337

protein, thus giving me information about the possible function of the protein. Example

databases/programs include PROSITE, AnDom, SMART (https://smart.embl-­heidelberg.

de/), and the ELM server (eukaryotic linear motifs; https://elm.eu.org/index.html). It is

always best to use several programs and compare the results, because this is the only way

to be sure that you have found a trustworthy match. Recurring conserved regions in mul­

tiple sequences can be found using multiple alignments. These allow to compare (align)

several sequences with each other. There are various programs for this, such as MUSCLE

(Multiple Sequence Comparison by Log-Expectation; https://www.ebi.ac.uk/Tools/msa/

muscle), MAFFT (Multiple Alignment using Fast Fourier Transform; https://www.ebi.

ac.uk/Tools/msa/mafft/) and Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/).

Multiple sequence alignments can be used to find conserved regions, possible domains, or

specific differences between different sequences. Another method is phylogenetic trees,

which can be created with PHYLIP (Phylogeny Inference Package; https://evolution.

genetics.washington.edu/phylip.html), for example. In addition to a multiple sequence

alignment, one can also find the evolutionary relationship between the sequences.

Question 11.12

Answer A, C, D.

In the chosen example for the “TAR protein”, both programs should have found a double

stranded RNA-binding domain (dsRBD), suggesting that binding occurs via double

stranded RNA molecules.

20.9

­

https://www.ncbi.

nlm.nih.gov/protein/60653021?report=fasta

20.9

Question 11.13

For

this:

https://www.rcsb.org/pdb/explore/explore.do?structureId=1HSG.

Then:

https://thegrantlab.org/teaching/material/Structural_Bioinformatcs_Lab.pdf; https://sbcb.

bioch.ox.ac.uk/users/greg/teaching/docking-­2012.html. Staining of hydrophobic residues

in

the

center.

Introduction

PyMOL

here:

https://pymolwiki.org/index.php/

Practical_Pymol_for_Beginners.

Questions 11.14 to 11.21

Cellular communication is an essential process in eukaryotic and prokaryotic cells in order

to regulate important processes or to react to an external stimulus. In prokaryotes, this is

usually done by direct control, e.g. via two-component systems. A sensor activates a

responder, which then immediately triggers transcription. In this way, a rapid response is

made to an external stimulus. In eukaryotes, on the other hand, regulation is more complex

20.11  Design Principles of a Cell