Bioinformatics Practicals

Practical 2
Date: 27-07-2009
Title
"Retrieval of protein sequence of HIV 1 Protease and predicting the length, molecular weight,
amino acid composition"
Objective
Understanding of Protein Primary database and study of retrieval and analyzing a protein
sequence
Introduction
Swissprot
Swiss-Prot is a manually curated biological database of protein sequences. Swiss-Prot was
created in 1986 by Amos Bairoch by the Swiss Institute of Bioinformatics (SIB) and the European
Bioinformatics Institute (EBI). Swiss-Prot strives to provide reliable protein sequences
associated with a high level of annotation (such as the description of the function of a protein,
its domains structure, post-translational modifications, variants, etc.), a minimal level of
redundancy and high level of integration with other databases.
Bioedit
BioEdit is biological sequence alignment software for windows. An intuitive multiple
document interfaces with convenient features makes alignment and manipulation of sequences
relatively easy for the desktop computer. By using Bioedit we can predict the protein sequence
molecular weight, length and amino acid composition.
SwissProt: P04585 (HIV-1 HXB2 POL) 99 amino acids (residues 57 to 155)
EMBL: K03455; AAB50259.1 [EMBL/GenBank/DDBJ]
Pfam: PF00558; UNKNOWN
SCOP: SSF50630 Acid protease
BLOCKS: P04585
Prosite: P04585
ProtoNet: P04585
ProtoMap: P04585
PDB: 1AAQ
Requirements for the analysis
OS: windows/Linux/Mac Os
Internet connection
Softwares Required: MS Office, Swissprot, Bioedit.
Methodology
I. Open the internet browser and use the url www.expasy,org
II. Enter the Swissprot Accession "P04585" of HIV 1 protease
III. Retrieve the Protein sequence in FASTA format
IV. Open the sequence in BIOEDIT software and analyse the length, molecular weight and
amino acid composition
V. Report the result
RESULTS
>Protease (Retropepsin) p15 (EC 3.4.23.16) - Human immunodeficiency virus
type 1 (HXB2 isolate) (HIV-1).
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLV
GPTPVNIIGRNLLTQIGCTLNF
Protein: Protease (Retropepsin) p15 (EC 3.4.23.16) - Human immunodeficiency virus type
1 (HXB2 isolate) (HIV-1).
Length = 99 amino acids
Molecular Weight = 10778.21 Daltons
Amino Acid Number Mol%
Ala A 3 3.03
Cys C 2 2.02
Asp D 4 4.04
Glu E 4 4.04
Phe F 2 2.02
Gly G 13 13.13
His H 1 1.01
Ile I 12 12.12
Lys K 6 6.06
Leu L 12 12.12
Met M 2 2.02
Asn N 3 3.03
Pro P 6 6.06
Gln Q 6 6.06
Arg R 4 4.04
Ser S 1 1.01
Thr T 8 8.08
Val V 7 7.07
Trp W 2 2.02
Tyr Y 1 1.01
Practical 3
Date: 29- 07-2008
Title
"Prediction of protein primary structure of HIV 1 Protease by ProtParam"
Objective
To study the protein primary structure of the protein for the given sequence
Introduction
ProtParam
ProtParam is a tool which allows the computation of various physical and chemical parameters
for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The
computed parameters include the molecular weight, theoretical pI, amino acid composition,
atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index
and grand average of hydropathicity
Methodology
I. Open internet browser and use the url http://www.expasy.org/tools/protparam.html
II. Copy and past the given sequence in the text box displayed in protparam tool
III. Click on compute parameters
IV. Report the results
RESULTS
Number of amino acids: 99
Molecular weight: 10778.7
Theoretical pI: 8.83
Total number of negatively charged residues (Asp + Glu): 8
Total number of positively charged residues (Arg + Lys): 10
Atomic composition:
Carbon C 488
Hydrogen H 802
Nitrogen N 130
Oxygen O 135
Sulfur S 4
Formula: C488H802N130O135S4
Total number of atoms: 1559
Practical 4
Date: 30-07-2009
Title
"Prediction of protein Secondary structure of HIV 1 Protease by Chou-Fasman"
Objective
To study the alpha helix, beeta sheets, coils and truns of HIV 1 Protease.
Introduction
Secondary Structure Prediction
Secondary structure in proteins consists of local inter-residue interactions mediated by
hydrogen bonds, or not. The most common secondary structures are alpha helices and beta
sheets. Other helices, such as the 310 helix and ð helix, are calculated to have energetically
favorable hydrogen-bonding patterns but are rarely if ever observed in natural proteins except
at the ends of á helices due to unfavorable backbone packing in the center of the helix.
Secondary structure of protein is mainly study of Alpha helix regions, Beeta sheets, coils and
turns. For predicting the secondary structure we have used an online server called SOPMA.
Chou-Fasman method
The Chou-Fasman method are an empirical technique for the prediction of secondary structures
in proteins, originally developed in the 1970s. The method is based on analyses of the relative
frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein
structures solved with X-ray crystallography. From these frequencies a set of probability
parameters were derived for the appearance of each amino acid in each secondary structure
type, and these parameters are used to predict the probability that a given sequence of amino
acids would form a helix, a beta strand, or a turn in a protein. The method is at most about 50-
60% accurate in identifying correct secondary structures, which is significantly less accurate
than the GOR method or modern machine learning-based techniques.
http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=misc1
Methodology
I. Open internet browser and use the url of Chou-Fasman online server
http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=misc1
II. Copy and paste the given sequence in the text box displayed in Chou-Fasman online tool
III. Click on SUBMIT
IV. Report the results
RESULTS
Practical 5
Date: 04 – 08 - 2008
Title
"Prediction of protein Secondary structure of HIV 1 Protease by SOPMA"
Objective
To study the alpha helix, beeta sheets, coils and truns of HIV 1 Protease.
INTRODUCTION
Secondary Structure Prediction
Secondary structure in proteins consists of local inter-residue interactions mediated by
hydrogen bonds, or not. The most common secondary structures are alpha helices and beta
sheets. Other helices, such as the 310 helix and ð helix, are calculated to have energetically
favorable hydrogen-bonding patterns but are rarely if ever observed in natural proteins except
at the ends of á helices due to unfavorable backbone packing in the center of the helix.
Secondary structure of protein is mainly study of Alpha helix regions, Beeta sheets, coils and
turns. For predicting the secondary structure we have used an online server called SOPMA.
SOPMA
SOPMA (Self-Optimized Prediction Method with Alignment) is an improvement of SOPM
method. These methods are based on the homologue method of Levin et al.. The improvent
takes place in the fact that SOPMA takes into account information from an alignment of
sequences belonging to the same family. SOPMA (Self-Optimized Prediction Method with
Alignment) is an improvement of SOPM method. These methods are based on the homologue
method of Levin et al.. This online server is available with swissprot. Following is the url to get
the server.
http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html
Methodology
V. Open internet browser and use the url http://npsa-pbil.ibcp.fr/cgibin/
npsa_automat.pl?page=npsa_sopma.html
VI. Copy and paste the given sequence in the text box displayed in SOPMA tool
VII. Click on SUBMIT
VIII. Report the results
RESULTS