Chart : Secondary Structure Chart

Display NMR Evidence for Protein Secondary Structure

This popup window is designed to collect together several kinds of NMR derived information to give a visual representation of evidence to indicate the regions of a protein chain with secondary structure, and what that structure might be. This system collects data from several sources from through-space (e.g. NOE) connectivity; from secondary chemical shifts; from a combined chemical shift index; from 3J H-Ha scalar couplings.

The main chart lists the residue sequence of the selected chain (see “Options”), the predicted secondary structure of the residues and various types of evidence of the secondary structure. The “Sec Struc” column may be set manually based on the contents of the table via the [Set ...] buttons at the bottom, or automatically via a program like DANGLE. In the table the eight through-space connectivity columns (d_aN i,i+1 to da_N i,i+2) are always displayed, but the other columns relating to chemical shift are optional and may be toggled via the top buttons. The connectivity columns are filled with a green colour if a given kind of connectivity is observed for a residue, additionally for the first three of these there is an extra distinction of strong (S) medium (M) and weak (W) categories. The name of a column indicates what kind of connectivity is present, for example d_aN i,i+1 represents the connection of an alpha position of one amino acid residue to the amide position of a residue one position further along (C-terminal) in the chain.

The Delta-delta columns indicate secondary chemical shifts for Ca, Cb, C’ and Ha atoms; the difference from recorded chemical shift to (sequence adjusted) random coil chemical shift. The random coil chemical shifts are calculated as specified in Schwarzinger et al. as detailed below. These secondary chemical shifts are combined to give the CSI values (calculated according to the methods in the papers listed below) indicating the secondary structure type; -1 indicates alpha-helix and +1 beta-strand. The last “3JHNHa” column lists any recorded scalar couplings between the amide and alpha hydrogens of a residue. These are indicative of the phi backbone angle, according to the Karplus relationship. These coupling values may be extracted and analysed in more detail using the Data Analysis : 3J H-Ha Coupling system.

The “Chart” tab shows a graphical representation of the secondary structure evidence data. This is the same data that is shown in the first table, it is merely presented differently, on a compact graphical form that may be printed out by making a PostScript file (right mouse menu). The order of the rows of data in the chart is the same order as the columns of the evidence table. The grey and white panels of the chart delineate the display into regions of ten residues. The text font used in the chart and the number or residues that are shown in a row, before the chart wraps back to start at the left again, are governed by settings in the last “Options Tab”.

The “Options” tab controls various aspects of how the data in the other tabs is displayed. The “Chain” naturally selects the sequence to use and “Shift List” is the source of the secondary chemical shift information. The “NOE Intensity Classes” section allows the user to set two values which distinguish between strong, medium and weak connection strength. Note that these values represent a peak intensity relative to the average in the peak list containing the connection. The lower table lists the peak lists that are used as sources of through-space connectivity information. The use can toggle to consider or reject particular peak lists by double clicking in the “Consider?” column. Any changes to any of these settings will be reflected one the user selects one of the first two tabs.

Caveats & Tips

The most accurate secondary structure prediction currently available in CCPN comes from the embedded DANGLE program. Although DANGLE has a separate graphical interface its secondary structure predictions, if committed, will be visible in this system via the displayed secondary structure classification.

Regions of a polypeptide backbone with stable secondary structure will tend to show more near-sequence (“short range”) though-space connectivities than unstructured, flexible regions; commonly termini and loops. Naturally alpha-helices will tend to show i to i+3 and i to i+4 connections, due to the periodicity of the helix. Beta strand regions will often show i to i+2 connectivity by lack i to i+3 and i to i+4, given that stands are extended conformations.

References

Secondary chemical shifts:

Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., Dyson, H. J. “Sequence-Dependent Correlation of Random Coil NMR Chemical Shifts”, J. Am. Chem. Soc. 123, 2970-2978 (2001)

Chemical Shift Index

Wishart DS, Sykes BD. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR. 1994 Mar;4(2):171-80.

Wishart DS, Sykes BD, Richards FM. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 1992 Feb 18;31(6):1647-51.

Main Panel

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Residue Data

A table of the evidence used to estimate the secondary structure type of residues

selector Column Options: Selects which of various secondary chemical shifts, chemical shift index or 3J H-Ha coupling data to display in the table and chart

Table 1
Residue The sequence number and residue type
Sec Struc The stated secondary structure type for the residue
d_αN i,i+1 Indicates residue that show an alpha(i) to amide(i+1) through-space/NOE connection
d_NN i,i+1 Indicates residue that show an amide(i) to amide(i+1) through-space/NOE connection
d_βN i,i+1 Indicates residue that show a beta(i) to amide(i+1) through-space/NOE connection
d_αN i,i+3 Indicates residue that show an alpha(i) to amide(i+3) through-space/NOE connection
d_αβ i,i+3 Indicates residue that show an alpha(i) to beta(i+3) through-space/NOE connection
d_αN i,i+4 Indicates residue that show an alpha(i) to amide(i+4) through-space/NOE connectio
d_NN i,i+2 Indicates residue that show an amide(i) to amide(i+2) through-space/NOE connection
d_αN i,i+2 Indicates residue that show an alpha(i) to amide(i+2) through-space/NOE connection
Δ δ13Cα Carbon alpha secondary chemical shift (difference to random coil value)
Δ δ13Cβ Carbon beta secondary chemical shift (difference to random coil value)
Δ δ13C’ Backbone carbonyl carbon secondary chemical shift (difference to random coil value)
Δ δ1Hα Hydrogen alpha secondary chemical shift (difference to random coil value)

button Set Alpha: Set the secondary structure type for the selected residue to “Alpha”

button Set Beta: Set the secondary structure type for the selected residue to “Beta”

button Set Coil: Set the secondary structure type for the selected residue to “Coil”

button Set Undef: Set the secondary structure type for the selected residue to “Undef”

button Read CSI File: Read CSI information for the residue from a CSI output file

button Make Chart: Display the secondary structure evidence information as a graphical chart, which may then be saved as a PostScript file

Chart

The secondary structure evidence information as a graphical chart, which may then be saved as a PostScript file

Options

The various parameters that control the data display, including which peak lists and molecule chain to use

pulldown Chain: Selects which molecular chain to secondary structure evidence for

pulldown Shift List: Selects which shift list chemical shifts are derived from, for calculating deltas etc.

Chart Font: Sets the typeface to use in the main chart display

pulldown Residue Wrap Width: Sets how wide, in terms of number residues, the main chart is; will cause sequences to wrap back to the start

NOE Intensity classes

float 1.5: The intensity value, relative to peak list average, that separates strong and medium NOE strength categories

float 0.3: The intensity value, relative to peak list average, that separates weak and medium NOE strength categories

NOE peak lists

Table 2
Spectrum The experiment:spectrum to which the through-space peak list belongs
Peak List The serial number of the through-space peak list within its spectrum
Consider? Whether the through-space peak list should be used to provide connectivity data for the secondary structure evidence table (Editable)

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