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Biomedical subjects

Guang Wu

Publications and source records attributed to Guang Wu.

13 recordsLinked to original sources
PubMed2003

Investigation of Zr-C, Zr-N, and potential agostic interactions in an organozirconium complex by experimental electron density analysis.

The crystal structure and electron density (ED) distribution of an imine coupling product with an open zirconocene, Zr(2,4-C(7)H(11))[(i-Pr)NCHPhCH(2)CMe=CHCMe=CH(2)] (C(7)H(11) = dimethylpentadienyl), have been derived from accurate synchrotron X-ray diffraction measurements. The molecular structure reveals asymmetric coordination of Zr by the pentadienyl (2,4-C(7)H(11)) ligand ( = 2.56(6) A), the butadiene fragment ( = 2.43(5) A), and the amide nitrogen atom (Zr-N = 2.0312(5) A) of the second ligand. The study of the ED and its topological analysis affords new insight into the bonding and electronic structure of the title zirconium complex. The interactions between the metal center and the ligands are represented by a Zr-N bond path and one Zr-C bond path with each of the pentadienyl and butadiene moieties, contrary to the usually depicted global metal-ligand bonding. The butadiene and pentadienyl groups exhibit a polarization of the corresponding pi-like ED in the C-Zr directions, indicating that the whole conjugated systems are nonetheless involved. The 4d atomic orbitals of Zr exhibit unusual populations according to ligand field considerations, which reveal a high degree of sigma-donation from the conjugated pi systems of both ligands. As deduced from numerical integration over the topologically defined atomic basins, the Zr to ligand charge transfer is 1.48 e to the C(17)NH(24) ligand and 0.68 e to dimethylpentadienyl. Topological analysis of a short intramolecular Zr.(C,H) contact provides no indication of the presence of agostic interactions, despite a small Zr-N-C angle of 102.87(4) degrees. Thus, no bond path and BCP (bond critical point) of the ED are found in the Zr.(C,H) region, which would have provided evidence for such direct interactions, nor is there any evidence for charge accumulation between the Zr and H atoms, or for lengthening of the C-H bond involved in the putative interaction. These characteristics, similar to those in other distorted situations, may be common for other electron-deficient d(0) complexes.

Journal Article↗
PubMed2003

Analysis of amino acid pairs sensitive to variants in human collagen alpha5(IV) chain precursor by means of a random approach.

In this data-based theoretical analysis, we use the random approach to analyze the amino acid pairs in 5(IV) chain precursor (CA54) in order to determine which amino acid pairs are more sensitive to 151 variants from missense mutant human CA54 protein. The rationale of this study is based on our hypothesis and previous findings that harmful variance is more likely to occur at randomly unpredictable amino acid pair position rather than at randomly predictable positions. This is reasonable to argue as randomly predictable amino acid pairs are less likely to be deliberately evolved, whereas randomly unpredictable amino acid pairs are probably deliberately evolved in connection with protein function. The results show that all 151 variants occurred at randomly unpredictable amino acid pairs and the chance of a variant occurring is markedly higher in randomly unpredictable amino acid pairs than in predictable pairs. Thus, randomly unpredictable amino acid pairs are more sensitive to variance in human CA54. The results also suggest that the human CA54 protein has a natural tendency towards variants.

Amino Acids↗
PubMed2003

Determination of amino acid pairs sensitive to variants in human beta-glucocerebrosidase by means of a random approach.

In this data-based theoretical analysis, we use the random approach to analyse the amino acid pairs in human beta-glucocerebrosidase in order to determine which amino acid pairs are more sensitive to 109 variants from missense mutant human glucocerebrosidase. The rationale of this study is based on our hypothesis and findings that the harmful variants are more likely to occur at randomly unpredictable amino acid pairs and the non-harmful variants are more likely to occur at randomly predictable amino acid pairs. This is because we argue that the randomly predictable amino acid pairs should not be deliberately evolved, whereas the randomly unpredictable amino acid pairs should be deliberately evolved with connection of protein function. The results show, for example, that 93.58% of 109 variants occur at randomly unpredictable amino acid pairs, which account for 71.40% of amino acid pairs in glucocerebrosidase, and the chance of occurrence of the variant is about 4.4 times higher in randomly unpredictable amino acid pairs than in predictable pairs. Hence the randomly unpredictable amino acid pairs are more sensitive to variants in human glucocerebrosidase. The results also suggest that human glucocerebrosidase has a natural tendency to variants.

Amino Acids↗
PubMed2002

Application of charge density methods to a protein model compound: calculation of Coulombic intermolecular interaction energies from the experimental charge density.

A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6-31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2-3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.

Biophysical Phenomena↗
PubMed2002

Excited-state structure by time-resolved X-ray diffraction.

X-ray crystallography has traditionally been limited to the study of the ground-state structure of molecules and solids. Recent technical advances are removing this limitation as demonstrated here by a time-resolved stroboscopic study of the photo-induced 50 micros lifetime excited triplet state of the [Pt(2)(pop)(4)](4-)ion [pop = pyrophosphate, (H(2)P(2)O(5))(2-)], performed at helium temperatures with synchrotron radiation. The shortening of the Pt-Pt bond by 0.28(9)A upon excitation is compatible with the proposed mechanism involving promotion of a Pt-Pt antibonding dsigma* electron to a weakly bonding p orbital. The contraction is accompanied by a 3 degree molecular rotation. The time-resolved diffraction technique described here is applicable to reversible light-driven processes in the crystalline solid state.

Journal Article↗
PubMed2002

Analysis of distributions of amino acids in the primary structure of tumor suppressor p53 family according to the random mechanism.

