computer modeling in molecular biology.pdf

6 Theory of Tkansport in Ion Channels 165curate ab initio quantum mechanical calculations on small molecular fragments;biased simulation techniques, necessary to overcome the sampling problems, are thenused to determine the potential of mean force (free energy simulation) and thecalculate the transition rate (activated dynamics trajectory); traditional phenomenologies(ERT and NP) provide a conceptual framework to relate the informationgained from the detailed molecular dynamics to the experimental macroscopic observables.Very similar approaches, sometimes involving other quantum chemicalmethods or biased sampling techniques, are now used to investigate dynamical transportproperties in widely different systems (see [96] and reference therein).Despite their sophistications it is also important to realize that modern computationalmethods have limitations, particularly in studying complex biological systems.Experimentally measured differences in ion permeabilities can often be accountedfor by changes of only a few kJ/mol in the activation energies. It should be clearthat such small differences may be beyond the accuracy of present computationalmethods. Thus, in a theoretical study of ion permeation based on a detailed atomicmodel, it is less the absolute transport rate than the analysis of the microscopic factorsnot directly accessible to experimental measurements that are of interest. In tryingto understand the transport properties of an ion channel, the potential of meanforce, W(x), an important concept in modern discussions of dynamical and rate processesin liquids [86, 941, provides essential insight. Although the description of thetransport properties remains incomplete without an investigation of the dynamics,the nature and the overall time-scale of the ion movements inside the channel areoften largely determined by the character of the free energy landscape in W(x). Togain more insight the various contributions to the potential of mean force can beanalyzed with the integrated mean force decomposition method; similarly, the frictionconstant can be linearly decomposed in terms of cross-coupling of the fluctuatingforces. The decomposition method, in combination with site-directedmutagenesis experiments, may be very useful to extract the effect of particularresidues on the factors affecting permeability. Decomposition of the microscopicquantities in terms of various contributions is important because it allows a detailedunderstanding of how an ion channel works in terms of its molecular structure.In future work the growing body of experimental data on the properties ofmodified gramicidin “channels” will be exploited. The gramicidin A is particularlywell suited for such structure-function studies in view of its structural and functionalsimplicity. Experiments involving amino acid substitutions will allow the investigationof the influence of particular side-chains on the permeation process [27, 97-99],and on the stability of monomer-monomer association in the lipid membrane [27].A tartaric acid linked channel showing rapid interruptions in ion flux measurements,similar to the “flickering” observed in biological channels [l], will permit the investigationof chapel gating kinetics [loo- 1021. Simulations of the GA channelembedded in realistic models of the phopholipids bilayer environment will be performed[103].