Re: Can we predict the function of a protein by its amino acid sequence ?

Yes and no. Amino acid sequence determines the secondary and tertiary structure of protein. On the other hand the biological function is closely related to the protein structure and conformational changes accompanying the protein activity. Thus we can say that there is close relationship between amino acid sequence (primary structure) and function of the protein. But the question is if we are able to predict theoretically protein function by knowing its primary structure only.

There are numerous tools, algorithms and programs which are to predict the secondary, tertiary or quarternary structure of proteins. The ones predicting the secondary structure do it with accuracy 50-75% depending on the algorithm. Some of them (non statistical ones) are claimed to give accuracy of more than 80%. These programs are powerful tools in such fields like protein modelling, protein engineering, theoretical protein biochemistry, bioinformatics etc. The other group are matrices and algorithms generated for comparative analysis of protein homology, multiple alignment, study of protein similarity, variability, evolution, fragments essential for their activity etc. Generally all protein databases are provided with such programs. Once you know the amino acid sequence of a protein of known function and if you know which fragments play important role, it is very likely that other proteins with similar fragments of homologous sequence have the same or similar function.

However the present knowledge is not sufficient enough to make 100% sure that a certain sequence will reveal a theoretically predicted function. Also we should remember that proteins are often multifunctional and not always all of them are known. We are able to predict some possible biological activities (like enzymatic activities, inhibitory activities, location of anitenic determinants), but there is no proof that this activity is the essential one. Anyway if you intend to construct a new protein with a specific activity by means of amino acid sequence determining its biological role - you can try it. It is possible (to some extent).