Bioinformatics of Myelin Membrane Proteins - Molecules: Nucleation, Aggregation and Crystallization - page 36

databases, one needs computers and sophisticated software. For proteins,
computerized sequence analysis and three-dimensional (3D) molecular
dynamics simulations may yield information on the following:

(i) the similarities between (groups of) proteins in terms of primary,
secondary and tertiary structure;
(ii) the secondary and tertiary structure of a given protein as predicted
from its amino acid sequence;
(iii) prediction of membrane-spanning α -helices;

(iv) prediction of membrane-spanning β -sheet structures;

(v) prediction of antigenic epitopes;
(vi) how membrane lipids influence protein structure and behavior;
(vii) prediction of crystallization conditions from the amino acid sequence.

For tackling some of the above, there are good methods available, e.g.
prediction of transmembrane segments in proteins; others are hopelessly
difficult, such as prediction of the crystallizability of a protein.

Definition of Bioinformatics

For the purposes of this review, the word “bioinformatics” is defined as
follows: “any use of computers to handle biological information”
(http://wiki.bioinformatics.org/Bioinformatics, 2008), which includes
analysis of all type of sequences stored in biological databases, e.g. amino
acid sequences of proteins, nucleotide sequences, structural information
on proteins, viruses, plants, and so on. These kinds of data are inputs for
computational data analysis as required by bioinformatics.

The Basis of Biological Membranes

Biomembranes enclose or separate cells, forming compartments. In these
compartments cells may maintain a chemical or biochemical environment
that differs from the environment outside. Membranes are composed of
bilayer-forming phospholipids, other kinds of lipids such as cholesterol,
and peripheral and integral proteins. Those proteins which are not soluble