Lecture 3 Protein structure and function

Question 1

Packing of secondary structures

Answer 1

The residues that form the interfaces between secondary structural elements are hydrophobic and the pakcing of secondary structural elements results in the formation of a protein structural domain with a hydrophobic core. Proteins contain one or more of these domains.

Question 2

Tertiary structure

Answer 2

The tree dimensional organization of the secondary structure elements in the protein domains.
The three dimensional arrangement of a-helices and ß-strands is known as the protein fold

Question 3

Structural domains

Answer 3

A structural domain is an element of the protein’s overall structure that is stable and often folds independently of the rest of the protein chain. A domain is typically 50-200 residues long and contains a well defined hydrophobic core.

Question 4

quatenary structure

Answer 4

The arrangement of subunits (polypeptide chains) in a multi-subunit protein complex.
The subunits can function either independitly or cooperatively so that the function of one subunit depends on the functional states of the others.

Question 5

SH1 domain

Answer 5

Catalyzes the transfer of phosphate groups from ATP to tyrosine residues on other proteins

Question 6

SH2 domain

Answer 6

Binds to phosphoryalted (charged) tyrosine residues in other proteins

Question 7

SH3 domain

Answer 7

Binds to peptide segments containing proline residues at specific positions.

Question 8

Hydrophobic core formation

Answer 8

When secondary structural elements pack against each other in folded proteins, their hydrophobic side chains are brought together, forming the hydrophobic core.

Question 9

Stability of the hydrophbic core

Answer 9

The hydrophobic core is the biggest contributer to the stability of the folded structure. Van der Waals interactions, hydrogen bonds and ionic interactions make only a small contribution to this.
The stability of the hydrobic core is mostly a result of the preference of the hydrophobic sidechains to be clustered together and away drom water.

Question 10

Hydrophobic effect

Answer 10

The hydrophobic effect is the dominant factor that drives protein folding (not hydrogen bonding).

Question 11

Formation of hydrogen bonds in protein folding

Answer 11

The backbone -NH and -C=O groups of the unfolded protein make hydrogen bonds with water. When the chain of the protein folds, the formation of the a-helices and ß-sheets results in hydrogen bonds with water being replaced by hydrogen bonds with other parts of the protein backbone.
Because of this exchange the net hydrogen bonding energy does not change much as the protein folds up.
One hydrogen bond is switched for another -> hydrogen bonding requirement is still satisfied

Question 12

Stability of secondary structure elements

Answer 12

Secondary elements appear fast but are not stable by themselves when the protein is unfolded.
An isolated peptide segments of an a-helix for example can’t form a hydrophobic core because the elements that it normally packs against are missing. These elements have to find each other to form the final form of the protein.

Question 13

Conformational change

Answer 13

A change in the structure of a molecule that occurs due to rotations of parts of the molecule around covalent bonds -> no covalent bonds need to be broken or remade

Question 14

Stereoisomers

Answer 14

Two structures with the same atoms and the same type of chemical bonds but which can’t be interconverted without braking and remaking covalent bonds
- NOT a conformational change

Question 15

Chirality of amino acids

Answer 15

Amino acids have 2 stereoisomer: L-form and D-form
All aminoacids that are made on the ribosome are L-form, so only the L-form of amino acids are found in genetically encoded proteins.
D-form is only used in certain situations and requeres a specialized enzyme

Question 16

Amide plane

Answer 16

The junction between 2 amino acid residues in a protein and is formed by the C=O and N-H groups of the first and second residues.
The four atoms in the peptide group are coplanar (plat) and define the amino plane.

Question 17

Trans peptide groups

Answer 17

The two Cα atoms or O and H atom are on opposite sides of the peptide bond.
Trans conformation is prefered.

Question 18

Cis peptide groups

Answer 18

The two Cα atoms or O and H atom are on the same side of the peptide bond.
Peptide groups in proteins are rarely in the cis conformation because it brings the Cα groups into close contact.
-> only proline can be in cis.

Question 19

Backbone torsion angles

Answer 19

Because of the planarity of the pepride groups, a protein backbone only has freedom to rotate at the points where the peptide groups meet.
Rotations around N-Cα -> Φ
Rotations around Cα-C -> ψ

Question 20

forbidden conformations

Answer 20

A molecular conformation in which some atoms are closer that the sum of their Van der Waals radii. The Van der Waals repulsion energy is so large for such conformations that favorable interactions that may occur cannot overcome the repulsion.
- Combination of Φ and ψ rotation that brings atoms to close

Question 21

Ramachandran diagram

Answer 21

Diagram that shows the energy of alanine dipeptide as a function of the backbone torsion angles Φ and ψ

Question 22

Loop types

Answer 22

Type I and type II
Proteins try to minimize the size of the loop

Question 23

Amphipatic α-helix

Answer 23

α-helices that have one hydrophobic face and one hydrophillic face.
Hydrophobic face interacts with hydrophobic subastances.
Hydrophilic face interacts with sulvant.

