Protein structure 3

Question 1

What are names given to different proteins with multiple chains

Answer 1

1. Identity & number (homo-dimer, hetero-trimer..)

2. Degree of obligation: quaternary (oligomer) vs. quinary (complex)

Question 2

What is the type of association between multiple chains

Answer 2

1. Mainly nonpolar
2. S-S bonds (membrane/secreted)
3. Covalent involving Lys (fibrous)

Question 3

Describe symmetry in oligomeric proteins

Answer 3

1. Oligomeric proteins tend to be symmetrical
2. 2-fold symmetry
3. 3-fold symmetry
4. Dihedral symmetry
5. Symmetry is usually formed by duplication of genes, and is probably another consequence of evolution’s general tendency towards parsimony, as it allows the cell to achieve a higher function using copies of the same structural unit.
6. Asymmetrical oligomers appeared only later in evolution.

Question 4

Describe 2-fold symmetry and give example

Answer 4

1. in dimeric triosephosphate isomerase.
2. The binding surfaces of the two subunits are identical and rotated 180º with respect to each other, making the interface ‘isologous’.

Question 5

Describe 3-fold symmetry and give example

Answer 5

1. in trimeric chloramphenicol acetyltransferase.

2. The interface includes two different binding surfaces, i.e., it is ‘heterologous’.

Question 6

Describe di-hedral symmetry and give example

Answer 6

1. in tetrameric β-tryptase, including two isologous interfaces.
2. Dihedral symmetry appears in most tetrameric and hexameric proteins.
3. The axes of symmetry are denoted in each structure.

Question 7

What are the Advantages of the quaternary structure

Answer 7

1. Allows the formation of versatile active sites
2. Enhances the regulation of protein activity
3. Increases stability by restraining internal motions
4. Insulin – hexamer in pancreas (days), monomer in blood (minutes)
5. Allows the formation of large structures (e.g. the cytoskeleton)

Question 8

What are some different post-translational modifications

Answer 8

1. Phosphorylation (Ser/Thr/ Tyr)
2. O-glycosylation (ser/thr)
3. N-acylation (Lys)
4. N-alkylation (Lys)

Question 9

What are two examples of acylations

Answer 9

1. N-Myristoylation (Gly)

2. S-Palmitoylation (Cys)

Question 10

What are two examples of alkylations

Answer 10

1. S-farnesylation (Cys)

2. S-geranyl-geranylation (Cys)

Question 11

What is phosphorylation

Answer 11

1. Occurs in both prokaryotes and eukaryotes
2. In eukaryotes: occurs on Ser, Thr or Tyr
3. Role: regulating protein activity
4. Mechanisms: conformational change, ligand binding, catalytic residues
5. Reversible: kinases vs. phosphatases

Question 12

Describe glycosylation

Answer 12

1. Occurs in both prokaryotes and eukaryotes
2. Creates glycoproteins and proteoglycans
3. N-linked: on Asn, context-dependent, in ER
4. O-linked: on Ser or Thr, context-independent, in Golgi
5. Roles: solubility, stabilization, protection, molecular recognition

Question 13

Describe acylation

Answer 13

1. Includes acetylation, myristoylation, palmitoylation and ubiquitinylation
2. Residues: Lys, Cys, Gly-α-amino
3. Direct effect: charge neutralization, mol. recognition
4. Role: regulation of protein activity and ligand binding, membrane attachment, degradation
5. The tumour suppression protein p53 can be either ubiquitinylated (when targeted for degradation) or acetylated (when it should remain active). The acetylation prevents ubiquitination.

Question 14

Describe alkylation

Answer 14

1. Examples: methylation, prenylation, adenylation
2. Residues: Lys, Arg, Cys, Tyr
3. Role: regulation of protein activity, molecular recognition, membrane attachment
4. The alkyl group is often attached to pyrophosphate, which leaves upon bond formation.

Question 15

Describe hydroxylation and sulfation

Answer 15

1. Residues: Pro, Lys, Asn, Glu (hydroxylation)
2. Tyr (sulfation)
3. Role: stabilization (e.g. HO-Lys/Pro in collagen), molecular recognition (e.g. ligand recognition by sulfate-CCR5)

Question 16

What is proteolysis

Answer 16

1. Usually carried out in hydrolytic enzymes

2. Role: activation

Question 17

How are Metal cation added and what is the role

Answer 17

1. E.g. Fe2+/Fe3+, Zn2+, Cu2+/Cu+, Mg2+, Mn2+/Mn3+, Mo3+/Mo4+/Mo6+, Co2+, Ni+
2. Metal bound directly or via a prosthetic group
3. Metal may appear in clusters
4. Role: stabilization (e.g. Zn-finger), ligand binding, electron transport, catalysis (e.g. bond polarization, TS stabilization)
5. Transition metals (Fe, Cu, Co, Mn) can acquire in multiple oxidation states → often used for electron transfer and redox catalysis

Question 18

Describe ADP-ribosylation

Answer 18

1. One or more ADP-ribosyl units
2. reversible (enzymatic: ADP ribosyltransferases)
3. There are also poly-ADP-ribosylations, which occur in eukaryotes, and are involved in cell signaling, DNA repair, gene regulation and apoptosis.
4. They are not carried out by ADP-ribosyltransferases, but rather by Poly-(ADP-ribose) polymerases (PARPs).

