Dissertations / Theses on the topic 'Amide resonance'

Final publication is available at http://link.springer.com/article/10.1007/s11060-014-1715-8
Kyoto University (京都大学)
0048
新制・課程博士
博士(医学)
甲第19605号
医博第4112号
新制||医||1014(附属図書館)
32641
京都大学大学院医学研究科医学専攻
(主査)教授 村井 俊哉, 教授 平岡 眞寛, 教授 山田 泰広
学位規則第4条第1項該当

Introduction Peritoneal metastasis is advanced disease and is usually widely disseminated at the time of discovery. It is crucial to detect peritoneal metastasis at an early stage and to allow precise patient selection for the right treatments. Both fluorodeoxyglucose positron emission tomography/computed tomography (FDGPET/CT) and magnetic resonance imaging (MRI) are used in peritoneal metastasis detection. Standardized uptake value (SUV), derived from FDGPET/ CT can evaluate glucose metabolism in cells, whilst apparent diffusion coefficient (ADC) derived from diffusion-weighted MRI (DWI) is used for quantitative analysis of tumour cellularity. Amide proton transfer (APT) MRI is a novel imaging technique based on exchangeable amide protons as endogenous contrast agent and can measure the increased amide proton signal in malignant tissues indirectly through bulk water proton signals. This thesis aims to: 1) compare the diagnostic performance of FDG-PET/CT and MRI in peritoneal metastasis evaluation; 2) study the relationship between SUV and ADC in peritoneal metastasis; 3) investigate the feasibility of APT in peritoneal metastasis evaluation. Materials and Methods Patients with peritoneal metastasis detected on FDG-PET/CT were prospectively recruited for MRI. FDG-PET/CT and MRI images were reviewed independently by two radiologists in separate sessions. Diagnostic characteristics were calculated for both imaging techniques. SUVmax and SUVmean were obtained by placing ROIs on PET, while ADCmin and ADCmean were calculated by contouring lesions on DWI. APT MRI was performed using a single-slice turbo spin echo sequence, with a block of presaturation pulses at 33 frequency offsets. ROIs were placed on peritoneal metastasis and muscle on APT. Mean of integrated asymmetrical magnetic transfer ratio (MTRasym) over 3-4 ppm with respect to water resonance was calculated for peritoneal metastasis and muscle. Results Eight patients were recruited in this study with 128 anatomical sites evaluated. DWI/MRI had good diagnostic performance (sensitivity = 92%, specificity = 99%, accuracy = 98%) compared to that of FDG-PET/CT (sensitivity = 90%, specificity= 100%, accuracy = 98%). Thirty-four peritoneal metastases were selected for quantitative analysis. Significant inverse correlation was found between ADCmean and SUVmax (r = -0.528, p = 0.001) and between ADCmean and SUVmean (r = -0.548, p = 0.001). ADCmin was significantly and negatively correlated with SUVmax (r = -0.508, p = 0.002) and SUVmean (r = -0.513, p = 0.002). In the above study cohort, 6 patients underwent APT imaging with 8 peritoneal metastases evaluated. Seven lesions showed positive APT signal and one had negative APT signal. The mean APT signal for peritoneal metastasis was 2.28%±1.76%, significantly different from that of muscle (-2.79%±0.95%, p < 0.001). Conclusions In conclusion, both DWI/MRI and FDG-PET/CT had good diagnostic performance in peritoneal metastasis evaluation. The negative correlation between SUV and ADC suggested an inverse relationship between tissue metabolism and cellularity. APT MRI is feasible to generate sufficient contrast signal for peritoneal metastasis and has potential to discriminate peritoneal tumours from its surrounding soft tissue using integrated MTRasym as a quantitative marker. These functional indices allow understanding of the biological behaviours of peritoneal tumours and could act as adjuncts in peritoneal metastasis imaging.
