15

(continued)

Biophysics

What are the biophysical properties (solubility, stability, helix content,

etc.) of my protein?

Imaging

How can proteins be visualized and images analyzed?

IT infrastructure

Computer infrastructure, service

Drug design

Helping to create new drugs to specifically target a protein

Glycomics

How sugar residues further modify proteins. In particular, this is how

cells recognise their cell neighbours, bacteria cling to glycoproteins.

Sugar-binding proteins are called lectins

How Do I Identify Important Amino Acids for Protein Function?

The PROSITE page is particularly helpful for this.

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https://prosite.expasy.org

This examines an entered protein sequence to determine whether or not certain sequence

motifs are preserved, for example signatures (hand-curated) or profiles (automatically cal­

culated, consensus sequences, taking different sequences into account) that indicate a par­

ticular enzyme function.

This allows me to check whether my protein sequence is really an active enzyme (then

all amino acids for catalysis are complete) or whether it only looks like one. If this happens

in a genome sequence, this is termed a “pseudogene”, a “false” gene regarding the enzyme

function because important catalytic amino acids are missing and the enzyme therefore

cannot function.

In addition, the independent folding units in the protein, the protein domains, are also

examined to see whether they are present in the protein, e.g. whether all parts, i.e. domains,

are present for a functional enzyme: at least one catalytic domain (50–150 amino acids)

that carries out the enzymatic reaction. This is then often joined by numerous other types,

e.g. DNA interaction if it is a transcription factor. Examples are:

• cofactor-binding domains (if the enzyme binds a cofactor),

• regulatory domains (for switching the enzyme on and off),

• interaction domains (with other proteins or to form dimers of two identical protein units

for the enzyme, e.g. glutathione reductase only functions as a dimer, so needs an inter­

action domain for its function),

• structural domains (e.g., if it is a structural protein, like collagen).

How Can I Estimate the Protein Structure?

Structure prediction with homology modelling, for example by SWISS-MODEL, is help­

ful for this.

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https://swissmodel.expasy.org

SWISS-MODEL offers the possibility to predict the three-dimensional structure of the

protein based on the sequence.

1.2  Protein Analysis Is Easy with the Right Tool