Exploring the nature of the translocon-assisted protein insertion

Abstract

The elucidation of the molecular nature of the translocon-assisted protein insertion is a challenging problem due to the complexity of this process. Furthermore, the limited availability of crucial structural information makes it hard to interpret the hints about the insertion mechanism provided by biochemical studies. At present, it is not practical to explore the insertion process by brute force simulation approaches due to the extremely lengthy process and very complex landscape. Thus, this work uses our previously developed coarse-grained model and explores the energetics of the membrane insertion and translocation paths. The trend in the calculated free-energy profiles is verified by evaluating the correlation between the calculated and observed effect of mutations as well as the effect of inverting the signal peptide that reflects the "positive-inside" rule. Furthermore, the effect of the tentative opening induced by the ribosome is found to reduce the kinetic barrier. Significantly, the trend of the forward and backward energy barriers provides a powerful way to analyze key energetics information. Thus, it is concluded that the insertion process is most likely a nonequilibrium process. Moreover, we provided a general formulation for the analysis of the elusive apparent membrane insertion energy, ΔG app , and conclude that this important parameter is unlikely to correspond to the freeenergy difference between the translocon and membrane. Our formulation seems to resolve the controversy about ΔG app for Arg.coarse-grain modeling | hydrophobicity scale | topology T he establishment of the correct functional topology of membrane proteins is a subject of great current interest (e.g., refs. 1-3). It is known that the protein-conducting channel named translocon (TR) plays a vital role in membrane proteins biogenesis (4). Although biochemical and structural (e.g., refs. 5 and 6) studies have provided crucial information about the insertion process, the understanding of this process is still limited. The difficulties in gaining detailed understanding are also apparent from the emerging problem in fully defining the molecular meaning of the intriguing results about the apparent free energy, ΔG app . That is, the concept of ΔG app , introduced by Hessa et al. (7) for the assessment of inserted versus secreted helical domains (Background), appeared in recent years to be more complex than previously thought. Apparently, the most logical implication of the original descriptions of ΔG app has been that it represents an equilibrium result of the partition between membrane and water. In fact, this was implied by the attempts to correlate ΔG app with the water-membrane partitions. However, different works (8-10) implied that the corresponding equilibrium constant corresponds to the equilibrium between the TR and the membrane (see also Background). Unfortunately, none of these works has offered a clear physical rationale for why one has to consider such equilibrium without considering the transfer to water. We note that eve...

Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel

“…Thus, we extended our previous study by the modeling intermediate states of the full Kv1.2 channel and evaluating their energetics, in order to obtain the complete free energy landscape at different voltages. In the current study, we used recent modifications of the CG energetics that included, in addition to the electrostatics effect of the protein, the electrolyte and the external voltage, also the hydrophobic contributions to the overall free energy using residue-and environment-specific hydrophobic scale with an implicit membrane model (27). The free energies were evaluated at two different voltages, −50 and 0 mV, taken as representative voltages for the low depolarization (less than −40 mV and greater than −90 mV) and the high depolarization regime (greater than −20 mV), respectively (28) ( Table S1).…”

Identification of Putative Substrates of SEC2, a Chloroplast Inner Envelope Translocase

“…For SEC2-mediated insertion of TIC40, the aminoproximal end of the TM would need to insert first. This occurs in other Sec systems if there are more positively charged residues on the carboxyl end than on the amino end flanking the TM (Rychkova and Warshel, 2013). This is called the positive inside rule (von Heijne, 1989).…”

Simulating the pulling of stalled elongated peptide from the ribosome by the translocon

“…The CG treatment used to obtain the insertion profile has been described in ref. 11. The EVB calculations used to obtain the chemical barrier in the ribosome and the details of the LD simulations are described in SI Text.…”