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Protein

From Molecular Biology Wiki

Proteins are large, complex molecules composed of amino acids. The sequence of the amino acids, and thus the function of the protein, is determined by the sequence of the base pairs in the gene that encodes it. Proteins are essential to the structure, function, and regulation of cells and the functioning of the whole body. Examples of proteins are hormones, enzymes, and antibodies.

The 4 most interesting photos from Flickr for the tag 'protein'


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Contents

Protein a History of Understanding

It was known in the early 1900s that the most common proteins in the body show on the average the following percentage of elements :

Carbon 50 -55 %

Hydrogen 6.57.3%

Nitrogen 15 -17.6%

Oxygen 19 -24 %

Sulphur 32.4%

Proteins were separated into three groups :

(1) simple proteins, such as protamines, albumins, and globulins;

(2) conjugated proteins, the glucopro teins, nucleoproteins, and chromoproteins ; and

(3) the products of protein hydrolysis, infraproteins, proteoses, peptones, and polypeptides.

These were been studied both by microchemical and macro chemical methods. In the former method reagents are applied to the microscopic objects and the changes in color, etc., indicate its constitution ; e.g., iron and phosphorus may be detected in this way. Parts showing affinity for acid stains like eosin are said to be acidophile or oxyphile ; those showing affinity for basic dyes, like methylene blue, are called basophile. The chromatin is basophile, whereas the linin and cytoplasm are oxyphile. In macrochemistry large quantities of the substances are collected and examined by ordinary laboratory methods.

Because of the importance that has been assigned to the chromatin, this substance was particularly interesting. Chromatin consists of nuclein, which is a conjugated protein containing nucleic acid, the latter being an organic acid, rich in phosphorus ; it was hence called nucleoprotein.


Nucleoproteins are found chiefly in the nucleus but also occur in the cytoplasm. They differed from one another in their protein content as well as in the character of their nucleic acid constituent. When treated with dilute acids nuclein was obtained, and when this was further subjugated to caustic alkali it decomposed into protein and nucleic acid.


Protein Structure

Main article: Protein structure

Image:Proteinviews-1tim.png
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: all-atom representation colored by atom type. Middle: simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).

Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state. Although many proteins can fold unassisted simply through the structural propensities of their component amino acids, others require the aid of molecular chaperones to efficiently fold to their native states. Biochemists often refer to four distinct aspects of a protein's structure:

Image:Protein Dynamics Cytochrome C 2NEW smaller.gif
NMR structures of the protein cytochrome c in solution show the constantly shifting dynamic structure of the protein. Larger version.

Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis. In solution all proteins also undergo variation in structure through thermal vibration and the collision with other molecules, see the animation on the right.

Image:Protein Composite.jpg
Molecular surface of several proteins showing their comparative sizes. From left to right are: Antibody (IgG), Hemoglobin, Insulin (a hormone), Adenylate kinase (an enzyme), and Glutamine synthetase (an enzyme).

Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins. Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural; membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane.

A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration, are called dehydrons.



A short video about protein primary, secondary, tertiary, and quaternary structure.

How Proteins Are Made

Flickr Extension: no images found for tag protein model


Proteins are made in the process of translation, where RNA is translated on ribosomes to synthesize proteins from amino acids.

RNA is synthesized from DNA, and enters the ribosome where protein translation and synthesis occurs.

Protein Translation Video

A video about protein translation, 3D animation of protein translation.

Protein Folding

The processes of protein folding and binding can be simulated using techniques derived from molecular dynamics, which increasingly take advantage of distributed computing as in the Folding@Home project. The folding of small alpha-helical protein domains such as the villin headpiece[2] and the HIV accessory protein[3] have been successfully simulated in silico, and hybrid methods that combine standard molecular dynamics with quantum mechanics calculations have allowed exploration of the electronic states of rhodopsins.[4]


The movie presents an animation of a protein GB1 folding from denatured to the native structure. The folding process of the 56-residue protein was explored by a multiscale modeling. The multiscale simulations are based on the idea of hierarchical approach. Coarse-grained effective search of the conformational space is followed by reliable transition into the all-atom resolution.


Electrophoresis

Protein
 

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