Flashcards in Lecture 5-7: Protein Folding Deck (69)
Short range repulsion,
van der waals interactions,
electrostatic forces (ion pairs and salt bridges)
Exclusion of water plays role in the folding and stability of proteins
Short range repulsion
2 like charges repel each other when too close and have no attraction when far apart----affects proteins folding
Van der waals interactions
interacting dipoles from distinct molecules in proteins. Transient.
Weaker than covalent, but longer than covalent bonds. FON can bond w/ H.
Ion pairs/ salt bridge
This forms a stability for tertiary structure. Ions interacting to cancel out charge.
Hydrophobic effect is
when 2 nonpolar substances come together in solvent(water) and cause water to be excluded from interior of the 2 nonpolar molecules
A helix (more flexible), B sheet (more rigid and structured). Also, omega loops can be added to give flexibility to B sheets
Has both interchain and intrachain disulfide interactions that comprise tertiary structure.
Disulfide bonds Intracellular or extracellular?
Extracellular, the cytoplasm is a reducing environment
Folding funnel timescale
1-rapid formation of 2 structure
2-formation of domains through cooperative aggregation(folding nuclei)
3-Formation of assembled domains (molten globule)
4-Adjustment of conformation
5-More rigid structure
A Ca++ senior that contains 4 similar A helices, in a single polypeptide. Each unit binds a Ca++ ion
Context-dependent; certain protein sequences can be B sheet or A helix based on context of protein location.
Ex of alternative conformation
Lymphotactin; Chemokine structure or glycosaminoglycan binding structure
Determinants of protein folding
2 structure allows for efficient packing, folding is hierarchal (folding funnel), hydrophobic effects, context-dependent
Molten globule state
An intermediate conformational states btw native and fully folded states of a globular protein.
Characteristics of molten globule state:
1-presence of native-like content of 2 struture
2-absence of a tertiary structure (produced by packing of AA side chains
3-Compactness in overall shape of protein, w/ radius 10-30% larger than that of the native state.
4-presence of loosely packed hydrophobic core that increases the hydrophobic SA accessible to solvent.
Molten globule is a compact globule w/ "molten" side chain structure that is primarily stabilized by:
Nonspecific hydrophobic interactions
Protein folding stability is governed by:
non-covalent interactions and hydrophobic interactions
T/F: protein folding is a cooperative process
DO proteins prefer higher or lower energy states?
Molten globule state is
btw native and fully folded state of globular protein
PRimary protein structure
AA linked by peptide bonds
Polypeptide chains that can fold into: A helices, B sheets, omega loops (B turns, hairpin turns)
Protein 2 structure stabilizing factors:
Short range repulsion,
van der waals ,
ion pairs and salt bridges
WAter soluble proteins fold into compact structures w/ nonpolar cores
Tertiary structure stabilizing factors:
Disulfide bonds, hydrophobic properties
Polypeptide chains can assemble into multisubunit structures
What determines 3D structure of proteins?