Serine-phosphoric acid cluster ions studied by electrospray ionization and tandem mass spectrometry

More than 310 kinds of cluster ions of S(m) P(n) H(k) (k+) are observed in a single ESI mass spectrum of a mixed solution of serine and phosphoric acid. Some typical cluster ions are selected, activated by collision in a FT ICR cell, and the dissociation pathways were deduced in detail. For large singly protonated ions, the collisions cause the ejection of subunits of serine or phosphoric acid subsequently producing the ions of S(2) P(4) H(1) (1+) , which can be further dissociated by the loss of phosphoric acid molecules in turn and form the protonated serine dimer and monomer. However, for the doubly protonated ions, the dissociation pathways change from the loss of a protonated serine dimer for the ions of S(7) P(9) H(2) (2+) to the neutral loss of H(3) PO(4) for the ions of S(7) P(12) H(2) (2+) or the neutral loss of serine or H(3) PO(4) for the larger clusters, indicating the effect of cluster sizes on the process of dissociation. The structure of S(2) P(4) H(1) (1+) is suggested based on B3LYP/6-31G(d,p) calculations. The diversity and structural orderliness of the hetero-cluster ions are mainly attributed to the network of hydrogen bonds inside the cluster ions and the extraordinary amphotericity of the components.     

Different Enzyme Conformations Induce Different Mechanistic Traits in HIV-1 Protease

The influence of the dynamical flexibility of enzymes on reaction mechanisms is a cornerstone in biological sciences. In this study, we aim to 1) study the convergence of the activation free energy by using the first step of the reaction catalysed by HIV-1 protease as a case study, and 2) provide further evidence for a mechanistic divergence in this enzyme, as two different reaction pathways were seen to contribute to this step. We used quantum mechanics/molecular mechanics molecular dynamics simulations, on four different initial conformations that led to different barriers in a previous study. Despite the sampling, the four activation free energies still spanned a range of 5.0 kcal ⋅ mol⁻¹. Furthermore, the new simulations did confirm the occurrence of an unusual mechanistic divergence, with two different mechanistic pathways displaying equivalent barriers. An active-site water molecule is proposed to influence the mechanistic pathway.     

A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa

Blood coagulation is an essential physiological process for hemostasis; however, abnormal coagulation can lead to various potentially fatal disorders, generally known as thromboembolic disorders, which are a major cause of mortality in the modern world. Recently, the FDA has approved several anticoagulant drugs for Factor Xa (FXa) which work via the common pathway of the coagulation cascade. A main side effect of these drugs is the potential risk for bleeding in patients. Coagulation Factor IXa (FIXa) has recently emerged as the strategic target to ease these risks as it selectively regulates the intrinsic pathway. These aforementioned coagulation factors are highly similar in structure, functional architecture, and inhibitor binding mode. Therefore, it remains a challenge to design a selective inhibitor which may affect only FIXa. With the availability of a number of X-ray co-crystal structures of these two coagulation factors as protein–ligand complexes, structural alignment, molecular docking, and pharmacophore modeling were employed to derive the relevant criteria for selective inhibition of FIXa over FXa. In this study, six ligands (three potent, two selective, and one inactive) were selected for FIXa inhibition and six potent ligands (four FDA approved drugs) were considered for FXa. The pharmacophore hypotheses provide the distribution patterns for the principal interactions that take place in the binding site. None of the pharmacophoric patterns of the FXa inhibitors matched with any of the patterns of FIXa inhibitors. Based on pharmacophore analysis, a selectivity of a ligand for FIXa over FXa may be defined quantitatively as a docking score of lower than −8.0 kcal/mol in the FIXa-grids and higher than −7.5 kcal/mol in the FXa-grids.     

Development of enzyme technology and enzyme engineering in China

Enzymes have been utilized in China for thousands of years for the production of various foods and alcoholic beverages. Today China manufactures and uses enzymes for not only the traditional areas of application, but is expanding the use of enzymes for a variety of nonfood areas. This report describes the present state of the art of enzyme manufacture and application in China today.     

Proteinase of germinated cotton seeds

A scheme has been developed to isolate and purify proteinase D from 3-day germinated cotton seeds. The physicochemical properties and substrate specificity were studied. It is found that cysteinic proteinase D cleaves auxiliary proteins to low-molecular-weight peptides and free amino acids.S. Yu. Yunusov Institute of the Chemistry of Plant Substances. Academy of Sciences of the Republic of Uzbekistan. Tashkent, fax (99871) 120 64 75. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 249–251, May–June, 2000.