 Protein sequence databases: Pfam, Swiss-Prot, PROSITE, NCBI…

 Protein structure databases: RCSB of PBD, Structural Classidication of

Protein…

 Protein model databases: Protein Model Portal, Swiss-model, ModBase…

 Protein expression databases: Human Protein Atlas

1. Sequencing DNA molecules is
so much easier and cheaper
2. Most of the corresponding
proteins have never actually
been isolated by anyone
3. Real proteins almost never
behave as you’d expect – post
translational modification
 Mass Spectrometry: the protein “sequencing” method based
on masses of particles and the elemental composition
 NMR: can determine the structure of many compounds by
studying the peaks of nuclear magnetic resonance spectra
 X-ray crystallography: the determination of the structure of a
crystal by the use of x-ray diffraction
Resolution
‐ 1.2 Å -- Excellent -- backbone and most sidechains very
clear. Some hydrogens may be resolved
‐ 2.5 Å -- Good -- backbone and many sidechains clear.
‐ 3.5 Å -- OK -- backbone and bulky sidechains mostly clear.
‐ 5.0 Å -- Poor -- backbone mostly clear; sidechains not clear.
1. Finding main physico-chemical properties Molecular weight
Extinction coefficients
Instability
Half-life
2. Digesting protein with proteases
3. Locating transmembrane segment Hydrophobic regions
Hydrophilic stretches
Coiled-coil regions
4. Predicting post-translational modifications
5. Scanning domains/motifs
6. …
7. 3D-structure works
 Search for UniProt database. There are 2 UniProt
Knowledgebases (UniProtKB) Swiss-Prot and TrEMBL.
Give the number of data in each UniProtKB. Whats is
difference between them? How can we know the data
in which UniProtKB? Protein database UniProt

 Search for protein name epidermal growth factor

receptor in human. How many results are given? How
many of them were reviewed by Swiss-Prot?
 Choose P00533, look for protein name and its
alternative name(s), length of canonical sequence
and other isoforms. How many publications were
included in this entry? List name and number of
function sites and function regions. Show the features
in graphic format.
 Search for neXtProt database. What is it? When is the
lastest release date? What are data sources supported
neXtProt? How many proteins exist in neXtProt?
 Search for P00533, give information for exons which
coding for different isoforms. Does UniProt provide Protein database
neXtProt
this kind of information?
 Go to The Human Protein Atlas. What types of atlas
are provided?
 Go to https://www.expasy.org/proteomics, look
for 5 tools which are used to predict the main
physico-chemical properties of protein. List names
and URL address.
 Use ProtParam tool to search for properties in Physico-chemical
properties
protein, report the results. What is pI, Extinction
&
coefficients, Instability and Half-life? Give 1 sentence
Protein digestion
for each definition.
 Using PeptideCutter in ExPASy to digest the given
protein by Clostripain, Enterokinase, Proteinase K
and Trypsin. Report the number of cleavages given
by each enzyme.
 Use 2 tools DAS-TMfilter and TMHMM v2.0
(http://mendel.imp.ac.at/sat/DAS/DAS.html,
http://www.cbs.dtu.dk/services/TMHMM/)
and 2 provided sequences, predict the trans-
membrane regions and compare the results. Primary structure
analysis
 Predict the post-translational modifications (PTMs)
&
by using Motif Scan in https://myhits.isb-
Post-translational
sib.ch/. Seach in all profiles and patterns, give modification
comparison and conclusion. Give 1-sentence
definition for those PTMs.
 Go to MEME tool in The MEME Suite
(http://meme-suite.org/). What is MEME?
 Do the searching with following parameters. Give
the result and make conclusion. What is e-value of
longest motif and shortest motif?
Domains/Motif scanning
 You already thought about interesting thing, now
give me the information:
 Organism & Gene name

 In which chromosome
Introduction
 Does it have data on GenBank? How many?
Which ID?
 Does it have information on UniProt database?
How many? Which ID?
 Remember, this will be your project.