The document discusses the chemical shift index (CSI) technique, which uses protein nuclear magnetic resonance spectroscopy data to identify and locate secondary protein structures like beta strands and helices. CSI analyzes backbone chemical shift values to detect differences from random coil values that indicate structure. It is a widely used and easy to implement method, though newer techniques have slightly better accuracy. CSI remains popular due to its simplicity and ability to identify structures without specialized software. The document also discusses limitations and examples of CSI's applications and implementation in analysis programs.

1. Chemical shift index
• Submitted to Mr. Inam ul Haq
• Submitted by Umair Iqbal
• Roll.no 3002

2. Contents
 Introduction
 Chemical shift index
 Chemical shift and structural restrains
 Limitation
 Utility

3. Introduction
 The chemical shift index or CSI is a widely employed technique in protein
nuclear magnetic resonance spectroscopy that can be used to display and
identify the location (i.e. start and end) as well as the type of protein
secondary structure (beta strands, helices and random coil regions) found in
proteins using only backbone chemical shift data [1][2] The technique was
invented by Dr. David Wishart in 1992 for analyzing 1Hα chemical shifts and
then later extended by him in 1994 to incorporate 13C backbone shifts. The
original CSI method makes use of the fact that 1Hα chemical shifts of amino
acid residues in helices tends to be shifted upfield (i.e. towards the right side
of a NMR spectrum) relative to their random coil values and downfield (i.e.
towards the left side of a NMR spectrum) in beta strands. Similar kinds of
upfield/downfiled trends are also detectable in backbone 13C chemical shifts.

4. Chemical shift index (CSI)
 trends like these led to the development of the concept of the chemical shift index* as
a tool for assigning secondary structure using chemical shift values.
 one starts with a table of reference values for each amino-acid type, which is
essentially a table of “random coil” Ha value

5. Chemical shifts and structural
restraints
 so CSI is a useful technique for identifying secondary structures from chemical shift
data
 explicit restraints on structure are also derivable from chemical shifts, analogous to
our nOe-derived distance restraints, our coupling-constant-derived dihedral angle
restraints and our hydrogen-exchange derived hydrogen bond restraints. However,
these are not in very wide use yet.

6. limitations
 The CSI method is not without some shortcomings. In particular, its performance
drops if chemical shift assignments are mis-referenced or incomplete. It is also
quite sensitive to the choice of random coil shifts used to calculate the secondary
shifts[5] and it generally identifies alpha helices (>85% accuracy) better than beta
strands (<75% accuracy) regardless of the choice of random coil shifts.[5]
Furthermore, the CSI method does not identify other kinds of secondary
structures, such as β-turns. Because of these shortcomings, a number of
alternative CSI-like approaches have been proposed. These include: 1) a prediction
method that employs statistically derived chemical shift/structure potentials
(PECAN);[11] 2) a probabilistic approach to secondary structure identification
(PSSI);[12] 3) a method that combines secondary structure predictions from
sequence data and chemical shift data (PsiCSI),[13] 4) a secondary structure
identification approach that uses pre-specified chemical shift patterns (PLATON)[14]
and 5) a two-dimensional cluster analysis method known as 2DCSi.[15] The
performance of these newer methods is generally slightly better (2-4%) than the
original CSI method.

7. Utility
 Since its original description in 1992, the CSI method has been used to
characterize the secondary structure of thousands of peptides and proteins.
Its popularity is largely due to the fact that it is easy to understand and can
be implemented without the need for specialized computer programs. Even
though the CSI method can be easily performed manually, a number of
commonly used NMR data processing programs such as NMRView,[16] NMR
structure generation web servers such as CS23D[17] as well as various NMR data
analysis web servers such as RCI,[18] Preditor[19] and PANAV [20] have
incorporated the CSI method into their software.

8. An Example
 for a-helices, Ca shifts are higher
than normal, whereas
 Cb shifts are lower than normal.
Note in your reading of the
 apo-calmodulin paper that Ca shifts
are used in characterizing
 the structure of the interdomain
linker

9. Summary
 CSI is a useful technique for identifying secondary structures from chemical shift
data.
 It is a very useful software for identify the location and secondary structure of
Protiens.
 It is used in Chemistry for identifying bonds in Protiens as well as it is also used in
biology.

10. Conclusions
 I have used it, it is very useful for me.
 It is very easy way for identifying locations of Protiens.
 It is also applicable for finding bonds Protiens.

11. Refrences
•CSI calculations via RCI webserver http://randomcoilindex.com
•CSI calculations via Preditor webserver http://preditor.ca
•Stand-alone CSI program for Linux/Unix http://www.bionmr.ualberta.ca/sykes/software/csi/latest/csi.html
•Chemical shift rereferencing for CSI calculations by Shiftcor http://shiftcor.wishartlab.com/
•Chemical shift rereferencing for CSI calculations by PANAV http://www.wishartlab.com/web_servers/pa