Creation of a Biological Calcium Sensor by the Rational Redesign of Calmodulin
Introduction
Calcium is the most abundant
mineral in the human body and serves many important biological functions.
Within the mammalian brain, the control of calcium-ion flow serves as
a basis for neuronal communication and is important in both learning and
memory. Calmodulin is a calcium-binding protein that is found in many
different cell types and in many different cellular locations. It undergoes
a large conformational change upon binding calcium, allowing it to perform
its downstream functions. Calmodulin is known to be important in nerve
cells, where it is a vital component in long term potentiation.
Recent
advances in magnetic resonance imagery (MRI) have led to the possibility
of using a molecular calcium sensor as a probe for high resolution analysis
of neural activity. We have employed computational methods in the task
of redesigning Calmodulin and one of its known binding partners (M13)
to yield an orthogonal binding pair. This pair could then be used to measure
calcium levels in living cells without perturbing the system
Methods
This task involves designing a Calmodulin mutant and an M13 mutant
that bind strongly to one another but weakly to the wild type structures.
This requires a method for mutating the wild type structures in silico
to create realistic structures for the mutants and then an accurate
energy function for evaluating these mutants. This allows the comparison
of the binding energy of the resulting mutants with the wild type binding
energy. This in turn allows the prediction of which mutations are likely
to yield the desired result. We initially used the techniques of dead-end
elimination [1] in combination with the A*
algorithm [2] to perform protein design. These tools
have proven to be very useful in reducing the enormous space of
protein conformational searches. We built the twenty replacement
analogues for each residue in the M13 sequence. The analysis of these
replacement analogues directed us to specific sites for mutagenesis.
More complex calculations were then performed on these specific
sites using CHARMM [3] to optimise the structure
of these mutants and calculate van der Waals interactions and differences
in solvent accessible surface area. The electrostatic interaction energy
and the desolvation penalty were then calculated on the resulting structures
using the Delphi program for calculating Poisson-Boltzmann continuum
electrostatics [4].
Current Progress
Analysis of the structure
of Calmodulin and the sequences of many of its known binding
partners [5] highlighted potentially productive sites for
mutation. Calculations were then performed to predict complementary mutations
on both sides of the interface that would produce a protein-peptide complex
with high binding affinity but minimal cross reactivity with the wild
type structures. The most promising mutations were those involving
the replacement of key hydrophobic anchor residue of M13 with charged
residues and the corresponding mutation of hydrophobic residues of
Calmodulin. The wild type and mutant interactions can be seen
in Figure 1 for the mutants W4R on M13 and V136D on Calmodulin.
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Wild type |
Mutant |
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Figure 1. The wild type and mutant structures
of M13 and Calmodulin. A section of the Calmodulin backbone is
shown in green and a section of the M13 backbone is shown
in blue. The important residues are shown as atom coloured sticks.
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Mutants such as this are
now being tested experimentally to investigate their in vitro behaviour.
Future Plans
This procedure has the potential to act as a powerful tool in the creation
of techniques for the study of this important biological system. We hope
to test all our predictions experimentally and design an orthogonal binding
pair for this system that can be used experimentally as a biological calcium
sensor. This methodology could then be applied to other systems of interest.
References:
[1] J. Desmet, M. De Maeyer, B. Hazes and I. Lasters.
The dead-end elimination theorem and its use in protein side-chain positioning.
Nature 356, p539\x{2013}542, 1992.
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space of protein side chains using dead-end elimination and the A* algorithm. Proteins 33, p227\x{2013}239, 1998.
[3] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D.
J. States, S. Swaminathan, and M. Karplus. CHARMM: A program for macromolecular
energy, minimization, and dynamics calculations. J. Comp. Chem.,
4, p187-217, 1983.
[4] M. K. Gilson and B. Honig. Calculation of the total
electrostatic energy of a macromolecular system: Solvation energies, binding
energies, and conformational analysis. Proteins, 4, p7-18, 1988.
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for calmodulin recognition. FASEB Journal, 11(5),
p331-340, 1997.
Accessibility
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