BCHM-3050 Lecture Notes - Lecture 9: Triosephosphate Isomerase, 310 Helix, Alphabeta
8 Jun 2018
School
Department
Course
Professor
Overview of structures
Primary structure: amino acid sequence makes up protein
Direct end of mRNA translation
•
Only peptide bonds present
Link indiv. AA
○
•
Peptide bond: b/w amine and carbonyl
Non rotational
○
•
Rotation on bonds other than peptide = psi and phi angles
Clockwise: positive angle
○
Counterclockwise: negative angle
○
•
Secondary structure: area of repeat main chain structure
Intermolecular forces (ex. H bond) form local regions of patterned
substructures
Helices and sheets
○
•
Rules:
Bond angles and bond lengths = similar to primary
Characteristics (ex. Nonpolar) in primary are found in
secondary
§
Amide group = planar
§
○
No two atoms will approach closer than allowed by van der waals
○
Noncovalent bonds help stabilize 3D structure
○
•
Tertiary structure: 3D spatial arrangement
Folding of secondary
•
Amino acids interact with other outside residue
Hydrophobic = fold to interior
○
Hydrophilic = fold to exterior
○
•
Could include cofactors
Non protein elements
Ex. Heme
§
○
Require folded 3D state
○
•
Quaternary structure: overall spatial arrangement
Multi subunit complex
•
Need 2+ polypeptide chain
•
Identical to tertiary in characteristics
•
Secondary structure
Alpha helix: side chain radiate out from helix axis
H bond: parallel to central axis
○
Amphiphilic
○
•
Beta sheets: stabilized by interchain H bond
Allow side chain to alternated sides of sheet
○
Parallel and antiparallel
Base on N and C termini
§
○
•
310 helix = rare
•
Parameters defining:
Residues per turn
Alpha helix = ~4
§
○
Rise
○
Pitch
○
•
Steric interaction determines peptide conformation
Some phi and psi angles result in steric hindrance
Atoms closer than van der waals radii
○
Conformation with steric hindrance is not allowed
○
•
Alpha helix: backbones w closely packed atoms
No steric clashes
○
•
Ramachandran plot: show sterically allowed phi and psi angles
White sections = sterically allowed angles
○
•
Bigger side chain = more steric hindrance
Less room for twists
○
•
Sheet: side chains as far away as possible
•
Representative secondary structure elements
Alpha helix: R groups jut out from center
Alignment of termini = helix dipole
C -> N
§
○
•
Beta sheets: antiparallel
•
Alpha helix v 310 helix
Alpha helix = 4 sides
Center = backbone atoms involved in packing
○
Main chain H bonds
○
•
310 = 3 sides
•
Polypeptide II helix
Not stabilized by H bonds
•
1/3 residues = proline
•
Prevalent in collagen
•
Turn and loop structure
Turns: characterized by number of peptide bonds b.w end residue
Connect via H bonds
4 for alpha turn
§
3 for beta turn
§
○
Beta turn = most common
○
Turns based on allowed phi and psi angles
○
Turns connect secondary structures
○
•
Loops: longer turns
On surface of protein
Indicates use of polar residue
§
○
Bury phi and psi angles
○
Role in folding and protein interactions
○
•
Random turn/coils
In "between state" b/w secondary and tertiary struct
•
Common in proteins that lack significant helical or sheet type
•
No repeating sequences of AA
•
Tertiary structure: fold classes
Classification of tertiary struct: helix and sheets with turns
•
Examples of fold class:
All alpha helix
○
All beta sheet
○
Alpha + beta
Not alternating
§
○
Alpha/beta
Alternating
§
○
•
More:
Globular
○
Membrane protein
○
Fibrous protein (coiled coil)
○
•
3 ways to represent protein ubiquitin
Surface model: surface of protein
Blue = + charge
○
Red = - charge
○
Green = neutral
○
•
Cartoon model: look at secondary struct
•
Stick model and close up: best for molecular interaction
Ex. Substrate to protein
○
•
Globular protein
Common features:
Hydrophobic interior and hydrophilic exterior
○
Beta sheets form barrel shape
○
Polypeptide chain can turn corners
○
•
Myoglobin: all alpha
•
Neuraminidase: all beta
•
Triosephosphate isomerase: alpha + beta
•
Large proteins = protein domains
~200 AA
○
Connect via loops and random coils
○
Can fold independently
○
May have multiple secondary structures
○
Have defined functions
○
•
Fibrous protein structure
Fibrous protein: elongate filamentous molecules
Defined secondary
○
Coiled tertiary
○
•
Keratin
Alpha keratin: large hydrophobic residues
Repeat every 4 positions
§
○
•
Fibroin
Silk fibroin: nothing but sheets
Very flexible
§
Held together by van der waal
§
○
•
Collagen: triple strand left hand helix
Matrix material in bone
○
Contain hydroxy proline (Hyp) and hydroxylysine
○
•
G-X-Y tripeptide motif
X= pro and Y = pro and Hyp
○
Chains cross linked with Hyp and glycosylated
○
•
Vitamin C: cofactor required for proline hydroxylation
Deficiency lead to breakdown of collagen
○
•
General protein folding
Anfinsen experiment: use bovine ribonuclease A
Specify info about tertiary struct based on AA sequence
○
•
Core features of tertiary structure
Unique
○
Stable
○
Once protein is folded it is at its most stable state
○
•
Heat enduced denaturation of RNAase
Let protein self fold and unfold
○
•
Thermodynamic hypothesis
High Tm = more stable protein
○
Tm = temperature at which protein exists 50% folded and 50%
unfolded
○
•
3 thermodynamic factors influence folding and protein stability
Favorable intramolecular enthalpic interactions
Noncovalent interactions
Salt bridgei.
