David C. Kombo
Wesleyan University
5 Papers
35 Citations
David C. Kombo is an academic researcher from Wesleyan University. The author has contributed to research in topics: Molecular dynamics & Protein crystallization. The author has an hindex of 4, co-authored 5 publications.
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Papers
Calculation of the Affinity of the λ Repressor-Operator Complex Based on Free Energy Component Analysis
TL;DR: In this article, the binding free energy of the u repressor-operator complex is calculated based on free energy component analysis, which is based on a thermodynamic cycle of seven steps decomposed into a total of 24 individual components.
One nanosecond molecular dynamics simulation of the N‐terminal domain of the λ repressor protein
TL;DR: Many amino acid residues, including those involved in DNA recognition, undergo a simultaneous transition in their side-chain conformations, consistent with the relationship between side- chain conformation and secondary structural elements, as observed in protein crystal structures.
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Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator
TL;DR: It is concluded that the binding of the repressor actually makes the N-7 atom of Gua8' more solvent exposed, thereby enhancing its reactivity to chemical methylation, and the nonconsensus flexible arm is more flexible and exhibits more conformations than its consensus counterpart.
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Molecular dynamics simulation accurately predicts the experimentally- observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions
TL;DR: A molecular dynamics simulation of the operator binding domain of the lambda repressor protein has been carried out and it is found that the atoms distributions in the environment of waters and Na+ ions are in excellent agreement with those derived from the analysis of water molecules in crystal structures and ion‐binding proteins.
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