PubMed · 10640136
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1999. Thermometers.. https://pubmed.ncbi.nlm.nih.gov/10640136/
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The molecular-replacement method works well with good models and simple unit cells, but often fails with more difficult problems. Experience with likelihood in other areas of crystallography suggests that it would improve performance significantly. For molecular replacement, the form of the required likelihood function depends on whether there is ambiguity in the relative phases of the contributions from symmetry-related molecules (e.g. rotation versus translation searches). Likelihood functions used in structure refinement are appropriate only for translation (or six-dimensional) searches, where the correct translation will place all of the atoms in the model approximately correctly. A new likelihood function that allows for unknown relative phases is suitable for rotation searches. It is shown that correlations between sequence identity and coordinate error can be used to calibrate parameters for model quality in the likelihood functions. Multiple models of a molecule can be combined in a statistically valid way by setting up the joint probability distribution of the true and model structure factors as a multivariate complex normal distribution, from which the conditional distribution of the true structure factor given the models can be derived. Tests in a new molecular-replacement program, Beast, show that the likelihood-based targets are more sensitive and more accurate than previous targets. The new multiple-model likelihood function has a dramatic impact on success.
In this paper, protein-drug interactions were studied by solid-phase microextraction (SPME) using diazepam binding to human serum albumin as a model system. Since drug compounds are normally polar and nonvolatile by nature, direct SPME is used in this work. The SPME extraction is an equilibrium process among the concentrations of the analyte partitioned onto the SPME fiber, free and bound drug in the solution. A calibration curve was first constructed by employing the amount of the analytes partitioned on the fiber versus the free analyte concentration in the solution in the absence of protein. In method I, the extraction was performed in the protein solution with known diazepam concentration. In method II, diazepam was first loaded onto the fiber by extracting in solution with known diazepam concentration. This fiber was subsequently transferred into the protein solution for desorption. The amount of the analyte left on the fiber was analyzed after the system reached equilibrium. The free drug concentration was then obtained from the calibration curve for both methods. The Scatchard plot was finally employed to obtain the number of binding sites and the equilibrium binding constants. Since only a very small amount of the protein solution is required (150 microL for each extraction), method II is very useful for circumstances where the protein amount is very limited. The direct measurement method proposed in this paper does not need a GC response factor, which significantly decreases the experimental error. The only measurement needed is the area count change (ratio) of the fiber injections before and after the protein was introduced into the solution. The difference between the direct measurement method for method I and method II is discussed. The result illustrated that the SPME direct measurement method provided both theoretical accuracy and simplicity in such applications.
The high-performance liquid chromatographic method with UV detection described below permits the selective determination of traces of palladium in human urine. After UV photolysis, during which the complete organic matrix was destroyed, the palladium was selectively enriched by solid-phase extraction (SPE). The reversed-phase C18 SPE column material was loaded with the ligand N,N-diethyl-N'-benzoylthiourea (DEBT) which shows an excellent complexing capacity for palladium in acidic solutions and at room temperature. The Pd(DEBT)2 complex was eluted with ethanol. After isocratic separation on the analytical column (MeOH/H2O 98:2 (v/v)), the complex was detected at 274 nm. The detection limit was 10 ng Pd/l. The relative standard deviations (RSD) of the within-series imprecision were in the range between 11% (75 ng Pd/l) and 7% (180 ng Pd/l). The between-day imprecision was 11% (75 ng Pd/l) and 5% (180 ng Pd/l). The recovery rates ranged between 94 and 96%. Using this method, urine samples of 44 persons from the general population were analysed. Only in one urine sample could palladium be detected. For comparison, 10 persons with occupational palladium exposure were examined. The urinary concentrations ranged from <10 to 2,538 ng/l.