Biomedical subjects

Yizhuang Xu

Publications and source records attributed to Yizhuang Xu.

10 recordsLinked to original sources

PubMed2006

PASA--a program for automated protein NMR backbone signal assignment by pattern-filtering approach.

We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13Calpha and/or 13Cbeta chemical shift matching. The pattern filter employs one or multiple constraints such as 13Calpha/Cbeta chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics.

Algorithms↗

PubMed2005

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to lanthanum and erbium ions.

Lanthanide ions and erythritol form metal-alditol complexes with various structures. Lanthanum nitrate and erbium chloride coordinate to erythritol to give new coordination structures. The lanthanum nitrate-erythritol complex (LaEN), 2La(NO3)3.C4H10O(4).8H2O, La3+ exhibits the coordination number of 11 (namely 11 polar atoms bound to one lanthanum) and is 11-coordinated to two hydroxyl groups from one erythritol molecule, six oxygen atoms from three nitrate ions and three water molecules. One erythritol molecule is coordinated to two La3+ ions and links the two metal ions together. The ratio of M:L is 2:1. The erbium chloride-erythritol complex (ErE), ErCl2.C4H9O(4).2C2H5OH was obtained from ErCl3 and erythritol in aqueous ethanol solution and the structure shows that deprotonation reaction occurs in the reaction process. The Er3+ cation is 8-coordinated with three hydroxyl groups of one erythritol molecule, two hydroxyl groups from another erythritol molecule, two ethanol molecules, and one chloride ion. Erythritol provides its three hydroxyl groups to one erbium cation and two hydroxyl groups to another erbium cation, that is, one hydroxyl group is coordinated to two metal ions and therefore loses its hydrogen atom and becomes a oxygen bridge. Another chloride ion is hydrogen bonded in the structure. The results indicate the complexity of metal-sugar coordination.

Crystallization↗

PubMed2005

New, rapid fluorescence stain method for histologic sections using lanthanide complexes.

A new stain method for histologic sections different from traditional hematoxylin and eosin (H&E) methodology used two newly developed stain reagents from the lanthanide series, the antibiotic ofloxacin chelate of europium(III) and the ciprofloxacin hydrochloride chelate of terbium(III), exhibiting excellent fluorescence. These complexes are unique due to their nontoxicity, attractive fluorescent properties, rapid staining, and high water solubility. In this article, we focus on the interactions between biomolecules and synthesized lanthanide complexes and on the staining effect applied for tissue staining.

Ciprofloxacin↗

PubMed2005

FT-IR spectroscopic study on the variations of molecular structures of some carboxyl acids induced by free electron laser.

Free electron laser has been developed as tunable lasers over a wide range of wavelengths. Devices irradiating in the region of 6-16 microm (1666-625 cm-1) are operable in the Beijing free electron lasers facilities (BFEL). For understanding the interactions between FEL and biological tissues, in this study wavelength-selective infrared-induced structure changes of substances under irradiation by FEL were measured using FT-IR spectroscopy. The carboxyl acids and carboxylates samples investigated include salicylic acid, sulfosalicylic acid, cholic acid, deoxycholic acid, sodium cholate and sodium deoxycholate. The changes of the FT-IR spectra of the molecules prove that the spectral variations of the samples induced by FEL are closely related to their hydrogen bond networks.

Carboxylic Acids↗

PubMed2005

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to neodymium ion.

A single crystal of a coordinated complex of neutral erythritol (C4H10O4,E) with a neodymium ion, NdE(II), was synthesized and studied using FT-IR and X-ray diffraction analysis. In NdE(II) (NdCl3.2.5C4H10O4.C2H5OH) the Nd3+ coordinates with one chloride ion and eight OH groups from three erythritol molecules. There are two neodymium centers linked by one erythritol molecule with same coordination structure in the molecule. Two erythritol molecules provide 1,3,4-hydroxyl groups to coordinate with a neodymium ion; another erythritol molecule coordinates to two Nd ions via its 1,2-hydroxyl groups and 3,4-hydroxyl groups, respectively. The OH groups of erythritol act as ligand to coordinate to neodymium ions, and OH groups of erythritol form hydrogen bond networks that link chain and layer together to build three-dimensional structures. The ratio of metal to ligand is 1:2.5. The structure of NdE(II) is more complicated than the previously reported NdE(I), which is NdCl3.C4H10O4.6H2O; in NdE(I), Nd3+ is coordinated to four hydroxyl groups from two erythritol molecules, four water molecules and one chloride ion. The results indicate the complexity of metal-sugar interaction.

Journal Article↗

PubMed2004

Complexation of trivalent lanthanide cations by erythritol in the solid state. The crystal structure and FT-IR study of 2EuCl3.2C4H10O4.7H2O.

Erythritol was chosen to study the interactions between metal ions and carbohydrates. FTIR spectroscopy results indicate that a EuCl3-erythritol complex different from a previously reported one was obtained. The crystal structure of EuCl3-erythritol complex, 2EuCl3.2C4H10O4.7H2O, Mr=443.49, a=13.846(3) A , b=7.4983(15) A, c=14.140(3) A, beta=116.39(3) degrees, V=1315.1(5) A(3), Z=4, mu=5.394 mm(-1) and R=0.0395 for 2965 observed reflections and 143 parameters, was determined. Characteristic of this complex is the presence of binuclear europium ions with different coordination structures. One Eu3+ ion is nine-coordinated, with five Eu-O bonds from water molecules, and four from hydroxyl groups of two erythritol molecules and another Eu3+ is eight-coordinated with two water molecules, two chloride ions, and four hydroxyl groups from two erythritol molecules. Erythritol provides two hydroxyl groups to one lanthanide ion and the other two to another rare earth ion. The OH, CO stretching and other vibrations are shifted in the IR spectra of the complexes and the results are consistent with the crystal structure.

