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The primary structure of a protein is easily obtainable from its corresponding gene sequence, as well as by experimental manipulation. Unfortunately, the primary structure is only indirectly related to the protein's function. In order to work properly, a protein must fold to form a specific three-dimensional shape, called its native structure or native conformation . The three-dimensional structure of a protein is usually understood in a hierarchical manner. Secondary structure refers to folding in a small part of the protein that forms a characteristic shape. The most common secondary structure elements are α-helices and β-sheets , one or both of which are present in almost all natural proteins.

Secondary structure: α-helix

α-helices, rendered three different ways. Left is a typical cartoon rendering, in which the helix is depicted as a cylinder. Center shows a trace of the backbone of the protein. Right shows a space-filling model of the helix, and is the only rendering that shows all atoms (including those on side chains).

Secondary structure: β-sheet

Cartoon representation

Different parts of the polypeptide strand align with each other to form a β-sheet. This β-sheet is anti-parallel , because adjacent segments of the protein run in opposite directions.

Ribbon representation

β-sheets are sometimes referred to as β pleated sheets, because of the regular zig-zag of the strands evident in this representation.

Bond representation

Each segment in this representation represents a bond. Unlike the other two representations, side chains are illustrated. Note the alignment of oxygen atoms (red) toward nitrogen atoms (blue) on adjacent strands. This alignment is due to hydrogen bonding, the primary interaction involved in stabilizing secondary structure.
Beta-sheets represented in three different rendering modes: cartoon, ribbon, and bond representations.
Tertiary structure refers to structural elements formed by bringing more distant parts of a chain together into structural domains . The spatial arrangement of these domains with respect to each other is also considered part of the tertiary structure. Finally, many proteins consist of more than one polypeptide folded together, and the spatial relationship between these separate polypeptide chains is called the quaternary structure . It is important to note that the native conformation of a protein is a direct consequence of its primary sequence and its chemical environment, which for most proteins is either aqueous solution with a biological pH (roughly neutral) or the oily interior of a cell membrane. Nevertheless, no reliable computational method exists to predict the native structure from the amino acid sequence, and this is a topic of ongoing research. Thus, in order to find the native structure of a protein, experimental techniques are deployed. The most common approaches are outlined in the next section.

Experimental methods for protein structure determination

A structure of a protein is a three-dimensional arrangement of the atoms such that the integrity of the molecule (its connectivity) is maintained. The goal of a protein structure determination experiment is to find a set of three-dimensional (x, y, z) coordinates for each atom of the molecule in some natural state. Of particular interest is the native structure, that is, the structure assumed by the protein under its biological conditions, as well as structures assumed by the protein when in the process of interacting with other molecules. Brief sketches of the major structure determination methods follow:

X-ray crystallography

The most commonly used and usually highest-resolution method of structure determination is x-ray crystallography . To obtain structures by this method, laboratory biochemists obtain a very pure, crystalline sample of a protein. X-rays are then passed through the sample, in which they are diffracted by the electrons of each atom of the protein. The diffraction pattern is recorded, and can be used to reconstruct the three-dimensional pattern of electron density, and therefore, within some error, the location of each atom. A high-resolution crystal structure has a resolution on the order of 1 to 2 Angstroms (Å). One Angstrom is the diameter of a hydrogen atom (10^-10 meter, or one hundred-millionth of a centimeter).

Questions & Answers

how can chip be made from sand
Eke Reply
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Almas
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Joseph
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There are lots of products of nano chemistry... Like nano coatings.....carbon fiber.. And lots of others..
learn
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da
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Giriraj
Preparation and Applications of Nanomaterial for Drug Delivery
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revolt
da
Application of nanotechnology in medicine
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narayan
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ya I also want to know the raman spectra
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Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
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Professor
Nasa has use it in the 60's, copper as water purification in the moon travel.
Alexandre
nanocopper obvius
Alexandre
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
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LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
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Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
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Rafiq
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Any one who tell me about Preparation and application of Nanomaterial for drug Delivery
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Bob Reply
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Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
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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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