published_or_final_version
Diagnostic Radiology
Master
Master of Philosophy

Stroke is one of the leading causes of death and adult disability worldwide. The major therapeutic intervention for acute ischemic stroke is the administration of recombinant tissue plasminogen activator (rtPA) to help to restore blood flow to the brain. This has been shown to increase the survival rate and to reduce the disability of ischemic stroke patients. However, rtPA is associated with intracranial haemorrhage and thus its administration is currently limited to only about 5% of ischemic stroke patients. More advanced imaging techniques can be used to better stratify patients for rtPA treatment. One new imaging technique, chemical exchange saturation transfer (CEST) magnetic resonance imaging, can potentially image intracellular pH and since tissue acidification happens prior to cerebral infarction, CEST has the potential to predict ischemic injury and hence to improve patient selection. Despite this potential, most studies have generated pH-weighted rather than quantitative pH maps; the most widely used metric to quantify the CEST effect is only able to generate qualitative contrast measurements and suffers from many confounds. The greatest clinical benefit of CEST imaging lies in its ability to non-invasively measure quantitative pH values which may be useful to identify salvageable tissue. The quantitative techniques and work presented in this thesis thus provide the necessary analysis to determine whether a threshold for the quantified CEST effect or for pH exists to help to define tissue outcome following stroke; to investigate the potential of CEST for clinical stroke imaging; and subsequently to facilitate clinical translation of CEST for acute stroke management.

In ischaemic stroke a disruption of cerebral blood flow leads to impaired metabolism and the formation of an ischaemic penumbra in which tissue at risk of infarction is sought for clinical intervention. In stroke trials, therapeutic intervention has largely been based on perfusion-weighted measures, but these have not been shown to be good predictors of tissue outcome. The aim of this thesis was to develop analysis techniques for magnetic resonance imaging (MRI) of chemical exchange saturation transfer (CEST) in order to quantify metabolic signals associated with tissue fate in patients with acute ischaemic stroke. This included addressing robustness for clinical application, and developing quantitative tools that allow exploration of the in-vivo complexity. Tissue-level analyses were performed on a dataset of 12 patients who had been admitted to the John Radcliffe Hospital in Oxford with acute ischaemic stroke and recruited into a clinical imaging study. Further characterisation of signals was performed on stroke models and tissue phantoms. A comparative study of CEST analysis techniques established a model-based approach, Bloch-McConnell model analysis, as the most robust for measuring pH-weighted signals in a clinical setting. Repeatability was improved by isolating non-CEST effects which attenuate signals of interest. The Bloch-McConnell model was developed further to explore whether more biologically-precise quantification of CEST effects was both possible and necessary. The additional model complexity, whilst more reflective of tissue biology, diminished contrast that distinguishes tissue fate, implying the biology is more complex than pH alone. The same model complexity could be used reveal signal patterns associated with tissue outcome that were otherwise obscured by competing CEST processes when observed through simpler models. Improved quantification techniques were demonstrated which were sufficiently robust to be used on clinical data, but also provided insight into the different biological processes at work in ischaemic tissue in the early stages of the disease. The complex array of competing processes in pathological tissue has underscored a need for analysis tools adequate for investigating these effects in the context of human imaging. The trends herein identified at the tissue level support the use of quantitative CEST MRI analysis as a clinical metabolic imaging tool in the investigation of ischaemic stroke.

Tridentate benzimidazole-based ligands, bis((1H-benzimidazol-2-yl)methyl)sulfide (BNSN) and bis((1H-benzimidazol-2-yl)methyl)amine (BNNN), along with dinonylnaphthalene sulfonic acid (DNNSA) as a synergist, were investigated as potential selective extractants for Ni2+ from base metals in a solvent extraction system using 2-octanol/Shellsol 2325 (8:2) as diluent and modifier. However, extraction studies show a lack of pH-metric separation of the later 3d metal ions with bis((1-octylbenzimidazol-2-yl)methyl)sulfide (BONSN) and bis((1- decylbenzimidazol-2-yl)methyl)amine (BDNNN) as extractants, but extractions occurred in the low pH range with an opportunity for back extraction. This investigation suggested that tridentate ligands (at least those of the nature investigated here) are not feasible extractants for separation of base metal ions due to their lack of stereochemical “tailor-making.”

