Hi! Looking for a FTIR or IR absorption spectroscopy library or simulation software it is possible to compare different spectral responses of biological molecular structures. Thank you
Dear Martin,
You may check the sources listed in the following publication:
Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot
J. Phys. Chem. B, 2015, 119 (41), pp 13079–13092
Infrared (IR) spectra from 1200 to 1800 cm–1 of the pure α-helix and β-sheet secondary structures have been extracted using a covariant least-squares procedure which relates a library of 40 infrared (IR) solution protein spectra from the work of Dong, Carpenter, and Caughey and amino acid fractions of the proteins based on assignments by STRIDE (secondary structure identification) of Eisenhaber and Argos. The excitonic splitting of the β-sheet structures is determined for this library of solution proteins. The method is extended to find a set of spectral basis functions that analyze IR spectra of protein samples for α-helix and β-sheet content. A rigorous error analysis including covariance, the correlations between the input library spectra, was used to justify the results and avoid less meaningful results. The utility of the results on α-helix and β-sheet regions is demonstrated by detecting protein changes due to cancer in imaging Fourier transform IR (FTIR) spectra of liver tissue slices. This work ends with a method to extract IR spectra of less prominent torsional angle distributions.
http://pubs.acs.org/doi/full/10.1021/acs.jpcb.5b08052
Hoping this will be helpful,
Rafik
Mr. Larsen,
There is not available protein IR-database for searching, because of, in general, there is a speculative task to assign, first, accurately IR-band position and integral intensities of vibrational modes of proteins, and, second, to determine their intensities, thus allowing to compare them quantitatively. The major reason for this is that, the characteristic modes of proteins associated with "amide" vibrations are observed within the framework of a narrow range of the electromagnetic spectrum as overlapped broad multi-component profile.
Given that, even employment of special experimental techniques (such as isotope labeling, D-exchange, polarized measurements and more); spectroscopic data-processing methods; and chemometric analysis (first derivative analysis; curve fitting; deconvolution; and mode) unable to assign accurately the bands to corresponding molecular vibrations.
There is possible to perturb the profile by techniques like chemical substitution; tuning of H-bonding network/conformations via protonation/deprotonation, isotope labeling and more, but generally, this frequently do not change the profile so significantly. Therefore even a qualitative comparative analysis is characterized with a low reliability. The quantitative analysis is almost unreliable.
Towards program packages, there are large set packages, using quantum chemical methods, allowing you to predict the vibrational profile of proteins and any other molecular object. Gaussian (www.gaussian.com) is an example in this respect, where the computation and visualization of the results are almost automatized. But this do not change the fact that even employment of quantum chemistry shall allow you to determine quantitatively proteins by IR.
You could pay attention to the attachment. It shows an example of a hexapeptide. There are given theoretical computations of IR-spectra by the program package mentioned above. As you can see, there is a significant change of the profile depending on protonation/deprotonation effect and molecular conformations. But generally, the characteristics are not "significant" in quantitative terms (attachment spectra 2 and 3). In fact, '5' "Amide I' modes are distinguished difficult even theoretically studying the COOH form. Furthermore, we are talking in this example about a hexapeptide, containing simple from a molecular chemistry point of view amino acid residues like 'gly'. With increasing of complexity of amino acid fragments (Arg, His fr example), there are obtained additional set characteristic IR-bands within spectroscopic regions of "amide" modes, which further complicates the IR-profile.
So, IR-data base rather for peptides, not proteins, would be meaningful if the objects are:(i) not so large; and/or (ii) not so complex as amino acid residues. Furthermore (iii), it should contain IR-spectra of given object at a large scale experimental conditions (different isotope labeling, spectra in large set solvent, P, T, solid-state at different P, T, and more). Such analysis only allows to assign the spectra on one the base on different perturbations of the IR-profiles.
Same is valid for databased of simulated spectra of peptides. They should account for many possible conformations; effects on medium (pH, solvent, T, P); and more.
Nevertheless that IR- is a cheap and easy for operation method, a creation of a meaningful in quantitative terms database of peptides, is associated with a large number independent experiments as mentioned above.
For peptide/proteins databases for structural analysis, the mass spectrometry is the method of choice.
Thanks for the answers. It was great help.
Is it possible to detect increase of low concentration plasma proteins in high concentration aqueous solutions where protein levels are low with FTIR spectroscopy, when the protein structure is known? Is it possible to see in the absorption IR spectrum whether there is an increase of albumin(ALB) or alanine aminotransferase(ALT)? Or will it be too much overlap and chaos to make sense from the results?