What Is Protein

This section provides a quick introduction of protein, which is a peptide found in living organisms in nature. A protein is usually a long chain of amino acid residues from the 20 common amino acids, coiled and folded into a 3-dimensional conformation.

What Is Protein? - A protein is a peptide found in living organisms in nature. A protein is usually a long chain of amino acid residues from the 20 common amino acids, coiled and folded into a 3-dimensional conformation.

What Is Protein Sequence? - A protein sequence is a sequence of abbreviations of amino acids whose residues are linked by peptide bonds to form the protein. The sequence starts from the amino-terminal (N-terminal) of the chain and stops at the carboxyl-terminal (C-Terminal) of the chain.

If we connect the peptide bonds and their neighbor bonds to central C atoms of neighbor amino acid residues, it forms the backbone of the protein sequence. This backbone is also called protein backbone.

For example, the smallest protein found in nature is called Trp-Cage, which has only 20 amino acid residues linked in the following sequence:

NLYIQWLKDGGPSSGRPPPS

The following picture shows the molecule structure of the Trp-Cage protein (source: biomolecular-modeling.com). The protein backbone is shown as a darker line in the picture.

Trp-Cage Protein - Molecule Structure
Trp-Cage Protein - Molecule Structure

The following picture shows the folded 3-dimensional conformation of Trp-Cage protein found in nature (source: biomolecular-modeling.com):

Trp-Cage Protein - Folded Conformation
Trp-Cage Protein - Folded Conformation

The largest protein is call Titin, which has 27,000 amino acid residues.

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

Protein and Amino Acid

 What Is Amino Acid

 The 20 Common Amino Acids

 Peptide, Peptide Bond, Amino Acid Residues

What Is Protein

 Protein Structure Levels

 Alpha Helix and Beta Sheet

 Protein Visualization - Ribbon Diagram

 Composed Proteins or Protein Complexes

 wwpdb.org - Worldwide PDB (Protein Data Bank)

 What Is FASTA

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB