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Nuclear magnetic resonance is a non-invasive way to observe material properties on a molecular level. Magnetic resonance imaging is an important diagnostic tool in medicine. Molecules of several metabolites in muscle tissue show similar interactions as molecules partially oriented in orienting media. These interactions could provide new information about processes in vivo, this can serve for diagnostics of metabolism. New insight into the function is gained by observation of metabolites in orienting media. Observable anisotropic interactions in muscle tissue in vivo could be used for diagnostic purposes. Anisotropic NMR interaction of solvent as a new method for observation of phase transition of hydrogel with temperature change or change of solvent composition. Use of magnetic resonance imaging in slices to observe the collapse of polyacrylamide in water-acetone mixtures. Use of diffusion-weighted magnetic resonance imaging to observe phase transition of PNIPAM-based semi-interpenetrating polymer.

Pin1 is an essential peptidyl-prolyl isomerase (PPIase) that catalyzes cis-trans prolyl isomerization in proteins containing phosphorylated serine/threonine-proline motifs (pSer/Thr-Pro). It has an N-terminal binding domain (WW) and a C-terminal PPIase domain. Pin1 targets pSer/Thr-Pro motifs by its WW domain and catalyzes isomerization through its PPIase domain. This dissertation is focused on elucidating the interactions between Pin1/substrate, the inter-domain dynamics upon binding, and the catalytic activity of Pin1 upon binding different substrates. Specifically, we investigated the Pin1-Histone H1 interaction and designed a series of chimeric peptides based on the H1.4 sequence (KATGAApTPKKSAKW). NMR titrations were performed for each peptide using both full-length Pin1 as well as the WW domain alone, to analyze the binding affinities. Here we combined 15N relaxation and residual dipolar couplings (RDCs) to monitor the degree to which peptide binding induced inter-domain interactions. We also investigated whether our chimeric sequences could alter catalysis (kex) using 1H-1H EXSY NMR experiments. Finally, when combined with molecular modeling, our results suggest a structural basis for how substrate binding can alter Pin1 inter-domain dynamics.

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Posttranslational modifications of nucleosomes play a crucial role for the proper functioning of the cell. One of the modifications called methylation is conducted by a family of SET-domain containing proteins called NSD1, NSD2, and NSD3. Recently, more evidence about the involvement of NSD proteins and their mutations in the oncogenesis has emerged. Various studies have found that post-SET domain and basic post-SET extension of NSD proteins are crucial for nucleosome interactions and for conducting enzymatic reactions. In this thesis, I attempt to define the role of post-SET domain basic extension on DNA binding, using nuclear magnetic resonance and isothermal titration calorimetry. Additionally, I have attempted to establish a methodology for obtaining nucleosomes, which could be used in future studies. NMR results showed that the post-SET domain extension is required for DNA to bind to NSD2 and NSD3 methyltransferases. The mutant form of NSD2, E1099K, exhibits stronger binding to DNA than does the wild type of NSD2. NMR results also show that the transplanted version of NSD3 containing the post-SET extension of NSD2 have an affinity similar to that of the NSD2 wild type. The NSD2 transplanted with a post-SET extension of NSD3 has close to 4 times less affinity towards DNA than does NSD2 wild type. The affinity of NSD3 T1232A and wild type could not be obtained, as the proteins could not be expressed in a sufficient amount for ITC experiments. However, the present literature confirms lower affinity of NSD3 (around 4 times less than NSD2) towards nucleosomes. Based on the empirical data and literature-based information, it can be assumed that post-SET domain basic extension determines the binding affinity of a NSD protein towards DNA. Additionally, a successful methodology for obtaining nucleosomes was established for future studies.

