Lecture 5 - Protein Strucute Flashcards
When amino acids are bonded together in a peptide of protein, they are referred to as…
… amino acid residues
How are the amino acid residues in a polypeptide chain numbered?
From the amino terminus to the carboxy terminus
How many chains do proteins have
Anywhere from one to several chains
- proteins with one chain are the most common variety
Because proteins are mostly globular, the main chain must….
Be able to form a more compact shape and be able to double back
Globular proteins will be mainly comprised of..
Primarily a-helix, B-helix structure and turns
How ,any levels of protien structure
- 4
- primary, secondary, tertiary and quanternary
All proteins have….
Some proteins have…..
All proteins have primary, secondary and tertiary structure
Some proteins have quanternary structure
Primary structure
The linear sequence of amino acids that make up the polypeptide
Secondary structure
- the 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues
- includes a-helices and b-sheets
Tertiary structure
- the 3D structure of a complete protein chain
Quanternary structure
- interchain packing and structure for a protien that contains multiple polypeptide chains (e.g haemoglobin)
The protein main chain and side chains atoms have bond which can…. And are somewhat….
The protein main chain and side chains atoms have binds which can rotate and are somewhat flexible
The main chain atoms in a protein are
N
Ca
C’
Bond angle between N and Ca is called
phi
Bond angle between Ca and C’ are called
Psi
Bong angles take on values ranging from
0 to +/- 180*
The chain angle between ‘ and N is called
w (omega)
W (omega) bond have the angle..
Very close to either 180 or 0
Main chain bond angles
Phi angle
Rotation around the N-Ca bond
Psi angle
Rotation angle around the Ca-C’
Omega
- rotation angle around the peptide bond
Main chain angles in the polypeptide shown
180
Phi-phi restrictions
Phi-Phi angles have restrictions in their values because of steric hinderance
What collision results form phi rotation
O-O collision
Phi rotation can lead to
O-O collision
Psi rotation can lead to collisions of
NH-NH
Psi rotation can lead to
NH-NH collisions
O-O collisions result from
Phi rotation
NH-NH collisions result from
Psi rotation
Steric hinderance between the hydrogen on the amide nitrogen and the carbonyl oxygen
What is w - omega
- third main chain angle
- angle of rotation around the peptide bond
Most peptide bonds are cis/trans
Trans
Angle of omega bond for a trans peptide bond
- w is about 180
- Ca atoms are found on opposite sides of the peptide bond
Steric crowding is increased for cis/trans peptide bonds
Cis
Bond angle of cis peptide omega bond angle
- in a cis peptide bond, the Ca atoms are found on the same side of the peptide bond, w is about 0
Once formed, the peptide bond angle usually does/does not rotate very much
Does not rotate very much
The combination of all the ____ and ____ around all of the ___ in a ___ leads to its overall ____ ____, which in turn, leads to the arrangement of all the side chains in the protien, which in turn leads to its function
The combination of all the rotations and twists around all the bonds in a protien leads to its overall 3D structure, which in turn, leads to the arrangement of all the side chains in the protien, which in turn leads to its function
Two canonical structures that are protien secondary structures
B-strand/B-sheet
a-helix
Strucutre of the a-helix
- the main chain spirals around the central axis like a spiral staircase
- no covalent interaction (hydrogen bond) between the carbonyl of residue “n” and the N-H of residue “n+4”
- hydrogen bonds help stabilise the a-helix structure
- slightly positive charge on the hydrogen
- slightly negative charge on the oxygen
Key properties of the a-helix
-3.6 residues/turn; 5.5A rise/turn; d=1.5A residue
- spiral is right handed
- side chains point out from the helix axis; help stabilise the a-helix
- stabilising hydrogen bond, 3-7kcal/mol or 12-28kj/mol
- some residues are ‘helic breakers’ e.g glycine, proline
- helic dipole exists, positive at N-terminus
Which way do the side chains point in an a-helix
Outwards
Energy in a-helix hydrogen bonds
- 3-7 kcal/mol
- 12-28 kj/mol
a-helix rotations
Which residues are considered “helix breakers”
- glycine
- proline
Do a-helixes have dipoles
Yes
Positive at N-terminus
Helix dipole depiction
Helix wheel
-3.6 residues/turn
-one full turn is 360*
- in an a-helix each amino acid side chain is separated by 100*
B-structure
• Stretches of residues with a more
extended structure than the a-helix.
• Each section of B structure is called a
B-strand
• Hydrogen-bonding occurs between
adjacent chains (strands)
• Adjacent chains can often form a B-
sheet, ≥ two B-strands
• 2 to 10 strands per sheet
• Average strand length contains ~ 6
amino acid residues
• Each strand may have up to 15
residues
• Two types of hydrogen bonding
interaction in a B-sheet:
each seaction of B strucutre os called a
B strand
Hydrogen bonding occurs between
Adjacent chains (strands)
Adjacent chains can often form
B-sheet
How many stands per B-sheet
2-10
How many amino acid residues in the average B-strand
6 amino acid residues
How many residues can a B-stand have
15
Two types of hydrogen bonding interaction in a B-sheet
Antiparallel: strands run in the opposite direction
- hydrogen bonding pattern is optimal (vertical)
Parallel: strands run in the same direction
- hydrogen bonds are zig zagged
B-pleated sheet
- extended
- pleated
B-sheet vs B-strand
- sheets not planar, pleated with R-handed twist
B- strucutre location of side chains
- side chains point above and below the sheet
Any NP-P-NP-P* stretch of residues commonly will form a
B-strand
B-structure in silk
- model sequence is (-Gly-Ser-Gly-Ala-Gly-Ala-) n
- all from one sheet is interdigitate with ala from other sheet
- silks from different species have different interdigitating groups and have differing physical properties
What is needed to form globular proteins
Turns
Structure of turns
Often short and hair pin like
How many residues are involved in turns
3 or 4
Almost __% of residues are involved in turns
300
High amounts of ____ and ____ in turns
Gly and pro
Turns often have an H-bon across _____
Width
Which types of turns are very common
Type 1 and type 2
How many types of turns are there
16
Features of glycine good for turns but not helies
- small side chains make glycine very flexible. It has a lot of conformational freedom.
What makes proline good for turns and bad for helicies
- proline is too rigid for helices but has a built-in turn because of the bonding between the R-group and the amino group
Why are protein structures challegenign to display clearly
- there are lots of atoms
- detailed internal cavities
- complicated shapes
- all the elements of protein structure
- a-helix, b-stands, turns, loops
Protein display structure
- helices shown as spirals (or cylinders)
- strands shown as arrows, pointing form N to C
- turns and random coil, shown as loops or rope like stretches
Protien structure shorthand
Protein short hand advantages
- easily visualise the main chain path of protein
- identify elements of secondary strucutre
- allows an appreciation of proteins as 3D objects
- allows comparison to other proteins
