抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become . heritable traits sic . We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein)ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein)ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard y1 y1 .

/pdf/automated-docking-using-a-lamarckian-genetic-algorithm-and-2t6y95r7fm.pdf

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

Mechanism of interaction of cysteine proteinases and their protein inhibitors as compared to the serine proteinase-inhibitor interaction.

Reaction of human GSH transferase P1-1 (GSTP1-1) with diethylpyrocarbonate (DEPC) at pH 7.0 and 4 degrees C resulted in covalent modification of an equivalent of one histidine and one tyrosine residue per subunit, with loss of activity. Sequence analysis showed that His-71 and Tyr-7 were modified. Reference to the three-dimensional structure of GSTP1-1 [Reinemer, Dirr, Ladenstein, Huber, Lo Bello, Frederici and Parker (1992) J. Mol. Biol. 227, 214-226] shows that the modification of Tyr-7 is most likely to affect enzyme activity. Kinetic analysis of the DEPC modification of Tyr-7 in GSTP1-1 gave a k2 approx. 150 times that of a peptide comprising residues 1-11 of GSTP1-1. The reaction of Tyr-7 of GSTP1-1 with DEPC was poorly inhibited by 1 mM GSH (14%) or 10 microM S-hexylglutathione (18%). DEPC treatment of the enzyme altered the absorbance at 290 nm in second-derivative spectra, suggesting that a significant amount of tyrosinate ion occurs in the enzyme. GSH, however, did not significantly alter the A290. The data provide the first evidence of unusual chemical reactivity of Tyr-7 and are consistent with its proposed role as a proton acceptor during catalysis.

Unusual reactivity of Tyr-7 of GSH transferase P1-1

http://www.flavins.info/Publications/PDF%20neu%20sortiert/Schramek%20J.%20Mol.%20Biol.,%20316,%20827-835%20(2002).pdf

Reaction mechanism of GTP cyclohydrolase I: single turnover experiments using a kinetically competent reaction intermediate.

Aspects of intramolecular light energy and electron transfer will be discussed for three protein cofactor complexes, whose three-dimensional structures have been elucidated by x-ray crystallography: Components of light harvesting cyanobacterial phycobilisomes, the purple bacterial reaction centre, and the blue multi-copper oxidases. A wealth of functional data is available for these systems which allow specific correlations between structure and function and general conclusions about light energy and electron transfer in biological materials to be made.

A structural basis of light energy and electron transfer in biology

http://www.flavins.info/Publications/PDF%20neu%20sortiert/Echt%20J.%20Mol.%20Biol.,%20341,1085-96%20(2004).pdf

Robert Huber

Papers

Mechanism of interaction of cysteine proteinases and their protein inhibitors as compared to the serine proteinase-inhibitor interaction.

Unusual reactivity of Tyr-7 of GSH transferase P1-1

Reaction mechanism of GTP cyclohydrolase I: single turnover experiments using a kinetically competent reaction intermediate.

A structural basis of light energy and electron transfer in biology

Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans.