Arabinose binding protein

Figure 4.21 The polypeptide chain of the arabinose-binding protein in E. coli contains two open twisted a/P domains of similar structure. A schematic diagram of one of these domains is shown in (a). The two domains are oriented such that the carboxy ends of the parallel P strands face each other on opposite sides of a crevice in which the sugar molecule binds, as illustrated in the topology diagram (b). [(a) Adapted from J. Richardson.)...

F. A. Quicho and N. K. Vyas, Novel stereospecificity of the L-arabinose binding protein,... 

Fig. 67. Stereo a-carbon drawing of the two domains of arabinose-binding protein (viewed perpendicular to the approximate 2-fold axis between domains), with the stretch of chain shown dark which joins the end of the first domain to the beginning of the second one.

Arabinose-binding protein domains 1 and 2 Dihydrofolate reductase Adenylate kinase Rhodanese domains 1 and 2 Glutathione reductase domains 1 and 2 Phosphoglycerate mutase Phosphoglycerate kinase domain 2 Pyruvate kinase domain 3 Hexokinase domains 1 and 2 Catalase domain 3 Aspartate aminotransferase... 

Fig. 8.2 Hot spots calculated for water sites with DrugScore in the binding pocket of arabinose binding protein (5abp).

Fig. 21. Stereodrawing of L-arabinose bound to L-arabinose-binding protein from Escherichia coli. The edge-to-face interaction between tryptophan-16 and phenylalanine-17 gives rise to a hydrophobic surface that interacts with the hydrophobic portion of the sugar. Reproduced with permission from Quiocho and Vyas (1984).

The GA approach has also been applied to the docking problem with dihydrofolatereduc-tase, arabinose binding protein, and sialidase... 

Arabinose binding protein in compiex with /3-L-arabinose (ARA)... 

Amino acids involved in binding M6P are shown in O Fig. 8. The phosphate moiety is coordinated by His 105, Asn 104, Asp 103 and divalent cation. Each hydroxyl of Man is hydrogen-bonded to binding site residues, while no interactions between the hydrophobic carbohydrate backbone and aromatic side chains are observed [148]. The multiple contacts between lectin and M6P, in contrast to that observed for many lectins which mediate cell surface interactions, are reflected in pM binding constants, reminiscent of bacterial arabinose-binding protein which functions as a sugar transport protein [149]. 

Figure 2. Calculated vs. observed free energies of binding for DHFR complexes (circles), the arabinose complex with arabinose binding protein (triangle), the lysine complex with lysine binding protein (diamond), the complexes of stearate and elaidate with muscular fatty acid binding protein (squares) and the complexes of retinol, retinoic acid, n-ethyl-retinamide and fenretinide with bovine plasma RBP (stars).

Most of the information on interdomain motions come from high-resolution crystal structures several reviews are available (Janin and Wodak 1983 Bennett andHuber 1984 Gerstein et al. 1994). Calculations ofhinge bending modes and domain motions in proteins other than lysozyme have been made. They include antibody molecules where the interdomain motions occur on a nanosecond time scale (McCammon and Karplus 1977 Oi et al. 1984), 1-arabinose-binding protein (Mao et al. 1982), liver alcohol dehydrogenase (Colona-Cesari et al. 1986) and the mouse... 

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