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PubMed2002

Molecular visualization of immunoglobulin switch region RNA/DNA complex by atomic force microscope.

Immunoglobulin heavy-chain (IgH) class switch recombination (CSR) is initiated by DNA breakage in the switch (S) region featuring tandem repetitive nucleotide sequences. Various studies have demonstrated that S-region transcription and splicing proceed to genomic recombination and are indispensable for CSR in vivo, although the precise molecular mechanism is largely unknown. Here, we show the novel physical property of the in vitro transcribed S-region RNA by direct visualization using an atomic force microscope (AFM). The S-region sense RNA, but not the antisense RNA, forms a persistent hybrid with the template plasmid DNA and changes the plasmid conformation from supercoil to open circle in the presence of spermidine. In addition, the S-region transcripts generate globular forms and are assembled on the template DNA into a large aggregate that may stall replication and increase the recombinogenicity of the S-region DNA.

Immunoglobulin Class Switching↗
PubMed2001

Decomposition of alkyl-substituted urea molecules at a hydroxide-bridged dinickel center.

The interactions between N-methylurea, N,N'-dimethylurea, N,N-dimethylurea, tetramethylurea, and thiourea and the hydroxide-bridged dinickel complex [Ni(2)(mu-OH)(mu-H2O)(bdptz)(H2O2](OTs)(3) were investigated. Structural characterization of [Ni(2)(mu-OH)(mu-H2O)(bdptz)(Me-urea)(CH3CN)](ClO4)(3) (1) and [Ni(2)(mu-OH)(mu-H2O)(bdptz)(thiourea)(CH3CN)](ClO4)(3) (2) provided insight into the interactions of the substrates with the dinickel center. In 1, the methylurea molecule coordinates to the dinickel complex through its carbonyl oxygen atom. Complex 2 has a similar geometry, with the thiourea molecule bound to a nickel ion through its sulfur atom. When the urea substrates are heated in the presence of the hydroxide-bridged dinickel complex, N-methylurea and N,N-dimethylurea react to form methylammonium cyanate and dimethylammonium cyanate, respectively. After long reaction times, thiourea reacts similarly, producing ammonium thiocyanate. The other substrates are unreactive. These results indicate that the dinickel complex promotes the elimination of alkylamines from urea substrates to form cyanate but cannot effect the direct hydrolysis of such substrates.

Alkanes↗
PubMedDate not supplied

Formation and characterization of two-dimensional crystals of photosystem II.

Photosystem II (PS II), a eukaryotic photosynthetic reaction center which converts solar energy to chemical energy, is also capable of evolving oxygen, making it uniquely important for our biosphere. We report the formation of two-dimensional crystals of the PS II complex. The crystals were tubular, approximately 0.2 by 1-2 microns. Characterization of the crystals by gel electrophoresis, immunoblotting, and absorption spectroscopy suggested that the crystals contain PS II exclusively, with no other protein complexes. Atomic force microscopy revealed that the complexes were closely packed, suggesting that the process of crystallization involves partial removal of lipid from the membrane. The structure of the complex was investigated using low-dose electron microscopy and image analysis. A projection map at 1.7 nm resolution was produced. The unit cell was 11.5 x 16.1 nm and consisted of two monomeric units arranged around a central cavity to form a dimer. Volume calculations suggested that each dimer consisted of two PS II complexes. The monomeric unit, which appears to be a single PS II complex, had four areas of density. The gap between the two PS II complexes was quite small, indicating that there may be a functional connection between the two halves of the dimer.

Crystallization↗
PubMed2002

Nickel(II) complexes with tetra- and pentadentate aminopyridine ligands: synthesis, structure, electrochemistry, and reduction to nickel(I) species.

