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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

Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
characteristics of micro business
for teaching engĺish at school how nano technology help us
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
what is the actual application of fullerenes nowadays?
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
Mostly, they use nano carbon for electronics and for materials to be strengthened.
is Bucky paper clear?
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
so some one know about replacing silicon atom with phosphorous in semiconductors device?
s. Reply
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Do you know which machine is used to that process?
how to fabricate graphene ink ?
for screen printed electrodes ?
What is lattice structure?
s. Reply
of graphene you mean?
or in general
in general
Graphene has a hexagonal structure
On having this app for quite a bit time, Haven't realised there's a chat room in it.
what is biological synthesis of nanoparticles
Sanket Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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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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