Protein structure 2

Question 1

What are the Two types of proteins

Answer 1

1. Globular

2. Fibrous

Question 2

What are the Characteristics of the globular structure

Answer 2

1. Compact (many molecules in cytoplasm)
2. Hydrophobic core (stability)
3. Hydrophilic surface (water soluble)
4. Brings together functional residues in 3D space –> formation of binding/catalytic/regulatory sites –> diverse functions (catalysis, transport, immunity, regulation)
5. Stabilized by non-covalent interactions –> flexible
6. But in some cases – also S-S bonds which anchor conformation of protein

Question 3

What is the architecture of globular proteins

Answer 3

1. Simple motif:
2. α (e.g. HLH)
3. β (e.g. β-hairpin, β-meander)
4. mixed (e.g. β-α-β)
5. Complex motifs:
6. (e.g. Ig, Rossmann, P-loop, TIM barrel, Horseshoe fold)
7. Domains :e.g. SH2, SH3, PH

Question 4

Give example of the (helix-loop-helix) HLH motif

Answer 4

1. EF-hand (Ca2+ binding)
2. Appears in signaling and muscle contraction proteins
3. Serves as a molecular ‘switch‘ in response to rise in cytosolic Ca2+ levels
4. The EF-hand motif is found in small proteins (e.g. calmodulin), or within the domains of larger proteins (e.g. myosin or calpain)
5. In these proteins calcium is bound by a helix-loop-helix structure that is formed by the E and F helices (letters assigned to helices in the order that they occur, starting at the N-terminus)
6. Ca2+ binds to polar side-chain and main-chain atoms in the loop region, and to water.
7. Binding –> small movement of helix –> conformational change in protein –> change of function (usually binding)
8. Calmodulin (CaM) - small protein, binds to enzymes and activates them upon Ca2+ binding, uses 4 EF-hand motifs
9. Some of these enzymes (e.g. Ca2+/CaM-dependent kinases) act on other proteins when activated

Question 5

What is bHLH

Answer 5

1. bHLH (DNA-binding)
2. Found in many transcription factors
3. Penetration of one of the helices into the major DNA groove allows tight binding and recognition of specific sequences in the DNA
4. Interacting residues – basic (bHLH)

Question 6

What is the zinc finger

Answer 6

1. β-hairpin packed against a helix

2. Common in proteins regulating gene expression

Question 7

What is the HTH

Answer 7

1. Helix-turn-helix (HTH)
2. Found in many proteins that regulate gene expression
3. In eukaryotes – important for development (e.g. homeodomain proteins)
4. Similar to the HLH motif but has shorter linker

Question 8

What are some Beta domain structures

Answer 8

1. Greek key
2. Jelly roll
3. Up-and-down barrels
4. b-propeller (WD40 protein beta-transducing repeat)

Question 9

Describe the greek key

Answer 9

1. Beta strands 2 and 3 fold over such that strand 2 is aligned adjacent and antiparallel to strand 1

Question 10

Describe the jelly roll

Answer 10

1. Antiparallel

2. One is up and 2 is down etc

Question 11

Describe the b-propeller (WD40 protein beta-transducing repeat)

Answer 11

1. Units come together to make a propeller
2. Each units have blade like structure
3. β-propeller proteins are interesting to study because the number of blades that the propeller contains, as well as the location of the propeller domain within the protein, could determine the function of the protein to some extent. For example, the following functions were identified for propellers with specific blade numbers:
4. 4 blades: Ligand binding
5. 5 blades: Ligand binding, transferase, hydrolase
6. 6 blades: Ligand binding, hydrolase, lyase, isomerase, signaling protein, structural protein
7. 7 blades: Ligand binding, hydrolase, lyase, oxidoreductase, signaling protein, structural protein
8. 8 blades: Oxidoreductase, structural protein
9. 10 blades: Signaling protein

Question 12

What is the most common mixed motif

Answer 12

1. The β-α-β motif
2. The most common mixed motif
3. Allows formation of parallel β-sheets
4. Allows efficient packing of nonpolar residues inside the core
5. 1st loop often participates in ligand binding to protein binding sites

Question 13

What are complex folds

Answer 13

1. Formed from combinations of simple folds/motifs
2. Their distribution in proteins exhibits a ‘power-law’:
3. Most folds appear in a small set of proteins
4. A few folds (‘superfolds’) appear in numerous proteins (commonest 10 - in more than ⅓ of the proteins)