A series of nickel(II) complexes with polydentate aminopyridine ligands N,N,N'-tris-[2-(2'-pyridyl)ethyl]ethane-1,2-diamine (L1), N,N,N'-tris-[2-(2'-pyridyl)ethyl]-N'-methylethane-1,2-diamine (L2), and N,N'-bis-[2-(2'-pyridyl)ethyl]-N,N'-dimethylethane-1,2-diamine (L3) were synthesized and characterized by elemental analysis and spectroscopic methods. Single-crystal X-ray diffraction studies showed that the Ni(II) ions have five-coordinate square-pyramidal geometry in [NiL2](ClO(4))(2), similar to that previously found in [NiL1](ClO(4))(2) x CH(3)NO(2) (Hoskins, B. F.; Whillans, F. D.J. Chem. Soc., Dalton Trans. 1975, 657), and square-planar geometry in [NiL3](ClO(4))(2). All three nickel(II) complexes are reduced by sodium borohydride or sodium amalgam in organic solvents to nickel(I) species, which were identified by highly anisotropic EPR spectra at 100 K: g(1) = 2.239, g(2) = 2.199, and g(3) = 2.025 for [NiL1](+); g(axially) = 2.324 and g(radially) = 2.079 for [NiL2](+) and [NiL3](+). Cyclic voltammetry of the nickel(II) complexes in acetonitrile exhibited reversible reduction waves at -1.01 V for [NiL1](2+), -0.91 V for [NiL2](2+), and -0.83 V for [NiL3](2+) versus SCE, potentials which are significantly less negative than those of most previously characterized Ni(II) complexes with nitrogen-only donor atoms. Complexes [NiL1](2+) and [NiL2](2+) showed high catalytic activity in the electroreduction of 1,2-trans-dibromocyclohexane to cyclohexene.

Aminopyridines↗
PubMed1987

Crystal structure of hexagonal MnAl(4).

A structure is proposed for the hexagonal form of MnAl(4), with a(H) = 28.4 A and c(H) = 12.43 A, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-A cubic structure of MnAl(4) and to the 14.19-A cubic structure of Mg(32)(Al,Zn)(49).

Journal Article↗
PubMed1990

Atomic structure of the actin:DNase I complex.

The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined by X-ray analysis at an effective resolution of 2.8 A and 3A, respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the beta- or beta- and gamma-phosphates, respectively. The motif of a five-stranded beta sheet consisting of a beta meander and a right handed beta alpha beta unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.

Actins↗
PubMed2001

Complexes of Li atoms with formaldehyde (LiOCH2) and formaldimine (LiNHCH2): stability via electrostatic and charge transfer interactions.

The Li atom adducts of formaldehyde (LiOCH2) and formaldimine (LiNHCH2) are produced in the gas phase by neutralization of the corresponding cations. Subsequent reionization, ca. 0.3 micros later, shows that the nominally hypervalent complexes LiXCH2 (X=O or NH) are stable, residing in potential energy minima. In the time span between the neutralization and reionization events, the LiXCH2 molecules dissociate partly into their constituents, Li + XCH2, the fragmentation extent of LiNHCH2 being more extensive. Ab initio calculations reveal three bound states for both Li atom complexes. Two (states A and B) resemble C-centered radicals carrying an ion pair, Li+*(-)X-CH2*, and can be viewed as lithiated derivatives of the hydroxymethyl (HOCH2*) or aminomethyl (H2NCH2*) radical; the third state (C) represents a conventional, electrostatically bonded Li-X=CH2 complex with an essentially intact X=C double bond and the unpaired electron located at the metal atom. States A and B are bound more strongly than state C for LiOCH2; the opposite is true for LiNHCH2, where C is the most stable arrangement and B only marginally bound. The larger degree of dissociation observed for LiNHCH2 vis à vis LiOCH2 upon neutralization-reionization points out that the experiment samples a considerable amount of state B which is barely bound for LiNHCH2.

Journal Article↗
PubMed2006

X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases.

Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing non-hydrolysable analogues of the scissile peptide bond. Until recent years, the positions of protons on the catalytic aspartates and the ligand in these complexes had not been determined with certainty due to the inadequate resolution of these analyses. There has been much interest in locating the catalytic protons at the active site of aspartic proteinases since this has major implications for detailed understanding of the mechanism of action and the design of improved transition state mimics for therapeutic applications. In this review we discuss the results of studies which have shed light on the locations of protons at the catalytic centre. The first direct determination of the proton positions stemmed from neutron diffraction data collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex at a resolution of 2.1 A provided evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. Atomic resolution X-ray studies of inhibitor complexes have corroborated this finding. A similar study of the native enzyme established that it, unexpectedly, has a dipeptide bound at the catalytic site which is consistent with classical reports of inhibition by short peptides and the ability of pepsins to catalyse transpeptidation reactions. Studies by NMR have confirmed the findings of low-barrier and single-well hydrogen bonds in the complexes with transition state analogues.

