Home News About Us Contact Contributors Disclaimer Privacy Policy Help FAQ

Home
Search
Quick Search
Advanced
Fulltext
Browse
Collections
Persons
My eDoc
Session History
Login
Name:
Password:
Documentation
Help
Support Wiki
Direct access to
document ID:


          Institute: MPI für Dynamik und Selbstorganisation     Collection: Biologische Physik und Evolutionäre Dynamik     Display Documents



  history
ID: 692258.0, MPI für Dynamik und Selbstorganisation / Biologische Physik und Evolutionäre Dynamik
Dynamics of High Molecular Weight Macromolecular Assemblies
Authors:Sharifi Sedeh, Reza; Hallatschek, Oskar; Bathe, Klaus-Jürgen
Language:English
Date of Publication (YYYY-MM-DD):2013-02-04
Title of Journal:Biophysical Journal
Volume:104
Issue / Number:2
Sequence Number of Article:227a
Review Status:Peer-review
Audience:Experts Only
Abstract / Description:Solvent-damped, thermally activated motions of high molecular weight proteins and nucleic acid assemblies are key to understanding and controlling their functions and activities. The finite element method is a well-established approach to analyzing protein conformational fluctuations that are not accessible to all-atom representations. However, like conventional all-atom normal mode analysis, the finite element method has previously been used only to model protein dynamics in vacuum. Here, we extend the finite element based modeling approach to incorporate solvent damping for proteins and nucleic acid assemblies to compute non-equilibrium conformational properties. The proposed model is computationally effective for calculating translational and rotational diffusion coefficients in addition to dynamical motions in solvent, as demonstrated for Taq polymerase and several nanometer-scale DNA assemblies. A distinct advantage of the finite element-based approach is that computational cost does not increase with increasing molecular weight, rendering the procedure applicable to long time-scale structure-based simulations of high molecular weight assemblies including chaperones, molecular motors, and nucleic acid nanostructures.
External Publication Status:published
Document Type:Article
Communicated by:Folkert Müller-Hoissen
Affiliations:MPI für Dynamik und Selbstorganisation/Biologische Physik und Evolutionäre Dynamik
External Affiliations:Massachusetts Institute of Technology, Cambridge, MA, USA
Identifiers:URL:http://bps2013.conferencespot.org/1166-Pos/
The scope and number of records on eDoc is subject to the collection policies defined by each institute - see "info" button in the collection browse view.