Michaela Knapp-Mohammady

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The MS(n) spectra of the [M + H](+) and b(5) peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b(4) ions derived from the first four peptides. The MS(2) spectra of the [M + H](+) ions show a substantial series of b(n) ions with enhanced cleavage at the amide bond C-terminal to His and(More)
When ionized by electrospray from acidic solutions, the tripeptides Pro-His-Xaa (Xaa = Gly, Ala, Leu) form abundant doubly-protonated ions, [M + 2H]2+. Collision-induced dissociation (CID) of these doubly-protonated species results, in part, in formation of b(2)(2+) ions, which fragment further by loss of CO to form a(2)(2+) ions; the latter fragment by(More)
Retinal proteins are excellent systems for understanding essential physiological processes such as signal transduction and ion pumping. Although the conjugated polyene system of the retinal chromophore is best described with quantum mechanics, simulations of the long-timescale dynamics of a retinal protein in its physiological, flexible, lipid-membrane(More)
Microcontact printing (μCP) of proteins is widely used for biosensors and cell biology but is constrained to printing proteins adsorbed to a low free energy, hydrophobic surface to a high free energy, hydrophilic surface. This strongly limits μCP as harsh chemical treatments are required to form a high energy surface. Here, we introduce humidified μCP(More)
The newly proposed close-packed motif for collagen and the more established 7/2 structure are investigated and compared. First-principles semi-empirical wave function theory and Kohn-Sham density functional theory are applied in the study of these relatively large and complex structures. The structures are refined, and comparable stability is displayed(More)
The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model(More)
Adiabatic electron affinities (AEA) and structural perturbations due to addition of an excess electron to each of the neutral guanine-cytosine (G-C), adenine-thymine (A-T), and hypoxanthine-cytosine (HX-C) base pairs were studied using the self-consistent charge, density functional tight-binding (SCC-DFTB-D) method, augmented by the empirical London(More)
Following up on an earlier theoretical report by Knapp-Mohammady (Phys Lett A 372:1881–1884, 2008) on the ground state of the neutral Ru complex NAMI-A (trans-imidazoledimethylsulfoxide-tetrachlororuthenate), we first report here a quantum-chemical study of the effect of both oxidation and reduction of the parent molecule to form the anionic and cationic(More)
Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor(More)