The nonplanar peptide unit. IV. Geometry and nonplanar distortions of the cis-peptide unit

Semiempirical quantum chemical calculations were carried out using the CNDO/2 and the INDO methods on the model compound cis-N-methylacetamide in order to get an insight into the problem of possible nonplanar distortions of the cis-peptide unit. In addition, the crystal structure data of cyclic peptides containing cis-peptide units were analyzed. These studies have indicated that the dihedral angles θ_N and Δ_ω are correlated approximately by the relation Δ_ω = ?θ_N, whereas θ_C is small and is uncorrelated with Δ_ω, as was found in the case of the trans-peptide unit. Both theory and crystal data suggest that out-of-plane distortions at the nitrogen atom of the peptide unit were quite likely to occur and should be included in the conformational calculations. The average geometry for the planar cis-peptide unit has also been obtained from the observed examples.     

Substrate directs enzyme dynamics by bridging distal sites: UDP-galactopyranose mutase

UDP-Galactopyranose mutase (UGM) is a flavoenzyme that catalyzes interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf); its activity depends on FAD redox state. The enzyme is vital to many pathogens, not native to mammals, and is an important drug target. We have probed binding of substrate, UDP-Galp, and UDP to wild type and W160A UGM from K. pneumoniae, and propose that substrate directs recognition loop dynamics by bridging distal FAD and W160 sites; W160 interacts with uracil of the substrate and is functionally essential. Enhanced Trp fluorescence upon substrate binding to UGM indicates conformational changes remote from the binding site because the fluorescence is unchanged upon binding to W70F/W290F UGM where W160 is the sole Trp. MD simulations map these changes to recognition loop closure to coordinate substrate. This requires galactose-FAD interactions as Trp fluorescence is unchanged upon substrate binding to oxidized UGM, or binding of UDP to either form of the enzyme, and MD show heightened recognition loop mobility in complexes with UDP. Consistent with substrate-directed loop closure, UDP binds 10-fold more tightly to oxidized UGM, yet substrate binds tighter to reduced UGM. This requires the W160-U interaction because redox-switched binding affinity of substrate reverses in the W160A mutant where it only binds when oxidized. Without the anchoring W160-U interaction, an alternative binding mode for UDP is detected, and STD-NMR experiments show simultaneous binding of UDP-Galp and UDP to different subsites in oxidized W160A UGM: Substrate no longer directs recognition loop dynamics to coordinate tight binding to the reduced enzyme.     

Synonymous codon usage pattern among the S,M, and L segments in Crimean-congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.     

Possible formation of the left-handed alpha-helix of poly-L-serine

A conformational study of poly-L -serine has shown that it can exist in the left-handed α-helical form. A study of a pair of peptide units with the serine sidegroup attached to the α carbon atom linking the two units showed that O? H ?O hydrogen bonds between the OH group of the side chain and a carbonyl oxygen of the first peptide group in the backbone can occur in two regions of ?, namely, ? = 15°–30° for χ₁ = 300° and for ? = 225°-230° for ? = 60°. The latter is close to a possible left-handed helix of poly-L -serine, stabilized by N? H ?O hydrogen bonds. From a study of contact criteria, the best conformation for this helix is found to be ? = 227°, Ψ = 238°, χ₁ = 65° which has n = 3.65, h = 1.51 A. The N? H ?O hydrogen bond has a length of 2.90 A. (6°) and the O? H ?O hydrogen bond is of length 2.60 A. (0°). There are no other bad short contacts in the structure. The cylindrical coordinates of the atoms, as well as a perspective view of the structure arc given in this paper.     

The approximate entropy of the electromyographic signals of tremor correlates with the osmotic fragility of human erythrocytes

Background  

The main problem of tremor is the damage caused to the quality of the life of patients, especially those at more advanced ages. There is not a consensus yet about the origins of this disorder, but it can be examined in the correlations between the biological signs of aging and the tremor characteristics.     

The specificity of protection against cationic antimicrobial peptides by lactoferrin binding protein B

A variety of Gram-negative pathogens possess host-specific lactoferrin (Lf) receptors that mediate the acquisition of iron from host Lf. The integral membrane protein component of the receptor, lactoferrin binding protein A specifically binds host Lf and is required for acquisition of iron from Lf. In contrast, the role of the bi-lobed surface lipoprotein, lactoferrin binding protein B (LbpB), in Lf binding and iron acquisition is uncertain. A common feature of LbpBs from most species is the presence of clusters of negatively charged amino acids in the protein’s C-terminal lobe. Recently it has been shown that the negatively charged regions from the Neisseria meningitidis LbpB are responsible for protecting against an 11 amino acid cationic antimicrobial peptide (CAP), lactoferricin (Lfcin), derived from human Lf. In this study we investigated whether the LbpB confers resistance to other CAPs since N. meningitidis is likely to encounter other CAPs from the host. LbpB provided protection against the cathelicidin derived peptide, cathelicidin related antimicrobial peptide (mCRAMP), but did not confer protection against Tritrp 1 or LL37 under our experimental conditions. When tested against a range of rationally designed synthetic peptides, LbpB was shown to protect against IDR-1002 and IDR-0018 but not against HH-2 or HHC10.