This module contains motivational and biochemical background material for a computer scientist beginning to learn about computational structural biology.
Topics in this module
Proteins and Their Significance to Biology and Medicine
Protein Structure
Experimental Methods for Protein Structure Determination
Protein Structure Repositories
Visualizing Protein Structures
Proteins and their significance to biology and medicine
Proteins are the molecular workhorses of all known biological systems. Among other functions, they are the motors that cause muscle contraction, the catalysts that drive life-sustaining chemical processes, and the molecules that hold cells together to form tissues and organs.
The following is a list of a few of the diverse biological processes mediated by proteins:
Proteins called enzymes catalyse vital reactions, such as those involved in metabolism, cellular reproduction, and gene expression.
Regulatory proteins control the location and timing of gene expression.
Cytokines, hormones, and other signalling proteins transmit information between cells.
Immune system proteins recognize and tag foreign material for attack and removal.
Structural proteins prevent cells from collapsing on themselves, as well as forming large structures such as hair, nails, and the protective, largely impermeable outer layer of skin. They also provide a framework along which molecules can be transported within cells.
The estimate of the number of genes in the human genome has been changing dramatically since it was annotated (the latest gene count estimates can be found in this
Wikipedia article on the human genome ). Each gene encodes one or more distinct proteins. The total number of distinct proteins in the human body is larger than the number of genes due to
alternate splicing . Of those, only a small fraction have been isolated and studied to the point that their purpose and mechanism of activity is well understood. If the functions and relationships between every protein were fully understood, we would most likely have a much better understanding of how our bodies work and what goes wrong in diseases such as cancer, amyotrophic lateral sclerosis, Parkinson's, heart disease and many others. As a result, protein science is a very active field. As the field has progressed, computer-aided modeling and simulation of proteins have found their place among the methods available to researchers.
Protein structure
An amino acid is a simple organic molecule consisting of a basic (hydrogen-accepting), amine group bound to an acidic (hydrogen-donating) carboxyl group via a single intermediate carbon atom:
An α-amino acid
A generic α-amino acid. The "R" group is variable, and is the only difference between the 20 common amino acids. This form is called a zwitterion, because it has both positive and negatively charged atoms. The zwitterionic state results from the amine group (NH2) gaining a hydrogen atom from solution, and the acidic group (COO) losing one. During the translation of a gene into a protein, the protein is formed by the sequential joining of amino acids end-to-end to form a long chain-like molecule, or
polymer . A polymer of amino acids is often referred to as a
polypeptide . The genome is capable of coding for 20 different amino acids whose chemical properties depend on the composition of their
side chains ("R" in the above figure). Thus, to a first approximation, a protein is nothing more than a sequence of these amino acids (or, more properly, amino acid
residues , because both the amine and acid groups lose their acid/base properties when they are part of a polypeptide). This sequence is called the
primary structure of the protein.
A polypeptide
A generic polypeptide chain. The bonds shown in yellow, which connect separate amino acid residues, are called
peptide bonds . The
Wikipedia entry on amino acids provides a more detailed background, including the structure, properties, abbreviations, and genetic codes for each of the 20 common amino acids.
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Source:
OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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