Aspartic Acid↗
PubMed2005

Subtle reactivity patterns of non-heteroatom-substituted manganese alkynyl carbene complexes in the presence of phosphorus probes.

The non-heteroatom-substituted manganese alkynyl carbene complexes (eta5-MeC5H4)(CO)2Mn=C(R)C[triple bond]CR'(3; 3a: R = R'= Ph, 3b: R = Ph, R'= Tol, 3c: R = Tol, R'= Ph) have been synthesised in high yields upon treatment of the corresponding carbyne complexes [eta5-MeC5H4)(CO)2Mn[triple bond]CR][BPh4]([2][BPh4]) with the appropriate alkynyllithium reagents LiC[triple bond]CR' (R'= Ph, Tol). The use of tetraphenylborate as counter anion associated with the cationic carbyne complexes has been decisive. The X-ray structures of (eta5-MeC5H4)(CO)2Mn=C(Tol)C[triple bond]CPh (3c), and its precursor [(eta5-MeC5H4)(CO)2Mn=CTol][BPh4]([2b](BPh4]) are reported. The reactivity of complexes toward phosphines has been investigated. In the presence of PPh3, complexes act as a Michael acceptor to afford the zwitterionic sigma-allenylphosphonium complexes (eta5-MeC5H4)(CO)2MnC(R)=C=C(PPh3)R' (5) resulting from nucleophilic attack by the phosphine on the remote alkynyl carbon atom. Complexes 5 exhibit a dynamic process in solution, which has been rationalized in terms of a fast [NMR time-scale] rotation of the allene substituents around the allene axis; metrical features within the X-ray structure of (eta5-MeC5H4)(CO)2MnC(Ph)=C=C(PPh3)Tol (5b) support the proposal. In the presence of PMe3, complexes undergo a nucleophilic attack on the carbene carbon atom to give zwitterionic sigma-propargylphosphonium complexes (eta5-MeC5H4)(CO)2MnC(R)(PMe3)C[triple bond]CR' (6). Complexes 6 readily isomerise in solution to give the sigma-allenylphosphonium complexes (eta5-MeC5H4)(CO)2MnC(R')=C=C(PMe3)R (7) through a 1,3 shift of the [(eta5-MeC5H4)(CO)2Mn] fragment. The nucleophilic attack of PPh2Me on 3 is not selective and leads to a mixture of the sigma-propargylphosphonium complexes (eta5-MeC5H4)(CO)2MnC(R)(PPh(2)Me)C[triple bond]CR' (9) and the sigma-allenylphosphonium complexes (eta5-MeC5H4)(CO)2MnC(R)=C=C(PPh(2)Me)R' (10). Like complexes 6, complexes 9 readily isomerize to give the sigma-allenylphosphonium complexes (eta5-MeC5H4)(CO)2MnC(R')=C=C(PPh2Me)R'). Upon gentle heating, complexes 7, and mixtures of 10 and 10' cyclise to give the sigma-dihydrophospholium complexes (eta5-MeC5H4)(CO)2MnC=C(R')PMe2CH2CH(R)(8), and mixtures of complexes (eta5-MeC5H4)(CO)2MnC=C(Ph)PPh2CH2CH(Tol)(11) and (eta5-MeC5H4)(CO)2MnC=C(Tol)PMe2CH2CH(Ph)(11'), respectively. The reactions of complexes 3 with secondary phosphines HPR(1)(2)(R1= Ph, Cy) give a mixture of the eta2-allene complexes (eta5-MeC5H4)(CO)2Mn[eta2-{R(1)(2)PC(R)=C=C(R')H}](12), and the regioisomeric eta4-vinylketene complexes [eta5-MeC5H4)(CO)Mn[eta4-{R(1)(2)PC(R)=CHC(R')=C=O}](13) and (eta5-MeC5H4)(CO)Mn[eta4-{R(1)(2)PC(R')=CHC(R)=C=O}](13'). The solid-state structure of (eta5-MeC5H4)(CO)2Mn[eta2-{Ph2PC(Ph)=C=C(Tol)H}](12b) and (eta5-MeC5H4)(CO)Mn[eta4-{Cy2PC(Ph)=CHC(Ph)=C=O}](13d) are reported. Finally, a mechanism that may account for the formation of the species 12, 13, and 13' is proposed.

