Computation of the protein molecular mechanism using adaptive dihedral angle increments

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

References

[1] Oyenarte I, Lucas M, Gómez García I, Martínez-Cruz L A. Purification, crystallization and preliminary crystallographic analysis of the CBS-domain protein MJ1004 from Methanocaldococcus jannaschii. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 2011, 67(Pt 3): 318-324

[2] Chirikjian, G.S.: A methodology for determining mechanical properties of macromolecules from ensemble motion data. TrAC Trends in Analytical Chemistry, 2003, 22(9): 549-553

[3] Kavraki L. Protein-Ligand Docking, Including Flexible Receptor, 2007

[4] Madden C, Bohnenkamp P, Kazerounian K, Ilies H T. Residue level three-dimensional workspace maps for conformational trajectory planning of proteins. The International Journal of Robotics Research, 2009, 28(4): 450-463

[5] Jeong J I, Lattman E E, Chirikjian G S. A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure. Acta Crystallographica Section D: Biological Crystallography, 2006, 62(Pt 4): 398-409

[6] Subramanian R, Kazerounian K, Fellow A. Improved molecular model of a peptide unit for proteins. Journal of Mechanical Design, 2007, 129(11): 1130-1136

[7] Diez M, Petuya V, Martínez-Cruzb L A, Hernándeza A. A biokinematic approach for the computational simulation of proteins molecular mechanism. Mechanism and Machine Theory, 2011, 46(12): 1854-1868

[8] Cornell W, Cieplak P, Bayly C, Gould I, Merz K, Ferguson D, Spellmeyer D, Fox T, Caldwell J, Kollman P. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 1995, 117(3): 5179-5197

[9] Diez M, Petuya V, Macho E, Hernandez A. Protein kinematic motion simulation including potential energy feedback. New Trends in Mechanism Science, 2010, 5: 83-90

Acknowledgements

The authors wish to acknowledge the financial support received from the Spanish Government through the Ministerio de Economía y Competitividad (Project DPI2011-22955), the European Union (Project FP7-CIP-ICT-PSP-2009-3) and the Regional Government of the Basque Country through the Departamento de Educación, Universidades e Investigación (Project IT445-10) and UPV/EHU underβprogram UFI 11/29.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg