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Determination of structure and dynamics of biomolecules by theoretical calculations of NMR spectroscopic parameters
Benda, Ladislav ; Sychrovský, Vladimír (advisor) ; Munzarová, Markéta (referee) ; Hrabal, Richard (referee)
iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...
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Determination of structure and dynamics of biomolecules by theoretical calculations of NMR spectroscopic parameters
Benda, Ladislav ; Sychrovský, Vladimír (advisor) ; Munzarová, Markéta (referee) ; Hrabal, Richard (referee)
iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...
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Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic N-15 chemical shielding anisotropy tensors
Emmer, J. ; Vavrinská, A. ; Sychrovský, Vladimír ; Benda, Ladislav ; Kříž, Z. ; Koča, J. ; Boelens, R. ; Sklenář, V. ; Trantírek, L.
Density functional theory was employed to study the influence of O-phosphorylation of serine, threonine, and tyrosine on the amidic N-15 chemical shielding anisotropy (CSA) tensor in the context of the complex chemical environments of protein structures.
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