Correlation between side chain mobility and conformation in protein structures

Thermal factors of protein atoms as determined by X-ray crystallographic techniques show a tendency to be larger in side chains with unfavourable local conformations rather than in those displaying conformational energy minima. It follows that side chain atoms are more mobile if they are in a non-rotameric configuration and that the stereochemistry of protein structures cannot be fully assessed or simulated without consideration of thermal factors that monitor flexibility in various regions of the protein. The observations should also prove useful in protein folding and design.      

Statistical validation of the root-mean-square-distance, a measure of protein structural proximity

Despite its well-documented limitations, the root-mean-square-distance (rmsd) between pairs of equivalent atoms is routinely used to monitor the degree of similarity between two optimally superposed protein three-dimensional structures. A robust method for assessing the statistical significance of the difference between two rmsd values is presented here. It is based on the comparison of two protein structures through the correlation coefficient between equivalent inter-atomic distances and the subsequent application of the Fisher transformation that allows one to estimate the probability of identity between two correlation coefficient values. The relationship between the rmsd and Fisher correlation coefficient allows then to estimate the statistical significance of the difference between two rmsd values. Such a procedure is exemplified with the analysis of the possible classifications of the immunoglobulin-like domains of filamin and is compared to related estimations of structural similarity. The possibility to estimate the probability of the difference between two rmsd values can be used to optimize the protein structural classifications and comparisons, independent of the procedure used to derive the rmsds.     

A novel biomimetic analysis system for quantitative characterisation of sclerosing foams used for the treatment of varicose veins

A novel analysis system for the quantification of sclerosing foam properties under clinically relevant conditions was developed with the purpose of establishing a robust methodology for comparative characterisation of different foam formulations and production strategies. The developed biomimetic-inspired model comprised of 4 or 10 mm inner diameter polytetrafluoroethylene tubing, filled with a blood substitute and fixed to a platform with an adjustable inclination angle. Sclerosing foams were produced by mixing polidocanol with either atmospheric air or 100 % CO₂, using a double-syringe system method. Individual foams were injected into the tube, while videos were captured simultaneously. Videos were then transferred to an in-house computational foam analysis system (CFAS) which performed a sequence of semi-automated operations, allowing quantitative characterisation of sclerosing foam dynamic behaviour. Using CFAS, degradation rates of different foams were measured and the effect of gas composition, liquid sclerosant concentration and time delay between foam production and injection were evaluated.     

Crystallisation and preliminary crystallographic analysis of recombinant Xenopus laevis Cu,Zn superoxide dismutase b

The recombinant Cu,Zn superoxide dismutase from the South African frog Xenopus laevis, expressed in E. coli, has been crystallized in a form suitable for high resolution crystallographic investigations. The crystals grow from polyethylene glycol solutions, at pH 6.0, 28 degrees C, and belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell edges a = 73.33, b = 68.86, c = 59.73 A, one protein dimer (32,000 M(r)) per asymmetric unit. Diffraction data have been collected to 3.0 A resolution, and a molecular replacement solution found for Xenopus laevis superoxide dismutase using the bovine enzyme as search model. The crystallographic R-factor corresponding to this solution is 0.412, in the 15.0-3.0 A resolution range.     

Correlation between occupancy and B factor of water molecules in protein crystal structures

An empirical relationship between occupancy and the atomic displacementparameter of water molecules in protein crystal structures hasbeen found by comparing a set of well refined sperm whale myoglobincrystal structures. The relationship agrees with a series ofindependent structural features whose impact on water occupancycan easily be predicted as well as with other known data andis independent of the protein fold. The estimation of the wateroccupancy in protein crystal structures may help in understandingthe physico-chemical properties of the protein–solventinterface and can allow the monitoring of the accuracy of theprotein crystal structure refinement.     

Mechanism of co-nanoprecipitation of organic actives and block copolymers in a microfluidic environment

Microreactors have been shown to be a powerful tool for the production of nanoparticles (NPs); however, there is still a lack of understanding of the role that the microfluidic environment plays in directing the nanoprecipitation process. Here we investigate the mechanism of nanoprecipitation of block copolymer stabilized organic NPs using a microfluidic-based reactor in combination with computational fluid dynamics (CFD) modelling of the microfluidic implementation. The latter also accounts for the complex interplay between molecular and hydrodynamic phenomena during the nanoprecipitation process, in order to understand the hydrodynamics and its influence on the NP formation process. It is demonstrated that the competitive reactions result in the formation of two types of NPs, i.e., either with or without loading organic actives. The obtained results are interpreted by taking into consideration a new parameter representing the mismatching between the aggregations of the polymers and actives, which plays a decisive role in determining the size and polydispersity of the prepared hybrid NPs. These results expand the current understanding of the co-nanoprecipitation mechanism of active and block copolymer stabilizer, and on the role exerted by the microfluidic environment, giving information that could be translated to the emerging fields of microfluidic formation of NPs and nanomedicine.     

Predicting residue solvent accessibility from protein sequence by considering the sequence environment

The solvent accessibility of each residue is predicted on thebasis of the protein sequence. A set of 338 monomeric, non-homologousand high-resolution protein crystal structures is used as alearning set and a jackknife procedure is applied to each entry.The prediction is based on the comparison of the observed andthe average values of the solvent-accessible area. It appearsthat the prediction accuracy is significantly improved by consideringthe residue types preceding and/or following the residue whoseaccessibility must be predicted. In contrast, the separate treatmentof different secondary structural types does not improve thequality of the prediction. It is furthermore shown that theresidue accessibility is much better predicted in small thanin larger proteins. Such a discrepancy must be carefully consideredin any algorithm for predicting residue accessibility.     

Vicinal disulfide turns

The formation of a disulfide bond between adjacent cysteineresidues is accompanied by the formation of a tight turn ofthe protein backbone. In nearly 90% of the structures analyzeda type VIII turn was found. The peptide bond between the twocysteines is in a distorted trans conformation, the omega torsionangle ranges from 159 to –133°, with an average valueof 171°. The constrained nature of the vicinal disulfideturn and the pronounced difference observed between the oxidizedand reduced states, suggests that vicinal disulfides may beemployed as a ‘redox-activated’ conformational switch. Received December 16, 2002; revised June 30, 2003; accepted July 30, 2003.