Lecture 1 revision Flashcards
History of protein complexity
1953 - DNA elucidated to be a ‘simple’ 3D double stranded helix
Was thought proteins may have similar simple structures
1959 - John Kendrew - X-ray crystallography low resolution of myoglobin illustrated a more complex and asymmetrical unit that wraps around haem group for protection (6 armstrongs)
Resolution can determine complexity
In 1977, 2 Armstrong myoglobin was discovered
Why does protein structure need to be so complex?
- Information storage and transfer from DNA is linear
- Codons code in a linear fashion for individual amino acids
- no need for complicated structure!
Three reasons for complexity:
1. Interactions in 3D - substrate recognition, interaction with macromolecules, binding of co-factors, allosteric regulation by glycans
- Must fit into environment - Membrane spanning a-helices in transmembrane protein, pH stability, hydrophilic/phobic sections
- Folding helps evade environmental change - evasion of proteolysis by other proteins - structure may hide cleavage site for proteases e.g. conversion of PrP to PrPSc (CJD).
Understanding protein structure and how it is helpful
- Structure critical to their function - assign function/mechanism to novel proteins
- Protein structures conserved through evolution - structure more conserved than primary sequences.
- Improves predictions of structure from primary sequences.
Protein hierarchy
- Primary structure - amino acid composition
- Secondary structure - Alpha helix, beta sheets, loops
- Tertiary structure - Overall three dimensional arrangement
- Quaternary structure - Arrangement in a multi-subunit complex
Simple topology diagrams
Beta sheets represented by short arrows
Arrow head at carboxyl end of strand
Can be mixed - used to represent both a-helices and B-pleated sheets (a-helices represented by cylinders)
TOPS
Topology of protein structure:
Circle - a-helix
Triangle - B-pleated sheet - direction of triangle represents direction of strand
Richardson schematics
More complex and complete representation of protein structure pioneered by Jane Richardson
Ribbons (a-helix), beta-sheet (arrows), loop regions between helices and sheets.
Motifs and Domains
- Super secondary structures
- Cofactors and modifications also contribute to protein structure
Secondary structures - a-helices and B-pleated sheets
Super secondary structures - a-hairpin (aa), B-a-B motif, B-hairpin (BB)
Motifs - aaaa, BaBaB, B-meander (BBB), BBBB
What do motifs and domains help with
- Describe protein tertiary structure diversity
- Provide vocabulary to identify common feature
- Explain evolutionary pressure for sequence conservation
Definition of protein motifs
Evolutionary conserved regions of amino acid sequences or 3D structure that are important to protein structure and/or function, both within the same species and across species
Sequence motifs - identified by AA sequence examination - FUNCTIONAL
Structural motifs - Motifs that share homology in 3D space - may not be identifiable by AA sequence alone -> functional and scaffolding structural motifs
Some structural motifs can also be sequence motifs
Explain sequence motifs
- Provide functional role e.g. metal chelation
- Readily identified by amino acid sequence/properties conservation from one protein to another
- Sequences of similar (polarity/hydrophobicity) or identical amino acids
Give an example of a sequence motif
RGD (arginine-glycine-aspartate) proteins
- Role of motif cause tight turn between a-helices that causes finger to point out
- Located at exposed flexible loop at protein surface
- Found in disintegrin domains of protein in ECM and certain proteins at cell surface e.g. ADAMs
- Interact with integrins during cell adhesion events
Where were RGD proteins originally identidied
Proteins from snake venom that interfere with platelet aggregation and prevent clotting
EF hands
- Sequence and structural motif
- Identified in muscle protein parvalbumin
- Found in several calcium ion binding proteins
- Primary sequence forms a helix-loop-helix structure (12 residues).
Calmodulin - 4 EF hands bind calcium through Asp residues
Regulatory function by causing conformational change in protein conveyed to downstream target proteins and calcium buffering to allow calcium sequestration.
Calmodulin pathway
Calmodulin -> (4 calcium ions) -> 4EF hands bound to calcium ions by Asp regions -> (CaM kinase) -> Forms CaM kinase peptide
Leucine zippers
Found in transcription factors e.g. Myc, Jun, Fos (identified by sequence alignment of these and other proteins)
Coiled-coil/supercoiled structure
Crick - supercoil of 2 a-helices reduces residues per turn from 3.6 to 3.5.
Made from heptad repeats
H-P-P-H-P-P-P - every 7th residue leucine
Leu residues interact
Basic region ‘furrow’ formed by motif interacting with DNA
Leucine rich repeats
Tandem repeat of 20-30 amino acid units arranged nose to tail each of which is rich is leucine
X-L-X2-L-X-L-X2-Z-X-L-X7-L-X3-L-X4
X - any amino acid
L - leucine
Z - Asparagine or cysteine
Found in ribonuclease inhibitors (16 repeats) and adenylate cyclase (20 repeats)
Horse-shoe tertiary structure
Zinc fingers (C2H2)
Repeat motif in DNA binding proteins
Klug (1985) identified in TFIIIA
Up to 50 repeats of motif
Two Cys separated by 2/3 AAs and two His separated by 3-5 AAs.
C-X2/4-C-X3-F-X5-L-X2-3-H-X3-5-H
F - Phe, Leu or branched AA
Residues 1-10 - antiparallel B-sheet
Residue 11 - loop
Residues 12-25 - a-helix
Cys from sheet and His from helix coordinate zinc atom
Residues at bottom of loop region are positively charged - interact with phosphate on DNA
- Residues in helix interact with base pairs in DNA (one helix 3-5bp)
Zinc finger C4
Bind hormone response element in DNA
Zn in C4 motifs maintain 3D conformation:
P-box a-helix can interact with DNA
D-box loop interacts with another molecule of glucocorticoid receptor (binds DNA when dimerized).
Zinc finger C2
Two zinc cluster containing two zinc atoms each bound to four cysteine residues
Found in yeast transcription factors e.g. GAL4
Zn holds tertiary structure in place so DNA binding region is of correct conformation to bind DNA
Functional structural motifs
An example of convergent evolution
‘The process by which organisms not closely related independently evolve similar traits as a result of adapting to environments or ecological niches’
Functional structural motifs that aren’t sequence motifs have conserved 3D conformation that is the optimal solution to biological requirements e.g. serine protease triad.
Scaffolding structural motifs
Scaffolding - motifs forming areas of substructure which serve to maintain the general architecture of protein
No immediate function
Consist of secondary structures joined by loops
Hair B-motif
B-strands linked by short loop region that run antiparallel
Short
Commonly single AA residue; loops of 3 or 4 AAs also common
Conformational constraints work against two residues
Greek key motifs
- 4 adjacent B-strands
- Found frequently in proteins
- Folded in many ways to achieve different types of protein architecture
B-a-B folds
Connect two parallel beta strands by an a-helix
Helix packs tight against B-sheet plane
Shields hydrophobic sheets from solvent at protein surface
Right-handed - Helix has a right handed twist as a-helix
Left handed - Helix has left handed twist (not found in any structures in theory)
