Protein-protein interactions

Core BMS

obligate PPIs are [blank] by themselves

unstable

85% of proteins form [blanks]

oligomers

obligate PPIs are [blank] by themselves

unstable

85% of proteins form [blanks]

oligomers

[blank] leads to enhanced stability, coding efficiency, new properties such as allostery, and increased local substrate concentrations

oligomerization

PPIs are used for [blank], signal transduction, cell metabolism, muscle contraction, etc

transport

[blank] fatty acid synthase is type I and is one giant gingerbread man looking protein

eukaryotic

[blank] fatty acid synthase is type II and requires reactions involving multiple proteins

bacterial/prokaryotic

types of PPIs include covalent bonds, post-translational interactions such as ubiquitination, and [blank] interactions

non-covalent

[blanks] are crucial for PPIs such as the SH2

domains

Y2H has the pros of being low-tech and [blank] but many cons such as false pos/neg, chimeric proteins, yeast, localization, and only two proteins

scalable

co-[blank] involves cell lysis by non-ionic denaturant, incubation of cell lysate with antibody, and removal of unbound protein

immunoprecipitation

Co-immunoprecipitation is often followed by mass spec or [blank] blot

western

[blank] purification involves binding of a host to a cross linking reagent attached to an affinity tag and beads

affinity

in mass spectrometry a [blank] is used to digest a protein mixture

protease

peptides are separated by gel [blank]

electrophoresis

MS/MS fragments peptides by breaking [blank] bonds

amide

[blank] techniques include size exclusion chromatography where interacting proteins are bigger

biophysical

AUC observes how fast proteins pellet and [blank] proteins pellet first

larger

[blank] methods are used to confirm the same answer

orthogonal

PPIs were considered undruggable due to violating Lipinski's rule of [blank] such as being much larger than small molecule protein

five

interface of PPIs is [blank] and not 3-D

flat

classically drugs target well-defined ligand binding site with a [blank] molecule

small

the methods of predicting PPIs are [blank], structure, and genome mining

docking

docking involves the [blanking] of two proteins

binding

genome mining involves eukaryote vs [blank] comparisons

prokaryote

[blank]-oligomers are the combination of identical units

homo

salt bridges, disulfide bonds, hydrogen bonds, and hydrophobic interactions are examples of [blank x 3]

protein protein interactions