Structural Analyses of Xyloglucan Heptasaccharide by the Post-source Decay Fragment Method Using Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

In the post-source decay (PSD) fragment spectrum of a reduced xyloglucan heptasaccharide (XXXGol) from tamarind seeds, eleven sodium-adduct fragment ions and a precursor ion [M + Na]⁺ were clearly observed by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Each fragment ion interval corresponded to the absence of unhydroxylose, unhydroglucose, and glucitol residues, indicating that PSD fragmentation cleavage in the sugar compound occurred only at glycosidic linkages close to the oxygen atom of saccharide ring members, and not in inner sugar ring bonds. The PSD fragment ions were classified into two series, one involving the reducing end and the other involving the non-reducing end. Structural information from both the reducing and non-reducing ends could therefore be simultaneously obtained from the measurement of the positive ion mode. Almost all the fragment ions from species larger than trisaccharide residues could be detected in this PSD fragment experiment. Such fragmentation information will enable the structural determination of xyloglucan oligosaccharides.     

A new analysis of the depolymerized fragments of lignin polymer using ToF-SIMS

Lignin in plant cell walls is a complex, irregular polymer built from phenylpropanoid C6-C3 units that are connected via various C-C and C-O linkages. A recent study using time-of-flight secondary ion mass spectrometry (ToF-SIMS) with Ga primary ion bombardment showed that lignin polymers can be characterized by specific positive ions possessing a substituted aromatic ring (so-called guaiacyl or syringyl rings), which are the basic building units of lignin. To study the relationship between the characteristic ions of lignin and the common interunit linkages, various lignin dimer model compounds were investigated using ToF-SIMS. The resulting dimer spectra showed that the characteristic ions with a guaiacyl ring at m/z 137 and 151 result from rupture of most common interunit linkages, not only 8-O-4' linkages, which are the most abundant in lignin, but also 8-1', 8-5', and 8-8'. There was no evidence of rupture of 5-5' linkages. These results show that ToF-SIMS offers a new tool for the direct analysis of the depolymerized fragments of lignin polymers. The mechanisms for the fragmentation of lignin dimer models in ToF-SIMS were proposed that allow ToF-SIMS fragmentation rules to be deduced. Adduct ions such as [M + 13]+ ([M + CH]+) were also produced in fragmentation of the dimers and are thought to arise from the combination of the molecules with their stable fragments.     

Nickel in subunit beta of the acetyl-CoA decarbonylase/synthase multienzyme complex in methanogens. Catalytic properties and evidence for a binuclear Ni-Ni site

The acetyl-CoA decarbonylase/synthase (ACDS) complex catalyzes the central reaction of acetyl C-C bond cleavage in methanogens growing on acetate and is also responsible for synthesis of acetyl units during growth on C-1 substrates. The ACDS beta subunit contains nickel and an Fe/S center and reacts with acetyl-CoA forming an acetyl-enzyme intermediate presumably directly involved in acetyl C-C bond activation. To investigate the role of nickel in this process two forms of the Methanosarcina thermophila beta subunit were overexpressed in anaerobically grown Escherichia coli. Both contained an Fe/S center but lacked nickel and were inactive in acetyl-enzyme formation in redox-dependent acetyltransferase assays. However, high activity developed during incubation with NiCl(2). The native and nickel-reconstituted proteins both contained iron and nickel in a 2:1 ratio, with insignificant levels of other metals, including copper. Binding of nickel elicited marked changes in the UV-visible spectrum, with intense charge transfer bands indicating multiple thiolate ligation to nickel. The kinetics of nickel incorporation matched the time course for enzyme activation. Other divalent metal ions could not substitute for nickel in yielding catalytic activity. Acetyl-CoA was formed in reactions with CoA, CO, and methylcobalamin, directly demonstrating C-C bond activation by the beta subunit in the absence of other ACDS subunits. Nickel was indispensable in this process too and was needed to form a characteristic EPR-detectable enzyme-carbonyl adduct in reactions with CO. In contrast to enzyme activation, EPR signal formation did not require addition of reducing agent, indicating indirect catalytic involvement of the paramagnetic species. Site-directed mutagenesis indicated that Cys-278 and Cys-280 coordinate nickel, with Cys-189 essential for Fe/S cluster formation. The results are consistent with an Ni(2)[Fe(4)S(4)] arrangement at the active site. A mechanism for C-C bond activation is proposed that includes a specific role for the Fe(4)S(4) center and accounts for the absolute requirement for nickel.     

