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Vol.1 , No. 3, Publication Date: Sep. 11, 2014, Page: 90-112
 loop conformation, G-actin flatness, conformation of nucleotide-binding cleft, rate of ATP hydrolysis, filament persistence-length, filament bending stiffness and axial stiffness, and actin-material elastic-stiffness matrix/moduli. These actin microstructural and property aspects are investigated using a combination of all-atom and coarse-grained molecular-level computational methods, and various coarse-graining and trajectory-data post-processing procedures. Wherever possible, the results obtained are compared with their experimental counterparts in order to validate the computational approach used. Also, by comparing the all-atom and the corresponding coarse-grained simulation results, it has been established that, for the most part, coarse-grained force-field functions derived are of sufficient accuracy/fidelity to yield reasonable data regarding actin microstructure and properties.&picture=http://www.aascit.org/aascit/decorators/img/journal/903.jpg)
| [1] | Angela Grujicic, Department of Bioengineering, Clemson University, Clemson SC 29634, USA. |
| [2] | Mica Grujicic, Department of Mechanical Engineering, Clemson University, Clemson SC 29634, USA. |
| [3] | Ramin Yavari, Department of Mechanical Engineering, Clemson University, Clemson SC 29634, USA. |
| [4] | Jennifer Snipes, Department of Mechanical Engineering, Clemson University, Clemson SC 29634, USA. |
| [5] | Subrahmanian Ramaswami, Department of Mechanical Engineering, Clemson University, Clemson SC 29634, USA. |
This paper deals with the study of microstructure and properties in actin monomers and polymers using advanced computational methods and tools. Specific aspects of actin microstructure and properties include: topological stability, DNase I-binding (DB) loop conformation, G-actin flatness, conformation of nucleotide-binding cleft, rate of ATP hydrolysis, filament persistence-length, filament bending stiffness and axial stiffness, and actin-material elastic-stiffness matrix/moduli. These actin microstructural and property aspects are investigated using a combination of all-atom and coarse-grained molecular-level computational methods, and various coarse-graining and trajectory-data post-processing procedures. Wherever possible, the results obtained are compared with their experimental counterparts in order to validate the computational approach used. Also, by comparing the all-atom and the corresponding coarse-grained simulation results, it has been established that, for the most part, coarse-grained force-field functions derived are of sufficient accuracy/fidelity to yield reasonable data regarding actin microstructure and properties.
Keywords
Actin, All-Atom Computational Analyses, Coarse-Grained Computational Analyses, Molecular Dynamics
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