Datasheet

The protein molecule itself is made when a free NH
2
group links chemically
with a COOH group, forming the peptide bond CO-NH. Figure 1-2 shows a
schematic picture of the resulting chain.
As a result of this chaining process, your protein molecule is going to be left
with an unused NH
2
at one end and an unused COOH at the other end. These
extremities are called (respectively) the
N-terminus and C-terminus of the
protein chain. This is important to know because scientific convention (in
books, databases, and so on) defines the
sequence of a protein — or of a
protein fragment — as the succession of its constituent amino acids, listed
in order from the N-terminus to the C-terminus. The sequence of our (short!)
demo protein is then
MAVLD= Met-Ala-Val-Leu-Asp= Methionine–Alanine-
Valine–Leucine-Aspartic
Working with protein 3-D structures
The precise succession of a protein’s constituent amino acids is what defines
a given protein molecule. This ribbon of amino acids, however, is not what
M A V L D
CO-NH CO-NH CO-NH CO-NH COOHNH2
Figure 1-2:
Amino acids
chained
together to
constitute a
protein
molecule.
M
COOH
NH2
L
COOH
NH2
A
COOH
NH2
V
COOH
NH2
D
COOH
NH2
C
COOH
NH2
Figure 1-1:
Free amino
acids
floating
around.
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Part I: Getting Started in Bioinformatics
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