Complex crystal structures

D. E. Palin and H. M. Powell. J. Chem. Soc. 1947, 208-21. Crystal structure complexes of hydroquinone-(small, volatile compounds). 

Also soon after the first crystal structure of ER, more traditional structure-based design work started to appear. The group of Stauffer et al. [113] used an acyclic amide structural template combined with the ER crystal structure to find additional hydrogen bonds and increase affinity. A number of separate groups, with just a few mentioned here [114-116], have utilized the crystal structure complexes to generate receptor-based alignment for a series of compounds, which were in turn used to generate predictive 3D-QSAR models. 

The third example in this chapter is about cellulase, Cel5A from Acidothermus cellulolyticus [69], Its crystal structure complexed with a natural substrate cellote-traose was resolved in 1996. Since then, the protein engineering study around this enzyme has attracted much attention. Especially, one of its mutants, Y245G, was found to increase the catalytic activity about 20 %, when combined with Cel7A. Indeed, one of the bottlenecks for effective biomass conversion is the low catalytic ability of cellulases. Theoretical investigations were carried out to understand the catalytic process using the hybrid QM/MM scheme. 

Crystal structure Complex cubic Complex cubic fee bcc... 

Diederich F, Jonas U, Gramlich V, Herrmann A, Ringsdorf H and Thilgen C 1993 Synthesis of a fullerene derivative of benzo[18]crown-6 by Diels-Alder reaction complexation ability, amphiphilic properties, and x-ray crystal structure of a dimethoxy-1,9-(methano[1, 2]benzomethano)fullerene[60] benzene clathrate Helv. Chim. Acta 76 2445-53... 

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

As a template for an intermediate conformation of protein kinase, the crystal structure of the binary complex of cAPK with adenosine (Ibkx.pdb in the Protein Data Bank) was used. As templates for open conformations... 

Fig. 2. Conformational free energy of closed, intermediate and open protein kinase conformations. cAPK indicates the unbound form of cAMP-dependent protein kinase, cAPKiATP the binary complex of cAPK with ATP, cAPKiPKP the binary complex of cAPK with the peptide inhibitor PKI(5-24), and cAPK PKI ATP the ternary complex of cAPK with ATP and PKI(5-24). Shown are averaged values for the three crystal structures lATP.pdb, ICDKA.pdb, and ICDKB.pdb. All values have been normalized with respect to the free energy of the closed conformations.

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Bode, W., Papamokos, E., Musil, D. The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Eur. J. Biochem. 166 (1987) 673-692... 

The catalytic subunit then catalyzes the direct transfer of the 7-phosphate of ATP (visible as small beads at the end of ATP) to its peptide substrate. Catalysis takes place in the cleft between the two domains. Mutual orientation and position of these two lobes can be classified as either closed or open, for a review of the structures and function see e.g. [36]. The presented structure shows a closed conformation. Both the apoenzyme and the binary complex of the porcine C-subunit with di-iodinated inhibitor peptide represent the crystal structure in an open conformation [37] resulting from an overall rotation of the small lobe relative to the large lobe. 

The structure of the metallocene cation energy minimised with the Car-Parrinello method agrees well with the experimentally obtained crystal structures of related complexes. Typical features of the structure as obtained from X-ray diffraction on crystals of very similar neutral complexes (e.g., the dichlorides), such as small differences in distances between C atoms within a cyclopentadienyl (Cp) ring, as well as differences in distances between the C atoms of the Cp ring and the Zr atom, were revealed from the simulations. 

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

Noble M E M, R K Wierenga, A-M Lambeir, F R Opperdoes, W H Thunnissen, K H Kalk, H Groendijk and W G J Hoi 1991. The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes. Proteins Structure, Function and Genetics 10 50-69. 

D, H W Hoeffken, D Crosse, J Stuerzebecher, P D Martin, B F P Edwards and W Bode 1992. Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed witli he 3 Benzamidine and Arginine-Based Thrombin Inhibitors NAPAP, 4-TAPAP and MQPA A Starting Point for Improving Antithrombotics. Journal of Molecular Biology 226 1085-1099. 

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. 

Syntheses, crystallization, structural identification, and chemical characterization of high nuclearity clusters can be exceedingly difficult. Usually, several different clusters are formed in any given synthetic procedure, and each compound must be extracted and identified. The problem may be compounded by the instabiUty of a particular molecule. In 1962 the stmcture of the first high nuclearity carbide complex formulated as Fe (CO) C [11087-47-1] was characterized (40,41) see stmcture (12). This complex was originally prepared in an extremely low yield of 0.5%. This molecule was the first carbide complex isolated and became the foremnner of a whole family of carbide complexes of square pyramidal stmcture and a total of 74-valence electrons (see also Carbides, survey). 

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