Genetic algorithm to design stabilizing surface-charge distributions in proteins

Journal of Physical Chemistry B

Volumn 106, Issue 26, 2002, Pages 6609-6613

  Ibarra Molero, Beatriz ^a   Sanchez Ruiz, Jose M ^a  

^a UNIVERSITY OF GRANADA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

SURFACE-CHARGE DISTRIBUTION;

COMPUTATIONAL METHODS; GENETIC ALGORITHMS; MATHEMATICAL MODELS; SURFACE CHEMISTRY;

PROTEINS;

EID: 0037019469     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp020483o     Document Type: Article

References (28)

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13. The development of the algorithm described in this work was based upon the simple and lucid description of genetic algorithms given by Marek Obitko in http://cs.felk.cvut.cz/̃xobitko/ga/.
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16. ASA values were calculated using a modification of the Shrake-Rupley algorithm (Shrake, A.; Rupley, J.A. J. Mol. Biol. 1973, 79, 351-372) that randomly places 2000 points on the surface of the expanded van der Waals sphere corresponding to each atom so that accurate atomic ASA values are obtained. We used a radius of 1.4 Å for the solvent probe and the Chothia set for the protein atoms (Chothia, C. J. Mol. Biol. 1976, 105, 1-12).
17. ASA values were calculated using a modification of the Shrake-Rupley algorithm (Shrake, A.; Rupley, J.A. J. Mol. Biol. 1973, 79, 351-372) that randomly places 2000 points on the surface of the expanded van der Waals sphere corresponding to each atom so that accurate atomic ASA values are obtained. We used a radius of 1.4 Å for the solvent probe and the Chothia set for the protein atoms (Chothia, C. J. Mol. Biol. 1976, 105, 1-12).
18. See, for instance, Liang, S.; Grishin, N.V. Protein Sci. 2002, 11, 322-331 and references therein.
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22. The accessibility is calculated as the ratio between the side-chain ASA value in the native protein and in a Gly-X-Gly tripeptide in which the conformation of the side chain is the same as that in the native protein.
23. Because the score is related to an energy, it might appear reasonable to use "Boltzmann selection" (i.e., the probability that a chromosome is selected for reproduction is made proportional to a Boltzmann exponential: exp(-Z/RT)). This, however, causes only a few chromosomes to be systematically selected in each GA cycle, with the concomitant loss of population diversity.
24. Our genetic algorithm program was written in Quickbasic 4.5 and made use of previously developed subroutines for the calculation of charge-charge interaction energies (see ref 1). The actual time required to complete typical GA runs, such as that shown in Figure 1, was on the order of minutes (using a PC computer with a Pentium III, 800-MHz processor). One of the reviewers of this paper has requested information about the availability of our program to other investigators. Our plan is to make our approach widely available after we have checked the practical details of its application through the comparison of the predictions with the experimental results for model proteins (work in progress).
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