H bonds ii.
Van der Waals
Packed proteins 1)
iii.
a.
1.
Unfavorable loss of conformation entropy
Primary is favored entropically more then tertiary
Folded state is not as chaotic i.
a.
2.
Favorable gain of solvent entropy by burying hydrophobic groups
Hydrophobic effect a.
3.
Disulfide bond: increase stability
Partly entropic
○
Reduce # of conformations possible in unfolded state
○
•
Dynamics of globular protein structure
Levinthal's paradox: not all possible states are sampled when trying to
find the lowest energy conformation
•
Molten globules: lack defined structural interaction
Free form tertiary structure
Can change at any time
§
○
Like an intermediate state
○
Helps guide protein into right conformation
○
•
Intermediate/off pathway states and help with folding
Cis isomer: unfavorable
•
Formation of non native disulfide bonds is corrected by protein disulfide
isomerase
•
Chaperonins: needed during times of heat stress
GroE1 = cup
○
GroES = lid
○
•
Chapter 6: 3D structure
Friday, June 1, 2018
10:08 PM
Overview of structures
Primary structure: amino acid sequence makes up protein
Direct end of mRNA translation
•
Only peptide bonds present
Link indiv. AA
○
•
Peptide bond: b/w amine and carbonyl
Non rotational
○
•
Rotation on bonds other than peptide = psi and phi angles
Clockwise: positive angle
○
Counterclockwise: negative angle
○
•
Secondary structure: area of repeat main chain structure
Intermolecular forces (ex. H bond) form local regions of patterned
substructures
Helices and sheets
○
•
Rules:
Bond angles and bond lengths = similar to primary
Characteristics (ex. Nonpolar) in primary are found in
secondary
§
Amide group = planar
§
○
No two atoms will approach closer than allowed by van der waals
○
Noncovalent bonds help stabilize 3D structure
○
•
Tertiary structure: 3D spatial arrangement
Folding of secondary
•
Amino acids interact with other outside residue
Hydrophobic = fold to interior
○
Hydrophilic = fold to exterior
○
•
Could include cofactors
Non protein elements
Ex. Heme
§
○
Require folded 3D state
○
•
Quaternary structure: overall spatial arrangement
Multi subunit complex
•
Need 2+ polypeptide chain
•
Identical to tertiary in characteristics
•
Secondary structure
Alpha helix: side chain radiate out from helix axis
H bond: parallel to central axis
○
Amphiphilic
○
•
Beta sheets: stabilized by interchain H bond
Allow side chain to alternated sides of sheet
○
Parallel and antiparallel
Base on N and C termini
§
○
•
310 helix = rare
•
Parameters defining:
Residues per turn
Alpha helix = ~4
§
○
Rise
○
Pitch
○
•
Steric interaction determines peptide conformation
Some phi and psi angles result in steric hindrance
Atoms closer than van der waals radii
○
Conformation with steric hindrance is not allowed
○
•
Alpha helix: backbones w closely packed atoms
No steric clashes
○
•
Ramachandran plot: show sterically allowed phi and psi angles
White sections = sterically allowed angles
○
•
Bigger side chain = more steric hindrance
Less room for twists
○
•
Sheet: side chains as far away as possible
•
Representative secondary structure elements
Alpha helix: R groups jut out from center
Alignment of termini = helix dipole
C -> N
§
○
•
Beta sheets: antiparallel
•
Alpha helix v 310 helix
Alpha helix = 4 sides
Center = backbone atoms involved in packing
○
Main chain H bonds
○
•
310 = 3 sides
•
Polypeptide II helix
Not stabilized by H bonds
•
1/3 residues = proline
•
Prevalent in collagen
•
Turn and loop structure
Turns: characterized by number of peptide bonds b.w end residue
Connect via H bonds
4 for alpha turn
§
3 for beta turn
§
○
