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Climate change is predicted to be the most pronounced in high latitude ecosystems, however very little is known about their vulnerability to the projected warmer temperatures. In particular, natural organic matter (NOM) in the high latitude cryosphere which includes dissolved organic matter (DOM) and cryoconite organic matter (COM) from glaciers and soil organic matter (SOM) in permafrost, is highly susceptible to climate change which may lead to severe consequences on both local and global carbon biogeochemical cycles. Examination of DOM in glacier ice by a novel 1H nuclear magnetic resonance (NMR) water suppression pulse sequence at its natural abundance revealed and quantified the composition and the organic constituents in ice samples from Antarctica. 1H NMR spectra of samples from several glaciers were acquired and compared to the dominant fluorescent DOM fraction. This comprehensive approach showed that glacier ice DOM was mainly composed of small, labile biomolecules associated with microbes. Examination of the organic debris found on glacier surfaces (COM) from both Arctic and Antarctic glaciers were determined to be derived from microbes. Samples from Arctic glaciers were more chemically heterogeneous with small inputs of plant-derived material detected after targeted extractions. Therefore the COM carbon composition was determined to be dependent on the local glacier environment, suggesting a site specific contribution to the carbon cycle. Finally, the distribution of extracted branched glycerol dialkyl glycerol tetraether (GDGT)microbial membrane lipids and the deuterium incorporation of plant-wax n-alkane biomarkers extracted from dated permafrost SOM (paleosols) were independently applied for Canadian Arctic climate reconstruction during the last glacial maximum. Overall, the branched GDGT based temperature reconstructions from the Arctic paleosols reconstruct higher temperatures, likely when bacterial activity was optimal. The deuterium composition of the C29 n-alkane plant lipids appears to integrate an average annual signal. Further analysis by both non-selective NMR spectroscopic and targeted biomarker techniques on these paleosol samples revealed that the major vegetative sources from this paleoecosystem originated from woody and non-woody angiosperms. This thesis demonstrates several novel analytical characterization techniques, along with the major sources and composition of NOM in the cryosphere while demonstrating its use in paleoclimate applications.

Climate change is predicted to be the most pronounced in high latitude ecosystems, however very little is known about their vulnerability to the projected warmer temperatures. In particular, natural organic matter (NOM) in the high latitude cryosphere which includes dissolved organic matter (DOM) and cryoconite organic matter (COM) from glaciers and soil organic matter (SOM) in permafrost, is highly susceptible to climate change which may lead to severe consequences on both local and global carbon biogeochemical cycles. Examination of DOM in glacier ice by a novel 1H nuclear magnetic resonance (NMR) water suppression pulse sequence at its natural abundance revealed and quantified the composition and the organic constituents in ice samples from Antarctica. 1H NMR spectra of samples from several glaciers were acquired and compared to the dominant fluorescent DOM fraction. This comprehensive approach showed that glacier ice DOM was mainly composed of small, labile biomolecules associated with microbes. Examination of the organic debris found on glacier surfaces (COM) from both Arctic and Antarctic glaciers were determined to be derived from microbes. Samples from Arctic glaciers were more chemically heterogeneous with small inputs of plant-derived material detected after targeted extractions. Therefore the COM carbon composition was determined to be dependent on the local glacier environment, suggesting a site specific contribution to the carbon cycle. Finally, the distribution of extracted branched glycerol dialkyl glycerol tetraether (GDGT)microbial membrane lipids and the deuterium incorporation of plant-wax n-alkane biomarkers extracted from dated permafrost SOM (paleosols) were independently applied for Canadian Arctic climate reconstruction during the last glacial maximum. Overall, the branched GDGT based temperature reconstructions from the Arctic paleosols reconstruct higher temperatures, likely when bacterial activity was optimal. The deuterium composition of the C29 n-alkane plant lipids appears to integrate an average annual signal. Further analysis by both non-selective NMR spectroscopic and targeted biomarker techniques on these paleosol samples revealed that the major vegetative sources from this paleoecosystem originated from woody and non-woody angiosperms. This thesis demonstrates several novel analytical characterization techniques, along with the major sources and composition of NOM in the cryosphere while demonstrating its use in paleoclimate applications.