Our understanding of the folding of membrane proteins lags behind that of soluble proteins due to the challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding landscapes, Chapter 2 investigates the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 $\mathit{\Chi}_{SDS}$), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal binding pocket is disrupted, with transmembrane residues becoming more solvent-exposed. Folding of pSRII from an SDS-denatured state harbouring a covalently-bound retinal chromophore shows deviations from an apparent two-state behaviour. SDS denaturation to form the sensory opsin apo-protein is reversible. This chapter establishes pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin. In Chapter 3, SDS-denatured pSRII, acid-denatured pSRII and sensory opsin obtained by hydroxylamine-mediated bleaching of pSRII were characterised by solution state NMR. 1D $^1$H and $^{19}$F NMR were first used to characterise global changes in backbone amide protons and tryptophan side-chains. Residue-specific changes in backbone amide chemical shifts and peak intensities in 2D [$^1$H,$^{15}$N]-correlation spectra were analysed. While only small changes in the chemical environment of backbone amides were detected, changes in backbone amide dynamics were identified as an important feature of SDS- and acid-denatured pSRII and sensory opsin. $^{15}$N relaxation experiments were performed to study the backbone amide dynamics of SDS-denatured pSRII, reflecting motions on different timescales, including fast fluctuations of NH bond vectors on the ps-ns timescale and the lack of exchange contributions on the µs timescale. These studies shed insight on differences in the unfolding pathways under different denaturing conditions and the crucial role of the retinal chromophore in governing the structural integrity and dynamics of the pSRII helical bundle. Hydrogen bonds play fundamental roles in stabilising protein secondary and tertiary structure, and regulating protein function. Successful detection of hydrogen bonds in denatured states and during protein folding would contribute towards our understanding on the unfolding and folding pathways of the protein. Previous studies have demonstrated residue-specific detection of stable and transient hydrogen bonds in small globular proteins by measuring $^1{\it J}_{NH}$ scalar coupling constants using NMR. In Chapter 4, different methods for measuring $^1{\it J}_{NH}$ scalar coupling were explored using RalA, a small GTPase with a mixed alpha/beta fold, as proof-of-concept. Detection of hydrogen bonds was then attempted with OmpX, a beta-barrel membrane protein, both in its folded state in DPC micelles and in the urea-denatured state. While $^1{\it J}_{NH}$ measurement holds promise for studying hydrogen bond formation, further optimisation of NMR experiments and utilisation of perdeuterated samples are required to improve the precision of such measurements in large detergent-membrane protein complexes. Naturally occurring split inteins can mediate spontaneous trans-splicing both in vivo and in vitro. Previous studies have demonstrated successful assembly of proteorhodopsin from two separate fragments consisting of helices A-B and helices C-G via a splicing site in the BC loop. To complement the in vitro unfolding/folding studies, pSRII assembly in vivo was attempted by introducing a splicing site in the loop region of the beta-hairpin constituting the BC loop of pSRII. The expression conditions for the N- and C-terminal pSRII-intein segments were optimised, and the two segments co-expressed. However, the native chromophore was not observed. Further optimisation is required for successful in vivo trans-splicing of pSRII and application of this approach towards understanding the roles of helices and loops in the folding of pSRII.

Etude structurale par spectrometrie raman de resonance des etats monocationique et triplet de quelques amines aromatiques, composes modeles de photochimie. Analyse des spectres de plusieurs especes structuralement proches. On montre que les etats ionises et triplet des benzenes substitues par des groupes mesomeres donneurs ont plusieurs points communs qui resultent d'interactions orbitalaires analogues entre le cycle benzenique et le substituant

Protein structure, including its dynamics, is of pervasive significance in biology. A protein’s structure determines its bindings with other molecules [1], and from that its roles in signal transduction, enzymatic activity and mechanical structure. Few cellular processes have no protein involvement. The relationship between a protein’s sequence of amino-acid residues and its three-dimensional structure, partial or otherwise, has long been of considerable interest [2]. A theory of protein folding is proposed in Section 4.10.4 (Hypotheses/Protein folding). This theory varies and extends the backbone-based theory proposed by Rose et al. [3]. This theory may prove to be the most significant offering of the thesis. Overall, this thesis investigates the variation in peptide group resonance and its implications for Resonance-Assisted Hydrogen Bonding [4, 5], RAHB, such as exists in inter-peptide group hydrogen bonding. Natural Bond Orbital [6], NBO, analysis is used for this investigation, and Section 2.1 summarizes the virtues of NBO. Chapter 3 is concerned with methods for computational investigation of protein structures, and finds that methods and basis sets most often used for these investigations are particularly unsuitable when any beta sheets are present due to poor modelling of amide resonance and hence of RAHB that features in the hydrogen-bonded chains of backbone amides of protein secondary structures such as beta sheets [7] and alpha helices [8]. Chapter 4 reports experiments quantifying the sensitivity of amide resonance to electrostatic field with component parallel or antiparallel to the amide C-N