Term
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Definition
- Has resonance structure conferring partial double bond so there is no rotation around that bond.
- Uncharged bond
- Forces Carboxy carbon and N and all attached atoms into same plane |
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Term
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Definition
| N and Ca rot angle, limited by size of atoms in back bone and R's |
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Term
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Definition
| C and Ca rot angle, limited by size of atoms in bb and R's |
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Term
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Definition
- Made using 500 diff proteins
- Plots Psi and phi
- Certain angles or pairs not found in nature
- Some clumped areas on plot, represent diff secondary structures (beta sheet with have larger phi and more positive phi angles whereas psi have less large) |
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Term
| Rigidity of peptide unit and allowed phi/psi angles are ... |
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Definition
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Term
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Definition
- Periodic structure (57 phi and 47 psi)
- 3.6 residues per turn
- CO of each residue makes H-bond to NH of residue four ahead (i and i+4)
- All CO and NH groups within helix are H-bonded
- Amino acids protrude outof helix at 100* intervals
- Most are right handed/clockwise |
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Term
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Definition
- Electrostatic
- Short range, below 3.3 A/.33 nm
- Distance and angle critical to force
- 1-3 kcal/mol |
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Term
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Definition
- Extended peices (B-strands) hydrogen bond between CO and NH groups
- Parallel and anti-parrallel variety; AP is more common more stable because H-bonds parallel to each other
- 130 phi and 125 psi; almost fully extended
- OFten right hand twisted and sheets can form barrells |
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Term
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Definition
- Aburpt change in dir of backbone at surface of protein
- Reverse turns
- Backbone Hbonds across hairpin stabilize
- Often connect two AP b strands
GLY, Ser, ASn or Pro (small r goups) |
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Term
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Definition
- No strict preiodic or regular structure
- Longer "excursion of backbone"
- Floppy/unstructured
- Often at surface of protein
- Mediate interaction with other molecules |
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Term
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Definition
- Overall 3D arrangement of secondary structure elements
- Structure beyond a single helix or B-sheet
- Arrangement of domains or folding units within a single chain |
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Term
| Tertiary Structures stabilized by: |
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Definition
In hi to low:
- Covalent bonds and metal ligands (co-ordination)
- Electrostatics (residues with diff charges formign salt bridges)
- H-bonds
- Vander Waals (nonpolar AA's, mostly for tightly packed proteins) |
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Term
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Definition
-Contributes to protein folding and 3d shape
- Apolar molecules clump together
- Usually for globular soluble proteins; hydrophonic AA's form the core and charged AA's or on surface |
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Term
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Definition
- Occurs as the protein emerges from ribosome
- Final step in transformation of genetic info to bio function
- Determined by primary structure
- Driven by hydrophobic effect and formation of intermediate structures |
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Term
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Definition
- In vivo doesnt allow proper folding; not enough water
- HSP 60 and 70 (diff kinds in cytosol, mito and ER)
- 3 domains; apical, intermediate and equatorial
- Chaperones recognize and capture the hydrophobic parts of unfolded protein via interactions with the rim of the barrell
- Protein is capped using ATP and then released using ATP (hopefully folded)
- Equatorial domain mediates contacts in ring structure |
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Term
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Definition
- Certain physio conditions such as pH, temp, stress, oxidation etc cause protein to mild fold and then aggregate
- Generally B strands
- Form oligomers that can eitehr create amorphous aggregates or protofibrils that form fibrils
- Misfolded proteins are usually degraded |
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Term
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Definition
- Prion protein acts as template to turn other proteins into nondegradable misfolded protein
- Normal conformation is PrP^c vs Diseased PrP^SC which forms large complexes
- Same primary structure but forms beta strands that encourage misfolding |
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Term
| Myoglobin secondary structure vs hvDAC1 |
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Definition
| Myoglobin is mostly helican while hVDAC1 is mostly b-stranded |
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Term
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Definition
- Modular units that can form independantly and usually are associated with specific structural or functional features of that protein
- 800 found and studied, maybe 2k total
- only 7% are vertebrate specific
- Evolved by fusion delm insertion of segmants that code for diff parts creating novel combinations |
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Term
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Definition
- Described by type and number of fomains
- aprox 25k protein coding genes
- function of aprox 10k of proteins are not known! |
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Term
Time Scale
1) Femto-pico
2) Pico - nano
3) Nano- micro
4) Micro - second |
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Definition
Amplitude and examples
1) .001-.1 A; bond stretchin/angle bending
2) .01- 10 A; unhindred surfice side chain
3) 1-100 A; Folding in small peptides
4) 10-1000 A; Protein folding |
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Term
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Definition
- Protein fluctuation key for function
- Occur across diff time and size scales |
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