A computational approach to study the energy transduction mechanism in the Na+/K+-ATPase
2008, Weidemüller, Christian, Hauser, Karin
The Na+/K+-ATPase pumps ions across the membrane which is necessary for maintaining the membrane potential. The energy for this active ion transport is provided by binding and hydrolysis of ATP and has to be transferred from the cytoplasmic nucleotide binding site to the transmembrane domain of ion transport. This transport cycle can also be induced experimentally by applying voltage jumps across the membrane. We simulated the applied electric field by an ionic capacitor and studied the impact on the Na+/K+-ATPase by a combination of multiconformation continuum electrostatics (MCCE) and molecular dynamics (MD). Our calculations show a selective activation of the helices M5, M6 and M8 by the electric field. Those helices are likely to act as energy transduction elements.
Thermal unfolding of a beta hairpin studied with IR spectra enhanced by site-specific isotope labeling
2007, Huang, Rong, Krejtschi, Carsten, Hauser, Karin, Kim, Joohyun, Keiderling, Timothy A.
To model formation of beta-sheets in proteins it is essential to understand the interaction and dynamics between separate strands. The simplest model for such interactions are beta-hairpins, of which the TrpZip model of Cochran is one of the most stable in aqueous solution. We have modified the TrpZip2 sequence by substituting Ala on the 1,3, and 10 positions to destabilize the hairpin somewhat and to facilitate isotopic labeling. If C=O groups on opposite strands are labeled with 13C, their coupling can lead to distinctive amide I bands whose intensity, and sometimes frequency can reflect local cross-strand coupling, and thus hairpin formation at that position in the sequence. For a fully formed hairpin the A1A10 forms a labeled outer (14-atom) H-bonded ring and the A3K8 an inner one, while the A3A10 forms a central (10 atom) H-bonded ring. Equilibrium studies show the A1A10 to be less well formed (non-degenerate) than the A3K8, and the A3A10 has a different pattern with distinct disruptive effects on the 12C=O coupling. Laser excited T-jump measurements show fast relaxation kinetics that varies with wavelength probed and initial temperature. The differences in kinetics for different positions in the hairpin suggest a multistate process consistent with observations by others on related systems. Spectral simulations have been obtained using QM level force fields and structural results from extended MD calculations.
Protonation of Ca2+ -ATPase Residues upon Ca2+ Release : [Abstracts of papers at the Fifty-Ninth Annual Meeting of the Society of General Physiologists]
2005, Andersson, Julia, Hauser, Karin, Barth, Andreas
We have studied protonation of the sarcoplasmic reticulum Ca2 -ATPase during Ca2 release and E2P formation (Ca2E1→E2P) using rapid scan Fourier transform infrared spectroscopy. The reaction has been investigated from pH 6.0 to 9.0. Infrared spectra show four signals in the spectral region of protonated carboxyl groups at pH 6.0–7.5 and only two at pH 8.0–9.0. The results show that at least two of the protonated carboxyl groups of E2P have a pK of 7.7. We have concluded that these carboxyl groups participate in H countertransport. To identify these carboxyl groups and to assign the IR bands, multiconformation continuum electrostatic calculations (MCCE) have been performed to calculate the residues’ ionization, at various pH, for the calcium-free and the calcium-occluded structure, respectively. The combination of infrared measurements and MCCE calculations clearly indicates that Asp800 is involved in the proton countertransport whereas Glu309 is not. The second carboxyl group involved in the countertransport might be Glu908. Our results also indicate a pH-dependent conformational change in a -sheet or turn structure of E2P. Additionally, we have tentatively assigned a band to the C O bond of the phosphorylated Asp 351. Based on infrared data, we concluded that the bond strength is essentially unchanged but is slightly reduced in E2P compared with Ca2E1P. This reduction is larger when Mg2 is bound to the aspartyl phosphate.