What are similarities amongst soluble globular proteins
mixtures of secondary structures (must include irregular structures along with regular secondary structures)
hydrophobic cores/hydrophilic exteriors
closely packed interiors
maximized H-bonds in the interior
What are differences amongst soluble globular proteins
secondary structure composition
prosthetic groups
presence of disulfides (only in extracellular proteins)
What are the tertiary structure rules for soluble globular proteins
hydrophobic interactions are critical (at least 2 layers must be present to bury hydrophobic groups + non-polar amino acids are usually buried, polar amino acids are usually on the surface)
extensive H-bonding occurs within secondary structural units, NOT BETWEEN THEM
knots do not form
Elements that are close in primary structure are usually
close in tertiary structure
What is the rossman rold?
common nucleotide binding motif found in many dehydrogenases (alternating stand a helix beta strand (BaB), forms a layered a/B structure
all right handed
Connections between sequential beta strands in a parallel beta sheet are
usually right handed
Tertiary structures are typically conserved better than sequence. What are the different classification systems?
What are they for?
SCOP: structural classification of proteins
CATH: class, architecture, topology and homology
Pfam: protein family
attempt to describe the structure of a protein (in search of common features and relationships)
usually described as overall features (a, B, a/B)
Super secondary structures in tertiary structures include motifs and domains. What are these?
motifs/folds: recognizable combinations of secondary structure that appear in a number of different proteins
domains: discrete, independently-folded compact units (may be composed of or include motifs) within a polypeptide
The burial of hydrophobic R groups, to exclude water, requires at least two layers of secondary structure. What motifs create two layers?
BaB
aa
Complex motifs can be built from simple ones, such as
a/B barrel (tim barrel) is formed by repeated B-a-B loop motifs, producing a central B barrel surrounded by a helices
What is a leucine zipper in terms of its structure
coiled coil containing two a helices (left handed superhelix) with leucine prominent in the helix:helix interface
A greek key describes
a type of structure motif
There are typically (blank) interactions than (blank) in a domain
intradomain
interdomain
What is a domain + what do they do?
distinct, stable, globular folded unit within a given polypeptide
they have structural/functional roles, and can be used to compare different proteins to each other
