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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

can someone help me with some logarithmic and exponential equations.
Jeffrey Reply
sure. what is your question?
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I don't understand what the A with approx sign and the boxed x mean
it think it's written 20/(X-6)^2 so it's 20 divided by X-6 squared
I'm not sure why it wrote it the other way
I got X =-6
ok. so take the square root of both sides, now you have plus or minus the square root of 20= x-6
oops. ignore that.
so you not have an equal sign anywhere in the original equation?
Commplementary angles
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algebra 2 Inequalities:If equation 2 = 0 it is an open set?
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or infinite solutions?
The answer is neither. The function, 2 = 0 cannot exist. Hence, the function is undefined.
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Kristine 2*2*2=8
Bridget Reply
Differences Between Laspeyres and Paasche Indices
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No. 7x -4y is simplified from 4x + (3y + 3x) -7y
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J, combine like terms 7x-4y
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Need to simplify the expresin. 3/7 (x+y)-1/7 (x-1)=
Crystal Reply
. After 3 months on a diet, Lisa had lost 12% of her original weight. She lost 21 pounds. What was Lisa's original weight?
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what's the easiest and fastest way to the synthesize AgNP?
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types of nano material
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Yes, Nanotechnology has a very fast field of applications and their is always something new to do with it...
Himanshu Reply
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In this morden time nanotechnology used in many field . 1-Electronics-manufacturad IC ,RAM,MRAM,solar panel etc 2-Helth and Medical-Nanomedicine,Drug Dilivery for cancer treatment etc 3- Atomobile -MEMS, Coating on car etc. and may other field for details you can check at Google
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after 100 year this will be not nanotechnology maybe this technology name will be change . maybe aftet 100 year . we work on electron lable practically about its properties and behaviour by the different instruments
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Prasenjit Reply
At high concentrations (>0.01 M), the relation between absorptivity coefficient and absorbance is no longer linear. This is due to the electrostatic interactions between the quantum dots in close proximity. If the concentration of the solution is high, another effect that is seen is the scattering of light from the large number of quantum dots. This assumption only works at low concentrations of the analyte. Presence of stray light.
Ali Reply
the Beer law works very well for dilute solutions but fails for very high concentrations. why?
bamidele Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
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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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