BT203IU Bioinformatics

Assignment 4

Protein localization & Prediction of protein structure

Due date: 20:00, 2 Dec. 2019

(Submission via email is acceptable)

Question 1: Performing Phobius for the following protein identifier, whether they have trans-
membrane segments if so specify how many are present and their position (the starting and ending
amino acids). Whether they have a signal peptide if so what are the starting and ending amino acids
of N-region, H-region and C-region. Prepare the results as a table.

a. Q6IWH7
b. P0C9J4
c. P14009
d. Q43495
e. P50927

Question 2: Performing ProtParam for the accession number P29139. Report the following
parameters:

a. Number of amino acids

- 326
b. Molecular weight
- 35173.62
c. Theoretical pI
4.73
d. Total number of negatively charged residues (Asp + Glu)
- 47
e. Total number of positively charged residues (Arg + Lys)
- 28
f. Extinction coefficient
- Extinction coefficients:

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient 26025

Abs 0.1% (=1 g/l) 0.740, assuming all pairs of Cys residues form cystines

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 Ext. coefficient 25900
Abs 0.1% (=1 g/l) 0.736, assuming all Cys residues are reduced.
g. In vivo half-life

30 hours (mammalian reticulocytes, in vitro).

>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).

h. The instability index (II)

- The instability index (II) is computed to be 29.84

i. Is this protein acidic or basic and stable or unstable?
-

Question 3: Performing Comparative modelling for P01326 (https://swissmodel.expasy.org/)

a. What can you say about the structural similarity of top-four templates? What ligands are present
in each of them?
b. Build model with a template 1efe.1.A. Report sequence identity. What can you conclude about
the quality of this modelling?
c. Build model with a template 1zei.1.A. Report sequence identity & types of ligands in this
template. What can you conclude about the quality of this modelling?

- ID : 1zei.1.
- Chain: A.
- coverage rate: 25.
- GMQE: 0.51 above 0.5, it means that this sequence stay at standard of reliability.
- QSQE: 0.54 below 0.7, it mean that this it can not be considered reliable to follow the
predicted quaternary structure in the modelling process.
- Resolution: 1.9Å.
- state of oligo: homo-hexamer.
- Identity: 96.79%.
- None types of ligands.

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- QMEAN -6.69. This below -4 are an indication of models with low quality.