Folding motifs of protein

Question 1

Thermodynamic hypothesis

Answer 1

The native structure is the global minimum of free energy

Question 2

Advantages of folding motifs

Answer 2

Information about function
Information for protein design
Prediction from amino acid sequence
Folding motif more conserved the amino acid sequence

Question 3

The helix bundle

Answer 3

The most usual way of packing α-helices in globular proteins

Usually ridges in grooves model

Can be either parallel or antiparallel

Question 4

Globin fold

Answer 4

One of the most important α helical structures

present in many proteins with unrelated functions

All organisms contain protein with globin fold

Evolved from a common ancestor

Human: myoglobin and hemoglobin

contain 8 α-helices forming a pocket for active site

Question 5

DNA binding protein

Answer 5

Dimeric

HTH-motif : C-terminal domain involved in protein dimerization.

Question 6

α/β Domains

Answer 6

TIM-barrel

Rossman fold

Question 7

TIM-barrel

Answer 7

Core of twisted parallel β-strands arranged close together. The α helices that connect the β-strands are on the outside of this barrel

closed α/β

Almost all closed α/β barrel observed have 8 parallel strands. strand nr.8 adjacent and H-bond to nr.1

minimun of 200 residues are required

Found in many different proteins, most enzymes with completely different amino acid sequences and functions.

β-strands and α-helices form structural framework and the active site is situated in a pocket created by 8 loops that connect carboxy end of the β-strand with the amino end of the α-helices

Question 8

Rossman fold

Answer 8

Twisted β-strand surrounded by α-helices on both sides

open α/β

Predictive rule exists to predict active sites in open α/β sheets.

The crevice occur when the strand order is reversed and the connections from β-strand go in opposite directions.

Loops connecting the top ends of the β-strand to helix are frequently associated with substrate binding sites.

Question 9

Flavodoxin

Answer 9

No geometric restriction on the number of strands involved.

Question 10

β-structures

Answer 10

Proteins folds which consists almost entirely of β-sheets exhibit completely or mostly anti-parallel arrangement. Many of these consists of 2 sheets packed against each other, with hydrophobic side chains forming the interface.

Question 11

Greek key barrel

Answer 11

4 β

see notes

Question 12

Upp and down barrel

Answer 12

8 β

see notes

Question 13

Gamma crystallin

Answer 13

two domains of gamma crystalline have sam topology, each composed of 2 greek key motifs.

Question 14

Staphylococcus nuclease

Answer 14

Greek key motif

Question 15

Jelly roll barrel

Answer 15

81274563
CN
see notes

Question 16

Immunoglobulin fold

Answer 16

Typ of protein domain that consists of 2 layer of 7-9 antiparallel β-strand arranged in 2 β-sheets with a Greek key topology.

Question 17

β-propeller

Answer 17

Whole subunit structure is a six blade propeller. Each blade consists 4 up and down antiparallel β-strands.

Forms Funnel like active site.

Question 18

Parallel β-helix

Answer 18

Tandem protein repeat structure formed by association of parallel β-strands in a helical pattern either 2 or 3 faces.