Matching Items (3)

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Characterizing nanomaterials and protic ionic liquids utilizing nuclear magnetic resonance spectroscopy

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Structural details of phosphonic acid functionalized nanomaterials and protic ionic liquids (PILs) were characterized using nuclear magnetic resonance (NMR) spectroscopy. It is well known that ligands play a critical

Structural details of phosphonic acid functionalized nanomaterials and protic ionic liquids (PILs) were characterized using nuclear magnetic resonance (NMR) spectroscopy. It is well known that ligands play a critical role in the synthesis and properties of nanomaterials. Therefore, elucidating the details of ligand-surface and ligand-ligand interactions is crucial to understanding nanomaterial systems more completely.

In an effort to further the understanding of ligand-surface interactions, a combination of multi-nuclear (1H, 29Si, 31P) and multi-dimensional solid-state NMR techniques were utilized to characterize the phosphonic acid functionalization of fumed silica nanoparticles using methyl phosphonic acid (MPA) and phenyl phosphonic acid (PPA). Quantitative 31P MAS solid-state NMR measurements indicate that ligands favor a monodentate binding mode. Furthermore, 1H-1H single quantum-double quantum (SQ-DQ) back-to-back (BABA) 2D NMR spectra of silica functionalized with MPA and PPA indicate that the MPA and PPA are within 4.2±0.2 Å on the surface of the nanomaterial.

The ligand capping of phosphonic acid (PA) functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of ligand exchange, solution and solid-state 31P NMR spectroscopy. In order to quantify the ligand populations on the surface of the QDs, ligand exchange facilitated by PPA resulted in the displacement of the PAs, and allowed for quantification of the free ligands using 31P liquid state NMR.

In addition to characterizing nanomaterials, the ionicity and transport properties of a series of diethylmethylamine (DEMA) based protic ionic liquids (PILs) were characterized, principally utilizing NMR. Gas phase proton affinity was shown to be a better predictor for the extent of proton transfer, and in turn the ionicity of the PIL, than using ∆pKa. Furthermore, pulsed field gradient (PFG) NMR was used to determine that the exchangeable proton diffuses with the cation or the anion based on the strength of the acid used to generate the PILs.

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Date Created
  • 2015

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Modeling protein ligand interactions using multi-scale computational approaches

Description

Molecular docking serves as an important tool in modeling protein-ligand interactions. Most of the docking approaches treat the protein receptor as rigid and move the ligand in the binding pocket

Molecular docking serves as an important tool in modeling protein-ligand interactions. Most of the docking approaches treat the protein receptor as rigid and move the ligand in the binding pocket through an energy minimization, which is an incorrect approach as proteins are flexible and undergo conformational changes upon ligand binding. However, modeling receptor backbone flexibility in docking is challenging and computationally expensive due to the large conformational space that needs to be sampled.

A novel flexible docking approach called BP-Dock (Backbone Perturbation docking) was developed to overcome this challenge. BP-Dock integrates both backbone and side chain conformational changes of a protein through a multi-scale approach. In BP-Dock, the residues along a protein chain are perturbed mimicking the binding induced event, with a small Brownian kick, one at a time. The fluctuation response profile of the chain upon these perturbations is computed by Perturbation Response Scanning (PRS) to generate multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, this approach was applied to a large and diverse dataset of unbound structures as receptors. Furthermore, the protein-peptide docking of PICK1-PDZ proteins was investigated. This study elucidates the determinants of PICK1-PDZ binding that plays crucial roles in numerous neurodegenerative disorders. BP-Dock approach was also extended to the challenging problem of protein-glycan docking and applied to analyze the energetics of glycan recognition in Cyanovirin-N (CVN), a cyanobacterial lectin that inhibits HIV by binding to its highly glycosylated envelope protein gp120. This study provide the energetic contribution of the individual residues lining the binding pocket of CVN and explore the effect of structural flexibility in the hinge region of CVN on glycan binding, which are also verified experimentally. Overall, these successful applications of BP-Dock highlight the importance of modeling backbone flexibility in docking that can have important implications in defining the binding properties of protein-ligand interactions.

Finally, an induced fit docking approach called Adaptive BP-Dock is presented that allows both protein and ligand conformational sampling during the docking. Adaptive BP-Dock can provide a faster and efficient docking approach for the virtual screening of novel targets for rational drug design and aid our understanding of protein-ligand interactions.

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Date Created
  • 2015

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Application of multivalent interactions for recognition imaging and delivery of therapeutics

Description

Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to

Multivalency is an important phenomenon that guides numerous biological interactions. It has been utilized in design of therapeutics and drug candidates. Hence, this study attempts to develop analytical tools to study multivalent interactions and design multivalent ligands for drug delivery and therapeutic applications.

Atomic Force Microscopy (AFM) has been envisioned as a means of nanodiagnostics due to its single molecule sensitivity. However, the AFM based recognition imaging lacks a multiplex capacity to detect multiple analytes in a single test. Also there is no user friendly wet chemistry to functionalize AFM tips. Hence, an uncatalyzed Click Chemistry protocol was developed to functionalize AFM tips. For multiplexed recognition imaging, recognition heads based on a C3 symmetrical three arm linker with azide functionalities at its ends were synthesized and the chemistry to attach them to AFM tips was developed, and these recognition heads were used in detecting multiple proteins simultaneously using AFM.

A bis-Angiopeptide-2 conjugate with this three-arm linker was synthesized and this was conjugated with anti-West Nile virus antibody E16 site specifically to target advanced West Nile virus infection in the Central Nervous System. The bis-Angiopeptide-2 conjugate of the antibody shows higher efficacy compared to a linear linker-Angiopeptide-2 conjugate of the antibody in in vitro studies and currently the efficacy of this antibody conjugate in studied in mice. Surface Plasmon Resonance imaging (SPRi) results indicate that the conjugation does not affect the antigen binding activity of the antibody very significantly.

A Y-shaped bisbiotin ligand was also prepared as a small sized antibody mimic. Compared to a monovalent biotin ligand, the y-Bisbiotin can cooperatively form a significantly more stable complex with streptavidin through intramolecular bivalent interactions, which were demonstrated by gel electrophoresis, SPR and AFM. Continuing on these lines, a four-arm linker was synthesized containing three single chain variable fragments (scFv) linked to the scaffold to form a tripod base, which would allow them to concomitantly interact with a trimeric Glycoprotein (GP) spike that has a “chalice” configuration. Meanwhile, a human IgG1 Fc is to be installed on the top of the tetrahedron, exerting effector functions of a monoclonal antibody.

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Date Created
  • 2016