Browsing by Subject "Biomolecules"
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Item Biomolecule interactions on calcium carbonate and stoichiometrically similar biomedical, optical and electronic materials(2004) Gooch, Erin Elaine; Belcher, Angela M.A combinatorial approach has been successfully used to characterize peptides that bind to four different surfaces of CaCO3 and six different oxide substrates that are chemically and stoichiometrically similar to CaCO3. A standard screening and a single substrate screening method were employed. Both methods used a bacteriophage combinatorial library with a complexity of 109 different random sequences. While geological (104) calcite screenings do not seem to show strong consensus, peptides screened against geological aragonite exhibit extraordinary consensus. Overall, peptides screened against aragonite were highly basic. Peptides screened against (110) geological aragonite show [LAIVG]P[WF][RKH] and triple [RKH] patterns. The most significant binding peptide, A21 (LPPWKHKTSGVA) was found in 4 separate screenings. The (110) geological aragonite sequences are highly enriched in prolines. Coincidently, peptides screened against the optical material LiNbO3 +Z show patterns similar to those found in the aragonite screenings. Other substrates that did not exhibit strong consensus include powdered LiNbO3, powdered BaTiO3, powdered PbTiO3, single crystal LiNbO3 –Z, and hydroxyapatite. A database and analysis program was written to catalog and evaluate the statistical significance of the many sequences. One peptide that was determined to be extremely significant in binding to aragonite, A20 (LPKWQERQMLSA), was modeled using umbrella sampling molecular dynamics techniques as well as analyzed by NMR. It was determined that there is a good probability that the peptide’s conformation is helical, but it is able to introconvert between α-helical, 3-10 helical and extended conformations fast enough that a stable secondary structure is not detectable by NMR. Engineered phage were constructed to display these significant peptides on the pVIII surface, increasing the expression level and the long range order in the hopes of building an aragonite nucleation surface. Hybrid organic-inorganic materials were grown on the phage resulting in a mixture of the three forms of CaCO3: calcite, vaterite, and aragonite. In addition, hybrid materials were grown on the optical waveguide material LiNbO3. Doubly engineered phage were shown to bind preferentially to the LiNbO3 +Z surface through the interaction of the A1 displayed peptide as well as nucleate semiconducting ZnS particles via the A7 peptide selected previously against ZnS.Item Computations of electrostatic potentials and energies of dynamic biomolecules(2016-05) Kim, Jerry Chil; Ren, Pengyu; Demkov, Alexander A.We present ongoing research into the simulation of biomolecules in a solvent. We first describe the various models used to model molecular electrostatics including the methods that attempt to modify the Poisson-Boltzmann equation due to its limitations. We then modify the boundary element solver MolEnergy, which solves the linearized Poisson-Boltzmann equation to determine the polarization energies of biomolecules. With our modifications it can now rely on an automated process, utilize a low-discrepancy pseudo-random number generator to yield different molecular configurations, and implement parallel computing to determine the potentials and energies of those configurations in parallel. Our modifications increase the accuracy and speed of MolEnergy.Item Design, synthesis, and calorimetric studies on protein-ligand interactions : apolar surface area, conformational constraints, and cation-[pi] interactions(2013-05) Myslinski, James Michael; Martin, Stephen F.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.Item Formation of noble metal nanocrystals in the presence of biomolecules(2007-05) Burt, Justin Lockheart, 1979-; Yacamán, M. JoseOne of the most promising, yet least studied routes for producing biocompatible nanostructures involves synthesis in the presence of biomolecules. I hypothesized that globular proteins could provide a suitable framework to regulate the formation of noble metal nanocrystals. As proof of concept, I designed two novel synthesis protocols utilizing bovine serum albumin (BSA) protein to regulate the formation of gold nanocrystals. In the first case, the standard protocol for polyol reduction was modified by replacing ethylene glycol with glycerin, replacing synthetic polymers with BSA as protecting agent, and decreasing the reaction temperature. In the second case, the BrustSchiffrin two-phase reduction