Sanbo Qin | PubMed Health

PubMed2005

Predicting protein secondary structure and solvent accessibility with an improved multiple linear regression method.

We have improved the multiple linear regression (MLR) algorithm for protein secondary structure prediction by combining it with the evolutionary information provided by multiple sequence alignment of PSI-BLAST. On the CB513 dataset, the three states average overall per-residue accuracy, Q(3), reached 76.4%, while segment overlap accuracy, SOV99, reached 73.2%, using a rigorous jackknife procedure and the strictest reduction of eight states DSSP definition to three states. This represents an improvement of approximately 5% on overall per-residue accuracy compared with previous work. The relative solvent accessibility prediction also benefited from this combination of methods. The system achieved 77.7% average jackknifed accuracy for two states prediction based on a 25% relative solvent accessibility mode, with a Mathews' correlation coefficient of 0.548. The improved MLR secondary structure and relative solvent accessibility prediction server is available at http://spg.biosci.tsinghua.edu.cn/.

Algorithms↗

PubMed2004

Thermal and conformational stability of Ssh10b protein from archaeon Sulfolobus shibattae.

The secondary structure of the DNA binding protein Ssh10b is largely unaffected by change in temperature between 25 degrees C and 85 degrees C, indicating that the protein is highly thermostable. Here, we report the temperature-dependent equilibrium denaturation of Ssh10b in the presence of guanidine hydrochloride (GdnHCl). It was found that the transition midpoint values of the temperature (T(m)), and changes of enthalpy (DeltaH(m)) and entropy (DeltaS(m)) of Ssh10b unfolding were linearly decreasing with increasing GdnHCl concentration. The true values of the thermodynamic parameters, T(m)=402 K, DeltaH(m)=590+/-40 kJ x mol(-1) and DeltaS(m)=1.4+/-0.15 kJ x T(-1) x mol(-1), were obtained by linear extrapolation to 0 M GdnHCl. The value of the heat capacity change of Ssh10b unfolding, DeltaC(p)=3.8+/-0.2 kJ x T(-1) x mol(-1) (approx. 19 J T(-1) x mol residue(-1)), was obtained from the measured thermodynamic parameters. This is significantly smaller than that of the average value for mesophilic proteins (50 J.K(-1) x mol residue(-1)) or the value calculated from the Ssh10b structural data (64 J T(-1) x mol residue(-1)). A consequence of the small DeltaC(p) is that the DeltaG of Ssh10b is larger than that of mesophilic proteins, while the values of DeltaH and T*DeltaS are smaller. The small DeltaC(p) of Ssh10b appears to result mainly from the presence of compactness in the denatured state.

Archaeal Proteins↗