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Normal mode analysis of macromolecular systems with the Mobile Block Hessian method

An Ghysels UGent, Veronique Van Speybroeck UGent, Dimitri Van Neck UGent, Bernard R. R. Brooks and Michel Waroquier UGent (2009) Proceedings ICCMSE 2009.
abstract
Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3Na 3Na matrix with Na the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible – but not necessarily optimized – geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
vibrational analysis, NMA, reduced dimension, partial optimization, IR spectrum
in
Proceedings ICCMSE 2009
pages
4 pages
conference name
ICCMSE 2009
conference location
Rhodos, Greece
conference start
2009-09-29
conference end
2009-10-04
language
English
UGent publication?
yes
classification
C1
additional info
This work is supported by the Fund for Scientific Research - Flanders (FWO) and the Research Board of Ghent University (BOF).
id
767051
handle
http://hdl.handle.net/1854/LU-767051
date created
2009-10-22 12:02:46
date last changed
2009-11-09 11:00:12
@inproceedings{767051,
  abstract     = {Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3Na 3Na matrix with Na the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.

Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible -- but not necessarily optimized -- geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.

In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.},
  author       = {Ghysels, An and Van Speybroeck, Veronique and Van Neck, Dimitri and R. Brooks, Bernard R. and Waroquier, Michel},
  booktitle    = {Proceedings ICCMSE 2009},
  keyword      = {vibrational analysis,NMA,reduced dimension,partial optimization,IR spectrum},
  language     = {eng},
  location     = {Rhodos, Greece},
  pages        = {4},
  title        = {Normal mode analysis of macromolecular systems with the Mobile Block Hessian method},
  year         = {2009},
}

Chicago
Ghysels, An, Veronique Van Speybroeck, Dimitri Van Neck, Bernard R. R. Brooks, and Michel Waroquier. 2009. “Normal Mode Analysis of Macromolecular Systems with the Mobile Block Hessian Method.” In Proceedings ICCMSE 2009.
APA
Ghysels, A., Van Speybroeck, V., Van Neck, D., R. Brooks, B. R., & Waroquier, M. (2009). Normal mode analysis of macromolecular systems with the Mobile Block Hessian method. Proceedings ICCMSE 2009. Presented at the ICCMSE 2009.
Vancouver
1.
Ghysels A, Van Speybroeck V, Van Neck D, R. Brooks BR, Waroquier M. Normal mode analysis of macromolecular systems with the Mobile Block Hessian method. Proceedings ICCMSE 2009. 2009.
MLA
Ghysels, An, Veronique Van Speybroeck, Dimitri Van Neck, et al. “Normal Mode Analysis of Macromolecular Systems with the Mobile Block Hessian Method.” Proceedings ICCMSE 2009. 2009. Print.