Structural elucidation of zwitterionic sugar cores from glycosphingolipids by nanoelectrospray ionization-ion-trap mass spectrometry

The use of electrospray ionization (ESI)-ion-trap mass spectrometry (ITMS) for analysis of zwitterionic, glycolipid-derived sugar cores of glycosphingolipids is described. The capability of the method to perform multiple steps of fragmentation (MS(n)) allows structural characterization of these compounds. No derivatization of the released oligosaccharides is necessary when using nano-ESI with sample solution flow rates of about 30 nL/min. Investigations of positive as well as negative ions in fragmentation experiments up to MS(4) permit determination of the sequence of sugar units, their linkage positions, and the exact location of the substituents phosphocholine and phosphoethanolamine. In the case of phosphocholine, chemical cleavage of this substituent was necessary to obtain all the linkage information. Approximately 150-250 ng of sample was needed for each analysis.     

Applications of natural orbitals for chemical valence in a description of bonding in conjugated molecules

Natural orbitals for chemical valence (NOCV) were used to describe bonding in conjugated pi-electron molecules. The 'single' C-C bond in trans-1,3-butadiene, 1,3-butadiene-1,1,4,4-tetra-carboxilic acid, 1,3,5,7-octatetraene, and 11-cis-retinal was characterized. In the NOCV framework, the formation of the sigma-bond appears as the sum of two complementary charge transfer processes from each vinyl fragment to the bond region, and partially to the other fragment. The formation of the pi-component of the bond is described by two pairs of NOCV representing the transfer of charge density from the neighboring 'double' C-C bonds. The NOCV eigenvalues and the related fragment-fragment bond multiplicities were used as quantitative measures of the sigma- and pi- contributions. The sigma-component of the 'single' C-C bonds appears to be practically constant in the systems analyzed, whereas the pi-contributions increase from butadiene (ca. 7.5%) to retinal (ca. 14%).     

莲子心碳苷黄酮与黄酮异构体的色谱质谱研究

采用电喷雾质谱法(ESI-MS),对从莲子心分离得到的碳苷类黄酮化合物进行质谱碎裂规律研究。结果表明,负离子模式下,六碳糖碳苷黄酮主要发生糖环裂解,通过丢失特征性的碎片(90 u、120 u、150 u)与氧苷黄酮区分;单糖取代的六碳醛糖氧苷黄酮直接丢失单糖部分(162 u),六碳醛糖种类无法通过质谱区分,但由于它们在液相上的保留时间不同,可通过液相色谱-质谱(LC-MS)联用方法分离鉴定;二糖取代的氧苷黄酮主要碎片离子通过丢失糖部分(146 u、162 u、308 u)所得,二糖的种类及连接方式可通过质谱图上的碎片离子峰及其相对丰度辨别。莲子心中多种碳苷黄酮和氧苷黄酮质谱的不同裂解规律,不仅有助于莲子心黄酮化合物的快速鉴定,而且可以通过与液相色谱联用实现莲子心中同分异构体的快速区分。     

Secondary ion mass spectrometry for sulfoglycolipids: application of negative ion detection

A series of underivatized sulfoglycolipids (SM4g, lyso-SM4g, SM4s, SM3, SM2, SB2, and SB1a) from various tissues were analyzed by both positive (POS-SI-MS) and negative (NEG-SI-MS) secondary ion mass spectrometry. By POS-SI-MS were detected the molecular ions of sulfoglycolipids in the form with sodium or potassium together with some fragment ions useful for the carbohydrate sequence determination. The analysis of monosulfogangliotriaosyl- or monosulfogangliotetraosylceramide and bis-sulfoglycolipid was difficult due to noise in the high mass region. On the other hand, NEG-SI-MS of sulfoglycolipids gave more intense signals from molecular ion of (M-H)- for monosulfoglycolipids and [M-H+Na)-H)- for bis-sulfoglycolipid. Many fragment ions useful for the elucidation of the carbohydrate sequences were also obtained with significant intensities. The fragmentation was assessed to occur at the glycosidic linkages to form ions of the oligosaccharides with or without ceramide. These ions were useful for sugar sequencing and also for distinguishing the differences in the position of the sulfate group. The intensities of saccharide ions without sulfate were lower than those with sulfates. In the case of SB2 and SB1a, containing 2 mol of sulfate ester groups, the molecular ion was detected as [M-H+Na)-H)-. Also, fragment ions with 2 mol of sulfate were detected as the sodium-additive form. It was concluded that NEG-SI-MS is a very useful technique for the structural elucidation of higher sulfoglycolipids.     