Shigella flexneri attacks cells of the intestinal tract, causing over 1 million deaths annually from bacterial dysentery. A type III secretion system (T3SS) initiates the host-pathogen interaction and transports virulence factors directly into host cells via a needle complex (NC) comprising an extracellular needle and membrane-spanning basal body. Rings formed by the single-pass membrane proteins MxiG and MxiJ are arranged concentrically within the inner membrane ring (IMR) of the NC. The Neterminal domain of MxiG (MxiG-N) is the predominant IMR cytoplasmic structure, however it was structurally and functionally uncharacterised. Determination of the solution structure of MxiG-N in this study revealed it to be a forkhead associated (FHA) domain, although subsequent analyses of conserved residues suggested it does not have the canonical role in cell-signalling via phospho-threonine recognition. Subsequent positioning of the structure in the electron microscopy (EM) density for the S. flexneri NC supported models with 24-fold symmetry in the IMR. Both MxiG and MxiJ also have significant periplasmic domains, which were purified to homogeneity in this study, facilitating preliminary characterisation of their structures and intermolecular interactions. In addition, the entire IMR within the context of intact basal bodies was isolated and visualised in vitro by EM. The essential function of MxiG-N could be to localise the putative cytoplasmic ring (Cering) at the base of the T3SS. Although absolutely required for secretion, the Csring component, Spa33, was structurally uncharacterised. The crystal structure of the Cvterminal domain of Spa33 (Spa33-C) was determined in this study, showing an intertwined dimer that aligned with homologous structures and exhibited a novel interaction with the N-terminus of the ATPase regulator, MxiN. Subsequently, Spa33-C was identified as an altemative translation product of spa33 that formed a 2: 1 complex with Spa33 in vitro. This complex oligomerised further, demonstrating for the first time that Spa33 has the propensity to form the ordered, high molecular weight assemblies that would be required for C-ring formation in S. flexneri.

Since its discovery in the 1950's, DNP has been a topic of significant interest in magnetic resonance. DNP is the transfer of polarization between single electrons and nuclei, driven by micro-wave irradiation. Since its renaissance at high field in the 90's, due to the introduction of gyrotrons as high-power, high-frequency microwave sources most application of this technique have been samples of biological interest in frozen solution. The long standing interest of our group in the characterization of surface species such as supported catalysts on silica lead us to apply this technique to the study of surfaces. The goal of this thesis is the development of this method, dubbed DNP Surface Enhanced NMR Spectroscopy. To that end, we first introduce new polarizing agents, soluble in organic solvents. The influence of the electron relaxation times on the DNP enhancements is demonstrated and efficient tailored polarizing agents are introduced. The optimization of the sample preparation to obtain optimal sensitivity is also discussed, as well as the interaction between the radical and the surface. These developments made it possible to apply the technique to many functionalized materials, with some examples developed in this manuscript. Finally, the issue of DNP on polarization conductors is discussed, and we show how microcrystals can be efficiently polarized using DNP.

The atomic resolution structure of a low populated and transiently formed on-pathway folding intermediate of the FF domain from human HYPA/FBP11 has recently been reported[1]. The structure was determined on the basis of backbone chemical shift and bond vector orientation restraints measured on the ‘invisible’ intermediate state using relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy that were subsequently input into the data-base structure determination program CS-Rosetta. This thesis focuses on the cross-validation of the structure so produced. We present here the solution NMR structure of a mimic of the folding intermediate that is highly populated in solution, obtained from the wild-type domain by protein mutagenesis. The ensemble of structures generated of the mimic are within 2Å of the relaxation dispersion/CS-Rosetta structures of the intermediate, with the non-native interactions in the intermediate also observed in the mimic. The results presented in this thesis strongly confirm the structure of the FF domain folding intermediate, in particular, and validate the use of relaxation dispersion derived restraints in structural studies of invisible excited states, in general.

The atomic resolution structure of a low populated and transiently formed on-pathway folding intermediate of the FF domain from human HYPA/FBP11 has recently been reported[1]. The structure was determined on the basis of backbone chemical shift and bond vector orientation restraints measured on the ‘invisible’ intermediate state using relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy that were subsequently input into the data-base structure determination program CS-Rosetta. This thesis focuses on the cross-validation of the structure so produced. We present here the solution NMR structure of a mimic of the folding intermediate that is highly populated in solution, obtained from the wild-type domain by protein mutagenesis. The ensemble of structures generated of the mimic are within 2Å of the relaxation dispersion/CS-Rosetta structures of the intermediate, with the non-native interactions in the intermediate also observed in the mimic. The results presented in this thesis strongly confirm the structure of the FF domain folding intermediate, in particular, and validate the use of relaxation dispersion derived restraints in structural studies of invisible excited states, in general.

