Volume difference mapping

Figure 10. Excluded volume map for active hexoses pictured in Figure 9. Volume map of alloxan and difference map showing small region of alloxan not accommodated by hexose map.

Typically, for Expression Difference Mapping experiments, chromatographic surfaces are used. The sample requirement is low (1-10 pg total protein per spot), and the sample volume can be freely chosen from 0.5 pL up to around 300 pL. After a short incubation period, unbound proteins and any contaminants on the spot surface are washed away. A solution of energy-absorbing molecules is applied to each of the spots, and the ProteinChip Array is ready for the analysis in the ProteinChip Reader, a highly sensitive laser desorption/ioniza-tion TOF-MS instrament. The results are initially visualized in a graph, with the mass... 

The molecular size and shape descriptors may indicate if a ligand molecule, L, does not fit the active site. Unfortunately, in many cases the receptor site cannot be described in simple terms of large , width , and depth . The MTD (minimal topologic difference) method allows a receptor site mapping in the frame of a series of bioactive compounds. The MVD (minimal volume difference) method is an improved variant of the MTD method, which takes into account the 3D extension of a molecule. These two methods are described here in some detail. The results obtained in the study of anti-carcinogenic activity of some retinoids and in the inhibition of carbonic-anhydrase (CA) by a series of sulfonamides are also presented in this chapter. 

MVD (molecular volume difference) method presented here was based on MCD method and on MTD multi-conformational method. MVD allows a logical construction of a start map of receptor, S, and assures the differentiation of the vertices in hypermolecule H, translating all the ligands into their vdW space. 

In this chapter we presented two structural measures of molecular shape that can be used as predictor variables in MLR (multiple linear regression) analysis of structure-activity studies - cylindrical (8,G) and ovality ( in, i = 1,2,3) molecular descriptors - and two inexpensive overlapping methods useful for quick receptor mapping - MTD (minimal topological difference) and MVD (minimal volume difference). A subsequent statistical analysis of QSAR models developed with these shape molecular descriptors explained well the variance in the observed reactivity data (8 descriptor of cylindrical shape) and biological activity of retinoids (MTD) and sulfonamides (MVD). 

We will first present an overview of the experimental findings in terms of structure diagrams temperature versus wax volume fraction maps that indicate the different structures found by SANS experiments for each of the investigated polymer-wax systems. This overview will be then followed by a detailed presentation of the structures and morphologies formed by the... 

In some depositional environments, e.g. fluviatile channels, marked differences in reservoir thickness will be encountered. Hence the assumption of a constant thickness, or a linear trend in thickness across the field will no longer apply. In those cases a set of additional maps will be required. Usually a net oil sand (NOS) map will be prepared by the production geologist and then used to evaluate the hydrocarbon volume in place. 

The essential feature of the AAA is a comparison of active and inactive molecules. A commonly accepted hypothesis to explain the lack of activity of inactive molecules that possess the pharmacophoric conformation is that their molecular volume, when presenting the pharmacophore, exceeds the receptor excluded volume. This additional volume apparently is filled by the receptor and is unavailable for ligand binding this volume is termed the receptor essential volume [3]. Following this approach, the density maps for each of the inactive compounds (in their pharm conformations superimposed with that of active compounds) were constructed the difference between the combined inactive compound density maps and the receptor excluded volume represents the receptor essential volume. These receptor-mapping techniques supplied detailed topographical data that allowed a steric model of the D[ receptor site to be proposed. 

The cytoskeleton also contains different accessory proteins, which, in accordance with their affinities and functions, are designated as microtubule-associated proteins (MAPs), actin-binding proteins (ABPs), intermediate-filament-associated proteins (IFAPs), and myosin-binding proteins. This chapter is focused on those parts of the cytoskeleton that are composed of microfilaments and microtubules and their associated proteins. The subject of intermediate filaments is dealt with in detail in Volume 2. 

Although this collision rule conserves momentum and energy, in contrast to the original version of MPC dynamics, phase space volumes are not preserved. This feature arises from the fact that the collision probability depends on AV so that different system states are mapped onto the same state. Consequently, it is important to check the consistency of the results in numerical simulations to ensure that this does not lead to artifacts. 

---