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Design, synthesis, and calorimetric studies on protein-ligand interactions : apolar surface area, conformational constraints, and cation-[pi] interactionsMyslinski, James Michael 11 July 2014 (has links)
Because bimolecular interactions in water are poorly understood, three tactics commonly used to improve binding affinity in ligand design were investigated: (1) increasing apolar surface area, (2) introducing a conformational constraint, and (3) targeting a cation-[pi] interaction. Thermodynamic parameters of binding ligands to the Grb2 SH2 domain were determined by isothermal titration calorimetry (ITC), and structural data was obtained by X-ray crystallography. The apolar surface area of the pTyr+1 residue in Ac-pTyr-Acnc-Asn-NH₂ was varied by incrementally increasing the size of the cyclic Acnc residue from a 3-membered to a 7-membered ring. Increasing apolar surface area resulted in an increase in Ka due to a more favorable [delta]H⁰ that was dominated a less favorable [delta]S⁰. Structural analyses showed that all ligands bound in a similar mode, so differences in binding thermodynamics were attributed to the pTyr+1 residue. The thermodynamics of binding tripeptides wherein pTyr+1 was an n-alkyl group were studied. Ka increased when Ala was mutated to Abu, but additional methylene groups had no effect on Ka due to strong entropy-enthalpy compensation. While [delta]H⁰ was weakly correlated with buried surface area, there was no change in [delta]H⁰ between one methylene and two methylene groups, presumably because an enthalpic penalty is associated with a gauche interaction between C-[beta] and C-[gamma] of the Xaa side chain that was noted in the crystal structure. An olefin was installed in an attempt to alleviate the energetic penalty incurred from the gauche interaction, but the introduction of the constraint resulted in equipotent ligands. A putative cation-[pi] interaction between Arg67 and various aromatic groups was probed by varying the [pi]-donating capability of groups attached to a tripeptide scaffold. Although crystal structures demonstrated that three of the aryl groups were close enough to Arg67 to form a cation-[pi] interaction, only a modest increase in Ka was observed relative to analogues having only an N-acetyl group. Furthermore, a simple cyclohexyl group in place of aryl groups resulted in ligands that were equipotent with indolyl- and phenyl- derived analogues, so any cation-[pi] interaction is not significant. / text
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Chromatography coupled with mass spectrometry in bioanalysisXia, Yang 12 1900 (has links)
No description available.
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Making sense of mixtures : chromatographic separations of plant, insect and microbial biomolecules.Brand, John Morgan. 11 October 2013 (has links)
No abstract available. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1996.
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Development and application of novel computational tools for structure based drug designBhat, Sathesh. January 1900 (has links)
Thesis (Ph.D.). / Written for the Dept. of Biochemistry. Title from title page of PDF (viewed 2008/01/11 ). Includes bibliographical references.
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Molecular aspects of biomolecule structure and functionRodger, Alison. January 2002 (has links)
Thesis (D. Sc.)--University of Sydney, 2003. / Title from title screen (viewed Apr. 28, 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Science to the School of Chemistry, Faculty of Science. Degree awarded 2003; thesis submitted 2002. Includes bibliographical references. Also available in print form.
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Molecular dynamics simulation studies of DNA and proteins force field parameter development for small ligands and convergence analysis for simulations of biomolecules /Loccisano, Anne Elizabeth. January 2007 (has links) (PDF)
Thesis (Ph.D.)--Duquesne University, 2007. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references (p. 32-55; 109-116; 185-191; 290-299; 330-332).
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Molecularly mediated assembly of nanoparticles towards functional nanostructuresLim, I-Im Stephanie. January 2008 (has links)
Thesis (Ph. D.)--State University of New York at Binghamton, Department of Chemistry, 2008. / Includes bibliographical references.
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Theoretical studies of biomacromolecules : collagen, collagen-like peptides & HIV-1 envelope glycoprotein GP120 /Quan, Jun-Min. January 2004 (has links)
Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2004. / Includes bibliographical references. Also available in electronic version. Access restricted to campus users.
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Techniques for improved mass spectrometric analysis of biologically relevant molecules produced by MALDI and ESI in the quadrupole ion trap /Goolsby, Brian James, January 2000 (has links)
Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references. Available also in a digital version from Dissertation Abstracts.
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Poly(para-phenyleneethynylene)s probing the biological interface with biomolecular materials /Phillips, Ronald Lee, III. January 2008 (has links)
Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Dr. Uwe H.F. Bunz; Committee Member: Dr. Andrew Lyon; Committee Member: Dr. Laren Tolbert; Committee Member: Dr. Nicholas Hud; Committee Member: Dr. Sherry Michele Owen. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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