PTM MarkerFinder,a software tool to detect and validate spectra from peptides carrying post‐translational modifications

Mass spectrometry (MS) analysis of peptides carrying post‐translational modifications is challenging due to the instability of some modifications during MS analysis. However, glycopeptides as well as acetylated, methylated and other modified peptides release specific fragment ions during CID (collision‐induced dissociation) and HCD (higher energy collisional dissociation) fragmentation. These fragment ions can be used to validate the presence of the PTM on the peptide. Here, we present PTM MarkerFinder, a software tool that takes advantage of such marker ions. PTM MarkerFinder screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, it reports and annotates the HCD and the corresponding electron transfer dissociation (ETD) spectrum (when present), and summarizes information on the type, number, and ratios of marker ions found in the data set. In the present work, a sample containing enriched N‐acetylhexosamine (HexNAc) glycopeptides from yeast has been analyzed by liquid chromatography‐mass spectrometry on an LTQ Orbitrap Velos using both HCD and ETD fragmentation techniques. The identification result (Mascot .dat file) was submitted as input to PTM MarkerFinder and screened for HexNAc oxonium ions. The software output has been used for high‐throughput validation of the identification results.     

Extensive digestion of Na+,K(+)-ATPase by specific and nonspecific proteases with preservation of cation occlusion sites.

This paper extends our recent report that renal Na+,K(+)-ATPase is digested by trypsin in the absence of Ca2+ and presence of Rb+ ions to a stable 19-kDa fragment and smaller membrane-embedded fragments of the alpha chain and essentially intact beta chain. These are referred to as "19-kDa membranes." Occlusion of both Rb+ (K+) or Na+ ions is preserved, but ATP-dependent functions are lost (Karlish, S. J. D., Goldshleger, R., and Stein, W. D. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4566-4570). We now show that extensive digestion with nonselective fungal proteases (Pronase and proteinase K) alone, in combination, or after tryptic digestion can remove up to 70% of membrane protein without destroying Rb+ occlusion. In the most heavily digested membranes, the 19-kDa fragment or a slightly shorter 18.5-kDa fragment and smaller fragments of the alpha chain remain, whereas the beta chain is largely digested, leaving smaller membrane-embedded fragments (13-15 kDa). For either trypsin or Pronase digestion, preservation of Rb+ occlusion and the specific fragmentation pattern is observed only in the absence of divalent metal ions (Mg2+ or Ca2+) and presence of either Rb+ or Na+ or congener ions. Tryptic digestion at pH 7.0 can split the beta chain into two fragments of approximately 50 and 16 kDa joined by an S-S bridge. The 16-kDa fragment is protected against further digestion by the presence of Rb+ ions, but probably is not directly involved in occluding cations. Tryptic 19-kDa membranes show a clear and reproducible fragmentation pattern in which all predicted membrane segments are identifiable. Families of fragments from 19-kDa membranes, including seven peptides of 7.6-11.7 kDa, have been separated by size-exclusion high performance liquid chromatography, concentrated, and resolved on 16.5% Tricine gels. N-terminal sequences of the different fragments have been determined after transfer to polyvinylidene difluoride paper. The most interesting findings are as follows. (a) Whereas the 19-kDa tryptic fragment begins at Asn831 as reported previously, the 18.5-kDa Pronase fragment begins at Thr834. (b) Fragments in tryptic 19-kDa membranes of 7.6-11.7 kDa begin at Asp68, Ile263, and Gln737, respectively. These include all putative transmembrane segments other than those in the 19-kDa fragment. (c) A Pronase fragment of 7.8 kDa begins at Thr834, i.e. apparently the 19-kDa fragment has been partially cut, without loss of Rb+ occlusion. (d) Tryptic 16- and approximately 50-kDa fragments of the beta chain begin at Ala5 and Gly143, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)     

