We have developed a fast computational method to study the conformation and energetics of several hundred base pairs long DNA loops. The DNA is modeled as a self-equilibrated electrically charged elastic rod. The ensemble of DNA loop conformations, attainable for a given geometry of the DNA ends, is generated as a set of numerical solutions to the equations of the Kirchhoff-Love theory of elasticity. The equations are augmented by electrostatic and steric repulsion force terms. The method provides the basis for multi-resolution modeling of protein-DNA complexes, e.g., through using the calculated forces in subsequent full atom molecular dynamics simulations.We demonstrate the application of the method in several test case studies of protein-DNA systems. One is the promoter DNA loop of E.coli, clamped by the lac repressor and possibly also bound by the catabolite gene activator protein (CAP). Two topologically alternative structures of the loop are found, which exchange the role of the global energy minimum for different DNA lengths. The changes of the loops structure and energy, introduced by CAP, provide insights into the mechanism of the cooperative DNA binding by CAP and the lac repressor, observed in the experiment.Another test system for the developed method is the nucleosom.We solve Kirchhoff equations with the introduced force terms in order to reproduce the experimentally known structure of nucleosomal DNA wound around the histone core. Structural and Functional Studies of Proteins withStructural genomics presents an enormous challenge with up to 100,OOO protein targets in the human genome alone. To speed the current rate of structure determination, judicious selection of targets and a system which allows efficient experimental testing, is neccessary.Pyrobaculum aerophifium (PA), a hyperthermophilic, archeaebacteria has recently been sequenced and annotated. The thermostable proteins from PA are easily purified and appear to crystallize more readily than their mesophilic homologs, providing a good experimental system for high throughput structure determination. A method to assign a probability that a sequence assumes a novel fold was developed and used in conjunction with traditional sequence analysis methods to target proteins from the genome (Mallick unpublished data). Targeted proteins have a probability greater than 0.88 of having a new fold and have disease related human homologs.Targeted proteins were cloned into E. coli expression vectors, over-expressed and purified.Crystal trials for X-ray crystallographic structure determination are underway. In addition functional studies of the proteins are in progress.Our approach to protein targeting will yield valuable protein topological information useful for fold recognition and drugdesign for human diseases. In addition PA will provide insights into thermostable enzymedproteins with potential industrial applications.Structural and functional importance of mutations in 1816 Hepatitis B virus pregenomic RNA studied by NMR 181 8 Prediction of protein foldi...
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