bond. This sensitivity allows electrostatic properties including permittivity of amino-acid residue sidechains to influence backbone amide resonance and hence secondary structure RAHB chains, giving a novel mechanism relating residue sequence to structure. Also, this variation in amide resonance is energetically significant even without considering a hydrogen bonding context. Variation of peptide group resonance is expected to vary the barrier height of prolyl isomerization [9]. Subsequent to quantifying this effect in isolated amides and in a RAHB chain, hypotheses are offered concerning the stability of beta sheets, amyloid fibrils [10] and polyproline helices [11]. An analogous sensitivity in nitrogenous base pairing [12] is conjectured. A hypothesis is offered concerning protein complexation and molecular chaperone [13] action. Chapter 5 is motivated by the observed increase of stabilization when cooperative hydrogen bonding chains are cyclized in non-protein contexts [6] and by the phenomena anticipated if these cycles exist in proteins as described in the chapter. The question of the optimal geometry for amide-amide hydrogen bonding is revisited with emphasis on the inequivalence of amide oxygen lone pairs. A possible avenue for the design of HB-chain polymers with improved stability is discussed. Chapter 6 studies a dependency of amino acid residue preference against beta sheet secondary structure by backbone hydration in the presence of cation, doing so by Quantum Molecular Dynamic simulation of a beta sheet with a full quantum mechanical treatment of each solvent molecule.
Thesis (Ph.D.) -- University of Adelaide, School of Physical Sciences, 2016

The thesis entitled “Exploring Diverse Facets of Small Molecules by NMR Spectroscopy” consists of six chapters. The main theme of the thesis is to exploit one and two dimensional NMR methodologies for understanding the diverse facets of small organic molecules, such as, weak intra- and inter- molecular interactions, chiral discrimination, quantification of enantiomeric excess and assignment of absolute configuration. Several new pulse sequences have also been designed to solve specific chemical problems, in addition to extensive utility of existing one and two dimensional NMR experiments. The results obtained on different problems, are discussed under six chapters in the thesis. The brief summary of each of these chapters is given below. Chapter 1 begins with the discussion on the importance of small molecules and their various facets, the analytical techniques available in the literature to study them. The role of NMR spectroscopy as powerful analytical technique to understand the diverse facets of organic molecules and their importance is set out in brief. A short introduction to the basic principles of NMR, the interaction parameters, the commonly employed one and two dimensional homo- and herero- nuclear NMR experiments are also given. The basic introduction to product operators essential for understanding the spin dynamics in the developed pulse sequences is given. The application of diffusion ordered spectroscopy (DOSY), the general problems encountered in the analysis of combinatorial mixtures and the matrix assisted method in circumventing such problems are discussed. Chapter 2 focuses on the chiral discrimination and the measurement of enatiomeric excess. The NMR approach to discriminate enantiomers using chiral auxiliaries such as, solvating agents, derivatizing agents, lanthanide shift reagents, the choice of such auxiliaries and the limitations are discussed in detail. The in-depth discussion on the new protocols developed using both the solvating and derivatizing agents for enantiomeric discrimination of chiral amines, hydroxy acids and diacids are discussed. The new three-component protocols that serve as chiral derivatizing agents for the discrimination of primary amines, diacids and hydroxy acids are discussed. Also the role of organic base such as DMAP in the chiral discrimination is explored for discrimination of acids using BINOL as a chiral solvating agent. Accordingly the discussion is classified into two sections. In the first section the protocol developed utilizing an enantiopure mandelic acid, a primary amine substrate and 2-formylphenylboronic acid that is ideally suited for testing the enantiopurity of chiral primary amines is discussed. The broad applicability of the protocols for testing enantiopurity has been demonstrated on number of chiral molecules using 1H and 19F NMR. The second section contains the results on the new concept developed for discrimination of hydroxy acids. The strategy involves the formation of three component protocol using chiral hydroxy acid, R-alphamethylbenzylamine and 2-formylphenylboronic acid for 1H-NMR discrimination of diacids. The section also includes the utility of ternary ion-pair complex for the discrimination of acids. The ternary ion-pair not only permitted the testing of enantiopurity of chiral acids, but is also found useful for the measurement of enantiomeric excess. Chapter 3 discusses the utilization of the developed three-component protocols for the assignment of absolute configurations of molecules of different functionality. The protocols for the assignments of absolute configuration of primary amines using 2-formylphenylboronic acid and mandelic acid yielded the substantial chemical shift differences between diastereomers. The consistent trend in the direction of change of chemical shifts of the discriminated proton(s) gave significant evidence for employing them as parameters for the assignment of spatial configuration of primary amines. Another protocol using 2-formylphenylboronic acid, hydroxy acids and enantiopure alphamethylbenzylamine permitted their configurational assignment. In the second section a novel solvating agent, obtained by the formation of an ion-pair complex among enantiopure