304 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II
ser81. Calmodulin ’ s four Ca 2+ - binding domains have a typical EF hand con-
formation (helix – loop – helix) and are similar to those described for other
Ca2+ - binding proteins. Each of the four EF - hand domains contains a Ca 2+ -
binding loop, and two short, double - stranded antiparallel β - sheets between
pairs of adjacent Ca 2+ - binding loops.
The PDB: 3CLN X - ray structure shows a large hydrophobic cleft in each
half of the molecule. These hydrophobic regions are believed to represent the
sites of interaction with many of the pharmacological agents and target pep-
tides known to bind to calmodulin. Some of these will be described below.
A more recent crystal structure at 1.0 Å resolution of calcium - saturated
calmodulin fromParamecium tetraurelia has been presented (PDB: 1EXR).^67
The reference 67 authors observe that binding of calmodulin to over 100 dif-
ferent proteins must require a considerable degree of structural plasticity.
Indeed, they fi nd at least 36 disordered amino acid residues in their struc-
ture — a surprisingly large 24% of the entire protein. The authors state that
atomic - resolution structures (resolution of approximately 1.2 Å ) usually
contain between 6% and 15% of residues in alternative conformations. In this
calmodulin structure the central helix contains 10 residues in alternate confor-
mations, including ser70, met72, ser81, glu87, and val85. There are two binding
pockets containing mostly hydrophobic amino acid residues, one for each
calcium - binding lobe of the protein. These pockets contain at least 16 residues
in alternative conformations and others in various disordered modes. The
hydrophobic cleft regions in calmodulin ’ s calcium - binding lobes are phenylala-
nine - and methionine - rich, and these residues provide hydrophobic binding
capability for target molecules and peptides. The reference 67 authors state
that specifi c phenylalanine (12, 68, 92, and 141) and methionine (36, 72, 76, and
144) residues present a deformable and polarizable surface that can adapt to
bond incoming target molecules. Analyses by these researchers indicate a large
number of conformational calmodulin substates in the crystalline environment
at the cryogenic temperature of their work (data collected at 100 K), and they
also infer that there might be an almost continuously changing set of calmodu-
lin conformations in solution at physiological temperatures. (See the discussion
of calmodulin structures that have been determined using NMR methods
below.) In addition to large conformation changes observed in going from apo -
calmodulin to calcium - saturated states (see Figure 6.22 ), they note that calcium -
saturated calmodulin undergoes additional conformational changes when
binding to (wrapping around) its targets. In fact, these additional changes opti-
mize calmodulin ’ s surface complementarity with its targets. The 28 residue
central helix (helix D/E) is intimately involved in target recognition and binding
because of its exposure to solvent as well as the fact that it can also adopt a
large variety of conformations depending on the binding requirements in
the calcium - binding lobes. Figure 6.22A illustrates the approximate 90 °
angles between helices A and B, C and D, E and F, and G and H in holo
(Ca2+ - saturated) calmodulin for the PDB: 1EXR structure. The secondary
structure for PDB: 1EXR is identifi ed as follows: (1) helices A (residues 2 – 18)