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RAMAKRISHNA MISSION VIVEKANANDA CENTENARY COLLEGE

RAHARA,KOLKATA-700118

PROJECT REPORT SUBMITTED BY Soumyadeep Saha Mondal

ADMIT ROLL NO-2023111184
COLLEGE ROLL NO-508
REGISTRATION NO-A01-1112-115-008-2023
Department of Zoology
TOPIC-3D STRUCTURE REPRESENTATION OF A DECAPEPTIDE MOLECULE
▶BY USING JMOL APPLICATION◀
For partial fulfillment of MULTIDISCIPLINARY COURSE (MD 1)
1ST YEAR (SEMESTER I)
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3-D STRUCTURE REPRESENTATION OF A DECAPEPTIDE

MOLECULE BY USING JMOL APPLICATION
➥DEFINITION OF DECAPEPTIDE-
A decapeptide is a polypeptide made up of a chain of ten amino acids.It is an oligopeptide
formed from ten amino acids.
In this 3-d representation project I’ll draw a decapeptide molecular structure with the help of
JMOL application.
A Decapeptide molecule is consists of 10 amino acids i.e.
1.Glycine
2.Arginine
3.Tryptophan
4.Alanine
5.Glutamine
6.Leucine
7.Methionine
8.Proline
9.Valine
10.Asparagine

Gly-Arg-Trp-Ala-Glu-Leu-Met-Pro-Val-Asp is the sequence of a decapeptide

STEP BY STEP PROCEDURE BY USING JMOL-
● STEP-1➤ At first we’ll open JMOL,after opening JMOL open get mol from File menu.
● STEP-2➤ And then through get mol we’ll placed a start codon i.e. Methionine,in
Methionine we’ll attach a peptide which is CONH2 by replacing a single bonded oxygen
atom using the model kit menu and adding Nitrogen to it.
3D-Structure using JMOL after opening Methionine➠
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● STEP-3➤ Now sequence wise we’ll add Glycine to the start codon i.e. Methionine by
adding one -CH2 & one -COOH group to it.
3D-Structure using JMOL after attaching attaching Glycine➠

● STEP-4➤ After addition of glycine according to the sequence we’ll attach Arginine to
the structure by replacing the single bonded Oxygen or -OH group and adding NH2 &
other groups like -COOH and the Carbon atoms to it serial wise with energy
minimizing.
3D-Structure using JMOL after attaching Arginine➠
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● STEP-5➤ In this step we’re going to attach Tryptophan by modifying the terminal
single bonded Oxygen atom or -OH group with NH2 & adding the α-amino group,an
α-carboxylic acid group,and a side chain indole respectively with energy minimizing.
3D-Structure using JMOL after attaching Tryptophan➠

● STEP-6➤ After adding tryptophan to the molecular structure we’ll connect Alanine to
it by replacing again the single bonded Oxygen atom or -OH group attached already
with Tryptophan & by formatting the other groups of alanine i.e. -COOH,CH3 with
energy minimizing.
3D-Structure using JMOL after attaching Alanine➠
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● STEP-7➤ Now in this step we’ll try to join the Glutamine according to the sequence,as
usual we’ll change the single bonded Oxygen atom or -OH group of Alanine with the
-NH2 group & place the other atoms like -CO,-COOH with energy minimizing.
3D-Structure using JMOL after attaching Glutamine➠

● STEP-8➤ In the current step we’ll draw & attach Leucine with respective structure by
modifying again the single bonded oxygen atom or -OH group with NH2 attached to
Glutamine and by joining two Methyl groups (-CH3) & one -COOH group to it with
energy minimizing.
3D-Structure using JMOL after attaching Leucine➠
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● STEP-9➤ Now we’ll add Proline with the respective structure by replacing again the
single bonded Oxygen atom attached already with Leucine & by attaching the -COOH
group to it with energy minimizing.
3D-Structure using JMOL after attaching Proline➠

● STEP-10➤ Now we’ve to join Valine with the sequence accordingly by replacing the
-OH (Hydroxyl group) with NH2 & by attaching the groups i.e. Methyl & -COOH group
with energy minimizing.
3D-Structure using JMOL after attaching Valine➠
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● STEP-11➤ At the end of the sequence of decapeptide we’ve to attach the Asparagine to
the sequence by again replacing the hydroxyl group (-OH) attached with Valine by
adding the two -NH2 groups,-CO group & one -COOH group to finish the decapeptide
structure.
Final 3D-Structure using JMOL after attaching Asparagine➠