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Protein Structure Students (1563)

Proteins have three main functions: catalysis, transport, and information transfer. They fold into complex three-dimensional structures determined by their amino acid sequence, including primary, secondary, tertiary, and sometimes quaternary structure. A protein's unique structure is crucial to its specific biological function. Predicting a protein's structure from its sequence remains a major challenge.

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27 views32 pages

Protein Structure Students (1563)

Proteins have three main functions: catalysis, transport, and information transfer. They fold into complex three-dimensional structures determined by their amino acid sequence, including primary, secondary, tertiary, and sometimes quaternary structure. A protein's unique structure is crucial to its specific biological function. Predicting a protein's structure from its sequence remains a major challenge.

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Protein Structure

Protein Functions

• Three examples of protein functions


Alcohol
dehydrogenase
– Catalysis: oxidizes alcohols
Almost all chemical reactions in a living to aldehydes or
cell are catalyzed by protein enzymes. ketones

– Transport:
Some proteins transports various
substances, such as oxygen, ions, and so Haemoglobin
carries oxygen
on.

– Information transfer:
For example, hormones. Insulin controls
the amount of
sugar in the
blood
Amino acid: Basic unit of protein

R Different side chains, R,


NH3 + C COO properties of 20 amino
- determine the
Amino group Carboxylic
acid group acids.
H
An amino acid
20 Amino acids

Glycine (G) Alanine (A) Valine (V) Isoleucine (I) Leucine (L)

Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine (N)

Glutamine (Q) Serine (S) Threonine (T) Tyrosine (Y) Cysteine (C)

Asparatic acid (D) Glutamic acid (E) Lysine (K) Arginine (R) Histidine (H)

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic


Each protein has a unique structure!

Amino acid sequence


NLKTEWPELVGKSVEEAK
KVILQDKPEAQIIVLPVGTI
VTMEYRIDRVRLFVDKLD

Folding!
Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
https://www.youtube.com/watch?v=q_n0Ij3K_Ho
Protein Assembly

• occurs at the ribosome


• involves polymerization of
amino acids attached to
tRNA
• yields primary structure
Primary Structure
primary structure of human insulin
CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
• linear
CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT • ordered
• 1 dimensional
• sequence of amino acid
polymer
• by convention, written
from amino end to
carboxyl end
• a perfectly linear amino
acid polymer is neither
functional nor
energetically favorable 
folding!
Protein Folding

• occurs in the cytosol


• involves localized spatial • yields secondary structure
interaction among primary
structure elements, i.e. the amino
acids
Secondary Structure

• non-linear
• 3 dimensional
• localized to regions of an
amino acid chain
• formed and stabilized by
hydrogen bonding,
electrostatic and van der
Waals interactions
Secondary structure

α-helix β-sheet

Secondary structures, α-helix


and β-sheet, have regular
hydrogen-bonding patterns.
Protein Packing

• occurs in the cytosol (~60% bulk


water, ~40% water of hydration)
• involves interaction between
secondary structure elements
and solvent
• yields tertiary structure
Tertiary Structure

• non-linear
• 3 dimensional
Protein Interaction
• occurs in the cytosol, in close proximity to other folded and
packed proteins
• involves interaction among tertiary structure elements of
separate polymer chains
Quaternary Structure
• non-linear
• 3 dimensional
3D structure of proteins

Tertiary
structure
Quaternary structure
Class/Motif

• class = secondary structure


composition,
e.g. all , all , / , +
• motif = small, specific combinations of
secondary structure elements,
e.g. -- loop /
• both subset of fold
Fold
• fold = architecture = the overall
shape and orientation of the
secondary structures, ignoring
connectivity between the
structures,
e.g. / barrel, TIM barrel
• subset of fold
families/superfamilies
Fold families/Superfamilies

• fold families = categorization that


takes into account topology and
previous subsets as well as
empirical/biological properties, e.g.
flavodoxin
• superfamilies = in addition to fold
families, includes
evolutionary/ancestral properties
CLASS: +
FOLD: sandwich
FOLD FAMILY: flavodoxin
Hierarchical nature of protein structure
Primary structure (Amino acid sequence)
↓
Secondary structure （α-helix, β-sheet）
↓
Tertiary structure （Three-dimensional structure
formed by assembly of secondary structures）
↓
Quaternary structure （Structure formed by more than
one polypeptide chains）
Protein structure and its function

Example of enzyme reaction Hormone receptor Antibody


substrates
enzyme A enzyme

B
Matching
Digestion
the shape
of A!
to A enzyme

Binding to A
Protein structure prediction has remained
elusive over half a century

“Can we predict a protein structure from


its amino acid sequence?”

Now, impossible!
• A fold
Summary

• Proteins are key players in our living systems.


• Proteins are polymers consisting of 20 kinds of amino acids.
• Each protein folds into a unique three-dimensional structure
defined by its amino acid sequence.
• Protein structure has a hierarchical nature.
• Protein structure is closely related to its function.
• Protein structure prediction is a grand challenge of
computational biology.

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