Lecture 1 - Motifs

Question 1

1953 thoughts about DNA and proteins

Answer 1

Believed structure of DNA was elucidated to be simple 3D double stranded helix

Thought proteins to be similar

Question 2

1959 enhanced knowledge of proteins

Answer 2

John Kendrew

X-ray crystallography low resolution structure of myoglobin

1958: 6A

1977- 2A

Question 3

Why is protein structure so complex

Answer 3

• Information storage and transfer from DNA is linear
• Codon code in linear fashion for individual amino acids
• Interactions in 3D - Substrate recognition, interaction with other macromolecules, binding of co-factorsm allosteric regulation
• Must fit into environment e.g. membrane spanning a-helices in transmembrane proteins
• Folding can evade environmental change - Evasion of proteolysis by other proteins - structure may hide cleavage site for proteases; e.g. conversion of PrP to PrPSc (CJD)

Question 4

Why is it important to understand protein structure

Answer 4

• Protein structure critical to their function - assign function/mechanism to novel proteins
• Structure conserved through evolution - Conserved more than primary sequence
• Helps predict structure of primary sequences

Question 5

Hierarchy of protein structure

Answer 5

Primary sequence - amino acid composition

Secondary sequence - Alpha helix, beta pleated sheet, loops

Tertiary structure - 3D arrangement

Quaternary structure - arrangement in multi-subunit complex

Question 6

Topology diagrams

Answer 6

Beta sheets represented by arrows (head = carboxyl group)
Cylinders represent a-helices

Question 7

Richardson schematics

Answer 7

Pioneered by Jane Richardson

Dominant diagram to represent protein structure

a-helices represented by twisted cylinder like structure
Arrows represent beta sheets (both parallel and antiparallel

Question 8

What are motifs and domains

Answer 8

Super secondary structures

Question 9

What others factors contribute to protein structure

Answer 9

Cofactors and modifications

Question 10

Importance of motifs/domains

Answer 10

Help to describe the diversity of protein tertiary structures

Provide a vocabulary to identify common feature

Can explain evolutionary pressure for sequence conservation

Question 11

Types of protein motifs

Answer 11

Sequence and structural

Question 12

Sequence motifs

Answer 12

Identified by examining AA sequences

FUNCTIONAL

Question 13

Structural motifs

Answer 13

Serve a functional role e.g. metal chelation

Identified by AA sequence convervation/properties between proteins

Question 14

What are RGD proteins

Answer 14

• Located at exposed flexible loop at protein surface
• Found in disintegrin domains of proteins in ECM and certain proteins at cell surface e.g. ADAMs
• Interact with integrins during cell adhesion events e.g. adhesion to ECM or other cells

Question 15

Types of structural motifs

Answer 15

Functional and ‘scaffolding’

Question 16

Functional structural motifs

Answer 16

Parvalbumin - Sequence and structural motif, found in calcium ion binding proteins, primary sequence forms helix-loop-helix (12 residue loop) - Discovered by Robert Kretsinger in 1973

EF hands II - Calmodulin - 4 EF hands binds calcium through Asp residues, calcium causes conformational change in protein conveyed to downstream target proteins, calcium buffering

Question 17

Leucine zippers

Answer 17

• Functional structural motif
• Found in transcription factors e.g. Fos, Jun, Myc,
• Coiled-coil/supercoiled,
• Supercoil of 2 a-helices reduces residues per turn from normal 3.6 to 3.5
• Made up of heptad repeats - every 7th residue in leucine
• Leu residues interact - hence ‘zipper
• Basic region ‘Furrow’ formed by motifs that interact with DNA

Question 18

Leucine rich repeats

Answer 18

Tandem repeats of 20-30 amino acid units arranged nose-to-tail each of which is rich in leucine

In some repeats residues may be missing or an extra residue may be inserted

Found in proteins with diverse functions
e.g. Ribonuclease inhibitor (16 repeats)
Adenylate cyclase (20 repeats)

Forms a ‘horse-shoe’ tertiary structure

Question 19

Zinc-finger motifs

Answer 19

• Repeat motif in DNA binding proteins

Aaron Klug (1985) identidied in TFIIIA (a transcription factor from Xenopus laevis) - Can be up to 50 repeats of motif (only 9 in TFIIA)

-Two Cys separated by 2/4 AAs and two His separated by 3-5 AAs:

• C-X2/4-C-X3-F-X5-L-X2-3-H-X3-5-H
• Phe can also be Tyr, Leu or another branched AA - quite vague motifs (but still sequence + structural)