Conclusions

The most direct and, perhaps, the only path to understanding the origins and earliest evolution of cellular life requires gaining advanced knowledge of contemporary cells and physico-chemical principles determining cellular organization and functions. This paper has been devoted to translating this idea into specific examples of protocellular functions through the application of molecular-level computer simulation methods. The ability to generalize the results for properly chosen models to other systems makes these methods particularly useful.

We have focused on the role of membranes as the main structures that distinguish a cell from other microenvironments. In particular, we stressed the role of membranes as barriers to charged species and explored it in two different contexts. We considered possible activated mechanisms for the formation of a proton gradient across protocellular walls than could be further utilized as an energy source. We paid special attention to the directionality of this process which was essential to sustain the gradient and showed that a simple gate-keeping mechanism could be created by placing a proton donor and two proton acceptors at proper locations in the membrane. This mechanism might also involve a water molecule. One example of such a system consists of two transmembrane, helical peptides. We also investigated how simple ions could permeate cell walls and showed that this process is facilitated by highly flexible membranes. Ion transport is accompanied by the formation of thinning defects in the membrane which are needed to reduce the high activation barrier to this process.

Despite considerable experimental [14] and theoretical [3] progress in establishing a molecular basis of protocellular life, most aspects of this problem remain poorly understood. In particular, catalytic systems and mechanisms leading to synthesis of essential cellular components (e.g amphiphiles, short peptides) are not known. Also, a specific, directional mechanism of capturing and utilizing energy has not yet been demonstrated. Solving these two problems are among the most important and challenging tasks in studies of protocellular life. Based on rapid increase in computational capabilities and fast progress in understanding membrane-based functions, we anticipate that computer simulations will be very useful to this end.