Molecules superimposition

While crystal structures of rubredoxins have been known since 1970 (for a full review on rubredoxins in the crystalline state, see Ref. (15)), only recently have both crystal and solution structures of Dx been reported (16, 17) (Fig. 3). The protein can be described as a 2-fold symmetric dimer, firmly hydrogen-bonded and folded as an incomplete /3-barrel with the two iron centers placed on opposite poles of the molecule, 16 A apart. Superimposition of Dx and Rd structures reveal that while some structural features are shared between these two proteins, significant differences in the metal environment and water structure exist. They can account for the spectroscopic differences described earlier. 

Often, one needs to compare different 3D structures or conformations of a molecule. That is done internally by the 3D stmcture generation program to weed out too similar conformations of fragments. Another aspect is the need of the computational chemist to compare different generated or experimental structures. A well-established measure is the so-called root mean square (RMS) value of all atom-atom distances between two 3D structures. The RMS value needed here is a minimum value achieved by superimposing the two 3D structures optimally. Before calculating the RMS, the sum of interatomic distances is minimized by optimizing the superimposition in 3D. 

Under the experiment conditions, the enzymatic cleavage occurs within seconds. Therefore, the observed release time of the tryptophan is also the actual disappearance time of the intermediate forms after the enzymatic cleavage. This dramatic enhancement of tail-unit release with the elimination-based system (dendritic molecule 19) compared to the cyclization-based system (dendritic molecule 18) is best viewed by superimposition of the graphs (Fig. 5.13). 

Even if the analyte is chemically perfectly pure it represents a mixture of different isotopic compositions, provided it is not composed of monoisotopic elements only. Therefore, a mass spectrum is normally composed of superimpositions of the mass spectra of all isotopic species involved. [11] The isotopic distribution or isotopic pattern of molecules containing one chlorine or bromine atom is listed in Table 3.1. But what about molecules containing two or more di-isotopic or even polyisotopic elements While it may seem, at the first glance, to complicate the interpretation of mass spectra, isotopic patterns are in fact an ideal source of analytical information. 

Structural alignments (ligand-based virtual screening) on the basis of a known active compound, molecules that show a good superimposition in shape and physicochemical features are searched for. 

The algorithm for the systematic conformation search starts with a minimized molecule. The rotatable bonds are selected along with the rotation increment and all possible conformations are created. At this point the search is terminated or each of the proposed conformations is energy minimized according to predefined parameters. After the database of conformers is finalized, each structure is compared to all the other structures through superimposition. Two... 

Meiler and Pfeifer (493) measured 13C and H NMR spectra of carbon monoxide, carbon dioxide, and benzene adsorbed on ZSM-5 and silicalite. The 13C signal from benzene was a superimposition of two lines corresponding to relatively mobile molecules (narrow Lorentzian line) and strongly adsorbed molecules (broad asymmetric line similar to that in polycrystalline benzene). Quantitative interpretation of the spectrum was possible via the measurement of the transverse proton relaxation times, T2, as a function of temperature and coverage. Recent work involving 13C NMR studies of sorbed species is summarized in Table XX. 

Fig. 11. Graphic representation for the first results in Fig. 5. The left-hand view shows the superimposition for the whole molecules, except for hydrogen atoms, and the right-hand view is for the relevant portions...

Fig. 12. The maximal common geometric pattern founded by COMPASS. In weighting atoms, different atomic species and atomic charge were considered. The distance allowance is 0.5 A. a Three-dimensional structures of haloperidide (left) and milenperone (right), b Display of the superimposition of their whole molecules and common parts, c Display of the common parts with electronic property...

The structural similarity of two molecules can be compared by superimposition with Spdbv ... 

Figure 15.3. Superimposition of two molecules with SPDBV. The structure superimposition of bovine ribonuclease (IRPH.pdb in blue) and rat ribonuclease (1RRA.pdb in red) is shown. The color for the superimposed molecules is assigned from the control panel as illustrated for 1RPH in blue. The corresponding color for color boxes of 1RRA is red. The align window shows sequence alignment of the two molecules.

Fig. 3.2 Unique trifoliolate structure of proline-/S-naphthylamidase.l7) Electron micrographic images of negatively stained molecules are rotationary averaged after superimposition of images each with 120° rotation from the others. Scale bar, 3 nm. (Reproduced with permission from K. Takahashi, FEBS Leu., 280, 298 (1991)).

Figure 12 Superimposition of an LFA-1 antagonist on the discontinuous epitope of ICAM-1 (pdb-code Ham, protein backbone shown as blue tube), which binds to LFA-1. Residues of the protein indicated in yellow contribute to LFA-1 binding and are mimicked perfectly by the small molecule...

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