BINOL, DMAP and chiral hydroxy acid for the assignment of the spatial configuration of hydroxy acids is discussed. Chapter 4 focuses on the development of novel NMR methodologies, and also the utility of existing two-dimensional experiments for addressing certain challenging problems. This chapter has been divided into three sections. In Section-I the utilization of well-known homonuclear 2D-J-resolved methodology for unravelling the overlapped NMR spectra of enantiomers, an application for chiral discrimination and the measurement of enantiomeric excess is discussed. The utilization of the chiral auxiliaries, such as, chiral derivatizing agents, chiral solvating agents and lanthanide shift reagents permits enantiodiscrimination and the measurement of excess of one form over the other. Nevertheless many a times one encounters severe problems due to small chemical shift difference, overlap of resonances, complex multiplicity pattern because of the presence of number of interacting spins, and enormous line broadening due to paramagnetic nature of the metal complex. This section is focused on combating such problems utilizing 2D-J-1JNH resolved spectroscopy where a 450 tilting of the spectrum in the F2 dimension, yielded the pure shift NMR spectrum. The method circumvents several problems involved in chiral discrimination and allows the accurate measurement of enantiomeric excess. In Section-II, the development of novel NMR experimental methodology cited in the literature as C-HetSERF and its application for the study of symmetric molecules, such as, double bonded cis- and trans- isomers, and extraction of magnitudes and signs of long range homo- and hetero- nuclear scalar couplings among chemically equivalent protons in polycylic aromatic hydrocarbons is discussed. The extensive utility of the new pulse sequence has been demonstrated on number of symmetric molecules, where the conventional one dimensional experiment fails to yield spectral parameters. In section III, yet another novel pulse sequence called RES-TOCSY developed for unravelling of the overlapped NMR spectrum of enantiomers and the measurement of enantiomeric contents, has been utilized for the accurate measurement of magnitudes and signs of 1H-19F couplings in fluorine containing molecules. The method has distinct advantages as the strengths of the couplings and their relative signs could be extracted on diverse situations, such as, couplings smaller than line widths, the spectrum where the coupling fine structures are absent. Chapter 5 covers the study of nature of intra- and inter- molecular hydrogen bond in amide and its derivative. The chapter is accordingly divided into two sections. In the first section the study of acid and amide hydrogen bonding is discussed and the hydrogen bonded interactions are probed by extensive utility of 1H, 13C and 15N-NMR. The temperature perturbation experiments, measurements of the variation in the couplings, monitoring of diffusion coefficients and the association constants, detection of through space correlation have given unambiguous evidence for the hydrogen bond formation. The results were also supported by DFT calculations. Similar interaction in the solid state has also been derived by obtaining the crystal structure of complex phenylacetic acid with benzamide. In the second section of the chapter the hydrogen bond interaction of organic fluorine in trifluoromethyl derivatives of benzanilides has been explored and the involvement of CF3 group in the hydrogen bonding has been detected. The evidence for the participation of CF3 group in hydrogen bond has been confirmed by number of experiments, such as, the detection of through space couplings, viz., 1hJFH, 1hJFN, and 2hJFF , where the spin polarization between the interacting spins is transmitted through hydrogen bond, the temperature and solvent dependent studies, variation in the 1JNH and two dimensional heteronuclear correlation experiments. In an interesting example of a molecule containing two CF3 groups situated on two phenyl rings of benzanilide, the simultaneous participation of fluorines of two CF3 groups in hydrogen bond has been detected. The confirmatory evidence for such an interaction, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, has been derived by 19F−19F NOESY. Significant deviations in the strengths of 1JNH, in addition to variable temperature, and the solvent induced perturbation studies yielded additional evidence. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated. The study revealed the rare observation and the first example of the C-F…H-N hydrogen bond in solution state in the molecules containing CF3 groups. Chapter 6 focuses on the mixture analysis using the diffusion ordered spectroscopy (DOSY). High Resolution-DOSY works when the NMR spectrum is well resolved and the diffusion coefficients of the combinatorial mixtures are substantially different from each other. DOSY technique fails when the mixture contains the molecules of nearly identical weights and similar hydrodynamic radii. Thus, the positional isomers, enantiomers consequent to their nearly identical rates of diffusion, are not differentiated. Some of these problems can be overcome by Matrix-Assisted Diffusion Order Spectroscopy (MAD-spectroscopy), where an external reagent acts as a matrix and aids in their diffusion edited separation, provided the molecules embedded in it possess differential binding abilities with the matrix. Such different binding properties of the matrix are the basis for resolution of many isomeric species. In the present study three different novel auxiliaries, micelles-reverse micelles, crown ether and cyclodextrin are introduced for the resolution of positional isomers, double bonded isomers, viz., fumaric acid and maleic acid and also enantiomers. Accordingly, the results of each of these studies are discussed in three different sections.

