High-resolution modeling

FIGURE 5-1 3 (A, B) Structure of a glutamate transporter. This bacterial glutamate transporter provides the first high-resolution model of a glutamate transporter [88]. The X-ray data indicate a trimeric structure. (A) A view of the trimer extracellularly and perpendicular to the bilayer. 

E. coli has a specific three-dimensional conformation featuring extensive intrachain base pairing. The predicted secondary structure of the rRNAs (Fig. 27-10) has largely been confirmed in the high-resolution models, but fails to convey the extensive network of tertiary interactions evident in the complete structure. 

The high-resolution model of the MT derived by docking tubulin into the 8-A reconstruction of the MT shows that the critical lateral contacts between protofilaments are established from the M loop of one side to loop H1-S2 and helix H3 of the other side (Fig. 3). While helix H3 is locked into its position, the M loop is flexible enough to accommodate different angles between protofilaments without compromising the interactions between subunits, thus allowing the formation of MT with different numbers of protofilaments [23, 24],... 

The initial observation that paclitaxel (PTX) stabilized the zinc sheet form of tubulin at nanomolar concentrations suggested that there was a high affinity binding site in these polymers like that found on microtubules. However, it was not a priori certain that the binding site on sheets would have the same geometry even if it were in the same location. The derivation of high resolution models of both polymers that show the same dimer structure supports the conclusion that, indeed, they share the same binding site. 

Gallicchio E, Levy RM (2004) AGBNP, An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling. J. Comput. Chem. 25 479-499... 

Table 19.1 Simulations perfonned with the high-resolution model area shown in Fig. 19.1b...

Nogales E, Whittaker M, Milligan RA, Downing KH. High-resolution model of the microtubule. Cell 1999 96 79-88. 

Many medium resolution structures of macromolecular assemblies (e.g., ribosomes), spherical and helical viruses, and larger protein molecules have now been determined by electron cryomicroscopy in ice. Four atomic resolution structures have been obtained by electron cryomicroscopy of thin 2D crystals embedded in glucose, trehalose, or tannic acid (11-14), where specimen cooling reduced the effect of radiation damage. One of these, the structure of bacteriorhodopsin (1 l)provided the first structure of a seven-helix membrane protein. The medium resolution density distributions can often be interpreted in terms of the chemistry of the structure if a high resolution model of one or more of the component pieces has already been obtained by X-ray, electron microscopy, or NMR methods. As a result, the use of electron microscopy is becoming a powerful technique for which, in some cases, no alternative approach is possible. Useful reviews [e.g., Dubochet et al. (9), Amos et al. (15), Walz and Grigorieff (16), and Baker et al. (17)] and a book [Frank (18)] have been written. 

Van Keken P. E., Kiefer B., and Peacock S. (2002) High-resolution models of subduction zones implications... 

Figure 9.7 Sensitivity tests to urban features with the DMI-HIRLAM high resolution model shown as the difference fields (runs without vs. with modifications) for the 2-m temperature (upper row) and 10-m wind velocity (lower row) separately with the inclusion of the AHF (left) and urban roughness (right) over the Copenhagen and Malmo metropolitan areas on 30 March 2005.

Schwab, D. J., Bennett, J. R., Liu, P. C., Donelan, M. A., 1984. Application of a Simple Numerical Wave Prediction Model to Lake Erie. Journal of Geophysical Research, 89(C3), 3586-3592. Seifert, T., Fennel, W., Kuhrts, C., 2007. High resolution model studies of transport of sedimentary... 

For dispersed systems the interfacial tension terms are generally more important in the high resolution models simulating details of the local flow close to each individual interface. 

This simplification is commonly called the hydrostatic approximation. The approximation states that, in the vertical direction, the most important forces acting on a parcel of air are the vertical pressure gradient and gravity. This approximation is common in dynamical models, although it neglects some phenomena such as sound waves, and is not appropriate for high resolution models. The ideal gas law can be used to substitute for p in the above equation to obtain... 

Thermal stability of hemicelluloses was performed using thermogravimetric analysis (TGA) on a thermal analyzer (TA Instruments High-Resolution Model Q-500). The apparatus was continually flushed with nitrogen. The samples weighed between 10 and 13 mg and were run fiom room temperature to 600 °C at a rate of 10 °C/min. 

CalKcchio, E., Levy, R.M. AGBNP An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem. 2004,25,479-99. 

Dose, E.V. and Guiochon, G.A., High-resolution modeling of capillary zone electrophoresis and isotachophoresis, AnaZ. Chem., 63, 1063, 1991. 

The resolution of a SIMION model is limited by manory constraints. The accuracy of ion trajectory simulations is highly dependent on the spatial resolution of the PA naturally, higher resolution models provide better approximations of smooth electrode surfaces and hence a better description of the electric field. Unfortunately, high-resolution models are memory-intensive each point in the PA requires 8-10 bytes of dynamic memory. SIMION v. 8.0 has an upper limit of 2x 10 points, which corresponds to ca 1.8 GB of RAM. Thus, the maximum cubic PA allowed is approximately 580x 580x 580 points. However, in order to run efficiently simulations of dynamic... 

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