<< Chapter < Page Chapter >> Page >

Unlike other structure determination methods, with x-ray crystallography, there is no fundamental limit on the size of the molecule or complex to be studied. However, in order for the method to work, a pure, crystalline sample of the protein must be obtained. For many proteins, including many membrane-bound receptors, this is not possible. In addition,a single x-ray diffraction experiment provides only static information - that is, it provides only information about the native structure of the protein under the particular experimental conditions used. As we will see later, proteins are often flexible, dynamic objects when in their natural state in solution, so a single structure, while useful, may not tell the full story. More information on X-ray Crystallography is available at Crystallography 101 and in the Wikipedia .


Nuclear Magnetic Resonance (NMR) spectroscopy has recently come into its own as a protein structure determination method. In an NMR experiment, a very strong magnetic field is transiently applied to a sample of the protein being studied, forcing any magnetic atomic nuclei into alignment. The signal given off by a nucleus as it returns to an unaligned state is characteristic of its chemical environment. Information about the atoms within two chemical bonds of the resonating nucleus can be deduced, and, more importantly, information about which atoms are spatially near each other can also be found. The latter information leads to a large system of distance constraints between the atoms of the protein, which can then be solved to find a three-dimensional structure. Resolution of NMR structures is variable and depends strongly on the flexibility of the protein. Because NMR is performed on proteins in solution, they are free to undergo spatial rearrangements, so for flexible parts of the protein, there may be many more than one detectable structures. In fact, NMR structures are generally reported as ensembles of 20-50 distinct structures. This makes NMR the only structure determination technique suited to elucidating the behavior of intrinsically unstructured proteins , that is, proteins that lack a well-defined tertiary structure. The reported ensemble may also provide insight into the dynamics of the protein, that is, the ways in which it tends to move.

NMR structure determination is generally limited to proteins smaller than 25-30 kilodaltons (kDa), because the signals from different atoms start to overlap and become difficult to resolve in that range. Additionally, the proteins must be soluble in concentrations of 0.2-0.5 mM without aggregation or precipitation.For more information on how NMR is used to find molecular structures, please see NMR Basics and The World of NMR: Magnets, Radio Waves, and Detective Work at the National Institutes of Health's The Structures of Life website.

Electron diffraction

Electron diffraction works under the same principle as x-ray crystallography, but instead of x-rays, electrons are used to probe the structure. Because of difficulties in obtaining and interpreting electron diffraction data, it is rarely used for protein structure determination. Nevertheless, ED structures do exist in the PDB. For more on ED, see this Wikipedia article .

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
Privacy Information Security Software Version 1.1a
Got questions? Join the online conversation and get instant answers!
Jobilize.com Reply

Get the best Algebra and trigonometry course in your pocket!

Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'Geometric methods in structural computational biology' conversation and receive update notifications?