Geometry of binding

D, J Sturzebecher and WBode 1991. Geometry of Binding of the N-Alpha-Tosylated Piperidides of weffl-Amidino-Phenylalanine, Para Amidino-Phenylalanine and para-Guanidino-Phenylalanine to Thrombin and Trypsin - X-ray Crystal Structures of Their Trypsin Complexes and Modeling of their Thrombin Complexes. FEBS Letters 287 133-138. 

In contrast to the effect of cycloheptaamylose, cyclohexaamylose depresses the rates of decarboxylation of unionized 8-keto acids (Straub and Bender, 1972). Since conformational effects depend largely on the geometry of binding, it is not surprising to find high sensitivity to the size of the cycloamylose cavity. Apparently, the smaller cyclohexaamylose cavity cannot accomodate the cyclic transition state for acidic decarboxylations. 

Aq. micelles affect excimer formation with change in geometry of binding... 

CTABr -I- amphiphilic azobenzenes. Light and dark reactions are compared Aq. micelles affect excimer formation with change in geometry of binding... 

An analysis by Chakrabarti [21] of protein structures in the PDB showed that metal ions approach the sulfur of methionine at about 38(5)° from the perpendicular to the C-S-C group. This is similar to values in the range foimd, as just described, for smaU-molecule crystal structures in which the metal ion is presumed to interact with a sulfur lone-pair orbital [18]. It was also found that metal ions approach cysteine residues such that the M- -S-C-C torsion angle is 90° or 180°, and that the conformation of the cysteine side chain is generally affected by the metal ion. The metal ions that readily bind to sulfur in proteins are copper, iron, mercury, and zinc. The geometry of binding of metal ions to methionine or cysteine did not appear to depend on the identity of the individual metal. 

Turk D, Stiirzebecher J, Bode W (1991) Geometry of binding of the Na-tosylated piperidines of ra-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin— X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes. FEES 287 133-138... 

Collins, J.B. Schleyer, P.V. Binkley, J.S. Pople, J.A. Self-consistent molecular-orbital methods. XVII. Geometries and binding energies of second-row molecules. A comparison of three basis sets J. Chem. Phys. 64 5142-5151, 1976. 

Self-Consistent Molecular Orbital Methods. XVn Geometries and Binding Energies of Second-Row Molecules. A Comparison of Three Basis Sets J. B. Collins, P. von R. Schleyer, J. S. Binkley and J. A. Pople The Journal of Chemical Physics 64 (1976) 5142-5151... 

Three basis sets (minimal s-p, extended s-p and minimal s-p with d functions on the second row atoms) are used to calculate geometries and binding energies of 24 molecules containing second row atoms, d functions are found to be essential in the description of both properties for hypervalent molecules and to be important in the calculations of two-heavy-atom bond lengths even for molecules of normal valence. 

Several model systems related to metalloenzymes such as carboxypeptidase and carbonic anhydrase have been reviewed. Breslow contributed a great deal to this field. He showed how to design precise geometries of bis- or trisimidazole derivatives as in natural enzymes. He was able to synthesize a modified cyclodextrin having both a catalytic metal ion moiety and a substrate binding cavity (26). Murakami prepared a novel macrocyclic bisimidazole compound which has also a substrate binding cavity and imidazole ligands for metal ion complexation. Yet the catalytic activities of these model systems are by no means enzymic. 

Fig.6 Binding energies of Cu (full lines) and Ag (broken lines) on a Si(lll) surface. The perpendicular distance between the adsorbate atoms and the plane of the surface silicon atoms is denoted by h. Hollow, top, and bridge positions of the adsorbate atoms are indicated by the labels A, B, etc. as shown in the insert, u corresponds to an unrelaxed and r to a relaxed geometry of the neighboring surface Si atoms (after Ref.47)...

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