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- All Subjects: Membrane Protein
- Creators: Ozkan, Banu
Description
The goal of this theoretical study of infrared spectra was to ascertain to what degree molecules may be identified from their IR spectra and which spectral regions are best suited for this purpose. The frequencies considered range from the lowest frequency molecular vibrations in the far-IR, terahertz region (below ~3 THz or 100 cm-1) up to the highest frequency vibrations (~120 THz or 4000 cm-1). An emphasis was placed on the IR spectra of chemical and biological threat molecules in the interest of detection and prevention. To calculate IR spectra, the technique of normal mode analysis was applied to organic molecules ranging in size from 8 to 11,352 atoms. The IR intensities of the vibrational modes were calculated in terms of the derivative of the molecular dipole moment with respect to each normal coordinate. Three sets of molecules were studied: the organophosphorus G- and V-type nerve agents and chemically related simulants (15 molecules ranging in size from 11 to 40 atoms); 21 other small molecules ranging in size from 8 to 24 atoms; and 13 proteins ranging in size from 304 to 11,352 atoms. Spectra for the first two sets of molecules were calculated using quantum chemistry software, the last two sets using force fields. The "middle" set used both methods, allowing for comparison between them and with experimental spectra from the NIST/EPA Gas-Phase Infrared Library. The calculated spectra of proteins, for which only force field calculations are practical, reproduced the experimentally observed amide I and II bands, but they were shifted by approximately +40 cm-1 relative to experiment. Considering the entire spectrum of protein vibrations, the most promising frequency range for differentiating between proteins was approximately 600-1300 cm-1 where water has low absorption and the proteins show some differences.
ContributorsMott, Adam J (Author) / Rez, Peter (Thesis advisor) / Ozkan, Banu (Committee member) / Shumway, John (Committee member) / Thorpe, Michael (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2012
Description
Secondary active transporters play significant roles in maintaining living cells' homeostasis by utilizing the electrochemical gradient in driving ions or protons as the source of free energy to transport substrate through biological membranes.A broadly recognized molecular framework, the alternating access model, describes the transport mechanism as the transporter undergoes conformational changes between different conformations and alternatingly exposes its binding site to intracellular and extracellular sides and, thus, exchanges ion and substrate in a cyclical manner.
Recent progress in structural biology brought the first-ever structural insights into the mammalian Cation-Proton Antiporters (CPA) family of proteins.
However, the dynamic atomic-level information about the interactions between the newly discovered structures and the bound ion or the corresponding substrate remains unknown.
With Molecular Dynamics (MD), multiple spontaneous ion binding events were observed in the equilibrium simulations, revealing the binding site topology of Horse Sodium-Proton Exchanger 9 (NHE9) and Bison Sodium-Proton Antiporter 2 (NHA2) in their preferred protonation state.
Further investigation into more CPA homologs compared various aspects, including sequence identity, binding site topology, and energetic properties, and obtained general insights into the similarities shared by the binding process of CPA members.
The putative binding site and other conserved residues in their actively ion-bound poses were identified for each model, and their similarities were compared.
The energetic properties accessed by the three-dimensional free energy profile, initially found to be binding unfavorable for the experimental structures, were recalculated based on the simulation data. The updated results show consistency with the correct binding affinity as indicated by the experimental methods.
This work provided a general picture of the structures and the ion-protein interaction of CPA proteins and serves as comprehensive guidance for any related future structural and computational work.
ContributorsZhang, Chenou (Author) / Beckstein, Oliver (Thesis advisor) / Ozkan, Banu (Committee member) / Ros, Robert (Committee member) / Singharoy, Abhishek (Committee member) / Arizona State University (Publisher)
Created2023