Divalent sulfur (S) forms a chalcogen bond (Ch-bond) via its σ-holes and a hydrogen bond (H-bond) via its lone pairs. The relevance of these interactions and their interplay for protein structure and function is unclear. Based on the analyses of the crystal structures of small organic/organometallic molecules and proteins and their molecular electrostatic surface potential, we show that the reciprocity of the substituent-dependent strength of the σ-holes and lone pairs correlates with the formation of either Ch-bond or H-bond. In proteins, cystines preferentially form Ch-bonds, metal-chelated cysteines form H-bonds, while methionines form either of them with comparable frequencies. This has implications for the positioning of these residues and their role in protein structure and function. Computational analyses reveal that the S-mediated interactions stabilise protein secondary structures by mechanisms such as helix capping and protecting free β-sheet edges by negative design. The study highlights the importance of S-mediated Ch-bond and H-bond for understanding protein folding and function, the development of improved strategies for protein/peptide structure prediction and design and structure-based drug discovery.

Variations in the acetolactate synthase (ALS) gene sequence were determined from 28 populations of corn poppy resistant (R) to tribenuron and from 6 populations susceptible (S) to this herbicide. The ALS gene fragment (634 bp) sequence revealed in R populations five point mutations at the codon Pro197, and among them the substitution of Pro197 by Ala was the most common. The sequencing chromatograms revealed that nine R individuals had only the mutant ALS gene and were homozygous (RR), 18 R individuals had both the wild type and the mutant ALS gene and were heterozygous (RS), whereas one R individual was heterozygous but with two different mutant ALS alleles (R1R2). The use of restriction digestion profile analysis to verify the DNA sequence results by detecting the existence of point mutations at the codon 197 managed to distinguish the R and S alleles and confirmed the results obtained from the sequencing chromatograms analysis. The secondary protein structure prediction suggested the formation of novel β-strands for each of the five mentioned amino acid substitutions that was not present in wild type ALS around the mutant site. These findings support the hypothesis that the substitution of Pro197 by Ser, Thr, Ala, Arg, or Leu resulted in altered secondary structure, which stabilizes an ALS tertiary conformation that prevents tribenuron binding and thus confers resistance to this herbicide.

To date, no structural study has been carried out on the effects of vitamin A deficiency (VAD) on hippocampal macromolecules. Therefore, in the present study, the effect of dietary VAD on the structure, content and function of rat hippocampal molecules was investigated using Fourier transform IF spectroscopy. Male Wistar rats were randomly divided into three groups: an experimental group maintained on a vitamin A-deficient liquid diet (VAD, n 7); a control group maintained on a vitamin A-supplemented liquid diet (CON, n 9); a pure control group maintained on standard solid laboratory chow (PC, n 7). The PC group was included in the study to ensure that the usage of liquid diet did not influence the outcomes of VAD. Both the CON and PC groups were successfully discriminated from the VAD group by principal component analysis and hierarchical cluster analysis. The spectral analysis indicated a significant decrease in the contents of saturated and unsaturated lipids, cholesteryl esters, TAG and nucleic acids in the VAD group when compared with the CON group (P≤ 0·05). In addition, a significant decrease in membrane fluidity and a significant increase in lipid order (e.g. acyl chain flexibility) were observed in the VAD group (P≤ 0·001). The results of the artificial neural network analysis revealed a significant decrease in the α-helix structure content and a significant increase in the turn and random coil structure contents, indicating protein denaturation, in the VAD group when compared with the CON and PC groups (P≤ 0·05). Dietary exclusion of vitamin A for 3 months apparently had an adverse impact on compositional, structural and dynamical parameters. These changes can be due to increased oxidative stress, confirming the antioxidant protection provided by vitamin A when used as a dietary supplement at low-to-moderate doses.

A simple approach to estimate the number of α-helical and β-strand segments from protein circular dichroism spectra is described. The α-helix and β-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given α-helix or β-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per α-helix and two residues per β-strand may be considered distorted in proteins. The number of α-helical and β-strand segments and their average length in a given protein were estimated from the fraction of distorted α-helix and β-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.