Question 14

What are some superfolds based on the β-α-β motif

Answer 14

1. The Rossmann fold
2. The P-loop fold
3. The TIM barrel fold

Question 15

Describe the immunoglobin fold

Answer 15

1. Found in immune system molecules (Ab, TCR, MHC) and other recognition molecules
2. Ab - antibodies
3. TCR – T-cell receptor
4. MHC – major histocompatibility complex
5. LgG light chain follows Greek key
6. Antibodies contain 2 heavy chains + 2 light chains
7. The antigen binds to the loops
8. Binding specificity results from electrostatic interactions
9. Electrostatic complementarity between an antibody (residues R61 and D53) and its cognate antigen
10. The antigen-binding site has very low evolutionary conservation - allows variability despite common structure
11. The need for variability in antibodies makes their functional sites non-conserved. In most other proteins functional sites are highly conserved because they bind same/similar ligands or carry out the same type of catalysis.
12. The variability results from both the sequence and the loops’ inherent flexibility.

Question 16

Describe the Rossmann fold

Answer 16

1. A common dinucleotide-binding motif
2. Built from two β-α-β-α-β units
3. malate dehydrogenase
4. Binds all three dinucleotide coenzymes
5. Redox enzymes: energy production, biosynthesis, detoxification, etc.- NADH, NADPH, FADH2
6. Gly residues –> efficient helix-strand packing –> stability

Question 17

Describe the P-loop fold-Rossmann fold in p21ras

Answer 17

1. The P-loop fold-Rossmann fold in p21ras
2. Binds mononucleotides (ATP, GTP)
3. One of the oldest and most common folds

Question 18

Describe the TIM barrel fold

Answer 18

1. Very common (~10% of protein structures), mainly in enzymes catalyzing diverse reactions
2. May act as scaffold or in catalysis (on one of the β–>α loops)
3. Like in the Ig fold, the TIM Barrel loops too provide functional diversity within a fold that has the same shape in all proteins in which it appears
4. Barrel center not hollow – densely packed with nonpolar residues - provides shielding from the external environment
5. When ligand is a nucleotide: positive binding site, interactions with backbone groups + Mg2+/Mn2+/Zn2+
6. Studies suggest divergent evolution of ancestral fold into many different functional forms
7. The basic structural unit of the fold – the (βα)4 ‘half barrel’

Question 19

Describe the horseshoe fold

Answer 19

1. Leucine-rich motifs
2. Helices on outer ring of molecule
3. Beta strands on inner core
4. Connected by loop structures filled with leucine residues
5. based on α (ring) -β (annulus) motif

Question 20

Why are superfolds so common?

Answer 20

1. Structural stability - amino acid packing, 2nd structures

2. Functional efficiency - create binding/active sites

Question 21

What are domains

Answer 21

1. Functional units of proteins
2. ‘Ideal’ domain: 100-250 residues, stable, repetitive, has own 2nd elements, has function
3. In reality: different definitions, by structure, sequence, function
4. Estimates: most proteins have > 1 domains, usually 2-5, 12 at the most
5. Domain versatility confers functional complexity to proteins- Different domains have different functions in molecules

Question 22

Describe Sequence-structure-evolution relationship classifications

Answer 22

1. Family (≥ 40% sequence identity, homologs): very similar structures, common evolutionary path
2. Superfamily (~20-30% identity): similar structures, far evolutionary relatives
3. Class: same overall organization of 2nd elements
4. The general fold of protein analogs is expressed in the types of secondary elements, their number, their relative orientation, and the way they are connected.

Question 23

Describe SCOP (Structural Classification Of Proteins)

Answer 23

1. Class
2. Fold
3. The fold category includes proteins with very different sequences, yet similar general fold (protein analogs). The fold is expressed in the types of secondary elements, their number, their relative orientation, and the way they are connected.
4. Superfamily
5. Family
6. Domain

Question 24

Describe Protein classification- CATH

Answer 24

1. Protein classification- CATH (Class, Architecture, Topology, Homologous superfamily)
2. class
3. Architecture
4. Topology/fold
5. Homologous Superfamily
6. Family, domain

Question 25

What are the Roles of ‘structural water’ inside proteins:

Answer 25

1. Masking polar groups (stabilization)
2. Assisting ligand-binding
3. Assisting catalysis (acid/base, polarizing bonds)
4. Assisting transport (channels, transporters)