I know very little about proteins so don't take my word as that of an expert. The problem I would see with your question is that of computational power. A protein is made up of particles but the various spin states and possible positions of the electrons would have to be integrated to build a potential function. That would only give the relative energy difference however. I think it might be better to consider the protein as a whole. Maybe pass an electric field through the protein to try to determine its dipole moment and then its polarizability. If you integrate the electric field over the volume of a protein (make it spherical!) and multiply it by the dipole moment you get the units of energy, although that would just give you the energy of the protein when subjected to an electric field, which mightnt be much use to you.

Thanks a lot Colm for your comment.

In m,y opinion for attain energy value of a protein, it's be better compute the energy which need to denature of a protein, for example if we want to measure the energy value of alpha-amylase we must use energy denaturation.

Regard

Depends on what energy you are determining. Analytically for phase transitions calorimetry or differential scanning calorimetry (from -180DegC to denaturation temp) would allow you to see the phase transformations over that temp range. Coupled with structural information from XRD (such as one would get from a sychrotron beam). If your looking for reaction energies then calorimetry. Was that helpful?

If you want to determine the protein energy just as a resutl of atomic electeric charge, it might be useful to apply APBS "Adaoptive Poisson Boltzman Solver" algorithm. But, if you wanna calculate the energy value of your interested protein as a result of anything els, such as ligand binding and etc. You can use more complicated methods like LIE, Umbrella Sampling, and even Jarzynski equation.

I you work experimentally, you can use methods like Optical Tweezers, Atomic Force Microscopy, DSC and so on. But, if you work on comutuing methods, PMV software, MD simulation and so on could be useful.

Best,

Mohammad

Best,

Mohammad

I am not Biophysic and my concepts of physics proteins are very limited. As a molecular biologist I am interested in studying proteins receptors at the cell surface from a specific pathway (VEGF receptors from endothelial cells). When a molecule reach is receptors there is a conformational change of the receptor. This alteration is due to electrostatic forces between molecule and receptor or due to resonance energy ? . So there was an energy that induced the conformational change of the receptor. I would like to know if there is any technique that could determine the resonance energy that induce conformational change ?

Thak you Vijay for your comment.

So maybe in sensory cells like olfactory cells, auditory cells, pulmonary cells wich all have cilium, in this case of cells they can have resonance energy that can induce conformational change of their receptors.

Thank you Luca I will have a look

Filipa: If I understand your question correctly, you know that a molecule binds a receptor and you want to know how much energy is involved. Either you want to measure this energy, so you can compare it to other molecules, or you want to predict this because the experiment is not possible. If you just want to measure it, I suggest you contact a biochemist or physical chemist in your institution and ask if they can suggest how best to measure it. There are many quantitative techniques available to measure energetics of binding (i.e. fluorescence, SPR, calorimetry, etc) but the choosing the right technique depends alot on the specifics of your system which you need a biochemist to determine. It might be easier than you think to measure it if you have access to lots of pure protein and the molecule of interest. If you want to predict it in a computer rather than just measure it, this is a very hard problem which the drug industry has tried for decades to solve with little success. There a few robust techniques, like the APBS program another commenter suggested, that work in very specific situations but you will very much have to have an extended conversation with a computational chemist or computational biophysicist to help you out and it will likely be much harder to do than just measuring it by experiment.

closest measurement would be in cm-1 (wavenumber) which is actually reciprocal of wavelength. from this one can compute, per time occurrence or something in Hz. Infrared technique can do this easily. Commonly, FT-IR is used. One studies change in the frequency of vibration and its amplitude of different constitutional bonds in proteins by FT-IR. Mostly, Amide I band is used to comment on conformation. Also, the H/D exchange of amide NH which resonates around 3500 cm-1. By designing a proper experiment with controls one can gain on change in frequency of constitutional bonds of proteins -/+ ligands or buffer conditions. Interesting question prompted me to reply. Good luck.

Thank you Alan and Ashish for your comments! I will try to find a biophysic since I have little background in this area.

Re. the special case of olfaction: Here is a link to a 6min video that might be of interest to you (also see the referenced paper by Klaus Schulten and references therein):

http://www.youtube.com/watch?v=Oe5PW2KqImI

Thank you Simon! Very interesting the study. Until know I think we didnt have the ideia about the mechanism of the interaction between receptor and the molecule. What I understand is that the molecule gives electrons to the receptor that alters the conformation of the receptor. This kind of study is very importante because Im working with electrical fields and I would like to understand why different cells have different response, direction, in electrical fields.

The answer is simple. An atom has an energy which is the electronic energy . For a molecule must be added to the electronic energy of all atoms, the repulsion energy of the nuclei. A quantum computation type ab initio (Hartree-Fock), allows to carry out this calculation with good accuracy, using appropriate software (Gaussian is the most common) for a molecule whose number of atoms of type H C, N, O, P, S, is not more than 20 or 30 atoms.

In the case of a protein, the number of atoms is a hundred to a thousand, this calculation is impossible for the moment. Only empirical approximations can estimate this energy.

This energy is expressed: in Hartree or Joules.

I really need to find a biophysic because most of the biophysical techniques I don't have any knowledge.Thank you Dan for your comment.

Thanks Felix! I already now about her work.