Laser-assisted field-desorption mass spectrometry of cyclomalto-hexaose and -heptaose and some 6-alkylthio derivatives

The use of laser-assisted field-desorption mass spectrometry for determination of molecular weight, elucidation of structure, and control of purity is demonstrated for cyclomalto-hexaose and -heptaose and their derivatives. Each compound gave an abundant [M + Na]⁺ ion. The [Na]⁺ ions originate from traces (～0.1%) of salts in the authentic samples. The fragmentation obtained is structurally highly significant, as the sequential loss of 1–5 sugar subunits is observed. Under these conditions, the elimination of water is negligible, but can be induced by applying higher thermal stress, e.g., using higher laser power. When fragmentation was induced, the cyclic oligosaccharides substituted at positions 6 lost substituted sugar units, thus confirming the synthesis pathway.     

Ab initio molecular dynamics simulations of beta-D-glucose and beta-D-xylose degradation mechanisms in acidic aqueous solution

Ab initio molecular dynamics simulations were employed to investigate, with explicit solvent water molecules, beta-D-glucose and beta-D-xylose degradation mechanisms in acidic media. The rate-limiting step in sugar degradation was found to be protonation of the hydroxyl groups on the sugar ring. We found that the structure of water molecules plays a significant role in the acidic sugar degradation pathways. Firstly, a water molecule competes with the hydroxyl group on the sugar ring for protons. Secondly, water forms hydrogen bonds with the hydroxyl groups on the sugar rings, thus weakening the C-C and C-O bonds (each to a different degree). Note that the reaction pathways could be altered due to the change of relative stability of the C-C and C-O bonds. Thirdly, water molecules that are hydrogen-bonded to sugar hydroxyls could easily extract a proton from the reaction intermediate, terminating the reaction. Indeed, the sugar degradation pathway is complex due to multiple protonation probabilities and the surrounding water structure. Our experimental data support multiple sugar acidic degradation pathways.     

Ring-cleaving dioxygenases with a cupin fold

Ring-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject to ortho or meta cleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an Fe(II) center for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O(2), resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O(2) is supported by model chemistry.     

Mass spectrum and uniformity of decomposition of certain 2-substituted 9-(o-chlorbenzyl)-8-azahypoxanthines

The regularities of mass spectrometric fragmentation under electron impact of new 9-(o-chlorobenzyl)-8-azahypoxantines with (N-aryl)amidocarbonylmethylthiomethyl substituents in position 2 were studied. The main fragmentation pathways are the elimination of Ar-NH+ and o-chlorobenzyl ions and cleavage of C-S bonds, characteristic of organic sulfides. During the fragmentations, some rearrangements occur, consisting in the transfer of labile hydrogen atoms from the alpha-positions to ions being eliminated. Fragmentation of 8-azapurine parts of the molecules does not prevail. Peaks of molecular ions are clearly visible in the mass spectra of all the substances studied. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 1; see also http://www.maik.ru.     

On the location of the divalent metal binding sites and the light chain subunits of vertebrate myosin.

