BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra

Abstract

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

The C‐terminal segment of collagenase in Grimontia hollisae binds collagen to enhance collagenolysis

“…The CD spectrum data were analyzed by using BESTSEL software available on the Web (http://bestsel.elte. hu/) to predict the proportion of the contents of secondary structures [17,18].…”

Endosomal pH favors shedding of membrane‐inserted amyloid‐β peptide

“…All CD curves were tested by a secondary structure calculation tool as described previously. 21,22 The results show that both Aβ40 and Aβ42 possessed a high content of α-helical structures at pH 7.4. At pH 5.5, this abundance of α-helices was lost.…”

Tetramer formation by the caspase‐activated fragment of the Par‐4 tumor suppressor

“…Results indicated approximately 60% beta content (sheet plus turn) in low salt (Fig. 1C) [49]. Beta content is often associated with misfolding and aggregation [60][61][62] For example, the conversion from a random coil to beta sheet structure plays a role in aggregation of the Tau protein in Alzheimer's disease [63].…”