Structural bioinformatics deals with prediction of 3-D structures of biological macromolecules such as proteins, DNA, RNA etc., basing on the data obtained from studies with the help of technique like X-ray crystallography, NMR etc. PDB is now essential for any study in structural biology. It is a freely accessible database of biological macromolecules.

1. STRUCTURAL
BIOINFORMATICS AND
PDB
Janmoni Borah
Assistant Professor
Department of Zoology
BarnagarCollege
Sorbhog, Barpeta,Assam 781317
Email-Janmoniborah16@gmail.com

2. Structural Bioinformatics
Structural Bioinformatics is the branch of bioinformatics
that is related to analysis and prediction of 3-D
structures of biological macromolecules such as
proteins, DNA, RNA etc.
The main objective of structural bioinformatics is the
creation of new methods of analysing and manipulating
biological macromolecular data in order to solve
problems in biology and generate new knowledge.
Structural bioinformatics plays important role in solving
problems of evolutionary biology, drug discovery etc.

3. PDB(Protein Data Bank)
The Protein Data Bank is a database for the 3-D structural data
of large biological molecules, such as proteins and nucleic acids.
The 3-D structures are submitted voluntarily by researchers
around the globe and are obtained by using techniques such as
X-ray crystallography, NMR spectroscopy, cryo-electron
microscopy etc.
The structures and all stored information are freely available on
the internet via the websites of the member organizations of
PDB like RCSB, PDBe, PDB etc.
It was announced in 1971 as a joint venture between Cambridge
Crystallographic Data Centre UK and Brookhaven National
Laboratory US.

4.  In 2003, wwPDB was established and PDB became an international
organization. The founding members were PDBe (Europe), RCSB
(Research Collaboratory for Structural Bioinformatics, USA) and
PDBj (Japan). In 2006, BMRB (Biological Magnetic Resonance Data
Bank) joined the collaboration.
The official websites are
(1) www.wwpdb.org
(2) www.pdbe.org
(3) www.rcsb.org/pdb
(4) www.bmrb.wisc.edu
(5)www.pdbj.org

5. Experimental
Method
Proteins NucleicAcids
Protein/Nucleic
Acid
complexes
Other Total
X-ray diffraction 135170 2097 6945 4 144216
NMR 11337 1325 264 8 12934
Electron
microscopy
3475 35 1136 0 4646
Hybrid 155 5 3 1 164
Other 286 4 6 13 309
Total: 150423 3466 8354 26 162269
Table-Total structures available in PDB as of April 1, 2020 (Source-
https://en.wikipedia.org/wiki/Protein_Data_Bank

7. Photo- Homepage of RCSB

8. Basics of Protein structure
Protein structure is the three dimensional arrangement
of atoms in an amino-acid chain molecule.
Proteins are polymers of amino acids. Proteins form by
amino acids undergoing condensation reactions, in
which the amino acids lose one water molecule per
reaction in order to attach to one another with a peptide
bond.
A chain under 30 amino acid residues is often termed as
a peptide, rather than a protein.

9. Fig:The carboxylic and amino groups of successive amino acids undergo
condensation reaction to form a peptide(covalent) bond.
Source-https://www.mun.ca/biology/scarr/iGen3_06-03.html

10. Levels of Protein structure
To be able to perform their biological functions, proteins fold
into one or more specific spatial conformations driven by a
number of non-covalent interactions such as hydrogen bonding,
ionic interactions, Van der Waals force, and hydrophobic
packing.
There are four distinct levels of protein structures. They are
termed as the primary, secondary, tertiary and quaternary
structures.

11. Primary structure of Protein
The simplest level of protein structure, primary structure is
simply the sequence of amino acids in a polypeptide chain.
The individual amino acid residues are held together by peptide
bonds in a polypeptide.
Each protein or polypeptide has its own set of amino acids,
assembled in a particular order. This order is determined by the
particular gene coding for the protein.
Each polypeptide chain has an N-terminus and a C-terminus.
For example, the hormone insulin has two polypeptide chains, A
and B.

12. Fig-Primary structure of Human insulin.
Source-https://www.quora.com/What-is-the-structure-of-insulin-primary-secondary-or-tertiary

13. Secondary structure
The next level of protein structure, secondary structure refers to
local folded structures that form within a polypeptide due to
interactions between the atoms of the backbone.
The backbone of a polypeptide refers to polypeptide chain apart
from the R-groups.
The most common types of secondary structures are the α-
helix and β pleated sheet.
Both α-helix and β pleated sheet are held in shape by hydrogen
bonds, which form between the carbonyl O of one amino acid
and the amino H of another.

14. Fig: Secondary structure of protein
(Modified from https://owlcation.com/stem/What-Are-Proteins-Part-3-of-3
Beta pleated sheet
Alpha helix
Loop

15. α-helix
In an α-helix, the carbonyl (C=O) of one amino acid is
hydrogen bonded to the amino H (N-H) of an amino acid
that is four down the chain.(eg., the carbonyl of amino acid
1 would form a hydrogen bond to the N-H of amino acid 5)
This pattern of hydrogen bonding pulls the polypeptide
chain into a helical structure that resembles a curled ribbon,
with each turn of the helix containing 3.6 amino acids.
The R groups of the amino acids in the helix stick outward
from the helix, where they are free to interact with other
chemiacal species.

16. Source-https://www.quora.com/What-level-of-protein-
structure-is-alpha-helix

17. https://www.dreamstime.co
m/illustration/alpha-
helix.html
https://www.researchgate.net/figure/a-helix-structure-
6_fig26_324706585

18. β pleated sheet
In β pleated sheet, two or more segments of a polypeptide chain
line up next to each other, forming a sheet-like structure held
together by hydrogen bonds.
The hydrogen bonds form between carbonyl and amino groups
of backbone, while the R groups extend above and below the
plane of the sheet.
The strands of the sheet may be parallel, pointing in the same
direction (meaning their N- and C-termini match up), or anti-
parallel, pointing in opposite directions (meaning that the N
terminus of one strand is positioned next to the C-terminus of
the other.)

19. Source-https://www.chegg.com/learn/chemistry/introduction-
to-chemistry/secondary-structure

20. Tertiary structure
The overall three dimensional structure of a polypeptide is
called its tertiary structure.
The tertiary structure is primarily due to interactions between
the R groups of the amino acids that make up the protein.
R group interactions that contribute to tertiary structure include
hydrogen bonding, ionic bonding, dipole-dipole interactions,
hydrophobic interactions etc.
Three dimensional or tertiary structure of a protein is crucial for
its function. An enzyme may become non-functional if it’s
tertiary structure is destabilized or lost.

21. Fig-3-D structure of a protein (Source-https://www.nature.com/articles/d41586-020-03348-4)

22. Quaternary structure
Many proteins are made up of a single polypeptide chain and have
only three levels of structure. However, some proteins are made up of
multiple polypeptide chains, also known as subunits. When these
subunits come together, they give the protein its quaternary structure.
n general, the same types of interactions that contribute to tertiary
structure (mostly weak interactions, such as hydrogen bonding and
dispersion forces) also hold the subunits together to give quaternary
structure.
For example, hemoglobin is made up of four subunits, two each of the
β types. Another example is DNA polymerase, an enzyme that
new strands of DNA and is composed of ten subunits^55start
end superscript.

23. Quaternary structure of haemoglobin
Source-
https://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/PS_2B3_Levels_Struct.html

24. ThankYou