Sequence-specific interactions, operator

Sequence-specific protein-DNA interactions recognize operator regions... 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

Valegard, K., et al. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific pro-tein-RNA interactions. /. Mol. Biol. 270 724-738,... 

The proteins impose precise distortions on the B-DNA in the complexes Sequence-specific protein-DNA interactions recognize operator regions... 

We have seen how an entire sequence of interactions between objects can be abstracted and described as a single joint action. We will next see how even in program code, an operation invocation itself has two sides the sender and the receiver. By using input and output parameters, a localized operation specification decouples the effect on the receiver from any information about the initiator. 

Inspection of the complete E. coli genome sequence reveals two sites within 500 bp of the primary operator site that approximate the sequence of the operator. Other lac repressor dimers can bind to these sites, particularly when aided by cooperative interactions with the lac repressor dimer at the primary operator site. No other sites that closely match sequence of the lac operator site are present in the rest of the E. coli genome sequence. Thus, the DNA-binding specificity of the lac repressor is sufficient to specify a nearly unique site within the E. coli genome. 

Both PSI and PSII are necessary for photosynthesis, but the systems do not operate in the implied temporal sequence. There is also considerable pooling of electrons in intermediates between the two photosystems, and the indicated photoacts seldom occur in unison. The terms PSI and PSII have come to represent two distinct, but interacting reaction centers in photosynthetic membranes (36,37) the two centers are considered in combination with the proteins and electron-transfer processes specific to the separate centers. 

A Catalysis joint action corresponds to a use case we prefer to separate the specification of the net effect of a joint action—its postcondition—from the interaction sequence (one of many possible) that realizes it. A joint action is an abstraction of that detailed interaction, just as an operation invocation is an abstraction of a language-specific call-return convention. We depict occurrences of joint actions on an interaction diagram we have not found any way to show this in UML. 

Specificity of conventional protein enzymes is provided by precise molecular fit. The mutual recognition of an enzyme and is substrate is the result of various intermolecular forces which are almost always strongly dominated by hydrophobic interaction. In contrast, specificity of catalytic RNAs is provided by base pairing (see for example the hammerhead ribozyme in Figure 1) and to a lesser extent by tertiary interactions. Both are the results of hydrogen bond specificity. Metal ions too, in particular Mg2+, are often involved in RNA structure formation and catalysis. Catalytic action of RNA on RNA is exercised in the cofolded complexes of ribozyme and substrate. Since the formation of a ribozyme s catalytic center which operates on another RNA molecule requires sequence complementarity in parts of the substrate, ribozyme specificity is thus predominantly reflected by the sequence and not by the three-dimensional structure of the isolated substrate. 

The NMR characterisation of polymeric systems requires first the search for the existence of networks. The observation of a time reversal effect, specific to residual spin-spin interactions, gives evidence for the presence of polymeric networks [3]. This property is reflected by so-called pseudo-solid spin-echoes formed by applying a suitable radiofrequency pulse sequence that results in a rotation of the spin operators (Figure 8.3). 

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