1. Principles of Protein Structure
PHAR 201/Bioinformatics I
Philip E. Bourne
School of Pharmacy & Pharm. Sci., UCSD
Prerequisite Reading: Structural Bioinformatics Chapters 1-2
Thanks to Eric Scheeff and Lynn Fink
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2. Remember ..
The first 2 lectures are not so much to teach/refresh your knowledge of protein/DNA/RNA structure, but for you to conceptualize, describe and subsequently analyze complex biological data
Assignment 1 will test this
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3. Remember..
All which we study is an abstraction to make comprehension of a complex entity more straightforward
We think of structures as static entities, but they are dynamic, sometimes to the point of being ill-definable – function requires this flexibility
The more we have the more we should know and use – contrast Kendrew to the PDB today
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4. Primary Structure - Amino Acids
It is the amino acid sequence (1940) that “exclusively” determines the 3D structure of a protein
20 amino acids – modifications do occur post translationally
2,3,4 completely encoded by primary structure
Linear polymer theory
Set of 20 amino acids not determined until 1940
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5. Amino Acids Continued…
It is the properties of the R group that determine the property of the aa and ultimately the protein
Different schemes exist for describing the properties Willie Taylor’s scheme is often employed in bioinformatics analyses
Hydrophobicity, polarity and charge are common measures
Learn the amino acid codes, structures and properties!
Subclasses – Aromatic or aliphatic; large and small
Static properties of the amino acid
Primary Structure
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6. Amino Acids Continued…
Chirality – amino acids are enatiomorphs, that is mirror images exist – only the L(S) form is found in naturally forming proteins. Some enzymes can produce D(R) amino acids
Think about a data structure for this information – annotation and a validation procedure should be included
Think about systematic versus common nomenclature
Primary Structure
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7. Peptide Bond Formation
Individual amino acids form a polypeptide chain
Such a chain is a component of a hierarchy for describing macromolecular structure
The chain has its own set of attributes
The peptide linkage is planar and rigid
Primary Structure
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8. Geometry of the Chain
A dihedral angle is the angle between two planes defined by 4 atoms – 123 make one plane; 234 the other
Omega is the rotation around the peptide bond Cn – Nn+1 – it is planar and is 180 under ideal conditions
Phi is the angle around N – Calpha
Psi is the angle around Calpha C’
The values of phi and psi are constrained to certain values based on steric clashes of the R group. Thus these values show characteristic patterns as defined by the Ramachandran plot
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Secondary Structure
From Brandon and Tooze

9. Ramachandran Plot Shows allowed and disallowed regions
Gly and Pro are exceptions: Gly has no limitation; Pro is constrained by the fact its side chain binds back to the main chain
Gray = allowed conformations. βA, antiparallel b sheet; βP, parallel b sheet; βT, twisted b sheet (parallel or anti-parallel); α, right-handed α helix; L, left-handed helix; 3, 310 helix; p, Π helix.
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Secondary Structure

10. Secondary Structure
The chemical nature of the carboxyl and amino groups of all amino acids permit hydrogen bond formation (stability) and hence defines secondary structures within the protein.
The R group has an impact on the likelihood of secondary structure formation (proline is an extreme case)
This leads to a propensity for amino acids to exist in a particular secondary structure conformation
Helices and sheets are the regular secondary structures, but irregular secondary structures exist and can be critical for biological function
Alpha and beta predicted by Pauling
Stabiliz
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Secondary Structure

11. Alpha Helix
A helix can turn right or left from N to C terminus – only right-handed are observed in nature as this produces less clashes
All hydrogen bonds are satisfied except at the ends = stable
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Secondary Structure

12. Alpha Helix Continued There are 3.6 residues per turn
A helical wheel will outline the surface properties of the helix
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Secondary Structure

13. Other (Rarer) Helix Types - 310
Less favorable geometry
3 residues per turn with i+3 not i+4
Hence narrower and more elongated
Usually seen at the end of an alpha helix
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4HHB
Secondary Structure

