1, the ar/R region has a diameter of ~ 2 Å and allows the passage of only one water molecule thus a single file water wire is formed along the channel [18, 32]. Such constriction has contributed to the dehydration penalty for the excess proton to pass through [18, 19]. On the other hand, it is suggested that the electrostatic repulsive interaction arising from the positive charge on Arg195 also contributes to the proton permeation free energy barrier which is about 15 kcal/mol higher compared with the channel mouth region [18]. Additionally, a predominant obstacle preventing proton leakage comes from the collective macro-dipole at the Asn-Pro-Ala domain (NPA) located at the center of the channel. This NPA domain is slightly wider in diameter than the SF domain and is considered as fingerprint of the aquaporin family. The two oppositely orientated Asn-Pro-Ala sequences at the center of the channel are highly conserved in all the aquaporins, with the positions of proline and alanine in several cases switched.
Recently, aimed on locating the cation filter in the prototypical water-specific AQP1, Beitz etc. explored cation permeation in a series of AQP1 channels[20]. The conductance of excess proton, sodium cation (Na+), and potassium cation (K+) in mutants AQP1-N76D, AQP1-H180A/R195V, and AQP1-N76D/H180A/R195V were measured. By point mutations at the SF domain, NPA motif or combined mutations at both domains, several proton leaking AQP1 channels were identified. Their results suggest that the effective blocking of alkali cations is likely to originate from the ar/R SF domain, while the excess proton blocking requires the collaboration of both the NPA motif and the ar/R SF region, which is consistent with our previous theoretical investigations [18, 19].
In the present study, to further theoreticcally explore the cation filtering mechanism of AQP1, single and combined mutants AQP1-N76D, AQP1-H180A/R195V, and AQP1-N76D/H180A/R195V have been examined. Molecular dynamics (MD) simulations were performed and the umbrella sampling technique [33, 34] was employed to obtain the...

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