Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A
✍ Scribed by Yuji Sugita; Akio Kitao
- Publisher
- John Wiley and Sons
- Year
- 1998
- Tongue
- English
- Weight
- 347 KB
- Volume
- 30
- Category
- Article
- ISSN
- 0887-3585
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✦ Synopsis
We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nose ´-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ⌬⌬G. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nose ´-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388-400, 1998.