Question 19

What is ADP-ribosylation involved in

Answer 19

1. cell signaling
2. DNA repair
3. Gene regulation
4. Apoptosis

Question 20

What is the clinical significance of ADP-ribosylation

Answer 20

1. Cancer (improper ADP-ribosylation)
2. infection (bacterial toxins)
3. Used by certain bacterial toxins to harm the host

Question 21

What are the Roles of membrane bound proteins

Answer 21

1. Transport of solutes
2. Communication and signal transduction
3. Cell-cell and cell-ECM recognition
4. Energy production and photosynthesis
5. Defense
6. Cellular trafficking
7. Membrane proteins constitute:
8. 20-30% of the protein-coding genes in humans
9. ~70% of drug targets

Question 22

Describe Integral membrane proteins

Answer 22

1. The membrane limits integral proteins to two general architectures
2. Electrostatic masking of polar groups is especially important in membrane proteins, since their trans-membrane (TM) segments are exposed to the nonpolar core of the membrane
3. alpha-helical (>90%)
4. TM segments are overall nonpolar
5. Leu, Ile, Val, and Phe – especially common
6. Polar residues are less common
7. Buried in core, masked by other polar groups and/or water molecules
8. Core is more polar than surface (unlike globular proteins)

Question 23

Describe length of integral membrane proteins

Answer 23

1. The length of TM segments matches the hydrophobic width of the membrane
2. Overall range - 15-39 residues
3. Average length - 21-26 residues
4. Strong preference for 20 residues (width of the nonpolar core)

Question 24

What are Common residues and where are they found

Answer 24

1. Small residues (Gly, Ala, Ser) – in closely packed helices
2. β-branched residues (Leu, Val, Ile)
3. Gly, Pro, mostly near kinks
4. Aromatic ‘belt’ – anchors protein to membrane (Trp and Tyr)
5. Arg, Lys – interact with lipids at cytoplasmic leaf

Question 25

What does Hydrogen-bonding polar backbone groups do

Answer 25

1. reduce desolvation penalty

Question 26

Describe α-helical membrane proteins

Answer 26

1. TM prolines serve as hinges of motion
2. channel/transporter gating
3. Shift between active/inactive receptor conformations
4. Other distortions in TM helices (40% in TM helices):
5. 310 and π-helices, discontinuous helices
6. The roles of distortions:
7. Allow greater proximity between helices
8. Create binding sites (e.g. reentrant loops in K+-channel)

Question 27

Describe β-sheet membrane proteins

Answer 27

1. Less common than α-helical MP (a few %)
2. Have a barrel shape (pairs the edges)
3. Most are porin channels (outer membrane of G- bacteria, mitochondria, chloroplasts)
4. Bacterial porins
5. Non-selective channels in outer membrane
6. Some are toxins (e.g. α-hemolysin)
7. Some are attachment sites for phages and bacterial toxins

Question 28

Describe tertiary structure as in globular proteins

Answer 28

1. Core - nonpolar, densely packed, conserved, and contains few functional polar residues
2. Loops – involved in ligand binding and signal transduction

Question 29

Describe tertiary structure in unlike globular proteins

Answer 29

1. Surface is less polar than core

2. Fold is often a helical bundle

Question 30

What are some Types of membrane bound receptors

Answer 30

1. Ion channels
2. Tyrosine kinases
3. Serine/threonine kinases
4. Guanylate cyclases
5. Cytokine receptors (defined by ligand type)
6. G protein-coupled receptors (GPCRs)

Question 31

Do you get GPCRs in plants

Answer 31

1. GPCRs seem to be missing in plants, although this matter is controversial.
2. G-proteins do exist in plants, but it has been claimed that they are activated by receptor-like kinases (RLKs) rather than by GPCRs.

Question 32

What are some ligands of GPCRs

Answer 32

1. Diverse ligands: proteins, peptides, small organic molecules, elemental ions, and even photons of light

Question 33

What are GPCRs involvement in disease

Answer 33

1. Participate in numerous physiological processes and involved in numerous diseases (targeted by 30-50% of the clinically prescribed drugs)
2. GPCRs are involved in diseases like hypertension, congestive heart failure, stroke, cancer, thyroid dysfunction, congenital bowel obstruction, abnormal bone development, night blindness, and neonatal hyperparathyroidism.
3. Their involvement may result from being either inactive or overactive.
4. For example, overactive GPCRs may affect the formation and spreading of tumors by trans-activating cancer-related receptors like epidermal growth factor receptor (EGFR), and by promoting cells migration during metastasis.

Question 34

Describe GPCRs structure

Answer 34

1. GPCRs have very similar structures despite low sequence identity
2. Rhodopsin and β2-AR: 21% identity, TM rmsd = 1.6 Å
3. The TMD is the most conserved, and contains 7 TM helices
4. Rhodopsin: the first solved structure, served as model for other GPCRs
5. GPCRs structural similarities
6. B1, B2 adrenergic receptor and A2A adenosine receptor
7. Very similar core structure
8. GPCRs differ mainly in their ECD