Journal Article↗
PubMed2002

Host-guest chemistry of the chromium-wheel complex [Cr8F8(tBuCO2)16]: prediction of inclusion capabilities by using an electrostatic potential distribution determined by modeling synchrotron X-ray structure factors at 16 K.

The structure and detailed electron density distribution (EDD) of the large octanuclear chromium-wheel host complex [Cr8F8(tBuCO2)16] (1) has been determined from synchrotron X-ray structure factors collected at 16(5) K. The complex has a central cavity with a minimum entry distance between carbon atoms of the pivalate methyl groups (pivalic acid = tBuCO2H) of 4.027(4) A on one side of the molecule and 7.273(4) A on the other. The screened side of the molecule can be "opened" by rotation of methyl groups to create a strained host structure, which is compensated for by improved host-guest and host-solvent interaction. The EDD of the 272-atom complex (1144 e-) was determined by multipole modeling based on the experimental structure factors. 3d orbital populations on the Cr atoms and topological analysis of the EDD show that the covalent part of the metal-ligand interactions consists mainly of sigma donation from the ligands, but that overall the interactions are predominantly electrostatic. The electrostatic potential (EP) has been calculated from the experimental EDD. Knowledge of the geometry of the naked complex 1 as well as the EP in the central cavity of this molecule allows us to deduce which characteristic properties guest molecules must have to be accepted into the void. To probe these predictions, a series of complexes of 1 with different guest inclusions were synthesized (2 = 1 + N,N'-dimethylformamide (DMF), 3 = 1 + N,N'-dimethylacetamide (DMA), 4 = 1 + DMA + DMF, 5 = 1 + 2CH3CN), and their structures were examined by using X-ray diffraction data measured at 120(1) K. Results of these studies indicate that in the crystalline state, the optimal guest molecule should be linear and possess a permanent dipole. Attempts to crystallize the host complex with cations incorporated into the cavity were fruitless, although electrospray ionization mass spectrometry showed that a [1 + potassium]+ entity pre-exists in solution and can be transferred intact into the gas phase.

Journal Article↗
PubMed1999

Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)-binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy.

Yeast centromeric DNA (CEN DNA) binding factor 3 (CBF3) is a multisubunit protein complex that binds to the essential CDEIII element in CEN DNA. The four CBF3 proteins are required for accurate chromosome segregation and are considered to be core components of the yeast kinetochore. We have examined the structure of the CBF3-CEN DNA complex by atomic force microscopy. Assembly of CBF3-CEN DNA complexes was performed by combining purified CBF3 proteins with a DNA fragment that includes the CEN region from yeast chromosome III. Atomic force microscopy images showed DNA molecules with attached globular bodies. The contour length of the DNA containing the complex is approximately 9% shorter than the DNA alone, suggesting some winding of DNA within the complex. The measured location of the single binding site indicates that the complex is located asymmetrically to the right of CDEIII extending away from CDEI and CDEII, which is consistent with previous data. The CEN DNA is bent approximately 55 degrees at the site of complex formation. A significant fraction of the complexes are linked in pairs, showing three to four DNA arms, with molecular volumes approximately three times the mean volumes of two-armed complexes. These multi-armed complexes indicate that CBF3 can bind two DNA molecules together in vitro and, thus, may be involved in holding together chromatid pairs during mitosis.

Centromere↗
PubMed2000

RecA-double stranded DNA complexes studied by atomic force microscopy.