Question 24

Amphipatic ß-strand

Answer 24

ß-sheets on the surface of proteins usually contain amphipathic ß strands, that have one hydrophobic face and one hydrophillic face.

Question 25

Helix propensity scale

Answer 25

The amino acids have different preferences either for or against being in a α-helix. The ranked list of these preferences is called a helix propensity scale.
These preferences arise due to differences in energy of the contacts made with the sidechain

Question 26

Most and least prefered amino acids in a α-helix?

Answer 26

Alanine, which has the smallest sidechain, is most preffered in a α-helix.
Glycine and proline tend to destabilize the α-helices.
Glycine has a lot of degrees of freedom, and is therefor not stable in a helix.
Proline loses the ability to form hydrogen bonds which is necessary in the α-helix so it often sits at the start of the helix

Question 27

Helix cap residues

Answer 27

Some amino acids have the preference to sit at the ends of helices. This can help satisfy the hydrogen-bonding requerements of -NH and -C=O at the end of the helix.
Glycine can provide a cap for the C-terminal end of the α-helix
Serine can provide a cap for the N-terminal end of the α-helix

Question 28

Structural motifs

Answer 28

A three-dimensional arrangement of two or more secondary structural elements. Motifs are typically components of larger domains, and more than one motif can be found in one domain.

Question 29

Helix-turn-helix

Answer 29

Simple motif that consists of two α-helices joined by a short turn region. They are commenly found in proteins that recognize specific regions in DNA. One of the helices than is inserted in the major groove of the DNA helix where the sidechains make sequence specific contact with the bases in the major groove.

Question 30

EF-hand motif

Answer 30

The loop region in this motif binds a calcium atom.

Question 31

Greek key motif

Answer 31

Antiparallel ß-strands are connected togehter by turns or hairpins. (looks like a greek motive)

Question 32

ß-α-ß motifs

Answer 32

The polypeptide chain turns twice, using loop regions. The motif is formed has a ß-strand followed by a loop, an α-helix, another loop and then the second ß-strand.

Question 33

Coiled coils

Answer 33

Two α-helices that coil around each other. Can be either parallel or antiparallel. (Common in muscle proteins because they are very long)

Question 34

Heptad repeat

Answer 34

In a coiled-coil structure, every seventh residue occupoes an identical position along the helix. This leads to a pattern of hydrophobic residues that repeats in groups of seven, known as the heptad repeat.

Question 35

Four helix bundle

Answer 35

The simplest and most frequent α-helical domain consists of four α-helices arranged in a bundle with the helical axes almost parallel to each other. Each helix is relatively straight and the sidechains of all helices are arranged so that hydrophobic sidechains are buried between the helices and the hydrophilic sidechains are on the outer surface of the bundle.

Question 36

Ridges and grooves of α-helices

Answer 36

α-helices pack against each other so that the ridge of one helix inserts in the groove of another helix. The ridges and grooves are formed by amino acids that are usually three or four residues apart.

Question 37

α/ß domains

Answer 37

Alternating α-helices and ß-strands forming a central parallel or mixed ß-sheets surrounded by α-helices, known as α/ß structures.
Binding crevices are formed by loop regions. Two major classes: barrel and open-sheet

Question 38

α/ß open sheet structure with α-helices on both sides

Answer 38

• A closed barrel can’t be formed
• There is a crevis outside the ß-sheet between 2 loops. Almost all ligand binding sites in this class of α/ß proteins are located in these crevises.
• Each ß-strand contributes hydrophobic sidechains to pack against α-helices in two similar hydrophobic core regions, one on each side of the ß-sheet.

Question 39

ß-barrels

Answer 39

A beta barrel is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last. Beta-strands in beta-barrels are typically arranged in an antiparallel fashion.

Question 40

ß-propeller

Answer 40

up-and-down ß-sheets in proteins that don’t form a barrel, but several small sheets each with a small number of ß-strands which are arranged like the blades of a propeller

Question 41

ß-helix

Answer 41

polypeptide coiled into a wide helix, formed by ß-strands and separated by loop regions.

Question 42

Catalytic / active sites

Answer 42

The region of an enzyme where substrate binds and a chemcial reaction is catalyzed.

Question 43

Membrane proteins

Answer 43

Proteins with at least one peptide segment that crosses the membrane bilayer are transmembrane proteins.
Proteins that are tightly associated with membranes, but do not traverse the membrane are known as peripheral membrane proteins. Such proteins can be bound to the membrane trough non-covalent interactions or covalenty attached to a membrane lipid.

Question 44

Bacteriorhodopsin

Answer 44

proton pump in light harvesting bacteria. It couples light energy to the generation of a proton gradient across the cell membrane.
Structure is reminiscent of G-protein-coupled-receptors.

Question 45

Porins

Answer 45

Important class of membrane proteins in bacteria with ß-barrel architecture. They form open water filled channels that allow the passive diffusion of nutrients and waste products across the outer membrane.