Beta turn = most common
○
Turns based on allowed phi and psi angles
○
Turns connect secondary structures
○
•
Loops: longer turns
On surface of protein
Indicates use of polar residue
§
○
Bury phi and psi angles
○
Role in folding and protein interactions
○
•
Random turn/coils
In "between state" b/w secondary and tertiary struct
•
Common in proteins that lack significant helical or sheet type
•
No repeating sequences of AA
•
Tertiary structure: fold classes
Classification of tertiary struct: helix and sheets with turns
•
Examples of fold class:
All alpha helix
○
All beta sheet
○
Alpha + beta
Not alternating
§
○
Alpha/beta
Alternating
§
○
•
More:
Globular
○
Membrane protein
○
Fibrous protein (coiled coil)
○
•
3 ways to represent protein ubiquitin
Surface model: surface of protein
Blue = + charge
○
Red = - charge
○
Green = neutral
○
•
Cartoon model: look at secondary struct
•
Stick model and close up: best for molecular interaction
Ex. Substrate to protein
○
•
Globular protein
Common features:
Hydrophobic interior and hydrophilic exterior
○
Beta sheets form barrel shape
○
Polypeptide chain can turn corners
○
•
Myoglobin: all alpha
•
Neuraminidase: all beta
•
Triosephosphate isomerase: alpha + beta
•
Large proteins = protein domains
~200 AA
○
Connect via loops and random coils
○
Can fold independently
○
May have multiple secondary structures
○
Have defined functions
○
•
Fibrous protein structure
Fibrous protein: elongate filamentous molecules
Defined secondary
○
Coiled tertiary
○
•
Keratin
Alpha keratin: large hydrophobic residues
Repeat every 4 positions
§
○
•
Fibroin
Silk fibroin: nothing but sheets
Very flexible
§
Held together by van der waal
§
○
•
Collagen: triple strand left hand helix
Matrix material in bone
○
Contain hydroxy proline (Hyp) and hydroxylysine
○
•
G-X-Y tripeptide motif
X= pro and Y = pro and Hyp
○
Chains cross linked with Hyp and glycosylated
○
•
Vitamin C: cofactor required for proline hydroxylation
Deficiency lead to breakdown of collagen
○
•
General protein folding
Anfinsen experiment: use bovine ribonuclease A
Specify info about tertiary struct based on AA sequence
○
•
Core features of tertiary structure
Unique
○
Stable
○
Once protein is folded it is at its most stable state
○
•
Heat enduced denaturation of RNAase
Let protein self fold and unfold
○
•
Thermodynamic hypothesis
High Tm = more stable protein
○
Tm = temperature at which protein exists 50% folded and 50%
unfolded
○
•
3 thermodynamic factors influence folding and protein stability
Favorable intramolecular enthalpic interactions
Noncovalent interactions
Salt bridgei.
H bonds ii.
Van der Waals
Packed proteins 1)
iii.
a.
1.
Unfavorable loss of conformation entropy
Primary is favored entropically more then tertiary
Folded state is not as chaotic i.
a.
2.
Favorable gain of solvent entropy by burying hydrophobic groups
Hydrophobic effect a.
3.
Disulfide bond: increase stability
Partly entropic
○
Reduce # of conformations possible in unfolded state
○
•
Dynamics of globular protein structure
Levinthal's paradox: not all possible states are sampled when trying to
find the lowest energy conformation
•
Molten globules: lack defined structural interaction
Free form tertiary structure
Can change at any time
§
○
Like an intermediate state
○
Helps guide protein into right conformation
○
•
Intermediate/off pathway states and help with folding
Cis isomer: unfavorable
•
Formation of non native disulfide bonds is corrected by protein disulfide
isomerase
•
Chaperonins: needed during times of heat stress
GroE1 = cup
○
GroES = lid
○
•
Chapter 6: 3D structure
Friday, June 1, 2018 10:08 PM
