This Presentation Deals With The Proteins And Their Different Structures. In This Presentation, You Will Learn About What Are Proteins, Importance Of Proteins, Structures Of Proteins, Primary Structure, Secondary Structure, Tertiery Structure, Quaternery Structure, Biological Examples With References For Further Studies.

1. ORDERS OF PROTEIN
STRUCTURE
Submitted By,
LOGESWARAN KA
P20BIT1013
I-MSC.BIOTECHNOLOGY
PERIYAR UNIVERSITY.

2. CONTENTS
 What are Proteins?
 Importance Of Protein Structure Determination
 Orders Of Protein Structure
 Primary Structure
 Secondary Structure
 Tertiary Structure
 Quaternary Structure
 Bioinformatics Tools For Protein Structure
Determination
 References

3. WHAT ARE PROTEINS?
 Essential Macromolecules Required By Every
Living Organisms To Perform Biological Functions.
 Proteins Consist Of Amino Acids Joined Together
By Peptide Bonds.
 20 Amino Acids Codes For Several Thousands Of
Different Proteins In The Living System.
 Proteins Plays Important Roles In Most Of The
Biological Processes Like,
1. Tissue Growth And Maintenance.
2. Immune System.
3. Metabolic Activities.
4. Cell Signalling And Structural Support.

4. IMPORTANCE OF PROTEIN
STRUCTURE DETERMINATION
 To Get Thorough Understanding Of Different
Proteins Structures And Working Mechanisms.
 To Design New Protocols, Drugs And Therapies
Based On Protein Studies.
 To Study The Complex And Important Roles Of
Proteins In Biological Processes.
 To Store The Informations Of Proteins Studies
(Sequence, Conformations, Findings And
Functions) At Protein Data Banks (eg. PDB) For
Future Protein Research.

5. ORDERS OF PROTEIN STRUCTURE
 Primary Structure
 Secondary Structure
1. α-Helix
2. β-Sheets
 Tertiary Structure
1. Covalent Interactions (Covalent Bonds)
2. Non-Covalent Interactions
(Ionic Bonds, Hydrogen Bonds, Van Der
Waals Force, Hydrophobic Reactions)
 Quaternary Structure
1º Structure  2º Structure  3º Structure  4º Structure
Amino Acid Local 3D Arrangement, More Proteins
Sequence Conformations Becomes Active Assembly

6. PRIMARY STRUCTURE
 1º Structure - Just Amino Acid Sequence.
 Determined By Genetic Code Directly.
 Very Important Structure Since It Determines The
Rest Protein Structures (Secondary, Tertiary And
Quaternary Structures).
Eg. Protamines. One Of The Most Simple Protein
With 50 Amino Acids Long Sequence. They Are
Important For Spermatogenesis.
Mus Musculus Protamine Sequence
MARYRCCRSKSRSRCRRRRRRCRRRRRRCCRRR
RRRCCRRRRSYTIRCKKY

8. SECONDARY STRUCTURE
 2º Structure - Local Conformations Of Polypeptide
Chains.
 They Are Stabilized By Hydrogen Bonds In
Polypeptide Backbone.
 The Most Common 2º Structures Are,
1. α-Helix
2. β-Sheets
 Common 2º Structures Has Torsion Angles φ (Phi) And
ψ (Psi).
 Undoubtedly, Ramachandran Plot Is A Important
Technique To Study These Protein 2º Structure
Relationships. It Is Developed By G.N. Ramachandran
In The Year 1963.

9. 1. ALPHA HELIX
 Rigid, Rod Like Structure Forms When Polypeptide
Chain Twists Into Helical Conformation.
 Direction Of Helical Conformation Can Be,
1. Right Handed / Clockwise
2. Left Handed / Anti-Clockwise
 α-Helix Found In Proteins Is Right Handed. In Right
Handed Helix, There Is Less Clash Between The Side
Chains.
 Usual Length  10-15 AA Residues
 Stabilized By Intrachain H-Bonds Between NH And CO
Groups.
 3.613 - Helix  Has 3.6 AA Per Turn And Single Turn
Involves 13 Atoms.

10.  Can Be Produced From Either D-AA Or L-AA Which
Has Only One Conformation.
 Cannot Be Produced From The Mixture Of D-AA
And L-AA.
 Higher Tendancy For Formation - Alanine,
Glutamine, Glutamate, Leucine, Methionine,
Arginine.
 Destabilization
1. Steric Clashes  Valine, Threonine
2. Presence Of H-Bond Donor And Acceptor In
Close Range  Serine, Asparagine
3. Lack Of NH Group  Proline

11. α-Helix Structure

12. 2. BETA SHEETS
 It Is Produced When Two Or More Polypeptide
Chains Are Lined Up Side By Side.
 Extended Conformation Where AA Are Present
In Front Of Eachother.
 Stabilized By Interchain Hydrogen Bonds Forms
Between NH And CO Groups.
 β Strand - Individual Segment Of β Sheets.
 Structures Of β-Sheets Can Be,
1. Parallel  Arranged In Same Direction
2. Antiparallel  Arranged In Opposite Direction
 Antiparallel Sheets Are More Stable Than Parallel Sheets
Due To Formation Of Collinear H-Bonds.

