I am measuring secondary structure of fish protein samples at concentration of 0.05 mg/ml. At the parametrs, i am supposed to enter the concentration in moles. there are few options; mol/L, m-mole/L and micro-mole/L.
What should I select?
And what should be the minimum ans maximum RMS value?
my values is sometimes above 90 and sometimes under 20.
Please guide me.
Dear Ziaur Rahman The answer on your question depends on numerous factors. Things I can come up with are:
-The equipment used, it’s settings and the software (for example what is the output of the (raw) spectrum)
-The experimental conditions (not only concentration but also the cell length used 0.1 cm or 1 cm etc.)
-The program used to perform the deconvolution
-Etc.
The following paper might be useful (I will send it to you):
Conformational and Rheological Changes in Catfish Myosin as Affected by Different Acids during Acid-Induced Unfolding and Refolding. Sivakumar Raghavan and Hordur G. Kristinsson
Journal of Agricultural and Food Chemistry 2007 55 (10), 4144-4153 DOI: 10.1021/jf063184v
When it comes to your mol question, there are two ways to resolve this matter:
-Use an average mass (estimate when you have a mixture or use SDS page approach when it is a single (unknown) protein and when it is one protein use a value you can find in the literature)
-Use a deconvolution program that ‘just’ use the shape of the CD spectrum (and then use the option with the ‘proper’ units to estimate the right value(s)). For this matter (and other issues) I highly recommend the following excellent paper (for example Fig. 6):
Article Tools and methods for circular dichroism spectroscopy of pro...
Regarding the RMS (NRMS?) it is in general required to keep this as low as possible (a few %) since the value reflect the difference between the experimental and the calculated spectrum.
Hope this answers your question somewhat.
Best regards.
PS. I might help to include an example of your measurements in your question.
convert the concentration of your fish protein samples from mg/mL to moles, you would need to know the molecular weight of the protein. Once you have the molecular weight, you can use the following formula:
moles = concentration (mg/mL) / molecular weight (g/mol) / 1000
For example, if the molecular weight of your fish protein is 100,000 g/mol, then the concentration of 0.05 mg/mL would be:
moles = 0.05 / 100,000 / 1000 = 5 x 10^-8 mol/L
Based on the options provided, you would select micro-mole/L as the concentration unit.
Regarding your second question, the RMS (root mean square) value is a measure of the deviation of your experimental data from a theoretical model. The minimum and maximum RMS values depend on the specific experimental conditions and the quality of your data. Generally, a lower RMS value indicates a better fit between your data and the model, while a higher RMS value indicates more deviations from the model.
In the case of measuring secondary structure of fish protein samples, a typical RMS value would depend on the method of measurement (e.g., circular dichroism, Fourier transform infrared spectroscopy), the quality of the protein samples, and the experimental conditions (e.g., temperature, pH). Therefore, it is difficult to provide a specific range for the minimum and maximum RMS values.
However, if your RMS value is sometimes above 90 and sometimes under 20, it may indicate that there is some inconsistency or variability in your experimental data. You may want to review your experimental procedures and conditions to ensure that you are obtaining consistent and reliable measurements.
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