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PROTEIN PHYSICSPROTEIN PHYSICS
LECTURE 24LECTURE 24LECTURE 24LECTURE 24
PROTEINS AT ACTION:PROTEINS AT ACTION:PROTEINS AT ACTION:PROTEINS AT ACTION:
BINDBIND TRANSFORMTRANSFORM RELEASERELEASEBIND BIND TRANSFORM TRANSFORM RELEASE RELEASE
BIND: repressorsBIND: repressors
αα-- turnturn--αα
ZnZn--fingersfingersfingersfingers
DNA & RNADNA & RNABINDINGBINDINGBINDINGBINDING
LeuLeu--zipperzipperLeuLeu zipperzipper
BINDBIND TRANSFORM TRANSFORM BINDBIND:: RepressorsRepressors
--BINDINGBINDING--INDUCED DEFORMATION INDUCED DEFORMATION MAKES REPRESSOR ACTIVE, and IT BINDS TO DNAMAKES REPRESSOR ACTIVE, and IT BINDS TO DNA
BIND:BIND: ImmunoglobulinsImmunoglobulins
ImmunoglobulinImmunoglobulin
BIND BIND TRANSFORM TRANSFORM RELEASERELEASE::ENZYMESENZYMESENZYMESENZYMES
chymotrypsinchymotrypsin
Note small Note small active siteactive site
Chymotrypsin catalyses hydrolysis of a peptide Chymotrypsin catalyses hydrolysis of a peptide
Spontaneous hydrolysis: very slowSpontaneous hydrolysis: very slow
Ch t iCh t iChymotrypsinChymotrypsinChymotrypsin is one of the serine proteases. Chymotrypsin is one of the serine proteases. Chymotrypsin is selective for peptide bonds withChymotrypsin is selective for peptide bonds withChymotrypsin is selective for peptide bonds with Chymotrypsin is selective for peptide bonds with aromatic or large hydrophobic side chains, such as aromatic or large hydrophobic side chains, such as Tyr, Trp, Phe and Met, which are on the carboxyl side Tyr, Trp, Phe and Met, which are on the carboxyl side of this bond. It can also catalyze the hydrolysis of of this bond. It can also catalyze the hydrolysis of easter bond. easter bond. The main catalytic driving force for Chymotrypsin is The main catalytic driving force for Chymotrypsin is the set of three amino acid known as catalytic triad. the set of three amino acid known as catalytic triad. This catalytic pocket is found in the whole serineThis catalytic pocket is found in the whole serineThis catalytic pocket is found in the whole serine This catalytic pocket is found in the whole serine protease family. protease family.
Properties of an Active SiteProperties of an Active SiteProperties of an Active SiteProperties of an Active Site
A shape that fits a specific substrate or A shape that fits a specific substrate or substrates onlysubstrates onlyyySide chains that attract the enzyme Side chains that attract the enzyme particular substrateparticular substrateparticular substrateparticular substrateSide chains specifically positioned to Side chains specifically positioned to speed the reactionspeed the reaction
The Catalytic TriadThe Catalytic TriadThe Catalytic TriadThe Catalytic Triad
chymotrypsinchymotrypsin
CHAIN CUTCHAIN CUT--INDUCED DEFORMATIONINDUCED DEFORMATIONMAKES ENZYME ACTIVEMAKES ENZYME ACTIVEMAKES ENZYME ACTIVEMAKES ENZYME ACTIVE
nonnon--activeactive↑↑
titi active active cat. sitecat. siteactive active
cat. sitecat. site
ChymotripsinChymotripsin ChymotripsinoChymotripsinogengeny py p y py p gg
SERSER--protease: protease: catalysiscatalysis
Chymotrypsin Protein Chymotrypsin Protein y ypy ypHydrolysisHydrolysis
Stage #1g
Chymotrypsin Protein Chymotrypsin Protein HydrolysisHydrolysis
Stage #2g
Chymotrypsin Protein Chymotrypsin Protein HydrolysisHydrolysis
Stage #3g
Chymotrypsin Protein Chymotrypsin Protein HydrolysisHydrolysis
Stage #4g
Chymotrypsin Protein Chymotrypsin Protein HydrolysisHydrolysis
Stage #5g
Chymotrypsin Protein Chymotrypsin Protein HydrolysisHydrolysis
Stage #6g
Transition State Transition State Stabilization Stabilization
Chymotrypsin KineticsChymotrypsin KineticsC y ot yps et csC y ot yps et cs
The initial "burst" inThe initial burst in chymotrypsin-catalysed hydrolysis of the p-nitrophenyl acetate
CHYMOTRYPSIN ACTIVE SITECHYMOTRYPSIN ACTIVE SITE with with INHIBITOR INHIBITOR
Catalytic antibodiesCatalytic antibodiesABZYM = AABZYM = AntyntyBBodyody enenZYMZYMABZYM AABZYM AntyntyBBodyody enenZYMZYM
Transition state (TS)Transition state (TS)Transition state (TS)Transition state (TS)
PreferentialPreferentialbinding binding
AntibodiesAntibodies
ggof TS:of TS:RIGIDRIGIDAntibodiesAntibodies
are are selectedselected
RIGIDRIGIDenzymeenzymeselectedselected
to TSto TS--likelikemoleculemolecule
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