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Frontiers of Mechanical Engineering

Front Mech Eng    2013, Vol. 8 Issue (1) : 104-108     https://doi.org/10.1007/s11465-013-0360-9
RESEARCH ARTICLE
Computation of the protein molecular mechanism using adaptive dihedral angle increments
Mikel DIEZ(), Victor PETUYA, Mónica URIZAR, Erik MACHO, Oscar ALTUZARRRA
Department of Mechanical Engineering, University of the Basque Country UPV/EHU, Bizkaia 48013, Spain
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Abstract

Protein motion simulation is still a troublesome problem yet to be solved, especially due to its high computational requirements. The procedure presented in this paper makes use of the proteins’ real degrees of freedom (DOFs). The procedure makes no use of any intermediate energy minimization processes that may alter the motion path or result in very high computational cost requirements. In order to reduce the computational cost, presented algorithms make use of the balls and rods approach for protein structure modelization. Also, structures are normalized in order to minimize inaccuracies introduced by experimental methods, providing a more efficient but still accurate structure for motion simulation.

Keywords kinematics      serial robot      proteins      folding      molecular mechanism     
Corresponding Author(s): DIEZ Mikel,Email:mikel.diez@ehu.es   
Issue Date: 05 March 2013
 Cite this article:   
Mikel DIEZ,Victor PETUYA,Mónica URIZAR, et al. Computation of the protein molecular mechanism using adaptive dihedral angle increments[J]. Front Mech Eng, 2013, 8(1): 104-108.
 URL:  
http://journal.hep.com.cn/fme/EN/10.1007/s11465-013-0360-9
http://journal.hep.com.cn/fme/EN/Y2013/V8/I1/104
Fig.1  Structural conformation, DOF of the protein
ProteinPrevious ProcedureNew Procedure
Rmsd/?Energy/%RP/(% atoms in favored regions)Rmsd/?Energy/%RP/(% atoms in favored regions)
1k9p 4.01796---
1k206.187.6925.486.292
3cln6.880955.523.792
1zac3.446.997---
Tab.1  Molecular mechanisms simulation results for previous and new procedures
Fig.2  Initial (a) and final (b) positions of 1k9p protein. The movement is concealed to the relative position of two -helixes. Represented with Pymol
ProteinNew Procedure with m=3, n=1 parameter values
Rmsd/?Energy/%RP/(% atoms in favored regions)Error reduction/%
1k9p 3.78a)6a)97a)5.7a)
1k205.294.8933.4
3cln5.343923.3
1zac3.0849810.4
Tab.2  Molecular mechanisms simulation results for the new procedure with modified and parameters
Fig.3  Initial (a) and final (b) positions of 3cln protein. The movement is represented by the formation of the central -helix and the rotation of the upper part of the protein. Represented with Pymol
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