Structural motifs

Structural keys describe the chemical composition and structural motifs of molecules represented as a Boolean array. If a certain structural feature is present in a molecule or a substructure, a particular bit is set to 1 (true), otherwise to 0 (false). A bit in this array may encode a particular functional group (such as a carboxylic acid or an amidelinkage), a structural element (e.g., a substituted cyclohexane), or at least n occurrences of a particular element (e.g., a carbon atom). Alternatively, the structural key can be defined as an array of integers where the elements of this array contain the frequency of a specific feature in the molecule. 

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C Bystroff, D Baker. Prediction of local structure m proteins using a library of sequence-structure motifs. J Mol Biol 281 565-577, 1998. 

Karlin, K.D. Metalloenzymes, structural motifs, and inorganic models. Science 261 701-708, 1993. 

Sternberg, M.J.E., et al. Analysis and prediction of structural motifs in the glycolytic enzymes. Phil. Trans. 

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Godovac-Zimmerman, J. The structural motif of p-lactoglobulin and retinol-binding protein a basic framework for binding and transport of small hydrophobic molecules Trends Biochem. Sci. 

As described in Chapter 2, the first complete protein structure to be determined was the globular protein myoglobin. However, the a helix that was recognized in this structure, and which has emerged as a persistent structural motif in the many hundreds of globular proteins determined subsequently, was first observed in x-ray diffraction studies of fibrous proteins. 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

A quite different structural motif is found in the curious cyclic hexamer [(BNMc2)6] which can be obtained as orange-red crystals by distilling the initial product formed by dehalogenation of (Me2N)2BCl with Na/K alloy ( >... 

Chain metasilicates Si03 formed by comersharing of Si04 tetrahedra arc particularly prevalent in nature and many important minerals have this basic structural unit (cf, polyphosphates, p, 528), Despite the apparent simplieily of their structure motif and stoichiometry considerable structural diversity is encountered because of the differing conformations that can be adopted by the linked tetrahedra. As a result, the repeat distance along the c -axis can be (1). 

A completely different structural motif has very recently been found in the red-brown phosphide CasPg, formed by direct fusion of Ca metal and red P in the correct atom ratio in a corundum crucible at 1000 C. The structure comprises Ca + cations and Pg anions, the latter adopting a staggered ethane conformation. (Note that P+ is isolobal with C and P with H so that C2H6 = [(P+)2(P"")6] = Ps - -) The internal P-P distance is 230.1pm and the terminal P-P distances 214.9-216.9 pm, while the internal PPP angles are 104.2-106.4° and the outer angles are 103.4-103.7°. 

A rather different structure-motif is observed in the chain polyphosphates these feature comer-shared PO4 tetrahedra as in the polyphosphoric acids (p. 522). The general formula for such anions is [Pn03 4.i] + , of which the diphosphates, P2O7 ", and tripolyphosphates, PsOjo , constitute the first two members. Chain polyphosphates have been isolated with n up to 10 and with n infinite , but those of intermediate chain length (10 < n < 50) can only be obtained as glassy or amorphous mixtures. As the chain length increases, the ratio (3n + l)/n approaches 3.00 and the formula approaches that of the polymetaphosphates [P03 ]oo-... 

A fascinating variety of discrete (or occasionally polymeric) polynuclear halogeno complexes of As, Sb and Bi have recently been characterized. A detailed discussion would be inappropriate here, but structural motifs include face-shared and edge-shared distorted (MXe) octahedral units fused into cubane-like and other related clusters or cluster fragments. Examples (see also preceding paragraph) are ... 

P4) is closely similar with P-P distances of 216 pm (smaller than for P4 itself, 221pm). Indeed, a whole series of complexes has now been established with the same structure-motif and differing only in the number of valency electrons in the cluster some of these are summarized in Table 13.11. The number of valence electrons in all these complexes falls in the range 30-34 as predicted by R. Hoffmann and his colleagues.Many other cluster types incorporating differing numbers of Group 15 and transition metal atoms are now known and have been fully reviewed. ... 

Finally, many disulfides have a quite different structure motif, being composed of infinite three-dimensional networks of M and discrete Sj units. The predominate structural types are pyrites, FeSa (also for M = Mn, Co, Ni, Ru, Os), and marcasite (known only for FeS2 among the disulfides). Pyrites can be described as a distorted NaCl-type structure in which the rodshaped S2 units (S-S 217 pm) are centred on the Cl positions but are oriented so that they are inclined away from the cubic axes. The marcasite structure is a variant of the rutile structure (Ti02,... 

A different structure motif occurs in S4N3CI. This very stable yellow compound features the S4N3+ cation (p. 732) and is obtained by many reactions, e.g. ... 

There is also a bewildering variety of structural motifs in polytelluride-ligand complexes as the brief selection in Fig. 16.10 indicates the original papers should be consulted for preparative routes and other details. Thus, dissolution of the alloy K2Hg2Te3 in ethylenedi-amine, followed by treatment with a methano-lic solution of [NBu JBr, yields the dark brown... 

Are the points randomly scattered, or are they clustered in certain regions of the plot If the latter, see if you can see any common structural motifs (see also Chapter 16, Problem 9). 

With the adequacy of lipid bilayer membranes as models for the basic structural motif and hence for the ion transport barrier of biological membranes, studies of channel and carrier ion transport mechanisms across such membranes become of central relevance to transport across cell membranes. The fundamental principles derived from these studies, however, have generality beyond the specific model systems. As noted above and as will be treated below, it is found that selective transport... 

This review will focus on the large family of EF-hand proteins characterized by a common structural motif, the EF-hand (Fig 1). 

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