Seconds motifs

One of these motifs, called the helix-turn-helix motif, is specific for DNA binding and is described in detail in Chapters 8 and 9. The second motif is specific for calcium binding and is present in parvalbumin, calmodulin, tro-ponin-C, and other proteins that bind calcium and thereby regulate cellular activities. This calcium-binding motif was first found in 1973 by Robert Kretsinger, University of Virginia, when he determined the structure of parvalbumin to 1.8 A resolution. 

A second motif observed by Strouse and coworkers is characterized by tightly packed herringbone-1 ike layers (Figure 67). Structures of this type were ob.served for ZufTtp-CI )PP -C -HvCI (o chlorotoluene). Zn T(p-... 

A second motif encountered in tetrapyridylporphyiin systems is typified by inclusion compounds with wet methanol and water that produce three-dimensional coordination polymers. Ttv/ni-pyridyl substituents on a Zn(TPyP) were ob.served to axially ligate the metal centers of adjacent porphyrin moieties generating a polymeric chain in one dimension. Cross-linking in a second dimension occurs when the original porphyrin molecule is coordinated by two pyridyl moieties from two additional porphyrin molecules... 

In principle, there are two different motifs of helical stacks commonly employed for columnar materials that are shown in Figure 9. One motif would use the side chains as a means to introduce point chirality that could then be transferred to the cores stacking. This chirality transfer would bias one helical stack versus another. A second motif would start with a structure that has a chiral core and use this as a subunit to stack into a helical column. 

We can shift the set of coordinates denoting the second motif into the same coordinate frame as the set denoting the first motif by replacing each value X(I), (A+l I A+B), by X(I)-(X(A+1)-X(D). All of these B replacement operations are executed in paraUel (with the first A PEs masked out so that the X values contained within them remain unchanged). Then, when the point Pi is broadcast from the MCU to determine its distance from the points P2,Pa... Pa (and to update the frequency distribution for the first database motif), it can simultaneously be compared with the coordinates for the points Pa+i,Pa+2 Pa+b> this corresponding to the calculation of the distances of these points from the point Pa+1 and thus providing the data for the updating of the frequency distribution for the second database motif. P2 is then broadcast, then P3, etc. etc. 

In a further step, molecules build a second motif in another direction in space, by matching sites C with D sites (rows 1-2, Fig. 15.3). This may require an arbitrary rotation of the whole molecule and/or further conformational adjustment. But the recognition motifs are always to some extent malleable, recall the estimated vibrational amplitudes in Table 12.11, and the whole construction adjusts itself so... 

Correspondingly G in the third strand binds to G in the duplex [21,22,23], The second motif often requires high divalent cation concentrations, and the third strand being G-rich, is prone to form self-associated structures involving G-quartets [24]. This is particularly pronounced when the third strand is a triplexforming oligonucleotide (TFO) [25,26]. Another competing structure, a G-A parallel duplex, can also interfere with triplex formation [27]. 

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