Lecture 1 - Motifs Flashcards
1953 thoughts about DNA and proteins
Believed structure of DNA was elucidated to be simple 3D double stranded helix
Thought proteins to be similar
1959 enhanced knowledge of proteins
John Kendrew
X-ray crystallography low resolution structure of myoglobin
1958: 6A
1977- 2A
Why is protein structure so complex
- 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)
Why is it important to understand protein structure
- 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
Hierarchy of protein structure
Primary sequence - amino acid composition
Secondary sequence - Alpha helix, beta pleated sheet, loops
Tertiary structure - 3D arrangement
Quaternary structure - arrangement in multi-subunit complex
Topology diagrams
Beta sheets represented by arrows (head = carboxyl group)
Cylinders represent a-helices
Richardson schematics
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
What are motifs and domains
Super secondary structures
What others factors contribute to protein structure
Cofactors and modifications
Importance of motifs/domains
Help to describe the diversity of protein tertiary structures
Provide a vocabulary to identify common feature
Can explain evolutionary pressure for sequence conservation
Types of protein motifs
Sequence and structural
Sequence motifs
Identified by examining AA sequences
FUNCTIONAL
Structural motifs
Serve a functional role e.g. metal chelation
Identified by AA sequence convervation/properties between proteins
What are RGD proteins
- 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
Types of structural motifs
Functional and ‘scaffolding’
Functional structural motifs
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
Leucine zippers
- 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
Leucine rich repeats
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
Zinc-finger motifs
- 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)
