Structure, three-dimensional motifs, structural

A general and precise description of stereoisomerism in polymers is suggested on the basis of the repetition theory which describes the distinct patterns along a line that can be obtained from a three-dimensional motif. The probability models for describing the" stero-sequence length in various possible cases of interest in stereoregular polymers are discussed. It is shown that for describing the stereosequence structure, the simplest probability model must involve a Markov chain with four probability parameters. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

Figure 2.20 Motifs that are adjacent in the amino acid sequence are also usually adjacent in the three-dimensional structure. Triose-phosphate isomerase is built up from four P-a-p-a motifs that are consecutive both in the amino acid sequence (a) and in the three-dimensional structure (b).

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

Most of the known antiparallel p structures, including the immunoglobulins and a number of different enzymes, have barrels that comprise at least one Greek key motif. An example is 7 crystallin, which has two consecutive Greek key motifs in each of two barrel domains. These four motifs are homologous in terms of both their three-dimensional structure and amino acid sequence and are thus evolutionarily related. 

Boumann, U., et al. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa, a two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 12 3357-3364, 1993. 

Figure 9.8 Schematic diagram of the three-dimensional structure of the Antennapedia homeodomain. The structure is built up from three a helices connected by short loops. Helices 2 and 3 form a helix-turn-hellx motif (blue and red) similar to those in procaryotic DNA-binding proteins. (Adapted from Y.Q. Qian et al.. Cell 59 573-580, 1989.)...

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 beta barrel is a three-dimensional protein fold motif in which beta strands connected by loops form a barrellike structure. For example, this fold motif is found in many proteins of the immunoglobulin family and of the chymotrypsin family of serine proteases. 

Due to their small size, many short polypeptides do not exhibit in solution a well-defined and stable three-dimensional structure, thus limiting potentially useful self-assembly-affecting motifs. Chemical modifications leading to the addition of unnatural... 

Figure 39-13. A schematic representation of the three-dimensional structure of Cro protein and its binding to DNA by its helix-turn-helix motif. The Cro monomer consists of three antiparallel p sheets (P1-P3) and three a-helices (a,-a3).The helix-turn-helix motif is formed because the aj and U2 helices are held at about 90 degrees to each other by a turn offour amino acids. The helix of Cro is the DNA recognition surface (shaded). Two monomers associate through the antiparallel P3 sheets to form a dimer that has a twofold axis of symmetry (right). A Cro dimer binds to DNA through its helices, each of which contacts about 5 bp on the same surface of the major groove. The distance between comparable points on the two DNA a-helices is 34 A, which is the distance required for one complete turn of the double helix. (Courtesy of B Mathews.)...

Fig. 1. Structural motifs of metal pnictides two- and three-dimensional (ladderlike aggregation).

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