Lecture 7 Flashcards
(16 cards)
structural constraints on protein conformation
- L-AAs
- –nearly all AAs are L - cis and trans configurations of peptide bonds.
- –all synthed by us are trans.
- –there’s an enzyme that can change a peptide bond to cis (usu never necessary) - other steric constraints on Phi and Psi
- –dots outside allowable area means plot unreliable - Proline (usu at bends) is found in cis config in 6% of pep bonds NEXT TO PROLINE
Generalizations from myogolobin structure
- predicted secondary structures exist
- very compact
- hydrophobic residues buried
- proline often at bends
- all species similar; 3D structure (globin fold) conserved in evolution
what agents/conditions denature proteins, and how
- Heat (disrupts H-bonds and others)
- Urea (disrupts hydrophobic interactions)
- Extremes of pH (disrupts ionic interactions)
- high [salt] (disrupts ionic interactions
- Detergents (disrupts Hydrophobic effect
- HS-CH2-CH2-OH (mercaptoethanol)
(disrupts disulfide bonds)
Anfinsen experiment (Rnase renaturation)
The experiment found that denatured Rnase could be renatured, implying that the plan for folding is encoded in the primary structure of the protein.
fibrous proteins
insoluble
- serve protective or structural role
- contain polypeptide chains that generally share a common secondary structure
globular proteins
soluble
globular (somewhat rounded) shape
motif
any distinct folding pattern for elements of secondary structure observed in one or more proteins
- can be simple or complex
- can represent all or just part of polypeptide chain
also called
- fold
- supersecondary structure
domain
distinct structural unit of a polypeptide
-may have separate functions and may fold as independent, compact units
fold
also called structural motif
simpler structural patterns found repeatedly in globular proteins
-any folding pattern with 2 or more segments of secondary structure
-4 SCOP classes.
Folds
classes
superfamilies
families
domain
distinct structural unit of a polypeptide
-may have separate functions and may fold as independent, compact units
TL;DR: independently stable cluster of AAs within polypeptide
can have a discrete function
renaturation
Refolding of an unfolded (denatured) globular protein so as to restore its native structure and function
renaturation
Refolding of an unfolded (denatured) globular protein so as to restore its native structure and function
hierarchy of supersecondary structures
I. Supersecondary structure
A. Folds/Motifs
—–any folding pattern from simple to complex (two or more elements of secondary structure)
1. Domains
——–independently stable segment
——–if separate segment, will fold on its own
——-folds can be domains, but not all folds are domains.
——-ex globin fold
hierarchy of supersecondary structures
I. Supersecondary structure
A. Folds/Motifs
—–any folding pattern from simple to complex (two or more elements of secondary structure)
1. Domains
——–independently stable segment
——–if separate segment, will fold on its own
——-folds can be domains, but not all folds are domains.
——-ex globin fold
Classes of Folds/Motifs (4)
- All a
- –ex: 4-helix bundle - All B
- –ex” single stranded LH B helix
- ——-barrel is helical but made of B segments. Looks like propellar if look from top down into it - a/B
- – alha and B segments interspersed (mixed tog) in protein
- ——-a/B Barrel Motif
- ———-B-a-B loop composes it. (helices on outside) - a+B
- – alpha and B segments, but segregated
maybe B-a-B Loop Motif
—connection between parallel B sheet segments is alpha helix
Classes of Folds/Motifs (4)
- All a
- –ex: 4-helix bundle - All B
- –ex” single stranded LH B helix
- ——-barrel is helical but made of B segments. Looks like propeller if look from top down into it - a/B
- – alpha and B segments interspersed (mixed tog) in protein
- ——-a/B Barrel Motif
- ———-B-a-B loop composes it. (helices on outside) - a+B
- – alpha and B segments, but segregated
maybe B-a-B Loop Motif
—connection between parallel B sheet segments is alpha helix