Nanoparticles (NPs) have become a key tool in medicine and biotechnology; as drug delivery systems, biosensors, and diagnostic devices. However, the mechanism of biocorona formation on nanoparticle surfaces and their impact on drug delivery remains speculative. Nevertheless, functionalized nanoparticles have demonstrated major success in medical applications; having been shown to effectively treat disease. The mechanistic details of protein behavior on nanoparticle surfaces remain poorly understood to date; due to difficulty in determining the orientation and structure of protein on NPs. Furthermore, surface crowding, orientation, and degree of disorder have been shown to perturb the efficacy of protein on NPs; dramatically reducing their benefits. NMR and other biophysical tools can be used to characterize the nanoparticle-protein surface interactions; leading to a better understanding of the biocorona structure. This dissertation investigates the structure, orientation, and function of proteins adsorbed on gold nanoparticles (P-AuNPs). Using hydrogen-deuterium exchange and methylation studies on P-AuNPs, we have elucidated the structure and orientation of proteins on AuNP surfaces. We have also designed fusion proteins that can effectively mitigate structural-, orientation-, and activity-perturbations of P-AuNPs. The benefits of our fusion protein approach have been verified via enzymatic assay; which monitored the enzymatic activity of these P-AuNPs. Biofilms are defined as surface-anchored, multi-cellular, three-dimensional, bacterial communities. Biofilms have a serious impact on public health; because of their role in infectious diseases and medical device-related infections. S. epidermidis is the most common biofilmorming bacteria. Therefore, understanding the mechanisms of biofilm formation could lead to novel therapeutics which prevent biofilm formation. One of the most recognized proteins in the biofilm formation mechanism is the S. epidermidis autolysin domain. Therefore, we have studied the structure and behavior of S. epidermidis autolysin repeat domain R2 (R2ab) via solution NMR and other biophysical techniques. This study has provided a deeper understanding of how R2ab interacts with foreign surfaces and blood proteins; which could lead to future methods of biofilm prevention. Over the course of this dissertation, the characterization of protein-surface interactions was achieved via solution NMR and other biophysical tools; providing insightful information to the fields of medicine and therapeutics.

Extremophiles are the organisms that survive in environments which are inhospitable to other creatures. This thesis made an attempt to understand the enviromental effects, in particular saline, on enzyme structure by using three dimensional NMR. The enzyme DHFR1 from halophile Haloferaxi volcanii is complexed with its coactor NADPH, and the saline effects on the complex are studied by comparison with its apoenzyme, hvDHFR1. Backbone chemical shift assignments of the hvDHFR1:NADPH complex were attained which can be functional (along with future work) in understanding the effect of salts on enzyme structure, function, and flexibility. A total of 27 amino acids were found to show a significant change upon binding of NADPH and their positions were identified on enzyme complex. The secondary structure of hvDHFR1:NADPH is also predicted and overall global structure is found to be similar with the crystal structure of hvDHFR1 with few changes.

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Kinetic isotope effect (KIE) study of enzymatic mechanisms has the potential for aiding the design of tight binding inhibitors, but is hampered by the need for isotopically labeled substrates. Recently, however, methods for measuring ¹³C and ²H KIEs at natural abundance by NMR spectroscopy have been developed, allowing KIEs to be measured at every NMR resolvable nucleus without isotopic substitution. Until this study, this technique had yet to be applied to an enzymatic system. KIEs provide information about transition states (TS) and since enzymes tightly bind structures resembling the TS, TS analogs can be used as powerful inhibitors and potential drugs. Glycosidases are enzymes that hydrolyze the acetals of carbohydrates. Inhibition of glycosidases has a large potential for therapeutic value. Methyl glucoside hydrolysis was used as a model substrate in the measurement of natural abundance KIEs. ¹³C KIEs were successfully measured on the acid and glucosidase catalyzed hydrolysis of methyl glucosides. The values of the primary ¹³C KIEs show that hydrolysis of β-methyl glucoside by β-glucosidase a more concerted ANON reaction. KIEs on the corresponding α-anomer suggest the opposite result, a ON*AN reaction. The experimental KIEs also matched well with calculated equilibrium isotope effects, lending support for the accuracy of the measurements. / Thesis / Master of Science (MSc)