Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force-field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp-cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein--a P12W mutant of the Trp-cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified the thermodynamically more stable variants in both cases and therefore can also be used as a tool for the relative measurement of protein stability. Finally, we will point out the important role played by dispersion energy, which contributes significantly to the total stabilization energy and whose role in aromatic pairs is clearly dominant. Surprisingly, the dispersion energy plays an even more important role in the interaction of prolines with aromatic systems.     

Investigation of a sulfate transfer during autohydrolysis of a fucoidan from the brown alga Fucus evanescens by tandem ESIMS

A fucoidan from the brown alga Fucus evanescens was effectively depolymerized by autohydrolysis. Negative-ion electrospray ionization mass spectrometry (ESIMS) revealed that the mixture contained sulfated mono- and oligosaccharides with polymerization degree (DP) up to 6, having from 1 to 4 sulfate groups per molecule. The prevalence of oligosaccharides with even DP was observed. It could be explained by the tendency of the 3-linked α-l-fucopyranose residues to hydrolyze faster than 4-linked ones. The intermolecular sulfate transfer during autohydrolysis was detected by ESIMS, when equimolar quantities of d-Rib and d-Glc were added as acceptors. The products were singly-sulfated and hexose was about four times more effective as an acceptor, than pentose. It was impossible to record MS/MS spectra of the sulfate transfer products, since intensities of their ions were too low.     

Structural resolution of the complex between a fungal polygalacturonase and a plant polygalacturonase-inhibiting protein by small-angle X-ray scattering

We report here the low-resolution structure of the complex formed by the endo-polygalacturonase from Fusarium phyllophilum and one of the polygalacturonase-inhibiting protein from Phaseolus vulgaris after chemical cross-linking as determined by small-angle x-ray scattering analysis. The inhibitor engages its concave surface of the leucine-rich repeat domain with the enzyme. Both sides of the enzyme active site cleft interact with the inhibitor, accounting for the competitive mechanism of inhibition observed. The structure is in agreement with previous site-directed mutagenesis data and has been further validated with structure-guided mutations and subsequent assay of the inhibitory activity. The structure of the complex may help the design of inhibitors with improved or new recognition capabilities to be used for crop protection.     

Investigation of new acyloxy derivatives of cholic acid and their esters as drug absorption modifiers

Skin penetration enhancers are used in the formulation of transdermal delivery systems for drugs that are otherwise not sufficiently skin-permeable. Intestinal absorption promoters/enhancers are used as excipients in oral formulations of poorly oral-bioavailable drugs. Series of fourteen acyloxy derivatives of 5β-cholic acid as potential drug absorption modifiers was generated by multistep synthesis. The synthesis of all newly prepared compounds is presented here. Structure confirmation of all generated compounds was accomplished by (1)H NMR, (13)C NMR, IR and MS spectroscopy methods. All the prepared compounds were analyzed using RP-TLC, and their lipophilicity (R(M)) was determined. The hydrophobicity (logP) and solubility (logS) of the studied compounds were also calculated using two commercially available programs. All the target compounds were tested for their in vitro transdermal penetration activity and as potential intestinal absorption enhancers. The anti-proliferative activity of all the final compounds was also assessed against the human cancer cell lines: T-lymphoblastic leukemia cell line and the breast adenocarcinoma cell line. Their cytotoxicity was also evaluated against the normal human skin fibroblast cells. Two compounds showed anti-proliferative effect on cancer cells without affecting the growth of normal cells, which should be promising in potential development of new drugs. Most of the target compounds showed minimal anti-proliferative activity (IC(50)>37 μM), indicating they would have low cytotoxicity when administered as chemical absorption modifiers. The relationships between the lipophilicity and the chemical structure of the studied compounds as well as the relationships between their chemical structure and enhancement effects are discussed in this article.     

Clinical efficacy of a GnRH-agonist implant containing 4.7 mg deslorelin, Suprelorin, regarding suppression of reproductive function in tomcats. Sandra.Pesch@vetmed.uni-giessen.de

The aim of the present study was to test for the efficacy of a slow release GnRH-agonist implant (4.7 mg deslorelin, Suprelorin®) in the male cat. Ten toms were implanted sc in the neck. Changes in testosterone (T) secretion, testicular size, body weight and behaviour (mounting, mating, urine marking) were monitored. T concentrations were significantly decreased (P < 0.0001) to basal levels (< 0.1 ng/mL) in 5 of 10 cats after 4 weeks and in all but one tom after 11 weeks (T < 0.1 ng/mL). In this respective tom only partial downregulation with T-values from 0.2 to 0.1 ng/mL was achieved until week 27. In weeks 28 and 32, T concentrations were below 0.1 ng/mL. Compared to pretreatment values, testicular volume was significantly decreased by about 60% in week 12 and about 73% after 36 weeks (P < 0.001). Penile spines disappeared 9.4 ± 1.0 weeks after treatment. Food intake was significantly increased during treatment period (P < 0.001). In all tomcats libido, mating behaviour and urine marking were significantly reduced (P < 0.0001) after an initial stimulation. In one tom, mating an oestrous queen on day 20 after implant administration resulted in pregnancy. Mating of another tom that had T-values between 0.1 and < 0.1 ng/mL since day 24 in week 8 revealed the presence of spermatozoa; however, this mating did not result in pregnancy.Subcutaneous implant administration was well tolerated by all tomcats without sedation or anaesthesia and no treatment related negative effects were observed.These results demonstrate the clinical efficacy of the 4.7 mg deslorelin implants (Suprelorin®) in the tom inducing all castration related effects.