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Biomedical subjects

J C Xuan

Publications and source records attributed to J C Xuan.

6 recordsLinked to original sources
PubMed1994

Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases.

Ab initio molecular orbital calculations with the STO-3G and 4-31G basis sets are performed to study the geometries and interactions of natural and "novel" Watson-Crick base pairs, as well as some non-Watson-Crick base pairs. First the optimized geometries of bases are determined using the STO-3G basis set, and then for the base pairs with the STO-3G and 4-31G basis sets. Interaction energies of these base pairs are evaluated, and their relative stabilities are discussed. Hydrogen bond features, partial charges and dipole moments of the base pairs are described. The calculated stabilities are in reasonable agreement with the limited available experimental data from thermal melting studies. Hydrogen bond geometries at the 4-31G level are in good agreement with the crystal structure data. The order of relative stabilities is found to be: iG:iC > G:C > G:T* > rG:rC > A*:C > Am:U > tau:kappa > chi:kappa > G*:T > A:C* > A:U = A:T where, A*, T*, G* and C* are tautomers, iG and iC are iso-G and iso-C, Am is 2-amino adenine, chi is xanthosine, kappa is 2,4-diaminopyrimidine, tau is 7-methyl oxoformycin B, rG is modified guanine with substitutions at positions 5 and 7, and rC is modified cytosine with a substitution at position 6. Pairing strengths with modified bases may affect the efficiency of protein production.

Adenine↗
PubMed1992

Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers.

The crystal structure of the dodecamer, d(CGCIAATTCGCG), has been determined at 2.4 A resolution by molecular replacement, and refined to an R-factor of 0.174. The structure is isomorphous with that of the B-DNA dodecamer, d(CGCGAATTCGCG), in space group P2(1)2(1)2(1) with cell dimensions of a = 24.9, b = 40.4, and c = 66.4 A. The initial difference Fourier maps clearly indicated the presence of inosine instead of guanine. The structure was refined with 44 water molecules, and compared to the parent dodecamer. Overall the two structures are very similar, and the I:C forms Watson-Crick base pairs with similar hydrogen bond geometry to the G:C base pairs. The propeller twist angle is low for I4:C21 and relatively high for the I16:C9 base pair (-3.2 degrees compared to -23.0 degrees), and the buckle angles alter, probably due to differences in the contacts with symmetry related molecules in the crystal lattice. The central base pairs of d(CGCIAATTCGCG) show the large propeller twist angles, and the narrow minor groove that characterize A-tract DNA, although I:C base pairs cannot form the major groove bifurcated hydrogen bonds that are possible for A:T base pairs.

Base Composition↗
PubMed1991

Crystal structure of interleukin 8: symbiosis of NMR and crystallography.

The crystal structure of a host defense system chemotactic factor, interleukin 8, has been solved by molecular replacement using as a model the solution structure derived from nuclear magnetic resonance experiments. The structure was refined with 2 A x-ray data to an R factor of 0.187 (0.217 at 1.6 A). A comparison indicates some potential differences between the structure in solution and in the crystalline state. Our analysis also predicts that residues 4 through 9 on the amino terminus and the beta-bend, which includes His-33, may be important for receptor binding.

Amino Acid Sequence↗
PubMed1987

Crystal structure determination of mung bean trypsin inhibitor Lys fragment-bovine trypsin complex--molecular replacement, electron density map at 3.0 angstron resolution.

The orientation and position of the trypsin molecule in the complex crystal cell mung bean trypsin inhibitor Lys fragment (MBILF)-bovine trypsin (BTRY) have been successfully determined by molecular replacement method with the model of the refined bovine trypsin molecule. Starting from the BTRY coordinates which were oriented and located in the correct azimuth and position in the complex cell according to the result from rotation function and translation function, sim-weighted Fourier map with coefficients 2/Fo/-/Fc/ at 3.0 A resolution was calculated. Besides the electron density which is obviously attributed to itself, in the vicinity of the active site of BTRY the dense contour levels corresponding to the MBILF and and its boundary could be clearly seen in this map. The size of MBILF was approximately estimated at 15 x 15 x 25 A.

Crystallography↗
PubMed1987

A molecular orbital study on adenosine phosphates.

AMP, ADP and ATP are calculated using the CNDO method, and ATP is studied by an ab initio calculation. The essential features of the electronic structure of these molecules are described in detail. Their ionization potentials, dipole moments and bond orders are given. The interaction between ATP with metal ions and enzyme molecules is discussed.

Adenosine Diphosphate↗