PubMed · 14298922
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K K MUSTAKALLIO. 1965. [DMSO].. https://pubmed.ncbi.nlm.nih.gov/14298922/
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We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths.
The toxic effects that organic solvents have on whole cells are important drawbacks in the application of these solvents in the production of fine chemicals by whole-cell stereoselective biotransformations. Although early studies found that organic solvents mainly destroyed the integrity of cell membranes by accumulating in the lipid bilayer of plasma membranes, the cellular metabolic responses to the presence of an organic solvent remain unclear. With the rapid development of genomics, it is possible to study cellular metabolism under perturbed conditions at the genome level. In this paper, the global gene expression profiles of Saccharomyces cerevisiae BY4743 grown in media with a high concentration of the organic solvent dimethyl sulfoxide (DMSO) were determined by microarray analysis of ~6,200 yeast open reading frames (ORFs). From cells grown in SD minimal medium containing 1.0% (v/v) DMSO, changes in transcript abundance greater than or equal to 2.5-fold were classified. Genomic analyses showed that 1,338 genes were significantly regulated by the presence of DMSO in yeast. Among them, only 400 genes were previously found to be responsive to general environmental stresses, such as temperature shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. The DMSO-responsive genes were involved in a variety of cellular functions, including carbohydrate, amino acid and lipid metabolism, cellular stress responses, and energy metabolism. Most of the genes in the lipid biosynthetic pathways were down-regulated by DMSO treatment, whereas genes involved in amino acid biosynthesis were mostly up-regulated. The results demonstrate that the application of microarray technology allows better interpretation of metabolic responses, and the information obtained will be useful for the construction of engineered yeast strains with better tolerance of organic solvents.
Both the aqueous and the lipid-induced structure of eledoisin, an undecapeptide of mollusk origin, have been studied by two-dimensional proton nuclear magnetic resonance spectroscopy and distance geometry calculations. Unambiguous nuclear magnetic resonance assignments of protons have been made with the aid of correlation spectroscopy experiments and nuclear Overhauser effect spectroscopy experiments. The distance constraints obtained from the nuclear magnetic resonance data have been utilized in a distance geometry algorithm to generate a family of structures, which have been refined using restrained energy minimization and dynamics. These data show that, while in water and dimethyl sulfoxide, eledoisin prefers to be in an extended chain conformation, whereas in the presence of perdeuterated dodecylphosphocholine micelles, a membrane model system, helical conformation is induced in the central core and C-terminal region (K4-M11) of the peptide. N terminus, though less defined, also displays some degree of order and a possible turn structure. The conformation adopted by eledoisin in the presence of dodecylphosphocholine micelles is similar to the structural motif typical of neurokinin-2 selective agonists and with that reported for kassinin in hydrophobic environment.