RecA-double stranded (ds) DNA complexes have been studied by atomic force microscopy (AFM). When the complexes were prepared in the presence of ATP gamma S, fully covered RecA-dsDNA filaments were observed by AFM. When the concentration of RecA proteins was lower, various lengths of filaments were found. The variation of the observed structures may directly reflect the real distribution of the intermediate complexes in the reaction mixture, as the mixture was simply deposited on a mica surface for AFM observation without special fixation or staining. The use of a carbon nanotube (CNT) AFM tip enabled high resolution to reveal the periodicity of RecA-dsDNA filaments. Our observations demonstrated the potential of the AFM method for the structural studies of the RecA-dsDNA complexes, especially their intermediate states.

Adenosine Triphosphate↗
PubMed1972

A study of heavy-light atom discrimination in bright-field electron microscopy using the computer.

The Z dependence of the phase angle of the complex atomic scattering amplitude can be used to separate the image due to the heavy atoms from that due to the light atoms of the object structure. The linear theory of image formation applied to a focus series of bright-field images leads to Schiske's formula for the calculation of the structure factor. A program system is described which uses this algorithm for computing both images from a set of digitized electron micrographs of a focus series of uranyl-stained DNA on a thin carbon film.

Carbon↗
PubMed2001

Biodegradability of ethylenediamine-based complexing agents.

Biological degradability of ethylenediamine derivatives depends on the type and number of substituents. The susceptibility to biodegradation decreases in the sequence of substituents -COCH3, -CH3, -C2H5, -CH2CH2OH, -CH2COOH and with polysubstitution. The biodegradability depends also on the kind and number of nitrogen atoms. Complexing agents with a single-nitrogen atom in the molecule (e.g. NTA) succumb relatively readily to biodegradation whereas, compounds with two or more tertiary amino groups are biologically highly stable and do not undergo biodegradation even in experiments with activated sludge adapted at an age of up to 30 days (EDTA, DTPA, PDTA, HEDTA). A lowering of the degree of substitution brings about an increased susceptibility to biodegradation. This holds, e.g., for replacement of tertiary amino groups with secondary ones; thus the symmetrically disubstituted ethylenediamine-N,N'-diacetic acid (EDDA) possesses still sufficient complexing ability while belonging already to the group of potentially degradable substances.

Biodegradation, Environmental↗
PubMed2005

Trapping and moving metal atoms with a six-leg molecule.

Putting to work a molecule able to collect and carry adatoms in a controlled way on a surface is a solution for fabricating atomic structures atom by atom. Investigations have shown that the interaction of an organic molecule with the surface of a metal can induce surface reconstruction down to the atomic scale. In this way, well-defined nanostructures such as chains of adatoms, atomic trenches and metal-ligand compounds have been formed. Moreover, the progress in manipulation techniques induced by a scanning tunnelling microscope (STM) has opened up the possibility of studying artificially built molecular-metal atomic scale structures, and allowed the atom-by-atom doping of a single C(60) molecule by picking up K atoms. The present work goes a step further and combines STM manipulation techniques with the ability of a molecule to assemble an atomic nanostructure. We present a well-designed six-leg single hexa-t-butyl-hexaphenylbenzene (HB-HPB) molecule, which collects and carries up to six copper adatoms on a Cu(111) surface when manipulated with a STM tip. The 'HB-HPB-Cu atoms' complex can be further manipulated, bringing its Cu freight to a predetermined position on the surface where the metal atoms can finally be released.

Benzene Derivatives↗
PubMed1999

DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy.

Specific and non-specific complexes of DNA and photolyase are visualised by atomic force microscopy. As a substrate for photolyase a 1150 bp DNA restriction fragment was UV-irradiated to produce damaged sites at random positions. Comparison with a 735 bp undamaged DNA fragment made it possible to separate populations of specific and non-specific photolyase complexes on the 1150 bp fragment, relieving the need for highly defined substrates. Thus it was possible to compare DNA bending for specific and non-specific interactions. Non-specific complexes show no significant bending but increased rigidity compared to naked DNA, whereas specific complexes show DNA bending of on average 36 degrees and higher flexibility. A model obtained by docking shows that photolyase can accommodate a 36 degrees bent DNA in the vicinity of the active site.

DNA↗