The divalent metal ion binding sites of skeletal myosin were investigated by electron paramagnetic resonance (EPR) spectroscopy using the paramagnetic (Mn(II) ion as a probe. Myosin possesses two high affinity sites (K less than 1 muM) for Mn(II), which are located on the 5,5'-dithiobis(2-nitrobenzoate) (DTNB) light chains. Mn(II) bound to the isolated DTNB light chain gives rise to an EPR spectrum similar to that of Mn(II) bound to myosin and this indicates that the metal binding site comprises ligands from the DTNB light chain alone. Myosin preparations in which the DTNB light chain content is reduced by treatment with 5,5'-dithiobis(2-nitrobenzoate) show a corresponding reduction in the stoichiometry of Mn(II) binding, but the stoichiometry is recovered on reassociation of the DTNB light chain. Chymotryptic digestion of myosin filaments in the presence of ethylenediaminetetraacetic acid yields subfragment 1, but digestion in the presence of divalent metal ions produces heavy meromyosin. Myosin with a depleted DTNB light chain content gives rise to subfragment 1 on proteolysis, even in the presence of divalent metal ions. It is proposed that saturation of the DTNB light chain site with divalent ions protects this subunit against proteolysis, which, in turn, inhibits the cleavage of the subfragment 1-subfragment 2 link. Either the DTNB light chain is located near the region of the link and sterically blocks chymotryptic attack, or it is bound to the subfragment 1 moiety and affects the conformation of the link region. When the product heavy meromyosin was examined by sodium dodecyl sulfate gel electrophoresis, an apparent anomaly arose in that there was no trace of the 19 000-dalton band corresponding to the DTNB light chain. This was resolved by following the time course of chymotryptic digestion of the myosin heavy chain, the DTNB light chain, and the divalent metal binding site. The 19 000-dalton DTNB light chain is rapidly degraded to a 17 000-dalton fragment which comigrates with the alkali 2 light chain. The divalent metal site remains intact, despite this degradation, and the 17 000 fragment continues to protect the subfragment 1-subfragment 2 link. In the absence of divalent metal ions, the 17 000-dalton fragment is further degraded and attack of the subfragment 1 link ensues. Mn(II) bound to cardiac myosin gives an EPR spectrum basically similar to that of skeletal myosin, suggesting that their 19 000-dalton light chains are analogous with respect to their divalent metal binding sites, despite their chemical differences. The potential of EPR spectroscopy for characterizing the metal binding sites of myosin from different sources and of intact muscle fibers is discussed.     

Collisionally induced fragmentation of protonated oligoalanines and oligoglycines.

In a hybrid instrument under minimal multiple-collision conditions, the collision-induced fragmentation of the [M + H]+ ions of tetraalanine and tetraglycine are dominated by the gamma 2 fragment, in distinction to the fragmentation of the [M + H]+ ions of hexa- and octaalanine and -glycine; these latter fragmentations are instead a distribution of b and y ions, and to a lesser extent a ions. This difference may be rationalized on the basis of control of the fragmentation by the most basic site in the peptide, which may be identified by taking internal hydrogen bonding into account. On increasing the collision energy from 10 to 150 eV, a, b and y ions of lower mass appear; and in several cases a peak due to a smaller b ion becomes the base peak. The ion distribution in the spectra of these protonated peptides serves as a baseline from which the effects of conformation on side-group rearrangements and other fragmentations may be explored.     

Direct voltammetry and electrocatalytic properties of catalase incorporated in polyacrylamide hydrogel films

The direct voltammetry and electrocatalytic properties of catalase (Cat) in polyacrylamide (PAM) hydrogel films cast on pyrolytic graphite (PG) electrodes were investigated. Cat-PAM film electrodes showed a pair of well-defined and nearly reversible cyclic voltammetry peaks for Cat Fe(III)/Fe(II) redox couples at approximately -0.46 V vs. SCE in pH 7.0 buffers. The electron transfer between catalase and PG electrodes was greatly facilitated in the microenvironment of PAM films. The apparent heterogeneous electron transfer rate constant (k(s)) and formal potential (E degrees ') were estimated by fitting square wave voltammograms with non-linear regression analysis. The formal potential of Cat Fe(III)/Fe(II) couples in PAM films had a linear relationship with pH between pH 4.0 and 9.0 with a slope of -56 mV pH(-1), suggesting that one proton is coupled with single-electron transfer for each heme group of catalase in the electrode reaction. UV-Vis absorption spectroscopy demonstrated that catalase retained a near native conformation in PAM films at medium pH. The embedded catalase in PAM films showed the electrocatalytic activity toward dioxygen and hydrogen peroxide. Possible mechanism of catalytic reduction of H(2)O(2) at Cat-PAM film electrodes was proposed.     

