Secondary-Structure Design of Proteins by a Backbone Torsion Energy

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both phi and psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the alpha-helix-forming-tendencies by lowering/raising the torsion-energy surface in the alpha-helix region and likewise increase/decrease the beta-sheet-forming tendencies by lowering/raising the surface in the beta-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming-tendencies by performing folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure

An epidemiological study on anemia among institutionalized people with intellectual and/or motor disability with special reference to its frequency, severity and predictors

BACKGROUND: To examine the type, frequency, severity, and predictors of anemia and its relationship with co-morbid conditions among institutionalized people with intellectual and/or motor disability. METHODS: We conducted a cross-sectional study at a public facility for people with intellectual and/or motor disability in Ibaraki prefecture, Japan. Health checkup data obtained in 2001 from 477 people with intellectual disability (male: 286, average age 40.6 ± 12.3; female: 191, average age 45.1 ± 11.6) were retrospectively reviewed. RESULTS: The prevalence of anemia among male participants was higher than in female participants for each disability category (intellectual disability, 41.1%, 4.2%; cerebral palsy, 37.5%, 4.8%; Down's syndrome, 15.0%, 0%; severe motor and intellectual disabilities, 61.9%, 16.7%). Most participants with anemia (93.8 – 100%) showed a normocytic normochromic anemia pattern. Multivariate analysis revealed that factors related to an increase in frequency included sex (male), low body mass index (BMI), use of anticonvulsants or major tranquilizers, and a high zinc sulfate turbidity test (ZTT) value. No clinically diagnosed co-morbid condition was found to be related to the presence of anemia. CONCLUSION: A high frequency of mild normocytic normochromic anemia in institutionalized people with intellectual and/or motor disability was observed, particularly among males. Medications and chronic inflammation may increase the risk of anemia

Substituent Effects in the Noncovalent Bonding of SO2 to Molecules containing a Carbonyl Group. The Dominating Role of the Chalcogen Bond

The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of the SO2 molecule, consistent with the disposition of the molecular electrostatic potentials of the two monomers. This S···O bond differs from the more commonly observed chalcogen bond in both geometry and origin. Substituents exert their influence via inductive effects that change the availability of the carbonyl O lone pairs as well as the intensity of the negative electrostatic potential surrounding this atom

Effects of Charge and Substituent on the S∙∙∙N Chalcogen Bond

Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of 37 kcal/mol for X = F. The binding is weakened to some degree when the H atoms are replaced by methyl groups in XMe2S+···NH3. The source of the interaction in the charged systems, like their neutral counterparts, is derived from a charge transfer from the N lone pair into the σ*(SX) antibonding orbital, supplemented by a strong electrostatic and smaller dispersion component. The binding is also derived from small contributions from a CH···N H-bond involving the methyl groups, which is most notable in the weaker complexes

Structural Conformers of (1,3-Dithiol-2-ylidene)ethanethioamides: The Balance Between Thioamide Rotation and Preservation of Classical Sulfur-Sulfur Hypervalent Bonds

The reaction of N-(2-phthalimidoethyl)-N-alkylisopropylamines and S2Cl2 gave 4-N-(2-phthalimidoethyl)-N-alkylamino-5-chloro-1,2-dithiol-3-thiones that quantitatively cycloadded to dimethyl or diethyl acetylenedicarboxylate to give stable thioacid chlorides, which in turn reacted with one equivalent of aniline or a thiole to give thioanilides or a dithioester. Several compounds of this series showed atropisomers that were studied by a combination of dynamic NMR, simulation of the signals, conformational analysis by DFT methods, and single crystal X-ray diffraction, showing a good correlation between the theoretical calculations, the experimental values of energies, and the preferred conformations in the solid state. The steric hindering of the crowded substitution at the central amine group was found to be the reason for the presence of permanent atropisomers in this series of compounds and the cause of a unique disposition of the thioxo group at close-to-right angles with respect to the plane defined by the 1,3-dithiole ring in the dithiafulvene derivatives, thus breaking the sulfur–sulfur hypervalent bond that is always found in this kind of compounds.Ministerio de Economıá y Competitividad, Spain (Project CTQ2012- 31611), Junta de Castilla y León, Consejería de Educación y Cultura y Fondo Social Europeo (Project BU246A12-1), and the European Commission, Seventh Framework Programme (Project SNIFFER FP7-SEC-2012-312411

Phase fluorometric method for determination of standard lifetimes

Rayleigh scatterers have long been used as standards for fluorescence lifetime determinations, but they have many drawbacks, including the well-known “color effect ’. To avoid these problems, various fiuorophores have been used as standards. Unfortunately, the lifetimes of these compounds are not agreed upon to better than 5%, and the compounds cited in the literature do not fully cover the 250–850 nm band of common fluorescence emission. We describe a multifrequency phase fluorometric method for accurately determining the lifetimes of monoexponential fluorophores (standards) without reference to another standard. Results are shown for some widely used standard fluorophores and some recently developed compounds. An Independent test of the accuracy of the method based on quenching experiments is presented. © 1988, American Chemical Society. All rights reserved