Supplementary MaterialsAdditional file 1 Desk S1 – /mo /mrow mrow mi
Supplementary MaterialsAdditional file 1 Desk S1 – /mo /mrow mrow mi k /mi /mrow /munder mrow mo class=”MathClass-open up” ( /mo mrow mo mathsize=”big” /mo mi a /mi msub mrow mi a /mi /mrow mrow mi X /mi mo class=”MathClass-rel” /mo mi Y /mi /mrow /msub mo class=”MathClass-bin” – /mo mo mathsize=”big” /mo mi a /mi msub mrow mi a /mi /mrow mrow mi Y /mi mo class=”MathClass-rel” /mo mi X /mi /mrow /msub /mrow mo class=”MathClass-close” ) /mo /mrow /mrow /math (1) where em CS /em may be the part of the substitution matrix. could be in touch with the solvent. The full total apolar (and the complementary polar) element of the entire accessible surface INCB018424 inhibitor database area of each protein in its quaternary form was calculated with the server GETAREA http://curie.utmb.edu/getarea.html with default settings . The contribution of different atomic types to the polar area, namely oxygens, side-chain oxygens, nitrogens and side-chain nitrogens was also investigated. To compare the different surface areas of halophilic and non-halophilic proteins, they were normalized by division by the total accessible surface area of the corresponding protein. The differences between the fraction of apolar accessible surface area in the unfolded and folded form of each protein considered ( em /em ApAU-F) were calculated through the web server http://roselab.jhu.edu/utils/unfolded.html. The differences between the em /em ApAU-F in each halophilic protein and in its corresponding homolog ( em /em ApAU-F) were calculated and statistically tested. Electrostatic potential calculation The surface electrostatic potential of the proteins in their quaternary form was calculated INCB018424 inhibitor database using the program DELPHI . Salt concentration was set equal to 0, since identical environmental conditions can better delineate differences between the electrostatic potential of the halophilic and non-halophilic homolog. Internal and solvent dielectric constants were set to 4.0  and 80.0 respectively. The other parameters used were set to the default INCB018424 inhibitor database values: grid scale = 1.2, box fill = 60%, probe radius = 1.4 ?, and van der Waals surface. To compare the potential of halophilic and non-halophilic proteins of different lengths, the average atomic potential (AAP) was calculated dividing the total electrostatic potential by the total number of atoms. Statistical tests Whenever possible, differences between the structural properties considered were calculated within the two samples: the SALTIN halophilic and non-halophilic homologs, and the OSMOL halophilic and non-halophilic pairs. Differences of structural properties are denoted by em /em : for example, em /em ACA indicates halophilic minus non-halophilic apolar contact areas. The INCB018424 inhibitor database em /em s between the structural properties of halophilic enzymes and their corresponding non-halophilic counterparts were tested within samples using two statistical tests, a paired em t /em -test and a non-parametric Wilcoxon signed-rank test . In the former case the null hypothesis is that the average em /em was 0 at 0.05 em p /em -value while in the latter case the null hypothesis is that the median of the em /em s was 0 at 0.05 em p /em Rabbit Polyclonal to C56D2 -value. The parametric em t /em -test assumes that the tested data come from a normal distribution, while the Wilcoxon test it is less restrictive since it does not require such a condition. To enhance robustness of the conclusions drawn from the structural comparisons, only differences resulting significant from both tests were considered em real /em significant outcomes. Set of abbreviations em /em : prefix indicating the difference between your real estate measured in the halophilic and in the non-halophilic homologous proteins; AAP: typical atomic potential; ACA: apolar contact region; ApA: apolar available region; em INCB018424 inhibitor database /em ApAU-F: difference between ApA in the unfolded and folded condition; ASA: solvent available surface; CHC: conserved hydrophobic contacts; OSMOL: halophilic organisms adopting the “osmolytes” technique; RMSD: Root mean square deviation; SALTIN: halophilic organisms adopting the “salt-in” technique; SCR: structurally conserved area. Authors’ contributions AS and MP gathered the data, completed the calculations and analysed outcomes. AP conceived the analysis, helped to analyse outcomes and to right the manuscript. SP analysed the outcomes, drafted the manuscript and participated in research style and coordination. All authors read and authorized the ultimate manuscript and declare no conflict of curiosity. Supplementary Material Extra file 1:Desk S1 – em /em ASA in the SALTIN and OSMOL samples at conserved residues. Variations of fractional accessibility surface ( em /em ASA) in the SALTIN and OSMOL samples for different course of atoms. The variations are between your surface area areas calculated in the halophilic proteins and the corresponding.