It is well known that the evolutionary process leads to the majority of amino acids clustering in some regions rather than being homogenously distributed along a protein. Among numerous factors affecting the evolutionary process is chance, whose impact therefore should be present in a protein primary structure. The issue of how to measure the random distribution of amino acids in a primary structure is of importance for the understanding of protein structure and functions. In this study, we use the random principle as a tool to analyze and compare the distributions of amino acids in the primary structure of the p53 protein family. The results, for example, show that the amino acids are distributed more randomly in mouse p53 and less randomly in common tree shrew p53, the distribution ranks of amino acids are relatively lower in the functional regions (about 0.5 on average) than in the whole sequences (about 1.2 on average) except for mouse p53. From the probabilistic distribution view, the composition of human p53 is relatively stable in the functional regions rather than in the whole sequence, which may suggest one of the potential effects on the mutations inducing human cancers. In general, we can use the distribution probability to present quantitatively a type of distribution of amino acids in a protein, to compare quantitatively the magnitude of clusters between different proteins and to track the effect of chance on the evolutionary process.

Amino Acids↗
PubMed2002

Estimation of amino acid pairs sensitive to variants in human phenylalanine hydroxylase protein by means of a random approach.

In this data-based theoretical analysis, we use a random approach to estimate amino acid pairs in human phenylalanine 4-hydroxylase (PAH) protein in order to determine which amino acid pairs are more sensitive to 187 variants in human PAH protein. The rationale of this study is based on our hypothesis and previous findings that the harmful variants are more likely to occur at randomly unpredictable amino acid pairs rather than at randomly predictable pairs. This is reasonable to argue as randomly predictable amino acid pairs are less likely to be deliberately evolved, whereas randomly unpredictable amino acid pairs are probably deliberately evolved in connection with protein function. 94.12% of 187 variants occurred at randomly unpredictable amino acid pairs, which accounted for 71.84% of 451 amino acid pairs in human PAH protein. The chance of a variant occurring is five times higher in randomly unpredictable amino acid pairs than in predictable pairs. Thus, randomly unpredictable amino acid pairs are more sensitive to variance in human PAH protein. The results also suggest that the human PAH protein has a natural tendency towards variants.

Amino Acids↗
PubMed1998

Multitemperature Resonance-Diffraction and Structural Study of the Mixed-Valence Complex [Fe(3)O(OOCC(CH(3))(3))(6)(C(5)H(5)N)(3)].

The Fe-O and Fe-N bond lengths at two iron sites of the mixed-valence complex [Fe(3)O(OOCC(CH(3))(3))(6)(C(5)H(5)N)(3)] show a pronounced temperature dependence; the bonds from two of the Fe atoms to the central oxygen atoms vary by more than 0.10 Å on cooling to 10 K whereas the bond from the third iron atom is essentially invariant. The variation is such that the longest Fe-O bonds at ambient temperature are the shorter ones at 10 K, with the crossover occurring at about 90 K. The bonds to the axial pyridine ligand show the opposite dependence. The variation is attributed to an equilibrium between different configurations, which interconvert through vibronic coupling, a process that involves electron transfer between the metal atoms. The position of the absorption edge for each of the iron atoms has been determined by resonance-diffraction experiments at the Fe K edge, performed at four different temperatures. At each temperature, the order of the absorption edges corresponds to that of the experimentally determined bond lengths. The crossover near 90 K is confirmed by the resonance experiments. The absorption-edge positions are related to the formal oxidation state by calibration with reference complexes of known oxidation state. The experiments demonstrate the close relation between the changes in coordination geometry and the oxidation states of the iron atoms.

Journal Article↗
PubMed1998

A multilayer recurrent neural network for solving continuous-time algebraic Riccati equations.

A multilayer recurrent neural network is proposed for solving continuous-time algebraic matrix Riccati equations in real time. The proposed recurrent neural network consists of four bidirectionally connected layers. Each layer consists of an array of neurons. The proposed recurrent neural network is shown to be capable of solving algebraic Riccati equations and synthesizing linear-quadratic control systems in real time. Analytical results on stability of the recurrent neural network and solvability of algebraic Riccati equations by use of the recurrent neural network are discussed. The operating characteristics of the recurrent neural network are also demonstrated through three illustrative examples.

Journal Article↗
PubMedDate not supplied

Squared correlation coefficient of measured values versus predicted values in linear and monoexponential regressions.

The correlation coefficient of measured values vs predicted values is widely used in pharmacokinetic and biopharmaceutical settings. When using linear and monoexponential regressions, we notice an interesting characteristic of the squared correlation coefficient of measured values vs predicted values, i.e. the squared correlation coefficient of measured y1 vs predicted (lambda)y2 is a constant regardless of different values of regression coefficients and is equal to the squared correlation coefficient of measured x1 vs measured y1.

Forecasting↗
PubMedDate not supplied

An extremely strange observation on the equations for calculation of correlation coefficient.

Various equations are used to calculate the correlation coefficient, these equations are presumed equally. However we find the extraordinary results when using r = square root of ((sigma(ŷi - y)2) / (sigma(yi - y)2)) and r2 = (sigma(yi - y)2 - sigma(yi - ŷi)2) / (sigma(yi - y)2) to calculate the correlation coefficient, for example, a line within 95% confidence band of a regressed line. The results are so extraordinary that we do not know whether or not we can still call the results as correlation coefficient, however we are sure that these results need to be presented.

Linear Models↗
PubMedDate not supplied

Calculation of steady-state distribution delay between central and peripheral compartments in two-compartment models with infusion regimen.

A lag time may exist between blood drug concentration and drug effect. Various factors can contribute to the lag time, among which the drug distribution delay is a significant one. The drug distribution delay can also exist between different compartments. An equation was derived to calculate the steady-state drug concentration delay between central and peripheral compartments in a two-compartment model with infusion regimen.

Algorithms↗