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Protein Structure and Function

Proteins are large biomolecules composed of chains of amino acids that carry out essential functions in the body. They have a primary structure defined by the sequence of amino acids in the chain. The chains fold into regular secondary structures like alpha helices and beta sheets that further organize into complex three-dimensional tertiary and sometimes quaternary structures essential for their function. The structures are determined by interactions between R groups of amino acids that allow proteins to perform diverse catalytic, structural, transport, and other vital roles in living organisms.

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46 views52 pages

Protein Structure and Function

Proteins are large biomolecules composed of chains of amino acids that carry out essential functions in the body. They have a primary structure defined by the sequence of amino acids in the chain. The chains fold into regular secondary structures like alpha helices and beta sheets that further organize into complex three-dimensional tertiary and sometimes quaternary structures essential for their function. The structures are determined by interactions between R groups of amino acids that allow proteins to perform diverse catalytic, structural, transport, and other vital roles in living organisms.

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bharat
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Protein Structure and function

Agneyo Ganguly
What Are Proteins?
• Large molecules
• Made up of chains of amino acids
• Are found in every cell in the body
• Are involved in most of the body’s functions
and life processes
• The sequence of amino acids is determined by
DNA
Structural Differences Between
Carbohydrates, Lipids, and Proteins
Amino acids share many features,
differing only at the R substituent
L and D forms
Essential, Nonessential, and
Conditional
• Essential – must be consumed in the diet
• Nonessential – can be synthesized in the body
• Conditionally essential – cannot be
synthesized due to illness or lack of necessary
precursors
– Premature infants lack sufficient enzymes needed
to create arginine
Amino Acids: Classification

• Common amino acids can be placed in five basic


groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
UV light Absorption by Proteins – due to 2 Amino Acids
Spectrophotometry

Transmittance is given by the equation:


T = I/Io
where I is the intensity of the light after it has gone
through the sample & Io is the initial light intensity.
Absorbance is related to the %T:
A = -logT = -log(I/ Io)
Absorbance
A = e.c.l
A is the absorbance
“e” is molar extinction in L/[(mole)(cm)]
“l” is the path length in cm
“c” is the concentration of the analyte
(sample) in mol/L
Molar extinction coefficient of protein

A protein comprising of 125 amino acids has 5 tryptophan, 10 tyrosin and


6 cystein residues. If a 1 ml sample of the protein gives absorbance of
0.3, calculate the amount of protein present in 1mL of solution.
Given : average molecular weight of amino is 110 Da
Cysteine can form Disulfide Bonds
Glycine Acid/Base Titration

Isoelectric point (pI)


= ½ ( pK1+pK2)
Compare Amino Acids to Simple Carboxylic Acids
and Amines
Glutamate has 3 pKa’s
Peptide Bond Formation
Structure of a Simple Peptide

Ser-Gly-Tyr-Ala-Leu or SGYAL
Naming peptides:
start at the N-terminus

• Using full amino acid names


– Serylglycyltyrosylalanylleucine
• Using the three-letter code abbreviation
– Ser-Gly-Tyr-Ala-Leu
• For longer peptides (like proteins) the one-
letter code can be used
– SGYAL
AEGK
Peptides: A Variety of Functions
• Hormones and pheromones
– insulin ( sugar)
– oxytocin ( childbirth)
Neuropeptides
– substance P (pain mediator)

• Antibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)

• Protection, e.g., toxins


– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)
Structure of the Protein
• Four levels of structure
– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure

Any alteration in the structure or sequencing


changes the shape and function of the protein
Terminology

• Conformation – spatial arrangement of


atoms in a protein
• Native conformation – conformation of
functional protein
Protein Structure: the early days

Robert Corey
Linus Pauling
First prediction of secondary structures:
Alpha helix and beta sheets

Pauling and Corey with their model of


the alpha helix, 1951
Ψ and ϕ angles
Alpha Helix

Phi angle: -570


Psi angle: -470
Beta-Sheets
• Beta-sheets
formed from
multiple side-by-
side beta-strands.
• Can be in parallel or
anti-parallel
configuration
• Anti-parallel beta-
sheets more stable
In a β strand, the torsion angle
of N-Cα-C-N in the backbone is
about 120 degrees.
Beta- Barrels

