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Assignment 5 - Protein Localization & Prediction of Protein Structure

This document provides instructions for an assignment on protein localization and structure prediction. It includes 3 questions: 1) Use Phobius to predict transmembrane segments and signal peptides for 5 protein IDs, reporting the results in a table. 2) Use ProtParam to analyze protein P29139 and report various parameters like molecular weight, pI, stability index. 3) Use comparative modeling on protein P01326 in SwissModel. Report the quality of models built using two different templates, including sequence identity, ligands, and model quality metrics.

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Việt Lê Nguyễn Hoàng
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126 views

Assignment 5 - Protein Localization & Prediction of Protein Structure

This document provides instructions for an assignment on protein localization and structure prediction. It includes 3 questions: 1) Use Phobius to predict transmembrane segments and signal peptides for 5 protein IDs, reporting the results in a table. 2) Use ProtParam to analyze protein P29139 and report various parameters like molecular weight, pI, stability index. 3) Use comparative modeling on protein P01326 in SwissModel. Report the quality of models built using two different templates, including sequence identity, ligands, and model quality metrics.

Uploaded by

Việt Lê Nguyễn Hoàng
Copyright
© © All Rights Reserved
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Download as DOCX, PDF, TXT or read online on Scribd
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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

1
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.

2
- QMEAN -6.69. This below -4 are an indication of models with low quality. 

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