[Protein-analysis] Re: A computer science student need some help from biologists!

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Tue Sep 26 04:09:40 EST 2006

sticker.ji at gmail.com wrote:

> So I need to know some basic protein structure knowledge in order to
> give a deeper discussion of my modeling methods' biological meanings.
> Can anyone give me some guide? Some websites or books will be useful.

This can be looked at in terms of primary structure (protein sequence)
and secondary/tertiary structure (folding of the protein chain in
space). The former point is covered in sequence data bases like Expasy,
the latter in structure data bases (Brookhaven PDB, for example on OCA).
There are some sites that try to classify proteins by secondary/tertiary
structure, e.g. SCOP, CATH and FSSP.

As for books, if you can wait a couple of weeks my own book
"Introduction to Protein Structure and Function", published by Springer,
will answer some of your questions. In the meantime, check some of the
standard books on Biochemistry (e.g. Lehninger) and Molecular Cell
Biology (e.g. Albers et al. or Lodish et al.). For a more general
overview see e.g. the Biology-textbook by Purves et al.

> * Similar functions of proteins usually results in similar sequencial
> expressions but the opposite saying is not correct.

No, proteins with similar functions have similar sequences only if they
have a common ancestor. If they developed by convergence sequences may
be quite different. On the other hand the presence of certain conserved
motives is often a good indicator for a general function, say,
nucleotide binding. 

> * The biological meanings of sequence alignments on protein sequences.

The idea here is that all life on earth ultimately descends from a
single primordial cell. In other words, all proteins also descent from a
small number of proteins present in that cell. Alignment of protein
sequences is an attempt to reconstruct the linage of todays proteins,
check for example "The Phylogenetics Handbook" by Salemi & Vandamme.

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