AlphaFold2: A role for disordered protein prediction?

The development of AlphaFold2 was a paradigm-shift in the structural biology community; herein we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that a naive use of Dictionary of Secondary Structure of Proteins (DSSP) to separate ordered from disordered regions leads to a dramatic overestimation in disorder content, and that the Predicted Aligned Error (PAE) provides a much more rigorous metric. In addition, we show that even when used for disorder prediction, conventional predictors can outperform the PAE in disorder identification, and note an interesting relationship between the PAE and secondary structure that may explain our observations and hints at a broader application of the PAE to IDP dynamics.

Graph Coverings for Investigating Non Local Structures in Proteins, Music and Poems

It is shown how the secondary structure of proteins, musical forms and verses of poems are approximately ruled by universal laws relying on graph coverings. In this direction, one explores the group structure of a variant of the SARS-Cov-2 spike protein and the group structure of apolipoprotein-H, passing from the primary code with amino acids to the secondary structures organizing the foldings. Then one look at the musical forms employed in the classical and contemporary periods. Finally, one investigates in much detail the group structure of a small poem in prose by Charles Baudelaire and that of the Bateau Ivre by Arthur Rimbaud.

Graph Coverings for Investigating Non Local Structures in Proteins, Music and Poems

It is shown how the secondary structure of proteins, musical forms and verses of poems are approximately ruled by universal laws relying on graph coverings. In this direction, one explores the group structure of a variant of the SARS-Cov-2 spike protein and the group structure of apolipoprotein-H, passing from the primary code with amino acids to the secondary structures organizing the foldings. Then one look at the musical forms employed in the classical and contemporary periods. Finally, one investigates in much detail the group structure of a small poem in prose by Charles Baudelaire and that of the Bateau Ivre by Arthur Rimbaud.

Beginners guide to circular dichroism

Circular dichroism (CD) is used to give information about the chirality or handedness of molecular systems. It is particularly widely applied to determine the secondary structure of proteins such as biopharmaceutical products.

Effect of High Blood Cortisol Concentration on the Spectroscopically Determined Secondary Structure of Proteins and Lipid Balance on the Example of Elite Women Volleyball Players

Cortisol is a stress hormone plays a crucial role in the balance between phospholipids and lipids level. In consequence, it affects the secondary structure of proteins. Currently cortisol concentration in plasma is determined by biochemical analysis. A new, optical method to estimate stress level is proposed in this work. Infrared and Raman spectroscopies were used to determine quantitative and qualitative changes in the lipids and proteins fraction in function of cortisol concentration in 49 samples of plasma collected from volleyball players at various stages of preparation for the competition. With the cortisol level increase, a decrease of structures related to PO2- phospholipids groups and amides III, II and I bonds was noticed in the transmission spectra. Changes in the secondary structure of protein were indicated as a frequency shift of α-helix and β-sheet vibrations observed in Raman spectra and second derivative of transmission spectra. Pearson correlation test presented positive correlations between phospholipids and proteins level and between cortisol concentration and phospholipids in transmittance spectra. Negative correlations between cortisol concentration and proteins and phospholipids level was observed in the Raman spectra. Both optical techniques are considered to become effective tools for estimating the concentration of cortisol in the plasma.

Peak Fitting Applied to Fourier Transform Infrared and Raman Spectroscopic Analysis of Proteins

FTIR and Raman spectroscopy are often used to investigate the secondary structure of proteins. Focus is then often laid on the different features that can be distinguished in the Amide I band (1600–1700 cm−1) and, to a lesser extent, the Amide II band (1510–1580 cm−1), signature regions for C=O stretching/N-H bending, and N-H bending/C-N stretching vibrations, respectively. Proper investigation of all hidden and overlapping features/peaks is a necessary step to achieve reliable analysis of FTIR and FT-Raman spectra of proteins. This paper discusses a method to identify, separate, and quantify the hidden peaks in the amide I band region of infrared and Raman spectra of four globular proteins in aqueous solution as well as hydrated zein and gluten proteins. The globular proteins studied, which differ widely in terms of their secondary structures, include immunoglobulin G, concanavalin A, lysozyme, and trypsin. Peak finding was done by analysis of the second derivative of the original spectra. Peak separation and quantification was achieved by curve fitting using the Voigt function. Structural data derived from the FT-Raman and FTIR analyses were compared to literature reports on protein structure. This manuscript proposes an accurate method to analyze protein secondary structure based on the amide I band in vibrational spectra.