Overview of Protein Structure

Proteins are complex molecules play a vital role and involved in every process within cells. The
Protein is a linear copolymer built from a sequence of molecules called amino acids, referred to
residue, arranged linearly. Naturally, there are 20 kinds of amino acids build up all proteins.
Amino acids are made of amine group (H2N), carboxyl group (COOH) and a side chain (R) that
differs from one amino acid to another. Amino acids are connected by peptide bonds between
the carboxyl and amino groups of any two adjacent amino acids to form one protein. Amino
acids can be classified into several groups according to some features and properties they may
have. They can be classified according to their charge, size and functional group. Such properties
play a main role in protein structure folding and protein-protein interactions. For example, the
location of some amino acids determined by its charge, while hydrophobic amino acids (i.e., Leu,
Ile, and Val) buried in the middle of the protein, hydrophilic amino acids like to be in the outer
shell of the protein.

Structure of Protein can be expressed to four levels as follow:

1. Primary Structure: refers to the sequence number and order presents of amino acids in the
protein.
2. Secondary structure: refers to a regular sub-conformational structure formed by consecutive
amino acids stabilized by hydrogen bonds (H-bonds). The most common examples of secondary

structures are alpha-helices (α-Helices), beta-sheets (β- Sheets), and turns/loops. The two secondary
structures, helices and sheets, are geometry stabilized by hydrogen bonds between amino acids peptide
groups. Different regions on the polypeptide chain may adopt different secondary structures according
to the primary sequence of amino acids in the protein.

1. i)  α-Helix: The conformation of the α-helix is stabilized by H-bonding between N-H group and
C=O group of peptide bonds four residues apart. The orientation of such a conformation
produces a helical coiling of the peptide backbone such that the side chain groups stem out of
the helix coil and perpendicular to its axis. Not all amino acids prefer forming alpha helices due
to some constraints of their side chains.
2. ii)  b. β-sheet: the second common conformation after α-helix. It is composed of two or more
different segments (strands) of stretches along the primary structure of the protein. The
conformation of the β-sheet is stabilized by H-bonding between N-H group of one strand with
C=O group of an adjacent strand.
3. iii)  c. Turns: refers to the close approach of two consecutive Cα atoms (less than 7Å) in which
residues do not form any kind of other secondary structure (i.e., α-helix or β-sheet). Turns can
be classified into many types according to the number of residues separate the two ends
residues.

3. Tertiary Structure: refers to the complete three-dimensional (3D) structure of a single protein
molecule. It defines the spatial relationship of different secondary structures to one another
within a polypeptide chain and describes the relationship of different domains to one another
within a protein.
 4. Quaternary Structure: refers to multiple polypeptide chains may form the protein molecule. The
quaternary structure is stabilized by the same non-covalent interactions and disulfide bonds as
the tertiary structure.

The Protein Data Bank (PDB) is an archive of experimentally determined 3D structures of biological
macromolecules that serves a global community of researchers, educators, and students. The data
contained in the archive include atomic coordinates, crystallographic structure factors and NMR
experimental data. Aside from coordinates, each deposition also includes the names of molecules,
primary and secondary structure information, sequence database references, where appropriate, and
ligand and biological assembly information, details about data collection and structure solution, and
bibliographic citations.

The pdb file format is a textual file format describing the 3D structures of molecules held in the Protein
Data Bank. For more information about the format of pdb files, you may visit
(http://www.wwpdb.org/documentation/file-format).