Structural bioinformatics
Three-dimensional structure of a protein
Structural bioinformatics is the branch of bioinformatics that is
related to the analysis and prediction of the three-dimensional
structure of biological macromolecules such as proteins, RNA,
and DNA.
It deals with generalizations about macromolecular 3D
structures such as comparisons of overall folds and local motifs,
principles of molecular folding, evolution, binding interactions,
and structure/function relationships, working both from
experimentally solved structures and from computational models.
The term structural has the same meaning as in structural
biology, and ……structural bioinformatics can be seen as a part
of computational structural biology.
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.
Protein structure
The structure of a protein is directly related to its function.
……..The presence of certain chemical groups in specific locations
allows proteins to act as enzymes, catalyzing several chemical
reactions.
In general, protein structures are classified into four levels
primary (sequences), secondary (local conformation of the
polypeptide chain), tertiary (three-dimensional structure of the
protein fold), and quaternary (association of multiple polypeptide
structures).
Structural bioinformatics mainly addresses interactions among
structures taking into consideration their space coordinates.
Thus, the primary structure is better analyzed in traditional
branches of bioinformatics. ……. However, the sequence implies
restrictions that allow the formation of conserved local
conformations of the polypeptide chain, such as alpha-helix, beta-
sheets, and loops
(Secondary structure ). …..Also… weak interactions (such
as hydrogen bonds) stabilize the protein fold.
Interactions could be intrachain, i.e., when occurring between
parts of the same protein monomer (tertiary structure),
or interchain, i.e., when occurring between different structures
(quaternary structure).
Finally, the topological arrangement of interactions, whether
strong or weak, and entanglements is being studied in the field of
structural bioinformatics, utilizing frameworks such as circuit
topology.
Structure visualization
Structural visualization of BACTERIOPHAGE T4
LYSOZYME (PDB ID: 2LZM). (A) Cartoon; (B) Lines; (C)
Surface; (D) Sticks.
Protein structure visualization is an important issue for structural
bioinformatics. …… It allows users to observe static or dynamic
representations of the molecules,…. also ….allowing the detection
of interactions that may be used to make inferences()االستدالالت
about mlecmoular mechanisms.
The most common types of visualization are:
Cartoon: this type of protein visualization highlights the secondary
structure differences. In general, α-helix is represented as a type of
screw(spiral), β-strands as arrows, and loops as lines.
Lines: each amino acid residue is represented by thin lines, which
allows a low cost for graphic rendering.
Surface: in this visualization, the external shape of the molecule is
shown.
Sticks: each covalent bond between amino acid atoms is
represented as a stick. This type of visualization is most used to
visualize interactions between amino acids...
DNA structure
The classic DNA duplexes structure was initially described
by Watson and Crick (and contributions of Rosalind Franklin).
…….The DNA molecule is composed of three substances:
a phosphate group, a pentose, and a nitrogen base
(adenine, thymine, cytosine, or guanine).
The DNA double helix structure is stabilized by hydrogen bonds
formed between base pairs: adenine with thymine (A-T) and
cytosine with guanine (C-G).
Many structural bioinformatics studies have focused on
understanding interactions between DNA and small molecules, which has
been the target of several drug design studies.