14. Other (Very Rare) Helix Types - Π
Less favorable geometry
4 residues per turn with i+5 not i+4
Squat and constrained
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Secondary Structure

15. Beta Sheets
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Secondary Structure

16. Beta Sheets Continued Between adjacent polypeptide chains
Phi and psi are rotated approximately 180 degrees from each other
Mixed sheets are less common
Viewed end on the sheet has a right handed twist that may fold back upon itself leading to a barrel shape (a beta barrel)
Beta bulge is a variant; residue on one strand forms two hydrogen bonds with residue on other – causes one strand to bulge – occurs most frequently in parallel sheets
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Secondary Structure

17. Other Secondary Structures – Loop or Coil
Often functionally significant
Different types
Hairpin loops (aka reverse turns) – often between anti-parallel beta strands
Omega loops – beginning and end close (6-16 residues)
Extended loops – more than 16 residues
1AKK
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Secondary Structure

18. Tertiary Structure
Myoglobin (Kendrew 1958) and hemoglobin (Perutz 1960) gave us the proven experimental insights into tertiary structure as secondary structures interacting by a variety of mechanisms
While backbone interactions define most of the secondary structure interactions, it is the side chains that define the tertiary interactions
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Tertiary Structure

19. Components of Tertiary Structure
Fold – used differently in different contexts – most broadly a reproducible and recognizable 3 dimensional arrangement
Domain – a compact and self folding component of the protein that usually represents a discreet structural and functional unit
Motif (aka supersecondary structure) a recognizable subcomponent of the fold – several motifs usually comprise a domain
Like all fields these terms are not used strictly making capturing data that conforms to these terms all the more difficult
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Tertiary Structure

20. Tertiary Structure as Dictated by the Environment
Proteins exist in an aqueous environment where hydrophilic residues tend to group at the surface and hydrophobic residues form the core – but the backbone of all residues is somewhat hydrophilic – therefore it is important to have this neutralized by satisfying all hydrogen bonds as is achieved in the formation of secondary structures
Polar residues must be satisfied in the same way – on occasion pockets of water (discreet from the solvent) exist as an intrinsic part of the protein to satisfy this need
Ion pairs (aka salt bridge) form important interactions
Disulphide linkages between cysteines form the strongest (ie covalent tertiary linkages); the majority of cysteines do not form such linkages
5EBX
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Tertiary Structure

21. Tertiary Structure as Dictated by Protein Modification
To the amino acid itself eg hydroxyproline needed for collagen formation
Addition of carbohydrates (intracellular localization)
Addition of lipids (binding to the membrane)
Association with small molecules – notably metals eg hemoglobin
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Tertiary Structure

22. There are Different Forms of Classification apart from Structural
Biochemical
Globular
Membrane
Fibrous
myoglobin
Bacteriorhodopsin
Collagen
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23. Quaternary Structure
The biological function of some molecules is determined by multiple polypeptide chains – multimeric proteins
Chains can be identical eg homeodimer or different eg heterodimer
The interactions within multimers is the same as that found in tertiary and secondary structures
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24. Cooperativity Co-location of Function Combination Structural Assembly
Hemoglobin:
Enhanced binding
capability of oxygen
Cooperativity
Glutamine sythetase:
Controlled use of
Nitrogen from
Multiple active sites
Co-location of
Function
Combination
Immunoglobulin:
Multiple receptor
responses
Structural
Assembly
Actin:
Giving the cell shape
and form
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Quaternary Structure

25. Quaternary Structure: Ferritin - The Bodies Iron Storage Protein
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Quaternary Structure

26. PHAR201 Lecture

27. Disorder?
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28. Additional Reading
Branden and Tooze (1999) Introduction to Protein Structure (2nd Edition) Garland Publishing.
An excellent introduction
Richardson (1981) The Anatomy and Taxonomy of Protein Structure Adv. Protein Chem. 34:
Good historical perspective
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