Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization

BMC Bioinformatics

Proceedings

Gaihua Zhang¹  Zhen Su¹ 

[1] State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100094, Beijing, People's Republic of China;

关键词: Secondary Structure;    Sequence Alignment;    Evolutionary Distance;    Structural Comparison;    Protein Structure Prediction;   

DOI  :  10.1186/1471-2105-13-S15-S12

来源: Springer

【 摘 要 】

BackgroundWork on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable.ResultsTo investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different.ConclusionProteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

【 授权许可】

CC BY   
© Zhang and Su; licensee BioMed Central Ltd. 2012