NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein.

The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.

Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations.

The lateral pressure profile of lipid bilayers has gained a lot of attention, since changes in the pressure profile have been suggested to shift the membrane protein conformational equilibrium. This relation has been mostly studied with theoretical methods, especially with molecular dynamics simulations, since established methods to measure the lateral pressure profile experimentally have not been available. The only experiments that have attempted to gauge the lateral pressure profile have been done by using di-pyrenyl-phosphatidylcholine (di-pyr-PC) probes. In these experiments, the excimer/monomer fluorescence ratio has been assumed to represent the lateral pressure in the location of the pyrene moieties. Here, we consider the validity of this assumption through atomistic molecular dynamics simulations in a DOPC (dioleoylphosphatidylcholine) membrane, which hosts di-pyr-PC probes with different acyl chain lengths. Based on the simulations, we calculate the pyrene dimerization rate and the lateral pressure at the location of the pyrenes. The dimerization rates are compared with the results of di-pyr-PC probes simulated in vacuum. The comparison indicates that the lateral pressure is not the dominant determinant of the excimer/monomer fluorescence ratio. Thus, the results do not support the usage of di-pyr-PC molecules to measure the shape of the lateral pressure profile. We yet discuss how the probes could potentially be exploited to gain qualitative insight of the changes in pressure profile when lipid composition is altered.

Protein shape change has a major effect on the gating energy of a mechanosensitive channel.

Increasing experimental evidence has shown that membrane protein functionality depends on molecular composition of cell membranes. However, the origin of this dependence is not fully understood. It is reasonable to assume that specific lipid-protein interactions are important, yet more generic effects due to mechanical properties of lipid bilayers likely play a significant role too. Previously it has been demonstrated using models for elastic properties of membranes and lateral pressure profiles of lipid bilayers that the mechanical properties of a lipid bilayer can contribute as much as ∼10 k(B)T to the free energy difference associated with a change in protein conformational state. Here, we extend those previous approaches to a more realistic model for a large mechanosensitive channel (MscL). We use molecular dynamics together with the MARTINI model to simulate the open and closed states of MscL embedded in a DOPC bilayer. We introduce a procedure to calculate the mechanical energy change in the channel gating using a three-dimensional pressure distribution inside a membrane, computed from the molecular dynamics simulations. We decompose the mechanical energy to terms associated with area dilation and shape contribution. Our results highlight that the lateral pressure profile of a lipid bilayer together with the shape change in gating can induce a contribution of ∼30 k(B)T on the gating energy of MscL. This contribution arises largely from the interfacial tension between hydrophobic and hydrophilic regions in a lipid bilayer.

Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol.

Lateral pressure profiles have been suggested to play a significant role in many cellular membrane processes by affecting, for example, the activation of membrane proteins through changes in their conformational state. This may be the case if the lateral pressure profile is altered due to changes in molecular composition surrounding the protein. In this work, we elucidate the effect of varying sterol type on the lateral pressure profile, an issue of topical interest due to lipid rafts and their putative role for membrane protein functionality. We find that the lateral pressure profile is altered when cholesterol is replaced by either desmosterol, 7-dehydrocholesterol, or ketosterol. The observed changes in the lateral pressure profile are notable and important since desmosterol and 7-dehydrocholesterol are the immediate precursors of cholesterol along its biosynthetic pathway. The results show that the lateral pressure profile and the resulting elastic behavior of lipid membranes are sensitive to the sterol type, and support a mechanism where changes in protein conformational state are facilitated by changes in the lateral pressure profile. From a structural point of view, the results provide compelling evidence that despite seemingly minor differences, sterols are characterized by structural specificity.