BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy

Abstract

Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu.

Multiple Timescale Dynamic Analysis of Functionally-Impairing Mutations in Human Ileal Bile Acid-Binding Protein

“…All the variants showed a cooperative and fully reversible thermal unfolding with a melting point close to 60 °C ( Supplementary Table S1 ). The secondary structure composition of the variants as a function of temperature was estimated from the CD spectra using the BeStSel method [ 40 , 41 ] ( Figure 2 B). The expectable error of the secondary structure estimation is around 5 percent in the absolute values [ 40 , 41 ], however, because of the similar spectral shape and amplitude of the WT and mutant proteins, it shows more accurately the structural changes in comparisons.…”

“…The secondary structure composition of the variants as a function of temperature was estimated from the CD spectra using the BeStSel method [ 40 , 41 ] ( Figure 2 B). The expectable error of the secondary structure estimation is around 5 percent in the absolute values [ 40 , 41 ], however, because of the similar spectral shape and amplitude of the WT and mutant proteins, it shows more accurately the structural changes in comparisons. These results show that the mutants are fully folded and their overall structure and stability is similar to the WT protein.…”

“…A two-state transition model described by Shih et al [ 57 ] showed a good fit to the fully reversible denaturation curves. Secondary structure composition was analyzed by the BeStSel webserver [ 41 ] ( accessed between 1 February 2022 and 31 May 2022).…”

“…Temperature dependence for all variants is shown in Supplementary Figure S1A . ( B ) Secondary structure composition was analyzed using the BeStSel method [ 40 , 41 ] as a function of temperature for wild-type hI-BABP and the two mutants. Secondary structure is summed up in three groups, α -helix, β -sheet, and turn+others.…”

The interaction between LC8 and LCA5 reveals a novel oligomerization function of LC8 in the ciliary-centrosome system

“…The spectra of LC8 at a concentration of 6 μM was recorded under the same experimental conditions as described before and subtracted from the individual CD spectra of the sLCA5-LC8 complexes. The baseline subtracted data were evaluated using the BeStSel web-server ( http://bestsel.elte.hu/index.php ) 46 , 47 . Thermal denaturation experiments were recorded at 222 nm between 10 and 80 °C using 1 °C/min heating rate.…”