Mr. Thapa,

The wording of your question, rather assumes a lack of comprehensive knowledge of the mass spectrometry (MS;) in particular, what the MS measurable variables represent, in fact. Why?

There are fluctuations of the experimental variables m/z- and 'intensity' values, which can deviate themselves from the normality. Given that, the information about normality of the datasets of variables over the whole time of the experimental MS measurements of the apo-form of the dimeric protein and its complex with the ligand should not provide any reliable results from the perturbation of the dimeric 3D structure of the protein molecules.

In order to obtain reliable information about 3D molecular conformations of the apo-dimeric protein and its complex with the ligand by mass spectrometry, there should be used our own-authored (mine and my co-author's approach according to the shown authorship) innovative method and model formulas applicable to quantify exactly the experimental MS variable 'intensity.' They connect among experimental MS outcomes, exact 3D structure of the analyte and the analyte concentration in solution, respectively. This is the only currently available method for exact quantification of fluctuations of mass spectrometric measurements reported in the literature worldwide.

Please, consider reference [1] in this context.

[1] Bojidarka Ivanova und Michael Spiteller

A stochastic dynamic mass spectrometric diffusion method and its application to 3D structural analysis of the analytes; Reviews in Analytical Chemistry, 38 (2019) 20190003; DOI: https://doi.org/10.1515/revac-2019-0003

If there is a lack of capability of performing high level of accuracy quantum chemical computations of your dimeric protein according to the established empirically connection of experimental mass spectrometric variables and free Gibbs energy parameter of the measured ion of dimeric protein according to [1], then you could focus your attention on the cited in reference [1] works by D. Clemmer.

Hi Bojidarka B. Ivanova ,

Thank you for the suggestions. I was just following few articles (https://www.nature.com/articles/srep20753, https://www.biorxiv.org/content/10.1101/676783v1.full.pdf, and there are few more) wherein they comment on the nature of the protein by studying the binomial isotope distribution. So, I wondered if I can also follow it up on similar lines with my enzyme (which is reported to be asymmetric nature on the basis of it crystal structure).

Our biochemical experiments have shown the increased activity of my enzyme due to its ability to bind to an interacting partner (that we were characterizing). Now several of our other biophysical experiments indicates clearly towards the change in the conformation of our enzyme leading to its increase activity after binding with the interacting partner. All our crystallographic and cryo EM trials did not yield the complex structure. Now using HDX MS studies we can show where the protein is more affected (catalytic sites in our case) due to the binding of the partner protein and indicating towards conformational changes. Therefore, I was interested to just look "IF" i can see such kind of transition based on the mode of spectral distribution from already obtained HDX data.

Of course i have relatively less knowledge on MS and therefore directing my questions here on RG to get proper directions.

I will go through the articles you kindly shared, but I cant find one of the article you suggested to refer. It says-

"

WITHDRAWN: Quantitative analysis of solid binary mixtures—Vibrational spectroscopy of β-lactam antibiotics within THz-region

-Bojidarka B.Ivanova MichaelSpiteller

This article has been withdrawn at the request of the editor. The Publisher apologizes for any inconvenience this may cause.

"

Mr. Thapa,

I am unable to provide to you the content of paper ''Quantitative analysis of solid binary mixtures—Vibrational spectroscopy of β-lactam antibiotics within THz-region; authors: Bojidarka Ivanova Michael Spiteller'' because of, we can publish the same text with other Publisher.

Toward the content of paper

https://www.biorxiv.org/content/10.1101/676783v1.full.pdf

you sould bear in mind that the crystallographic structure corresponds to local minimum of the energy, while the mass spectrometry provide information both in solution and in the solid state. The phase transition between these condense phases can yield to conformational changes.

Please, consider in this context work [2], where we have detailed such example.

[2] Journal of Molecular Structure, 1179 (2019) 192-204

3D structural analysis of copper(II) complex of glycine – Experimental mass spectrometric and theoretical quantum chemical approach

Bojidarka Ivanova, Michael Spiteller