This document discusses methods for protein sequencing, including studying the N-terminus using Sanger and Edman degradation methods, studying the C-terminus using carboxylpeptidases, and cleaving polypeptides into peptides using specific enzymes or chemical reactions. It provides an example of using these various methods to determine the amino acid sequence of a peptide segment. The grand strategy is to separate and sequence all peptides from one cleavage to determine the full protein sequence.
Compare and contrast the chemical (Maxam/Gilbert) and chain termination (Sanger) sequencing methods.
List the components and molecular reactions that occur in chain termination sequencing.
Discuss the advantages of dye primer and dye terminator sequencing.
Derive a text DNA sequence from raw sequencing data.
Describe examples of alternative sequencing methods, such as bisulfite sequencing and pyrosequencing.
Maxam/Gilbert chemical sequencing
Sanger chain termination sequencing
Pyrosequencing
Array sequencing
With addition of enzyme (DNA polymerase), the primer is extended until a ddNTP is encountered.
The chain will end with the incorporation of the ddNTP.
With the proper dNTP:ddNTP ratio, the chain will terminate throughout the length of the template.
All terminated chains will end in the ddNTP added to that reaction.
The collection of fragments is a sequencing ladder.
The resulting terminated chains are resolved by electrophoresis.
Fragments from each of the four tubes are placed in four separate gel lanes.
Cycle sequencing is chain termination sequencing performed in a thermal cycler.
Cycle sequencing requires a heat-stable DNA polymerase.
Fluorescent dyes are multicyclic molecules that absorb and emit fluorescent light at specific wavelengths.
Examples are fluorescein and rhodamine derivatives.
For sequencing applications, these molecules can be covalently attached to nucleotides.
In dye primer sequencing, the primer contains fluorescent dye–conjugated nucleotides, labeling the sequencing ladder at the 5′ ends of the chains.
In dye terminator sequencing, the fluorescent dye molecules are covalently attached to the dideoxynucleotides, labeling the sequencing ladder at the 3′ ends of the chains.
Compare and contrast the chemical (Maxam/Gilbert) and chain termination (Sanger) sequencing methods.
List the components and molecular reactions that occur in chain termination sequencing.
Discuss the advantages of dye primer and dye terminator sequencing.
Derive a text DNA sequence from raw sequencing data.
Describe examples of alternative sequencing methods, such as bisulfite sequencing and pyrosequencing.
Maxam/Gilbert chemical sequencing
Sanger chain termination sequencing
Pyrosequencing
Array sequencing
With addition of enzyme (DNA polymerase), the primer is extended until a ddNTP is encountered.
The chain will end with the incorporation of the ddNTP.
With the proper dNTP:ddNTP ratio, the chain will terminate throughout the length of the template.
All terminated chains will end in the ddNTP added to that reaction.
The collection of fragments is a sequencing ladder.
The resulting terminated chains are resolved by electrophoresis.
Fragments from each of the four tubes are placed in four separate gel lanes.
Cycle sequencing is chain termination sequencing performed in a thermal cycler.
Cycle sequencing requires a heat-stable DNA polymerase.
Fluorescent dyes are multicyclic molecules that absorb and emit fluorescent light at specific wavelengths.
Examples are fluorescein and rhodamine derivatives.
For sequencing applications, these molecules can be covalently attached to nucleotides.
In dye primer sequencing, the primer contains fluorescent dye–conjugated nucleotides, labeling the sequencing ladder at the 5′ ends of the chains.
In dye terminator sequencing, the fluorescent dye molecules are covalently attached to the dideoxynucleotides, labeling the sequencing ladder at the 3′ ends of the chains.
Protein Sequencing
Introduction
Protein Sequencing
History of Protein Sequencing
Determining Amino Acid Composition
N-terminal amino acid analysis
C-terminal amino acid analysis
Edman degradation
The Edman degradation reaction
Limitations of the Edman degradation
Mass spectrometry
Nucleic Acid Sequencing
Introduction
Nucleic Acid Sequencing
Type of Nucleic Acid Sequencing
DNA Sequencing
Method of DNA Sequencing
Application of DNA Sequencing
DNA Sequencing Institutes
Conclusion
Reference
Introduction
What is Protein Sequencing?
History
Determination of amino acid composition
Sequencing methods
N terminal sequencing
C terminal sequencing
Mass spectrometer
Application
Reference
Notes* for the subject 'Advanced Pharmaceutical Analysis'Sanathoiba Singha
As per the syllabus prescribed by Rajiv Gandhi University of Health Sciences, Karnataka, for M. Pharm (Pharmaceutical Analysis) 1st semester.
*not all topics have been included in this collection of notes.
Introduction.
History of Protein Sequencing.
Determining Amino Acid Composition.
N-terminal amino acid analysis.
C-terminal amino acid analysis
The Edman degradation reaction.
Limitations of the Edman degradation.
Mass spectrometry
Importance
Conclusion
Reference
Solid-phase peptide synthesis (SPPS), pioneered by Robert Bruce Merrifield,[1] caused a paradigm shift within the peptide synthesis community, and it is now the standard method for synthesizing peptides and proteins in the lab.
