Configurationally and conformationally homogeneous cyclic n-aryl sulfimides—IV : Synthesis,configuration and stereochemistry of the rearrangement of 1,3-di-thiane-1-N-p-chlorophenylimides

1,3-Dithiane-1-N-p-chlorophenylimides (1,4-9) were prepared and their configuration and conformation was determined by ¹H and ¹³C NMR. The compounds were rearranged to the corresponding 2-(2'-amino-5'-chlorophenyl)-1, 3-dithianes (1U,4U,9U). The rearrangement reactions took place with ?95% stereospecifity. The mechanism of the reaction was investigated with the aid of analogs specifically deuterated at C-2.     

A new perspective on beta-sheet structures using vibrational Raman optical activity: from poly(L-lysine) to the prion protein

The vibrational Raman optical activity (ROA) spectrum of a polypeptide in a model beta-sheet conformation, that of poly(l-lysine), was measured for the first time, and the alpha-helix --> beta-sheet transition monitored as a function of temperature in H(2)O and D(2)O. Although no significant population of a disordered backbone state was detected at intermediate temperatures, some side chain bands not present in either the alpha-helix or beta-sheet state were observed. The observation of ROA bands in the extended amide III region assigned to beta-turns suggests that, under our experimental conditions, beta-sheet poly(L-lysine) contains up-and-down antiparallel beta-sheets based on the hairpin motif. The ROA spectrum of beta-sheet poly(L-lysine) was compared with ROA data on a number of native proteins containing different types of beta-sheet. Amide I and amide II ROA band patterns observed in beta-sheet poly(L-lysine) are different from those observed in typical beta-sheet proteins and may be characteristic of an extended flat multistranded beta-sheet, which is unlike the more irregular and twisted beta-sheet found in most proteins. However, a reduced isoform of the truncated ovine prion protein PrP(94-233) that is rich in beta-sheet shows amide I and amide II ROA bands similar to those of beta-sheet poly(L-lysine), which suggests that the C-terminal domain of the prion protein is able to support unusually flat beta-sheets. A principal component analysis (PCA) that identifies protein structural types from ROA band patterns provides a useful representation of the structural relationships among the polypeptide and protein states considered in the study.     

Retention behavior of humic substances in reversed phase HPLC

Recovery as well as appearance and abundance (in percent) of different fractions of humic substances are found to depend on injected sample amounts in reversed phase HPLC. Sample amounts have been varied both by varying sample concentration and sample volume. In case of lowest amounts injected only two fractions were obtained for a commercial humic acid sodium salt, i.e. one for excluded molecules and one for hydrophobic components. The abundance of excluded molecules decreases upon increasing amounts injected. Another three fractions are obtained upon increasing amount injected: a hydrophilic fraction and two hydrophobic ones. This behavior is explained by auxiliary equilibria between excluded components and humic molecules previously adsorbed on the stationary phase.     

A general formalism of deriving the pair potential of polymer chains for arbitrary interaction potentials between isolated chain segments at and close to the theta-point

A formalism has been worked out which allows to transform any non-punctiform segment-segment potential of isolated polymer segments ε of fairly short-ranged character into the pair-potentialU operating between linear polymer chains with a certain reference to the arguments as they have been originally put forward byFlory andKrigbaum. Although no restrictions are made in the derivation as to the repulsive or attractive contribution of the segment-segment potential ε because of some known general deficiencies of theFlory-Krigbaum treatment for exclusively repulsive interaction, the resulting equations are primarily intended to describe the thermodynamic situation at and close to the θ-point where repulsion and attraction—though working at different ranges of segment separation—cancel. As the equation derived is somewhat complicated two different approximate forms have been developed: The first one is based on aTaylor series expansion retaining terms up to the fourth order which allows to characterizeU by the second and the fourth moment of the pair segment-segment distribution function, β and γ (β being the so-called binary cluster integral of segment-segment interaction, which is considered to be zero for θ-conditions). In this caseU may be represented by an expression of the general form $$U/kT = A(1 - BR^2 )\exp \{ - bR^2 \} .$$ The second method is based on a separate integration over the repulsive and attractive ranges of ε giving the repulsive (U ₊) and the attractive (U _?) part ofU finally after some approximations leading to an equation of the general form $$U/kT = (U_ + + U_ - )/kT = A_1 \exp \{ - b_1 R^2 \} - A_2 \exp \{ - b_2 R^2 \} .$$ In both cases the knowledge of the exact form of ε is dispensable, only β and γ—or for the second case their repulsive (β₊ and γ₊) and attractive (β_? and γ_?) parts have to be known. It is shown that the approximations are in excellent accordance with the exact form so that they may be conveniently used to describe pair potentials of polymer chains and to analyze pair potentials of segment-segment interactions under the limitations and conditions indicated.     

A study of alpha-helix hydration in polypeptides, proteins, and viruses using vibrational raman optical activity

A vibrational Raman optical activity (ROA) study, supplemented by protein X-ray crystal structure data, of alpha-helices in polypeptides, proteins, and viruses has suggested that ROA bands in the extended amide III spectral region may be used to distinguish between two types of right-handed alpha-helix. One type, associated with a positive ROA band at approximately 1300 cm(-1), dominates in hydrophobic environments and appears to be unhydrated; the other, associated with a positive ROA band at approximately 1340 cm(-1), dominates in hydrophilic environments and appears to be hydrated. Evidence is presented to support the hypothesis that unhydrated alpha-helix corresponds to the canonical conformation alpha(c) and hydrated alpha-helix to a more open conformation alpha(o) stabilized by hydrogen bonding of a water molecule or a hydrophilic side chain to the peptide carbonyl. Alpha-helical poly(L-lysine) and poly(L-ornithine) in aqueous solution and poly(L-alanine) in dichloracetic acid display both bands, but alpha-helical poly(l-glutamic acid) in aqueous solution and poly(gamma-benzyl L-glutamate) in CHCl(3) display only the approximately 1340 cm(-1) band and so may exist purely as alpha(o) due to enhanced stabilization of this conformation by particular side chain characteristics. The ROA spectrum of poly(beta-benzyl L-aspartate) in CHCl(3) reveals that it exists in a single left-handed alpha-helical state more analogous to alpha(o) than to alpha(c).     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.