The structural determination of interacting proteins, both as individual proteins and in their complex, complemented by thermodynamical studies are vital in order to gain in-depth insights of the phenomena leading to the highly selective protein-protein interactions characteristic of numerous life processes. This thesis describes an investigation of the structural and thermodynamical basis for molecular recognition in two different protein-protein complexes, formed between so-called affibody proteins and their respective targets. Affibody proteins are a class of engineered binding proteins, which can be functionally selected for binding to a given target protein from large collections (libraries) constructed via combinatorial engineering of 13 surface-located positions of the 58-residue three-helix bundle Z domain derived from Staphylococcal protein (SPA). In a first study, an affibody:target protein pair consisting of the ZSPA-1 affibody and the parental Z domain, with a dissociation constant (Kd) of approximately 1 µM, was investigated. ZSPA-1 was in its free state shown to display molten globule-like characteristics. The enthalpy change on binding between Z and ZSPA-1 as measured by isothermal titration calorimetry, was found to be a non-linear function of temperature. This nonlinearity was found to be due to the temperature dependent folded-unfolded equilibrium of ZSPA-1 upon binding to the Z domain and, the energetics of the unfolding equilibrium of the molten globule state of ZSPA-1 could be separated from the binding thermodynamics. Further dissection of the binding entropy revealed that a significant reduction in conformational entropy resulting from the stabilization of the molten globule state of ZSPA-1 upon complex formation could be a major reason for the moderate binding affinity. A second studied affibody:target complex (Kd ~ 0.1 µM) consisted of the ZTaq affibody protein originally selected for binding to Taq DNA polymerase and the anti-ZTaq affibody protein, selected for selective binding to the ZTaq affibody protein, thus constituting an "anti-idiotypic" affinity protein pair. The structure of the ZTaq:anti-ZTaq affibody complex as well as the free state structures of ZTaq and anti-ZTaq were determined using NMR spectroscopy. Both ZTaq and anti-ZTaq are well defined three helix bundles in their free state and do not display the same molten globule-like behaviour of ZSPA-1. The interaction surface was found to involve all of the varied positions in helices 1 and 2 of the anti-ZTaq, the majority of the corresponding side chains in ZTaq, and also several non-mutated residues. The total buried surface area was determined to about 1670 Å2 which is well inside the range of what is typical for many protein-protein complexes, including antibody:antigen complexes. Structural rearrangements, primarily at the side chain level, were observed to take place upon binding. There are similarities between the ZTaq:anti-ZTaq and the Z:ZSPA-1 structure, for instance, the binding interface area in both complexes has a large fraction of non-polar content, the buried surface area is of similar size, and certain residues have the same positioning. However, the relative orientation between the subunits in ZTaq:anti-ZTaq is markedly different from that observed in Z:ZSPA-1. The thermodynamics of ZTaq:anti-ZTaq association were investigated by isothermal titration calorimetry. A dissection of the entropic contributions showed that a large and favourable desolvation entropy of non-polar surface is associated with the binding reaction which is in good agreement with hydrophobic nature of the binding interface, but as in the case for the Z:ZSPA-1 complex a significant loss in conformational entropy opposes complex formation. A comparison with complexes involving affibody proteins or SPA domains suggests that affibody proteins inherit intrinsic binding properties from the original SPA surface. The structural and biophysical data suggest that although extensive mutations are carried out in the Z domain to obtain affibody proteins, this does not necessarily affect the structural integrity or lead to a significant destabilization. / QC 20110118

The research work reported in this thesis deals with the development of novel NMR experimental techniques for the spectroscopic discrimination of enantiomers dissolved in a chiral liquid crystalline medium. The information on the chemical shifts and coupling constants pertaining to each enantiomer has been derived on the investigated chiral molecules. The enantiomeric excess (ee), a parameter which is of profound importance in pharmaceutical industry and in asymmetric synthesis, has also been measured. A special attention is paid to the use of high sensitivity of H NMR for chiral discrimination. Typical analyses of H NMR spectra are severely hindered due to enormous spectral inhomogeneous broadening arising from too many unresolved transitions, in addition to superposition of spectra from both the enantiomers. Therefore, the major part of the work is focused on the design and application of pulse sequences to overcome many of these drawbacks. This helps to achieve very high resolution, discerning of overlapped transitions, identification of resonances pertaining to each enantiomer and simplification of the spectrum for easy extraction of spectral parameters, in addition to the accurate measurement of ee. Initially a brief discussion is provided on enantiomers, diastereomers, basic principles of NMR spectroscopy, the several interaction Hamiltonians responsible for yielding the NMR spectra, introduction to product and polarization operator formalisms that gives insight into the spin dynamics for designing appropriate two-dimensional (2D) NMR experiments. This sets the foundation to understand the complex multiplet structures of the diagonal peaks and cross peaks in the resulting 2D spectrum. Subsequently, a brief introduction is given for the available techniques for NMR spectroscopic discrimination of enantiomers in isotropic medium, where only chemical shifts are employed as a measurable parameter. The limitations of these techniques are circumvented by the introduction of other anisotropic NMR parameters, such as homo-and hetero-nuclear dipolar couplings, quadrupolar couplings and chemical shift anisotropies. To achieve this goal the enantiomers are dissolved in weakly aligning chiral liquid crystalline (CLC) medium. To understand this, a general introduction to liquid crystals and their utility as an alignment medium in NMR spectroscopy and the anisotropic interactions affecting the NMR spectrum has also been provided. The preparation of the CLC phase of Poly-γ-Benzyl-L-Glutamate (PBLG) employed in the present study and its orientational behaviour has been discussed. The detection of NMR spectra of various nuclei and the interaction parameters utilized for chiral discrimination will be enumerated. A brief summary of the experiments employed for the spectral analyses of the enantiomers dissolved in PBLG will also be presented.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2005. / Härtill 5 uppsatser.