Cations↗

PubMed2004

Interactions between metal ions and carbohydrates: the coordination behavior of neutral erythritol to transition metal ions.

The single crystals of coordinated complexes of neutral erythritol (C4H10O4) with various transition metal ions were synthesized and studied using FT-IR and single crystal X-ray diffraction analysis. Two CuCl2-erythritol complexes (denoted as CuE(I) and CuE(II)) were obtained. In CuE(I), Cu2+ coordinates with two chloride ions and four OH groups from two erythritol molecules. Two copper centers are linked by one erythritol molecule to form a zigzag chain. For CuE(II), each Cu2+ coordinates with two OH groups from an erythritol molecule and two chloride ions. The crystal of CuE(II) contains complexed and free erythritol, the dimers of [Cu2Cl4(C4H10O4)] further form a [Cu2Cl4(C4H10O4)]infinity chain via secondary Cu...Cl bonds, both the dimer unit of [Cu2Cl4.(C4H10O4)] and non-coordinated C4H10O4 unit exist side by side in the crystal. MnCl2-erythritol complex whose structure is similar to CuE(I) is also acquired. The OH groups of erythritol act as ligand to coordinate to metal ions on one hand, one the other hand, OH groups form hydrogen bonds network that link chain and layer together to build three-dimensional structures.

Carbohydrates↗

PubMed2004

Interactions between metal ions and carbohydrates: the coordination behavior of neutral erythritol to zinc and europium nitrate.

The single crystals of coordinated complexes of neutral erythritol (C4H10O4) with zinc nitrate and europium nitrate were synthesized and studied using FT-IR and single crystal X-ray diffraction analysis. In the structure of Zn(NO3)2.C4H10O4, ZnEN (E denotes erythritol, N represents nitrate), Zn2+ is coordinated to four hydroxyl groups from two erythritol molecules and two oxygen atoms from two nitrates. Two Zn2+ are connected by one erythritol molecule to form Zn(C4H10O4)(NO3)2 chain, and layers formed by above chain pile to produce 3D structures. In the structure of Eu(NO3)3.C4H10O4.C2H5OH, EuEN, Eu3+ is 10-coordinated by six oxygen atoms from three nitrate ions, three hydroxyl groups from one erythritol molecule and one hydroxyl group from ethanol. In the above erythritol complexes, two hydroxyl groups of erythritol coordinate to one metal ion and the other two to another metal ion or erythritol acts as three-hydroxyl groups donor. The OH groups of erythritol act as ligand to coordinate to metal ions on one hand, one the other hand, OH groups form hydrogen bonds network to build three-dimensional structures.

Journal Article↗

PubMed2003

Interactions between metal ions and carbohydrates. Coordination behavior of neutral erythritol to Ca(II) and lanthanide ions.

The study of the sugar-metal ion interactions remains one of the main objectives of carbohydrate coordination chemistry because the interactions between metal ions and carbohydrates are involved in many biochemical processes. This paper presents a comparison of coordination structures of erythritol with alkaline-earth-metal and lanthanide chloride and nitrate in the solid state using FT-IR and X-ray diffraction. Neutral, nondeprotonated erythritol (E) reacts with CaCl(2) to give three CaCl(2)(-)erythritol (CaE(I), CaE(II), CaE(III)) complexes, showing that three of the five general features of calcium-carbohydrate complexes deduced in the reference encounter contrary examples. Different coordination structures have been observed for calcium and lanthanide chloride and nitrates. The coordination of carbohydrates to metal ions is complicated, and erythritol, chloride ions, nitrates, water molecules, and ethanol (crystallization medium and reaction solvents) have the chance to coordinate to metal ions. IR spectral results show that different lanthanide ions, from LaCl(3) to TbCl(3), have similar coordination structures with erythritol. The results show that erythritol can act as two bidentate neutral ligands (CaE(I), CaE(II), CaE(III), CaEN, PrE, NdE) or as a three-hydroxyl donor (NdEN). The IR results are consistent with the crystal structures.

Calcium↗

PubMed2002

A new mechanism of Raman enhancement and its application.

Strong electronic Raman bands corresponding to the transition between 4I9/2 and 4I11/2 manifolds of Nd3+, caused by a Raman-enhancement effect, are observed in the FT-Raman spectrum of Nd2O3. Neither resonance enhancement (RR) nor surface enhancement (SERS) accounts for the Raman enhancement observed here. We propose a new mechanism of Raman enhancement called the "feed-back" mechanism. A YAG laser excites the final state of the Raman transition (4I11/2 of Nd3+) to the 4F3/2 state and causes a significant decrease in the population of Nd3+ at the 4I11/2 state. This causes the population ratio of Nd3+ at 4I9/2 and 4I11/2 to deviate from the value required by Boltzmann's law. To restore equilibrium, Raman scattering is enhanced so that more Nd3+ ions are brought from the 4I9/2 state to the 4I11/2 state. This hypothesis gets support from the temperature-variable FT-Raman spectroscopic results. Additionally, obvious differences between the Stokes and anti-Stokes Raman spectrum of Nd3+ provide further evidence to support the feed-back mechanism. The Raman-enhancement effect confers on the electronic Raman bands a special ability to reflect the variation of coordinated structure around metal ions. The structural variations in polymer-metal ion composites and biomineralization systems have been investigated by using the electronic Raman bands.

Journal Article↗