Papers by Rainer Böckmann
Journal of Molecular Biology, 2006
Escherichia coli DsbD transports electrons from cytoplasmic thioredoxin to periplasmic target pro... more Escherichia coli DsbD transports electrons from cytoplasmic thioredoxin to periplasmic target proteins. DsbD is composed of an N-terminal (nDsbD) and a C-terminal (cDsbD) periplasmic domain, connected by a central transmembrane domain. Each domain possesses two cysteine residues essential for electron transport. The transport proceeds via disulfide exchange reactions from cytoplasmic thioredoxin to the central transmembrane domain and via cDsbD to nDsbD, which then reduces the periplasmic target proteins. We determined four high-resolution structures of cDsbD: oxidized (1.65 Å resolution), chemically reduced (1.3 Å), photo-reduced (1.1 Å) and chemically reduced at pH increased from 4.6 to 7. The latter structure was refined at 0.99 Å resolution, the highest achieved so far for a thioredoxin superfamily member. The data reveal unprecedented structural details of cDsbD, demonstrating that the domain is very rigid and undergoes hardly any conformational change upon disulfide reduction or interaction with nDsbD. In full agreement with the crystallographic results, guanidinium chloride-induced unfolding and refolding experiments indicate that oxidized and reduced cDsbD are equally stable. We confirmed the structural rigidity of cDsbD by molecular dynamics simulations. A remarkable feature of cDsbD is the pKa of 9.3 for the active site Cys461: this value, determined using two different experimental methods, surprisingly was around 2.5 units higher than expected on the basis of the redox potential. Additionally, taking advantage of the very high quality of the cDsbD structures, we carried out pKa calculations, which gave results in agreement with the experimental findings. In conclusion, our wide-scope analysis of cDsbD, encompassing atomic-resolution crystallography, computational chemistry and biophysical measurements, highlighted two so far unrecognized key aspects of this domain: its unusual redox properties and extreme rigidity. Both are likely to be correlated to the role of cDsbD as a covalently linked electron shuttle between the membrane domain and the N-terminal periplasmic domain of DsbD.
Nature Structural Biology, 2002
The mitochondrial membrane protein FoF1-ATP synthase synthesizes adenosine triphosphate (ATP), th... more The mitochondrial membrane protein FoF1-ATP synthase synthesizes adenosine triphosphate (ATP), the universal currency of energy in the cell. This process involves mechanochemical energy transfer from a rotating asymmetric gamma-'stalk' to the three active sites of the F1 unit, which drives the bound ATP out of the binding pocket. Here, the primary structural changes associated with this energy transfer in F1-ATP synthase were studied with multi-nanosecond molecular dynamics simulations. By forced rotation of the gamma-stalk that mimics the effect of proton motive Fo-rotation during ATP synthesis, a time-resolved atomic model for the structural changes in the F1 part in terms of propagating conformational motions is obtained. For these, different time scales are found, which allows the separation of nanosecond from microsecond conformational motions. In the simulations, rotation of the gamma-stalk lowers the ATP affinity of the betaTP binding pocket and triggers fast, spontaneous closure of the empty betaE subunit. The simulations explain several mutation studies and the reduced hydrolysis rate of gamma-depleted F1-ATPase.
Biophysical Journal, 2015
Biophysical Journal, 2014
The journal of physical chemistry. B, Jan 26, 2015
A molecular description of the lipid-protein interactions underlying the adsorption of proteins t... more A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding t...
Angewandte Chemie (International ed. in English), Jan 13, 2004
Biophysical journal, 2003
Electrostatic interactions govern structural and dynamical properties of membranes and can vary c... more Electrostatic interactions govern structural and dynamical properties of membranes and can vary considerably with the composition of the aqueous buffer. We studied the influence of sodium chloride on a pure POPC lipid bilayer by fluorescence correlation spectroscopy experiments and molecular dynamics simulations. Increasing sodium chloride concentration was found to decrease the self-diffusion of POPC lipids within the bilayer. Self-diffusion coefficients calculated from the 100 ns simulations agree with those measured on a millisecond timescale, suggesting that most of the relaxation processes relevant for lipid diffusion are faster than the simulation timescale. As the dominant effect, the molecular dynamics simulations revealed a tight binding of sodium ions to the carbonyl oxygens of on average three lipids leading to larger complexes with reduced mobility. Additionally, the bilayer thickens by approximately 2 A, which increases the order parameter of the fatty acyl chains. Sodi...
