1-42 Mutations and Proteins Flashcards
the ramachandran plot shows us
the possible dihedral angles that can be observed in a given amino acid sequence
forces that restrict the forms that a protein can take on
protein structure works to maximize favorable charge-charge pairings
satisfy all hydrogen bonds
maximize van der Waals interactions
arrange hydrophobic residues such that they are not interacting directly with water.
All of these forces restrict the forms the protein can take on, influencing its folding heavily.
alpha helices
Often contain stretches of hydrophobic residues and act as transmembrane domains.
beta sheets
Alternating hydrophobic/hydrophilic residues make them the secondary structure of choice for the proteins of Gram-negatives’ porins; the hydrophobic parts face the membrane, and the hydrophilic parts line the inside of the channel.
gram negative porin secondary structure
beta sheets
hydrophobic parts face membrane, hydrophilic line the channel
reverse (beta) turn
tight turns in protein
usually contains proline
found in any protein sequence with sharp turns, including multi-pass transmembrane proteins
loops
referred to as “irregular structure”.
frequently forms binding site for other proteins/substrate.
proteins can share similar scaffolding, different loops sequences give rise to different functions
helix-turn-helix
motif found in homeodomains and other DNA binding proteins in all kingdoms of life
zinc finger
motif that binds DNA less strongly than helix-turn-helix.
many are used together by transcription factors to bind DNA
coiled-coil domain
extremely stable domains found in fibrous proteins like myosin. also observed as DNA-binding domains in trancription factors.
problems with folding in vivo
overcome with?
while protein transitions between different intermediates, some intermediates have exposed hydrophobic residues that can interact with neighbors.
overcome with chaperone proteins which cover exposed hydrophobic regions and help folding happen more smoothly
Hsp70
used for small proteins
binds proteins and covers exposed hydrophobic patches during folding
Hsp60
for larger proteins
takes misfolded proteins into its hydrophobic cavity.
ATPase puts a tight cap on the cavity, which changes it’s conformation and reveals charged residues lining the cavity
the protein quickly sequesters its hydrophobic regions within the protein structure
Hsp100
uses atp to disassemble harmful protein aggregates
role of h-60 and hp70 is mainly to
prevent interactions that cause misfolding or aggregating
