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Ranking by energy

Protein conformations are not only geometric objects but are characterized by energetic stability. You have seenthat there are many empirical ways to compute the potential energy of a conformation. Functions such as CHARMM are very involved for the purpose of this assignment. Therefore, let us notworry about all the energetic terms to be considered from the atomic interactions. Consider only unfavorable interactions due to collisionsbetween atoms, also referred to as steric clashes. Think about a simple energy function that checks for steric clashes. Yourfunction should report high energies for conformations with collisions and low energies for collision-free conformations. You can model each atom asa sphere with a certain radius known as the Van der Waals (VDW) radius. Even though different atoms have different VDW radii, you can assume thatall atoms have the same radius of 1.7 A. To assist you in devising a function that checks for collisions over all pairs of atoms, consider the following:

For all different atoms i and j, make sure that the distance between their centers C is more than twice their radiuses. In this simpleexample we are using the same radius R.

    Evaluating rotations by energy

  • Now think about the effect of the dihedral rotation of the last bond the energetic stability of the new conformation. Please answer Q2 .
  • When you rotated a dihedral bond in the middle of the backbone until you reached a conformation that had collisions, you verified the presence ofsteric clashes by visualizing the conformation. You can quantify the presence of steric clashes now through your energy function. Please answer Q5 .

Again, as in dihedral rotations, you are encouraged to use Matlab. After you have the cartesian coordinates of the manipulated conformation, you caniterate over the atoms and check whether they are in collision with one another. You can do this with a double loop. Assume that the radius of everyatom is the same, 1.7 A. In order to avoid reporting collisions for bonded atoms, you can consider only pairs of atoms that are 4 positions apart. Thatis, check atom i with atom i+4 for a possible steric clash.

For submission

NOTE: remember that in order to open a .crd file in VMD (to attach it to a loaded structure) it has to contain a dummy first line. If your implementation writes out ASCII coordinates, remember to add an empty/dummy line at the beginning before opening with VMD. Please follow this list of deliverables closely:


  • Q1

    Superimpose the conformation resulting from rotating the dihedral bond between the N and CA of the last aminoacid by 30 degrees over the native backbone conformation. Prepare an image that clearly shows which atoms' locations have changed. Submit this image.
  • Q2

    Now you need to quantify the energetic cost of rotating this dihedral bond by 30 degrees by reporting whether this rotation causes any steric clashes. Please test your energy function on the conformation you obtained from rotating the last dihedral bond by 30 degrees. Please report the answer of your energy function. It should be compatible with what you can visualize from the image you prepared above.
  • Q3

    Provide the index of the dihedral bond you need to rotate to generate a large scale motion that results on collisions between atoms. Report on the amount of rotation that you need to perform in order to obtain a conformation that contains steric clashes. Plot this conformation superimposed on the native backbone conformation so as to show that it is very different from the native. Render this image and submit it.
  • Q4

    Zoom in on that part of your conformation that contains collisions. Make sure that this image clearly shows steric clashes and submit this image.
  • Q5

    Compute the energy of the above conformation with your energy function. Report the answer that your energy function returns. Make sure that this answer reflects the fact that there are steric clashes. Please provide the atomic distances for the atom pairs that your function reports in collision.
  • Bonus

    Upon a situation when the energy of the conformation resulting from a dihedral rotation is high, how would you minimize the energy of this conformation? Provide a discussion and pseudo-code on how you would perform the minimization.
Note: While you are welcome to use any programming language, please typeset your deliverables and make sure that the quality of your images is good. You can use any visualization software to produce your images. You are welcome to perform the asked rotations either through the Denavit-Hartenberg derivation provided in our [PDF] document , or through simple rotations around arbitrary vectors. If you choose the latter, please note that there is a typo in the formula for therotation matrix Ri in Zhang-Kavraki, 2002 [PDF] on page 2: The second column, first row entry of this matrix is given as u x v y 1-cos(theta) v z sin(theta) , but it should be v x v y 1-cos(theta) v z sin(theta) .

Questions & Answers

anyone know any internet site where one can find nanotechnology papers?
Damian Reply
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
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Akash Reply
it is a goid question and i want to know the answer as well
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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
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what is biological synthesis of nanoparticles
Sanket Reply
what's the easiest and fastest way to the synthesize AgNP?
Damian Reply
types of nano material
abeetha Reply
I start with an easy one. carbon nanotubes woven into a long filament like a string
many many of nanotubes
what is the k.e before it land
what is the function of carbon nanotubes?
I'm interested in nanotube
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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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