Step 6 Evaluating Protein Models

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

One important experimental result was available, the quantitative measurement of the fraction of each secondary structural element by circular dichroism (CD) on purified lipid-protein complexes. This provided a constraint that allowed a careful evaluation of the secondary structure predictions derived from the various approaches, some of which were developed for water-soluble proteins and therefore of uncertain reliability for proteins in a lipid environment. The data from these analyses were combined using an integrated prediction method to arrive at a consensus secondary structure model for each protein. The integrated method involved 36 steps, with independent predictions at each step. The final model was based on an evaluation of the various predictions, with judicious intervention by the authors. As an aid to developing the appropriate weighting of all the data, they carried out the analysis for apoE-3 without reference to the available crystal structure (Wilson et al., 1991), then used the known structure of the HDL-binding amino-terminal domain of apoE-3 as feedback to reevaluate the weighting. 

Fig. 1. CPU times (in hours) for 1 ps MD runs for various proteins using three different methods, direct velocity Verlet with a time-step 0.5 fs, r-RESPA with direct evaluation of electrostatic forces and an overall time-step of 4.0 fs, and r-RESPA/TFMM with an overall time-step 4.0 fs (combination of (2,2,2,2) in force breakup).The energy conservation parameter log AE for the three methods are comparable. The CPU time (hours) is for RISC6000 /MODEL 590 computer.

During AEDA, interactions between the odorants are not taken into consideration, since every odorant is evaluated individually. Therefore, it may be possible that odorants are recognized which are possibly masked in the food flavor by more potent odorants. Furthermore, the odor activity values only partially reflect the situation in the food, since OAVs are mostly calculated on the basis of odor thresholds of single odorants in pure solvents. However, in the food system, the threshold values may be influenced by nonvolatile components such as lipids, sugars or proteins. The following examples will indicate that systematic sensory model studies are important further steps in evaluating the contribution of single odorants to the overall food aroma. 

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