Conformation Crystal structures

Chain Conformation, Crystal Structures, and Structural Disorder in Stereoregular Polymers... 

The free ligand, or its protonated form dien-H ( = 0-3), has the potential to adopt the cis,cis (37), cis,trans (38) or trans,trans (39) conformations. Crystal structures of dien-H"+ (n = 2, 3) (Table 8) salts show that both the counter ion and degree of protonation determine which form is adopted. 

The sequence of amino acids in the long chain defines the primary structure of a protein. A secondary structure is determined when several residues, linked by hydrogen bonds, conform to a given combination (e.g., the a-helix, pleated sheet, and P-turns). Tertiary structure refers to the three-dimensional folded conformation of a protein. This is the biologically active conformation (crystal structure). A quaternary structure can result when two or more individual proteins assemble into two or more polypeptide chains. Conjugated proteins are complexes of proteins with other biomolecules, such as glycoproteins (sugar-proteins). 

Figure 7. X-ray crystal structure of meso-octamethylcalix[4]pyrrole-methanol complex, 1-21916014. The calixpyrrole adopts a 1,3-alternate conformation. Crystal structure originally published in Allen, W. E. Gale, P. A. Brown, C. T. Lynch, V. M. Sessler,. L. j. Am. Chem. Soc. 1996, /18, 12471. Diagram produced using data from the Cambridge Crystallographic Database.

The reinforcement of polypropylene and other thermoplastics with inorganic particles such as talc and glass is a common method of material property enhancement. Polymer clay nanocomposites extend this strategy to the nanoscale. The anisometric shape and approximately 1 nm width of the clay platelets dramatically increase the amount of interfacial contact between the clay and the polymer matrix. Thus the clay surface can mediate changes in matrix polymer conformation, crystal structure, and crystal morphology through interfacial mechanisms that are absent in classical polymer composite materials. For these reasons, it is believed that nanocomposite materials with the clay platelets dispersed as isolated, exfoliated platelets are optimal for end-use properties. 

Summary We present ab initio calculations and crystal structures of halo- and hydrido-substituted cyclodisilazanes as well as the synthesis and crystal structure of the first amino-chloro functional cyclodisilazane in the cw-conformation. Crystal structure determinations of cyclotrisilazanes are shown. 

Keywords Azacalixarene - Conformation Crystal structure Inclusion property Macrocyclization... 

Keywords Calixfurans Conformation Crystal structure Heterocalixarenes ... 

The first technique is very intuitive. Out of the few proteins that could be crystallized in a number of different conformations, adenylate kinase is probably the best-studied example. By combining nine observed crystal structures and interpolating between them, a movie was constructed that visualized a hypothetical path of its hinge-bending transition (jVonrhein et al. 1995]). 

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. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

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.

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. 

It may be desirable to predict which crystal structure is most stable in order to predict the products formed under thermodynamic conditions. This is a very difficult task. As of yet, no completely automated way to try all possible crystal structures formed from a particular collection of elements (analogous to a molecular conformation search) has been devised. Even if such an effort were attempted, the amount of computer power necessary would be enormous. Such studies usually test a collection of likely structures, which is by no means infal-... 

Pyran, 2,6-dimethyl-4-(p-nitrophenylimino)-crystal structure, 3, 621 Pyran, 4,4-diphenyl-synthesis, 3, 757 Pyran, 2,6-diphenyltetrahydro-conformation, 3, 629 Pyran, ciY-diphenyltetrahydro-synthesis, 3, 774 Pyran, epoxydihydro-synthesis, 1, 475 Pyran, 2-ethoxytetrahydro-dehydration, 3, 773 Pyran, 2-formyl-5-methyl-3,4-dihydro-synthesis, 3, 771... 

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