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Can local energy minimization refine the PDB structures of different resolution universally?

Content Provider	Springer Nature Link
Author	Godsie, M. G. Gromova, A. P. Oferkin, I. V. Mirov, P. V.
Copyright Year	2009
Abstract	Local energy minimization was statistically tested as the refinement strategy for PDB structure pairs of different resolution. The 13 pairs of structures with the only difference being the resolution were extracted from PDB and represented structures of 11 identical proteins obtained with different x-ray diffraction techniques. The rmsd distribution was calculated for these pairs before and after local energy minimization of each structure. MMFF94 was used for energy calculations and the quasi-Newtonian method was used for local energy minimization. By comparison of these two rmsd distributions, the local energy minimization was proved to statistically increase the structural differences in pairs, so it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in the multidimensional space of atomic coordinates. For these randomized structures the rmsd distribution was calculated and compared with the one for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by x-ray analysis for PDB. Some other results we obtained exploring the energy surface near these conformations are also presented. These results are expected to be useful for the development of new protein refinement strategies based on energy minimization.
Starting Page	442
Ending Page	447
Page Count	6
File Format	PDF
ISSN	00063509
Journal	Biophysics
Volume Number	54
Issue Number	4
e-ISSN	15556654
Language	English
Publisher	SP MAIK Nauka/Interperiodica
Publisher Date	2009-12-09
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	energy minimization protein structure refinement MMFF94 x-ray analysis protein conformation PDB structures protein energy surface molecular mechanics Biophysics and Biological Physics
Content Type	Text
Resource Type	Article
Subject	Biophysics

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