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The Quantum Mechanics of Biomolecules

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Systems of unprecedented size can be studied by ab initio quantum mechanical methods on modern top end computing systems such as HPCx. Using such machines and software designed to exploit them we are now able to study new subject areas using standard methods from quantum chemistry or materials science. Structural Biology is one such area. However the simulation of systems one or two orders of magnitude larger than previously calculated present a whole new set of problems

Crambin

 

 

Crambin is a very small protein from the Abyssinian cabbage (Crambe Abyssinica) with 1284 atoms per unit cell. Hartree Fock studies using the CRYSTAL03 code have been performed using using a variety of basis sets.

 

 

 

 
 

Isosurface of the charge density at 0.1Å resolution. In principle this information can be obtained at any resolution. This can be compared with experimental results from Synchrontron Radiation data.

 

Charge density isosurface coloured according to electrostatic potential. This is useful to determine possible chemically active groups.

 

Rusticyanin

 

Rusticyanin, a blue copper protein, has about 6300 atoms and is involved in redox processes.

We have started calculations using over 30000 basis functions.

In collaboration with S Hasnain (SRS,DL) we aim to calculate redox potentials for rusticyanin and associated mutants.

Rusticyanin has a large potential of 680mV.

 

 

CRYSTAL on HPCx: ab initio studies of proteins,
I J Bush, Capability Computing, Issue 2, (2003), 10-12
http://www.hpcx.ac.uk/about/newsletter/HPCxNews02.pdf

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