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Calcium Binding Proteins |
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Fig. 1: Click here to get a 16.3 kByte ribbon representation of calmodulin in the fully activated state (4 calcium ions), ~1,400 heavy atoms:
Calcium binding proteins regulate many important cellular processes such as smooth muscle contraction and the crossbridge motion in skeletal muscle. Calmodulin is a rather ubiquitous calcium-sensing protein belonging to a class of loop-helix-loop cation binding proteins of similar structure and function. Molecular Dynamics simulations of calmodulin uncover important dynamical aspects of the regulatory mechanisms of this class of proteins (Pascal-Ahuir, Mehler, Weinstein: Molecular Engineering 1, 231-247, 1991). For instance, the structural flexibility of the central alpha-helical tether is believed to be an essential element in the calcium-dependent recognition of target-peptides.
Fig. 2: Click here to get a 45.1 kByte image of calmodulin, solvated in a 44 A radius sphere of waters (only oxygens shown) with counterions at physiological ionic strength 0.15 mol/l, ~33,000 atoms (red: Cl-, grey: Na+, blue: Ca++):
We have carried out a 3 ns simulation of the system on the Cray T3D in Pittsburgh. We study the reorientation of the two major domains of calmodulin and the flexibility of the tether. The simulations shed light on the time-dependent availability of various target-specific structures of calmodulin. We find that the central tethering helix, which has been shown to undergo large conformational changes upon binding to target proteins, bends over its length and that the two calcium-binding domains reorient with respect to each other. This rearrangement of the structure brings the domains to a more favorable position for target binding, poised to achieve the orientation observed in the CaM-myosin-light-chain-kinase complex (Ikura et al., Science (1992) 256:632).
Our 3 ns trajectory allows for the first time a near-complete sampling of the counterion distribution about a protein. In Fig. 3 we compare the three-dimensional histogram of sodium ions sampled from the 3 ns trajectory with the electostatic field surrounding the protein calculated from the Poisson-Boltzmann equation at the ionic strength of the simulation. The Figure demonstrates that the counterions are more localized in regions of negative electrostatic potential.
Fig. 3: Click here to get a 133 kByte image of counterion distribution and electrostatic field surrounding calmodulin:
Left: Three-dimensional histogram of sodium ion distribution in calmodulin's vicinity sampled from the 3 ns trajectory. The grid width of the histogram is 1.4 A. The colors code for the ion density values 0.003 (blue), 0.005 (yellow), and 0.008 (red). Right: Contour of the electrostatic potential at -200 mV near the surface of the negatively charged protein. The contour was calculated with the program Grasp at 150 mM ionic strength.
Willy R. Wriggers
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Material on this site is copyrighted.
wriggers@ks.uiuc.edu