碩士
國立中正大學
化學暨生物化學研究所
102
An AT-rich region of DNA often involved in DNA transcription and DNA-drug interactions. Thus a molecular probe that can recognize a particular DNA sequence is important. The previous research indicated bis(1-methyl-3-vinylpyrazinium-4-phenyl) amine diiodide (BMVPA4) selectively interacting with AT-rich region of DNA through minor groove binding. Since BMVPA4 is lack of fluorescence, we measured resonance Raman spectra of BMVPA4 complexed with a G-quadruplex d[TAG3(T2AG3)3] (Hum23) and a double helix d[(GC)2A2T2(GC)2] (LD12). In comparison with calculated Raman spectra by the density functional method, we attempted to identify the interacting moieties of BMVPA4 with these DNA sequences. The absorption peak of BMVPA4 at 480 nm shows a red shift of 27 nm when BMVPA4 mixed with Hum23 while the peak is red shifted 67 nm upon interacting with LD12. The difference resonance Raman spectrum of BMVPA4/LD12 relative to the BMVPA4 excited by 488 nm laser light shows more substantial deviations than the difference resonance Raman spectrum of BMVPA4/Hum23 relative to BMVPA4. We utilized the theoretical normal Raman modes to assign the experimental resonance Raman peaks. Several vibration frequencies of the pyrazine group are red shifted (e.g. 941、1027、1481、1545 cm-1 peaks) upon interacting with LD12. Some peaks intensity decreased. They are assigned as the vibrational modes of pyrazine group (e.g. 1027、1184 cm-1 peaks). These results reflect that the pyrazine groups play an important role in binding to LD12. The angle and length of the BMVPA4 structure allow BMVPA4 snugly fitted into the minor groove of the double helix of LD12. LD12 and BMVPA4 bind together through the electrostatic interaction. When BMVPA4 was mixed Hum23, the spectra varied slightly. We speculated that BMVPA4 combined with periphery phosphate backbone of Hum23. We also use several aprotic solvents to discussion hydrogen bond of BMVPA4. The resonance Raman spectra of BMVPA4 dissolved in different solvents showed no large shift of Raman peaks. So, we think BMVPA4 does not form the hydrogen bond with water. Finally, we use a different laser (405 nm) to excite the second electronic transition band (378 nm) of BMVPA4. One resonance Raman peak of about pyrazine group decreased in intensity (compared with 488 nm excited). The result indicated that the second excited electronic state has a similar potential surface relative to the electronic ground state along that pyrazine vibrational coordinate. In constrast, the first excited electronic transition state has a substantial change relative to the electronic ground state along this pyrazine vibrational mode.

