Abstract
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.
Highlights
Secondary structures such as ␣-helices, -strands and coils are commonly used to describe, understand and visualize protein tertiary structures [1]
This is true for nuclear magnetic resonance (NMR)-based protein structure determination where secondary structure is used to help in structure generation and refinement [2,3]
To demonstrate the utility of Chemical Shift Index (CSI) 3.0 we evaluated its performance for both secondary and super-secondary structure identification using a set of 13 proteins with known 3D structures
Summary
Secondary structures such as ␣-helices, -strands and coils are commonly used to describe, understand and visualize protein tertiary structures [1]. In particular we combined a high-end secondary structure calculation algorithm (CSI 2.0) with a high-performing torsion angle calculator (TALOS-N), an accurate measurement method for backbone flexibility (random coil index (RCI) ) and a robust method for calculating fractional accessible surface areas (fASAs) (Side-chain RCI)––all of which use NMR chemical shifts as input. CSI 2.0 uses chemical shift and sequence data to accurately identify three types of secondary structures: helices, -strands and coil regions.
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