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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld Jan 2006

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld

Retrospective Theses and Dissertations

This dissertation presents a modular software pipeline that searches collections of RNA sequences for novel RNA motifs. In this case the motifs incorporate elements of primary and secondary structure. The motif search pipeline breaks up sets of RNA sequences into shortened segments of RNA primary sequence. The shortened segments are then folded to obtain low energy secondary structures. The distance estimation module of the pipeline then calculates distances between the folded bricks, and then analyzes the resulting distance matrices for patterns;An initial implementation of the pipeline is applied to synthetic and biological data sets. This implementation introduces a new ...


A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne Jan 2006

A Penalty Function Method For Constrained Molecular Dynamics , Ajith Gunaratne

Retrospective Theses and Dissertations

We propose a penalty-function method for constrained molecular dynamic simulation by defining a quadratic penalty function for the constraints. The simulation with such a method can be done by using a conventional, unconstrained solver only with the penalty parameter increased in an appropriate manner as the simulation proceeds. More specifically, we scale the constraints with their force constants when forming the penalty terms. The resulting force function can then be viewed as a smooth continuation of the original force field as the penalty parameter increases. The penalty function method is easy to implement and costs less than a Lagrange multiplier ...


Coordinated Effects Of Distal Mutations On Environmentally Coupled Tunneling In Dihydrofolate Reductase, Lin Wang, Nina M. Goodey, Stephen J. Benkovic, Amnon Kohen Jan 2006

Coordinated Effects Of Distal Mutations On Environmentally Coupled Tunneling In Dihydrofolate Reductase, Lin Wang, Nina M. Goodey, Stephen J. Benkovic, Amnon Kohen

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

One of the most intriguing questions in modern enzymology is whether enzyme dynamics evolved to enhance the catalyzed chemical transformation. In this study, dihydrofolate reductase, a small monomeric protein that catalyzes a single C-H-C transfer, is used as a model system to address this question. Experimental and computational studies have proposed a dynamic network that includes two residues remote from the active site (G121 and M42). The current study compares the nature of the H-transfer step of the WT enzyme, two single mutants, and their double mutant. The contribution of quantum mechanical tunneling and enzyme dynamics to the H-transfer step ...