Margaret S. Cheung
Pacific Northwest National Laboratory
Folding (chemistry)Energy landscapePhysicsBiophysicsComputational chemistryChemical physicsMacromolecular crowdingChemistryMaterials scienceProtein foldingCalmodulinComputer scienceProtein structureBiochemistryMolecular dynamicsDynamics (mechanics)CrystallographyMotor protein
Publications 128
In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an open-source software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blend...
#1Fabio C. Zegarra (UH: University of Houston)H-Index: 2
#2Dirar Homouz (UH: University of Houston)H-Index: 16
Last. Margaret S. CheungH-Index: 27
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Pseudomonas aeruginosa apoazurin (apo, without the copper cofactor) has a single disulfide bond between residues 3 and 26 and unfolds in a two-state reaction in vitro. The disulfide bond covalently connects the N-termini of β-strands 1 and 3; thereby, it creates a zero-order loop or a "cinch" that restricts conformational space. Covalent loops and threaded topologies are emerging as important structural elements in folded proteins and may be important for function. In order to understand the rol...
1 CitationsSource
#1Jules Nde (UH: University of Houston)H-Index: 5
#2Pengzhi ZhangH-Index: 4
Last. Margaret S. CheungH-Index: 27
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Calmodulin (CaM) is a calcium-binding protein that transduces signals to downstream proteins through target binding upon calcium binding in a time-dependent manner. Understanding the target binding process that tunes CaM’s affinity for the calcium ions (Ca2+), or vice versa, may provide insight into how Ca2+-CaM selects its target binding proteins. However, modeling of Ca2+-CaM in molecular simulations is challenging because of the gross structural changes in its central linker regions while the...
#1Pengzhi ZhangH-Index: 4
#2Jaebeom HanH-Index: 10
Last. Margaret S. Cheung (UH: University of Houston)H-Index: 27
view all 4 authors...
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of its unique coordination chemistry that involves surrounding atoms required for its stability. In this work, we extracted a wide variation of Ca2+ binding loop conformations from Ca2+ binding protein calmodulin (CaM) that adopt the most populated ternary structure types from the MD simulations, followed by ab initio quantum mechanical (QM) calculations on the 12 amino acids from entire...