The β barrel structure in porins, which are transmembrane proteins


that facilitate transfer of small molecules
Bonds holding the tertiary structure of
Proteins

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Levinthal paradox

If a protein comprise of n number of residues, possible torsional angles is


2n. If 3 possible stable conformations are possible for each of these, the
total possible conformation will be 32n (approx. 10n)

If the rate of reorientation of a single bond is 1013/s


The time required for a protein to explore all possible conformations will be:

t= 10n/1013 s-1 For a small protein of 100 aa, this would be 1087 s >> age of
the universe ( 13.7 billion years = 4.3x 1017 s)
Levinthal paradox
Protein Folding
• occurs in the cytosol • tumbles towards conformations
• involves localized spatial that reduce E (this process is
interaction among primary thermo-dynamically favorable)
structure elements, i.e. the • yields secondary structure
amino acids
• may or may not involve
chaperone proteins
Protein Packing
• occurs in the cytosol (~60% bulk
water, ~40% water of hydration)
• involves interaction between
secondary structure elements and
solvent
• may be promoted by chaperones,
membrane proteins
• tumbles into molten globule states
• overall entropy loss is small enough
so enthalpy determines sign of E,
which decreases (loss in entropy
from packing counteracted by gain
from desolvation and reorganization
of water, i.e. hydrophobic effect)
• yields tertiary structure
X-Ray Crystallography
• crystallize and immobilize
single, perfect protein
• bombard with X-rays,
record scattering
diffraction patterns
• determine electron density
map from scattering and
phase via Fourier
transform:

• use electron density and "All crystallographic models are not equal. ... The brightly colored stereo views of a

biochemical knowledge of protein model, which are in fact more akin to cartoons than to molecules, endow
the model with a concreteness that exceeds the intentions of the thoughtful
crystallographer. It is impossible for the crystallographer, with vivid recall of the
the protein to refine and massive labor that produced the model, to forget its shortcomings. It is all too easy
for users of the model to be unaware of them. It is also all too easy for the user to
determine a model be unaware that, through temperature factors, occupancies, undetected parts of
the protein, and unexplained density, crystallography reveals more than a single
molecular model shows.“

- Rhodes, “Crystallography Made Crystal Clear” p. 183.


Fluorescence Resonance Energy Transfer
• FRET described as a “molecular ruler”
• segments of a protein are tagged with fluorophores
• energy transfer occurs when donor and acceptor interact, falls
off as 1/d6 where d is separation between
donor and acceptor
• donor and acceptor must be within 50 Å,
acceptor emission sensitive to distance change
• can determine pairs of side chains that are separated when
unfolded and close when folded
Protein Data Bank
• Coordinates database
RCSB Protein Data Bank (PDB)
– has many structures, partly due
to minor differences in structure
resolution and annotation
– has much fewer fold families,
Cumulative increase in the partly due to evolved pathways
number of domains
and mechanisms
– .pdb = data from experiment,
with missing parameters and
multiple conformations

Cumulative increase in the


number of folds and
superfamilies
Molecular Modeling DataBase
• Comparative database
NCBI Molecular Modeling DataBase (MMDB)
– subset of PDB, excludes theoretical structures, with native
.asn format
– .asn = single-coordinate per-atom molecules, explicit bonding
and SS remarks
– suited for computation, such as homology modeling and
structure comparison
Protein Function
• Catalysis – enzymes
• Structural – keratin
• Transport – hemoglobin
• Trans-membrane transport – Na+/K+ ATPases
• Toxins – rattle snake venom, ricin
• Contractile function – actin, myosin
• Hormones – insulin
• Storage Proteins – seeds and eggs
• Defensive proteins – antibodies

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Protein Classification
Fibrous –
1) polypeptides arranged in long strands or
sheets
2) water insoluble (lots of hydrophobic AA’s)
3) strong but flexible
4) Structural (keratin, collagen)

Globular –
1) polypeptide chains folded into spherical or
globular form
2) water soluble
3) contain several types of secondary structure
4) diverse functions (enzymes, regulatory
proteins)
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