Biophysical journal, 2003
According to the different nucleotide occupancies of the F(1)-ATPase beta-subunits and due to the... more According to the different nucleotide occupancies of the F(1)-ATPase beta-subunits and due to the asymmetry imposed through the central gamma-subunit, the beta-subunit adopts different conformations in the crystal structures. Recently, a spontaneous and nucleotide-independent closure of the open beta-subunit upon rotation of the gamma-subunit has been proposed. To address the question whether this closure is dictated by interactions to neighbored subunits or whether the open beta-subunit behaves like a prestressed "spring," we report multinanosecond molecular dynamics simulations of the isolated beta-subunit with different start conformations and different nucleotide occupancies. We have observed a fast, spontaneous closure motion of the open beta(E)-subunit, consistent with the available x-ray structures. The motions and kinetics are similar to those observed in simulations of the full (alpha beta)(3)gamma-complex, which support the view of a prestressed "spring,&quo...
Nature structural biology, 2002
The mitochondrial membrane protein FoF1-ATP synthase synthesizes adenosine triphosphate (ATP), th... more The mitochondrial membrane protein FoF1-ATP synthase synthesizes adenosine triphosphate (ATP), the universal currency of energy in the cell. This process involves mechanochemical energy transfer from a rotating asymmetric gamma-'stalk' to the three active sites of the F1 unit, which drives the bound ATP out of the binding pocket. Here, the primary structural changes associated with this energy transfer in F1-ATP synthase were studied with multi-nanosecond molecular dynamics simulations. By forced rotation of the gamma-stalk that mimics the effect of proton motive Fo-rotation during ATP synthesis, a time-resolved atomic model for the structural changes in the F1 part in terms of propagating conformational motions is obtained. For these, different time scales are found, which allows the separation of nanosecond from microsecond conformational motions. In the simulations, rotation of the gamma-stalk lowers the ATP affinity of the betaTP binding pocket and triggers fast, spontan...
The adsorption of proteins on solids and soft materials plays a vital role in biotechnical and bi... more The adsorption of proteins on solids and soft materials plays a vital role in biotechnical and biomedical applications, for example for the biocompatibilty of implant material or in dental health care. Not only the properties of the sorbent surface can be changed, but also the proteins might undergo conformational changes during adsorption. To investigate such processes in molecular detail, but still reaching appropriate time scales (microseconds), coarse-grained molecular dynamics simulations were applied here. As a model system, the adsorption of lysozyme and human serum albumin to a simple, slightly negatively charged, single-layer solid surface were studied at various ion concentrations. Adsorption rates of the two proteins, protein diffusion before and after attachment to the surface, and the orientation of the proteins on the surface were analyzed.
The pentadecapeptide gramicidin forms a cation-specific ion channel in membrane environment. Two ... more The pentadecapeptide gramicidin forms a cation-specific ion channel in membrane environment. Two conformations are known up-to-date: the head-to-head helical dimer (HD) and the intertwined double helical form (DH). These two conformations are favored depending on the specific conditions, but the biologically active form is still a matter of debate. Nevertheless, due to its small size, the gramicidin serves as an excellent ion channel model for both computational and experimental studies. In this comparative study, we focus on the energetics of single potassium ion permeation by means of the potential of mean force (PMF) for both gramicidin conformations using molecular dynamics simulations. Our results show that the DH has a significantly decreased central barrier with respect to HD, implying an increased ion conduction. The barrier to ion passage is found to be closely related to the channel flexibility. Multiple ion permeation for the DH conformation is probably facilitated due to its opposing pore water dipole moments at the pore entrances.
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Papers by Rainer Böckmann