The guanosine monophosphate synthetase (GMPS) is a class I glutamine amidotransferase, involved in the de-novo purine nucleotide biosynthesis. The enzyme catalyzes the biochemical transformation of xantosine (XMP) into guanosine monophosphate (GMP) in presence of ATP, Mg2+ and glutamine. All GMPSs consist of two catalytic sites 1) for GATase activity 2) for the ATPPase activity. The two catalytic sites may be housed in the same polypeptide (two-domain-type) or in separate polypeptides (two-subunit-type). Most of the studies have been performed on two-domain-type GMPSs, while only one study has been reported from two-subunit-type GMPS (Maruoka et al. 2009). The two-subunit-type GMPS presents an example where the component reactions of a single enzymatic reaction are carried out by two distinct subunits. In order to get better understanding of structural aspects and mechanistic principle that governs the GMPS activity in two-subunit-type GMPSs, we initiated the study by taking GMPS of Methanocaldococcus jannaschii as a model system. The GMPS of M. jannaschii (Mj) is a two-subunit-type protein. The GATase subunit catalyzes the hydrolysis of glutamine to produce glutamate and ammonia. The ATPPase subunit catalyses the amination of XMP to produce GMP using the ammonia generated in GATase subunit. Since the two component reactions are catalysed by two separate subunits and are coupled in the way that product of one reaction (ammonia) acts as a nucleophile in the second reaction. The cross-talk between these two subunits in order to maximise the efficiency of overall GMPS warrants investigation. The GATase activity is tightly regulated by the interaction with ATPPase domain/subunit, in all GMPS except in the case of P. falciparum. This interaction is facilitated by substrate binding to the ATPPase domain/subunit. Though, the conditions for the interaction between two subunits is known in a two-subunit-type GMP synthetase from P. horikoshii, the structural basis of substrate dependent interaction is not known. As a first step to understand the structural basis of interaction between the Mj GATase and Mj ATPPase subunits, we have determined the structure of Mj GATase (21 kDa) subunit using high resolution, multinuclear, multidimensional NMR spectroscopy. Sequence specific resonance assignments were obtained through analysis of various 2D and 3D hetero-nuclear multidimensional NMR experiments. NMR based distance restraints were obtained from assignment of correlations observed in NOE based experiments. Data were acquired on isotopically enriched samples of Mj GATase. The structure of Mj GATase (2lxn) was solved by using cyana-3.0 using NMR based restraints as input for the structure calculation. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35±0.06 Å for backbone atoms and 0.8±0.06 Å for all heavy atoms. Attempts were also made to obtain assignments for the 69.6 kDa dimeric ATPPase subunit. Partial assignments have been obtained for this subunit. The GATase subunit is catalytically inactive. So far, there has been only one published report on a two-subunit-type GMPS from P. horikashii. The study has shown that the catalytic activity of GATase is regulated by the GATase-ATPPase interaction which is facilitated by the substrate binding to the ATPPase subunit. For the first time, we have provided the structural basis of interaction between GATase-ATPPase (112 kDa) in a two-subunit-type GMPS. Observed line width changes were used to identify residues in GATase residues that are involved in the Mj GATase-ATPPase interaction. Our data provides a possible explanation for conformational changes observed in the Mj GATase subunit upon GATase-ATPPase interaction that lead to GATase activation. Ammonia is generated in GATase subunit and is very reactive and labile. Thus, the faithful transportation of ammonia from GATase to ATPPase subunit is very crucial for optimal GMPS activity. Till date, a PDB query for GMPS retrieves only one structure which belongs to two-subunit-type GMPS, where authors have determined the structures of GATase and ATPPase subunits separately. However, the structure of holo-GMPS is not determined yet. Using interface information from experimental data and HADDOCK, we have constructed a model for the holo-GMPS from M. jannaschii. A possible ammonia channel has been deduced using the programs MOLE 2.0 and CAVER 2.0. This ammonia channel has a length of 46 Å, which is well within the range of the lengths calculated for similar channels in other glutamine amidotransferase. It had been suggested earlier that in addition to the magnesium required for charge stabilization of ATP, additional binding sites were present on GMPS. The effect of excess Mg2+ requirement on the GMPS activity has been studied in two-domain-type GMPS. However, the interaction between GATase and Mg2+ has been not investigated in any GMPS. This prompted us to investigate the effect of MgCl2 on Mj GATase subunit. For the first time, using chemical shift perturbation, we have established interaction between Mj GATase and Mg2+. The dissociation constant (Kd) of the Mj GATase-Mg2+ interaction was determined. The Kd value was found to be 1 mM, which indicates a very weak interaction. The substrate of the GATase subunit is glutamine. The condition of the hydrolysis of the glutamine is known in GMPS. However, the binding of the glutamine and associated conformational changes in GATase have been not studied in GMPS. Furthermore, till date there is no structure available for the glutamine bound GMPS/GATase. Using isotope edited one dimensional and two-dimensional NMR spectroscopy; we have shown that the Mj GATase catalytic residues are not in a compatible conformation to bind with glutamine. Thus, a conformational change in Mj GATase subunit is a pre-requisite condition for the binding of glutamine. These conformational changes are brought by the Mj GATase-ATPPase interaction.