CALCIUM-DEPENDENT MOLECULES 301
This section has concentrated on the role of magnesium ions in catalytic
RNA. Other important topics related to biological magnesium ion chemis-
try — in kinases, ATPases, and large systems such as chlorophyll — will not be
treated here. In general, cations enable catalysis in the following ways: (1) as
general bases perhaps as metal - hydroxo species, activating the nucleophile; (2)
as general acids perhaps as metal - aqua species, aiding in the protonation of
the leaving group; and (3) as charge neutralizers, stabilizing transition states.
The fi rst two criteria could be considered as functional roles whereas the third
would be a structural as well as a functional role. For the group I intron, mag-
nesium ions play an important structural role in bringing intron and exon
together productively. In a functional manner, magnesium ions are involved
in the activation of the guanosine nucleophile in an analogous manner to metal
cofactor activation in protein metalloenzymes. Finding out whether a metal
ion plays solely a structural role, or also takes part in the actual catalytic activ-
ity, is a diffi cult experimental problem. The phosphorothioate metal rescue
(PS - rescue) experiment described in the preceding sections (see Section 6.2.2 ,
for instance) can be successful in predicting sites of catalytic activity, although
the situation is complicated by the fact that ribozyme active sites undergo
several conformational changes between ground, pre - transition, and transition
states. Although the number of magnesium ions playing a functional role in
the group I intron may be somewhat uncertain, researchers are in general
agreement that Mg 2+ has a catalytic role in this ribozyme. At the time of this
writing, the role of metal ions in hammerhead ribozyme catalysis is much
less certain. Probably metal ions, specifi cally Mg 2+ , play a structural role in
assisting rapid and effi cient ribozyme folding. Whether or not these ions play
a functional/catalytic role remains a question requiring further research.
6.3 CALCIUM - DEPENDENT MOLECULES
6.3.1 Introduction,
Calcium homeostasis has been discussed in Section 5.2.3. The present and fol-
lowing sections will provide some detail on two calcium - containing biomole-
cules: calmodulin and calcium ATPase. Binding of Ca 2+ to calmodulin (Section
6.3.2 ) activates enzymes such as protein kinases. Ca 2+ - ATPases (Section 6.4.2)
are cross - membrane calcium pumps that bind and release calcium ions to
foster muscle relaxation. Other proteins and enzymes requiring calcium ions
are, for example, (1) Troponin C — binding of three to four Ca 2+ ions results in
muscle contraction; (2) extracellular digestive enzymes such as staphylococcal
nuclease (one calcium site), phospholipase A 2 (two calcium sites), and trypsin
(one calcium site); (3) structural and storage enzymes that sequester many
calcium ions per protein unit including thrombin, phosphodentine (material
in teeth), and calsequestrin (calcium storage in the sarcoplasmic reticulum).
Calsequestrin is the major calcium - buffering protein localized in the lumen of