Crystal structure of beta-cyclodextrin-dimethylsulfoxide inclusion complex

beta-Cyclodextrin (beta-CD) crystallizes from 27% DMSO-water as beta-CD.0.5DMSO.7.35H(2)O in the monoclinic space group P2(1) with unit cell constants: a=15.155(1), b=10.285(1), c=20.906(1) A, beta=109.86(1) degrees. Anisotropic refinement of 888 atomic parameters against 9,127 X-ray diffraction data converged at an R-factor of 0.055. The beta-CD macrocycle adopts a 'round' conformation stabilized by intramolecular, interglucose O-3(n) triplebond O-2(n+1) hydrogen bonds. In the beta-CD cavity, DMSO, water sites W-1, W-3 (occupancies 0.5, 0.25, 0.75) are not located concurrently with the water site W-2 because the interatomic distances to W-2 are too short (1.56-1.75 A). DMSO is placed in the beta-CD cavity such that its S-atom is shifted from the O-4 plane center to the beta-CD O-6-side ca. 0.9 A and the C-S bond which is inclined 13.6 degrees to the beta-CD molecular axis. It is maintained in position by hydrogen bonding to water site W-3 and the O-31-H group. 7.35 water molecules are extensively disordered in 13 positions both inside (W-1-W-4) and outside (W-5-W-13) the beta-CD cavity. They act as hydrogen bonding mediators contributing significantly to the stability of the crystal structure.     

Studies on adsorption of dyes on beta-cyclodextrin polymer

Beta-cyclodextrin (beta-CD) polymers are used for the removal of various dyes from aqueous solutions. Three insoluble polymers with different degrees of beta-CD were used. Results of adsorption experiments showed that these polymers exhibited high sorption capacities toward dyes. The mechanism of adsorption was both physical adsorption and hydrogen bonding due to the polymer and the formation of an inclusion complex due to the beta-CD molecules through host-guest interactions.     

A new crystal form of beta-cyclodextrin-ethanol inclusion complex: channel-type structure without long guest molecules

A new crystal form of beta-cyclodextrin (beta-CD)[bond]ethanol[bond]dodecahydrate inclusion complex [(C(6)H(10)O(5))(7).0.3C(2)H(5)OH.12H(2)O] belongs to monoclinic space group C2 (form II) with unit cell constants a=19.292(1), b=24.691(1), c=15.884(1) A, beta=109.35(1) degrees. The beta-CD macrocycle is more circular than that of the complex in space group P2(1) [form I: J. Am. Chem. Soc. 113 (1991) 5676]. In form II, a disordered ethanol molecule (occupancy 0.3) is placed in the upper part of beta-CD cavity (above the O-4 plane) and is sustained by hydrogen bonding to water site W-2. In form I, an ethanol molecule located below the O-4-plane is well ordered because it hydrogen bonds to surrounding O-3[bond]H, O-6[bond]H groups of the symmetry-related beta-CD molecules. In the crystal lattice of form I, beta-CD macrocycles are stacked in a typical herringbone cage structure. By contrast, the packing structure of form II is a head-to-head channel that is stabilized at both O-2/O-3 and O-6 sides of each beta-CD by direct O(CD)...O(CD) and indirect O(CD)...O(W)...(O(W))...O(CD) hydrogen bonds. The 12 water molecules are disordered in 18 positions both inside the channel-like cavity of beta-CD dimer (W-1[bond]W-6) and in the interstices between the beta-CD macrocycles (W-7[bond]W-18). The latter forms a cluster that is hydrogen bonded together and to the neighboring beta-CD O[bond]H groups.     

Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme

The effects of various metal ions on cleavage activity and global folding have been studied in the extended Schistosoma hammerhead ribozyme. Fluorescence resonance energy transfer was used to probe global folding as a function of various monovalent and divalent metal ions in this ribozyme. The divalent metals ions Ca²⁺, Mg²⁺, Mn²⁺, and Sr²⁺ have a relatively small variation (less than sixfold) in their ability to globally fold the hammerhead ribozyme, which contrasts with the very large difference (>10,000-fold) in apparent rate constants for cleavage for these divalent metal ions in single-turnover kinetic experiments. There is still a very large range (>4600-fold) in the apparent rate constants for cleavage for these divalent metal ions measured in high salt (2 M NaCl) conditions where the ribozyme is globally folded. These results demonstrate that the identity of the divalent metal ion has little effect on global folding of the Schistosoma hammerhead ribozyme, whereas it has a very large effect on the cleavage kinetics. Mechanisms by which the identity of the divalent metal ion can have such a large effect on cleavage activity in the Schistosoma hammerhead ribozyme are discussed.