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Title Modeling the structure, dynamics, and interactions of biological molecules
URL
Publication Date
Date Accessioned
Degree PhD
Discipline/Department Biomedical Engineering
Degree Level doctoral
University/Publisher University of Texas – Austin
Abstract Biological molecules are essential parts of organisms and participate in a variety of biological processes within cells. Understanding the relationship between sequence, structure, and function of biological molecules are of fundamental importance in life science and the health care industry. In this dissertation, a multi-scale approach was utilized to develop coarse-grained molecular models for protein and RNA simulations. By simplifying the atomistic representation of a biomolecular system, the coarse-grained approach enables the molecular dynamics simulations to reveal the biological processes, which occur on the time and length scales that are inaccessible to the all-atom models. For RNA, an "intermediate" coarse-grained model was proposed to provide both accuracy and efficiency for RNA 3D structure modeling and prediction. The overall potential parameters were derived based on structural statistics sampled from experimental structures. For protein, a general, transferable coarse-grain framework based on the Gay-Berne potential and electrostatic point multipole expansion was developed for polypeptide simulations. Next, an advanced atomistic model was developed to model electrostatic interaction with high resolution and incorporates electronic polarization effect that is ignored in conventional atomistic models. The last part of my thesis work involves applying all-atom molecular simulations to address important questions and problems in biophysics and structural biology. For example, the interaction between protein and miRNA, the recognition mechanism of antigen and antibody, and the structure dynamics of protein in mixed denaturants.
Subjects/Keywords Structural modeling; Molecular dynamics; Protein; RNA; Coarse-grained model; Atomistic model; RNA silencing; Influenza; Polarizable force field
Contributors Ren, Pengyu (advisor)
Language en
Country of Publication us
Record ID handle:2152/21875
Repository texas
Date Retrieved
Date Indexed 2019-09-12
Grantor The University of Texas at Austin
Note [] text; [department] Biomedical Engineering;

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…energy in solution ...................73 4.4.2 Proline and glycine conformational free energy in solution .......75 4.5 Conclusions .............................................................................................76 5 Molecular Dynamics

…Simulations of Ago Silencing Complexes .......................83 5.1 Introduction .............................................................................................83 5.2 Methods for Molecular Dynamics Simulations…

…predicted by 2D-WHAM simulations. (b) Average of ala-2, ala-3, and ala-4 residues in replica exchange molecular dynamics simulation of the (Ala)5 peptide. The trajectory at 298 K was used. (c) The PDB data are from ref [269…

…The structure of the guide-target heteroduplex for the wild-type during the 100-ns molecular dynamics simulation. The conformational change is shown by superimposing the final snapshot (shown in blue) to the starting native structure (…

…simplified molecular models for protein and nucleic acid, respectively. By simplifying the atomistic representation of a biomolecular system, coarse-grained approach enables the molecular dynamics simulations to reveal the biological processes, which occur on…

molecular dynamics (DMD) and the tailored force fields to predict RNA folding dynamics. RNA secondary structure information is not required as input. The replica exchange molecular dynamics (REMD) [28] are implemented to enhance…

…chains and united peptide groups. These coarse-grained particles are connected through virtual bonds. To parameterize the various energy terms, both quantum mechanical ab initio methods and all-atom molecular dynamics simulations were used. 10 2 Coarse…

…for Protein Structure and Dynamics ...............7 2 Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures 11 2.1 Introduction .............................................................................................11 2.2…

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