Browsing by Author "Wang, Yingjie"

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    Development of fragment-based quantum mechanical methods and combined quantum mechanical and molecular mechanical methods
    (2014-08) Wang, Yingjie
    This thesis is dedicated to develop fragment-based QM methods and QM/MM schemes: For the first part, the fragment-based explicit polarization (X-Pol) method has been extended in three aspects: I. the inclusion of exchange repulsion terms in the X-Pol model is examined by antisymmetrizing the X-Pol Hartree-product wave function; this yields X-Pol with full eXchange, called X-Pol-X; II. the original X-Pol method, where all fragments are treated using the same electronic structure theory, is extended to a multilevel representations, called multilevel X-Pol, in which different electronic structure methods are used to describe different fragments; III. a fragment-based variational many-body (VMB) expansion method is described to directly account for exchange repulsion, charge delocalization (charge transfer) and dispersion interactions in the X-Pol method. For the second part, a universal QM/MM scheme, the projected hybrid orbital (PHO) method, is proposed to handle the covalent boundary at QM/MM interface at ab initio level with arbitrary basis sets. As an extension to the generalized hybrid orbital (GHO) method in which hybrid orbitals are constructed using the valence orbitals on the boundary atom, the PHO method further represents the core and valence electrons with a secondary, minimal basis set by projecting the original (primary) basis set used in the QM system. The PHO method is then validated on several aspects: geometry optimization, charge population and proton-affinity calculation. Comparison with standard QM results shows that PHO is a robust and balanced QM/MM scheme that yields satisfactory structural, electronic, and energetic properties.
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    The role of the αC-β4 loop in regulating cooperativity interaction in Protein Kinase A
    (2024-02-19) Olivieri, Cristina; Veglia, Gianluigi; Veliparambil Subrahmanian, Manu; Wang, Yingjie; vegli001@umn.edu; Veglia, Gianluigi; Veglia Lab
    This investigation examines the cooperative modulation of Protein Kinase A (PKA) activity by ATP and substrates, with a specialized focus on the enzyme's catalytic subunit (PKA-C), utilizing NMR-restrained molecular dynamics simulations complemented by advanced Markov Model analysis. Herein, we deposit chemical shift datasets for the PKA-C mutant F100A, both in its apo form and in complex with nucleotides and inhibitors, and activity assay data providing a comprehensive insight into the enzyme's allosteric regulation mechanisms.