was modified by replacing alkylthiols with BSA as protecting agent, which facilitated a strictly aqueous phase synthesis. Due to superior product yield and rapid reduction at room temperature, the aqueous protocol became the foundation for subsequent studies. I extended this approach to produce well-dispersed ~2nm silver, gold, and platinum nanocrystals. Having demonstrated the feasibility of BSA-functionalized nanocrystals, some potential uses were explored. BSA-functionalized silver nanocrystals were employed in a broader study on the interaction of silver nanocrystals with HIV. BSA-functionalized gold nanocrystals were utilized for in vivo dosage of a contrast enhancing agent to bacteria. BSAfunctionalized platinum nanocrystals were studied as hydrogenation catalysts. Since many intriguing uses for protein-functionalized nanocrystals involve incorporation into biosystems, I sought to enhance biocompatibility by using ascorbic acid as reducing agent. Initial experiments revealed elongated and branched nanocrystals. Such structures were not observed in previous synthesis protocols with BSA, so I hypothesized ascorbic acid was driving their formation. To test my assertion, I reduced ionic gold in an aqueous solution of ascorbic acid, thereby discovering a new method for producing multiply-branched gold nanocrystals. Two conditions were necessary to achieve multiply-branched structures: rapid kinetics, and strongly acidic pH. By exploiting ascorbic acid complexation with BSA to moderate reaction kinetics, and using sodium hydroxide to provide basic pH, the two conditions for branching were negated, and well-dispersed ~2.5nm gold nanocrystals were obtained. This protocol represents a novel, environmentally benign approach to producing biocompatible nanocrystals, relying on proteins, ascorbic acid, sodium hydroxide, and water, all at ambient temperature.Item Semiconductor nanocrystals, nanorods, nanowires and applications in biomolecular integration(2005) Shieh, Felice; Korgel, Brian A.Inorganic nanostructures interfaced with biological molecules have recently generated much interest in biology, oncology, and medical fields. Semiconductor II-VI nanocrystals have found much use in biological applications for fluorescence cell imaging, tracking, and sorting. Due to quantum confinement effects, nanocrystal size and shape alters optical and electrical properties. A general method of shape control for cadmium chalcogenide nanocrystals, specifically CdSe, CdS, CdTe, was developed and extended to the synthesis of mixed-semiconductor heterostructures. Cadmium chalcogenide nanocrystals were synthesized by thermal decomposition of organometallic precursors. A single injection of chalcogenide precursor resulted in farily monodisperse spherical nanoparticles; whereas multiple injections resulted in nanorods elongated along their c-axis. Nanoparticles and nanorods were primarily wurzite in structure, but spherical nanoparticles exhibited a greater amount of stacking faults. The shape evolution of nanocrystals was indicated by a red shift in emission spectra and decrease in photoluminescence intensity. Injection of a different chalcogenide precursor yielded both types I and II linear heterostructures. Thus the shape of anisotropic nanocrystals may be kinetically controlled by rate of chalcogenide injection. Due to their near-infrared emission, CdTe nanocrystals were chosen as fluorescent markers for prostate carcinoma cell labeling purposes. Shape and size monodisperse CdTe nanocrystals were rendered water-soluble and biocompatible prior to conjugation with prostate-specific membrane antigen (PSMA) aptamers. CdTe-aptamer, and ZnS/CdSe-aptamer bioconjugates specifically labeled both live and fixed cells and overexpressing PSMA in vitro. In preparation for in vivo studies, CdTe-PSMA bioconjugates were tested for long term luminescence and photostability in biological environment as well as depth of penetration for specific labeling of tissue phantoms. Biomolecules may also be integrated with non-colloidal nanocrystals. Peptides selective for germanium nanowires and wafers were isolated using phage display. Peptides expressed on the minor protein coat of bacteriophage were incubated with germanium substrates to find the sequences with greatest affinity for its substrate. Binding affinities were quantified by fitting titer measurements to an adsorption isotherm. Peptides selected using phage display was found to be morphologically selective for germanium substrates. Much research has yet to be conducted with the integration of inorganic with biomaterials, as the potential applications of these integrated materials continues to expand.