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Protein Sequencing
Introduction
Protein Sequencing
History of Protein Sequencing
Determining Amino Acid Composition
N-terminal amino acid analysis
C-terminal amino acid analysis
Edman degradation
The Edman degradation reaction
Limitations of the Edman degradation
Mass spectrometry
Nucleic Acid Sequencing
Introduction
Nucleic Acid Sequencing
Type of Nucleic Acid Sequencing
DNA Sequencing
Method of DNA Sequencing
Application of DNA Sequencing
DNA Sequencing Institutes
Conclusion
Reference
Introduction
What is Protein Sequencing?
History
Determination of amino acid composition
Sequencing methods
N terminal sequencing
C terminal sequencing
Mass spectrometer
Application
Reference
Notes* for the subject 'Advanced Pharmaceutical Analysis'Sanathoiba Singha
As per the syllabus prescribed by Rajiv Gandhi University of Health Sciences, Karnataka, for M. Pharm (Pharmaceutical Analysis) 1st semester.
*not all topics have been included in this collection of notes.
Introduction.
History of Protein Sequencing.
Determining Amino Acid Composition.
N-terminal amino acid analysis.
C-terminal amino acid analysis
The Edman degradation reaction.
Limitations of the Edman degradation.
Mass spectrometry
Importance
Conclusion
Reference
Solid-phase peptide synthesis (SPPS), pioneered by Robert Bruce Merrifield,[1] caused a paradigm shift within the peptide synthesis community, and it is now the standard method for synthesizing peptides and proteins in the lab.
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2. Introduction
• Protein sequencing is the method of studying the
covalent structure and amino acid sequence of a mature
polypeptide.
• Protein sequencing is a part of posttranslational
modifications.
• There are three main categories of protein sequencing :
- Studying N-terminus
- Studying C-terminus (very few methods, mostly using
enzyme carboxylpeptidases).
- Cleavage of polypeptides into peptides.
3. Studying N-terminus
• Sanger method :
- Most common reagent is DNFB (1-fluoro-2,4-dinitrobenzene).
- The reagents produce coloured derivatives and only qualitative analysis is
required.
- They all react with amine groups and will therefore also bind to amine
groups in the side chains of amino acids such as lysine - for this reason it is
necessary to be careful in interpreting chromatograms to ensure that the right
spot is chosen.
4. Studying N-terminus
• Edman degradation :
- Can sequence peptides up to 50 amino acids long.
- Relies upon the removal of the N-terminus amino acid residue from the
polypeptide as the (PITC)-amino acid. The (PITC)-amino acid from each step
can be positively identified by high-pressure adsorption chromatography.
https://www.researchgate.net/figure/Edman-degradation-in-3-steps-with-different-reaction-conditions-
1-mildly-alkaline_fig40_283380515
5. Cleavage of polypeptide into peptides
- Using specific enzyme : Protein needs to be unfolded before cleavage.
Specific enzyme Cleavage site R group (amino acid)
Citraconylation + trypsin C-terminal Arg
Trypsin C-terminal Lys, Arg
S.aureus protease C-terminal Glu, Asp
Chymotrypsin C-terminal Phe, Tyr, Trp (aromatic)
Thermolysin N-terminal Leu, Ileu, Val, Phe
6. Cleavage of polypeptide into peptides
- Using chemical reaction :
* Cyanogen Bromide (BrCN) : Cleavage C-terminal of Met.
* Mild bromination (Br+ ) : Cleavage at C-terminal of Trp.
* 2-nitro-5-thiocyanatobenzoate : Cleavage N-terminal of Cys.
H
N
NH
O
NH N
H
O
HN
O
O
O
H3N
Br+
7. A theoretical example
*A peptide segment has been purified from a digest of certain protein. Consider the
following information.
(A) : Complete acid hydrolysis in 6 M HCl :
(1) : Arg, Glu, 2 Gly, Ileu, Leu, Lys, Phe, Ser, Val
(B) : React with DNFB forms (2) : DNB-Val
(C) : Using enzyme trypsin : (3): (Arg, Glu, Gly, Val) ; (4) : (Gly, Lys, Phe, Ser)
(5):(Ileu, Leu).
(D) : Edman degradation :
(E) : Carboxylpeptidase : Ileu
*Solution :
From (B), the N-terminus is Val.
From (C) and (D) : peptide (3) is Val-Glu-Gly-Arg ; (4) is Phe-Ser-Gly-Lys
From (E), the C-terminus is Ile, so the peptide (5) is Leu-Ile.
So the peptide segment is : Val-Glu-Gly-Arg-Phe-Ser-Gly-Lys-Leu-Ile.
Peptide Cycle
1 2
(3) Val Glu
(4) Phe Ser
8. Conclusion
-The grand strategy for determining the sequence of a polypeptide directly is to
separate and sequence all of the peptides from one particular cleavage.
-However, the sequences of polypeptides are now possibly determined by
sequencing DNA complementary to the messenger RNA that encodes them.
References
[1] Structure in Protein Chemistry , 1995 – Jack Kyte – University of
California, San Diego.
[2] Example is from Chemistry Olympiad of gifted high schools in the North
of Vietnam 2016 (Not original).
[3] http://www.ehu.eus/biofisica/juanma/papers/EdmanDegradation.pdf
[4] https://nptel.ac.in/courses/102103017/pdf/lecture%2018.pdf
(All links are accessed on Dec.6th.2018)