13. (a) Parallel Sheets (b) Antiparallel Sheets

14. Ramachandran Plot - Protein 2º Structure Determination

15. TERTIARY STRUCTURE
 3º Structure - Compact, 3D - Folded Arrangement Of
Proteins Under Physiological Conditions.
 Very Important Structure Where The Proteins
Becomes Functional.
 Stabilized By Following Biochemical Interactions
Includes,
 Covalent Interactions
 Non-Covalent Interactions
1. Ionic Bonds
2. Hydrogen Bonds
3. Van Der Waals Forces
4. Hydrophobic Interactions

16. COVALENT INTERACTIONS
 Covalent Bond Present In 3° Structure Of Proteins
Is Disulfide Bond.
 It Is Formed Between 2 Cysteine Residues Due To
Oxidation.
 The Oxidized Form Of Cysteine Residue Is Called
“Cystine”.
 Two Types Of Interactions Are There.
1. Polar Covalent Bonds  Electron Pairs Shared
Unequally Due To Different Electronegativity.
Eg.Hydrogen Fluoride(HF).
2. Non-Polar Covalent Bonds  Electron Pairs
Shared Equally And Same Electronegativity.
Eg. Hydrogen(H2).

17. NON-COVALENT INTERACTIONS
Weak In Nature Compared To
Covalent Interactions.
Bond Strength Is Very Less.
Minimum Energy Is Enough To Break
Non-Covalent Interactions Since They
Are Weak.
 Required Energy To Break  1-5 Kcal/Mol

18. IONIC BONDS
Formed Due To Electrostatic
Interactions Between Positive And
Negative Ions.
It Is Formed When Electronegativity
Between Two Groups Is Large.
In Proteins, Ionic Bonds Are Formed
Between Two Charged Groups Of AA.
i.e. Basic And Acidic AA.

19. HYDROGEN BONDS
 It Is Stronger Than Most Non-Covalent
Interactions.
 Bond Strength Of H-Bonds Is Depends On
The Alignment Of Atoms.
 H-Bonds Can Be Intermolecular Or
Intramolecular In Nature.
 H-Bonds Plays Some Important Roles In
Structure Of Proteins Includes,
1. Regular Shape To Polypeptide Chains.
i.e. α-Helix, β-Sheets.
2. Molecular Stability Of Proteins.

20. VAN DER WAALS FORCE
Weak, Intermolecular Interactions.
The Strength Of Van Der Waals
Forces Will Increase When Two
Atoms Comes Closer To
Eachother.
Bond Energy  1 Kcal/Mol

21. HYDROPHOBIC INTERACTIONS
 Occurs Among Non-Polar, Hydrophobic R-Groups
Of Proteins.
 Very Important For Protein Folding Process.
Protein Folding And Hydrophobic Bonds
 Linear Polypeptide Will Fold Into A Shape Where
Hydrophobic AA Comes In Close Contact With
Eachother Inside The Cellular Environment.
 The Peptide Chain Of Globular Protein Folds Into
Spherical Shape And Desired Surface Area Is
Achieved.
 Unwanted Interactions With Water Is Reduced And
Protein Folding Is Successful.

22. Protein Tertiary Structures And Protein Folding

23. QUATERNARY STRUCTURE
 Multi-Subunit Organization Of Proteins.
 Assembly Or Aggregation Of Two/More Polypeptide
Chains Occurs And Those Were Held Together By
Non-Covalent Interactions.Eg.Hydrogen Bonds.
S.NO PROTEIN NAME PROTEIN TYPE NO.OF
CHAINS
1. ALBUMIN GLOBULAR 1
2. INSULIN GLOBULAR 2
3. COLLAGEN FIBROUS 3
4. HEMOGLOBIN GLOBULAR 4
Quaternary Structures Of Proteins

25. 2° STRUCTURE TOOLS
JPred4
RaptorX
PredictProtein 2013
PROTEUS2
PEP2D

26. 3° STRUCTURE TOOLS
SWISS MODEL
PHYRE2
PEP FOLD3
ORION
Robetta

27. 4° STRUCTURE TOOLS
PIPSA
MolSurfer
PDBePISA
TRAPP
STRING

28. Orders Of Protein Structure

29. REFERENCES
 James.D Watson, Tania.A Baker, Molecular Biology Of The Gene,
Pearson Publishers, 7th Edition, Pg 121-129.
 Lehninger, David.L Nelson, Michael.M Cox, Principles Of
Biochemistry, W.H.Freeman And Company(NY), 6th Edition,
Pg 115.
 U.Satyanarayana, U.Chakrapani, Biochemistry, Books And
Allied(P)Ltd, 5th Edition, Pg 52.
 https://courses.lumenlearning.com/introchem/chapter/protein-
structure/
 https://www.khanacademy.org/science/biology/macromolecules/p
roteins-and-amino-acids/a/orders-of-protein-structure
 https://bio.libretexts.org/Courses/University_of_California_Davis/
BIS_2A%3A_Introductory_Biology_(Britt)/Readings/16%3A_Prot
ein_Structure
 https://molbiol-tools.ca/Protein_secondary_structure.htm
 https://molbiol-tools.ca/Protein_tertiary_structure.htm
 https://molbiol-tools.ca/Protein_quaternary_structure.htm

30. THANKS FOR YOUR PATIENCE….