学霸归纳-蛋白质与蛋白质组

蛋白质与蛋白质组伍乘风出品Chapter1.Proteinstructure1.Regulationofproteinfunction:Expression,Transportationandlocalization,Modification,Interaction,Degradation.2.Proteinsgenerallyhave50aminoacidresidues.3.Levelsofstructure:1)Aminoacidresiduesequence2)Structuralelements3)Specific3-dimensionalstructure4)Arrangementofsubunitsinmulti-subunitprotein4.Thereareover300naturallyoccurringaminoacidsonearth,butthenumberofdifferentaminoacidsinproteinsisonly20.5.Classificationofaminoacids:1)Acidic:aspartate(Asp,D),glutamate(Glu,E).2)Basic:lysine(Lys,K),arginine(Arg,R),histidine(His,H).3)Aromatic:tyrosine(Tyr,Y),tryptophan(Trp,W),phenyl-alanine(Phe,F).4)Sulfur:cysteine(Cys,C),methionine(Met,M).5)Unchargedhydrophilic:serine(Ser,S),threonine(Thr,T),asparagine(Asn,N),glutamine(Glu,Q).6)Inactivehydrophobic:glycine(Gly,G),valine(Val,V),leucine(Leu,L),isoleucine(Ile,I).7)Specialstructure:proline(Pro,P)isoftenlocatedattheturnofapeptidechain.6.InteractionbetweenpositiveandnegativeRgroupsmayformasaltbridge,whichisanimportantstabilizingforceinproteins.7.Thesynthesisofallpeptidechainsstartsfrommethionine.8.Twoadditionalaminoacids:selenocystein(硒半胱氨酸,UGA)andpyrrolysine(吡咯赖氨酸,UAG).Theunusualaminoacidisspecifiedbyacanonical(标准的)stopcodon.9.TheappropriatetRNAisinitiallychargedwithserine,whichissubsequentlymodifiedtoselenocysteine.However,tRNAcanbedirectlychargedwithpyrrolysine,whichrepresentsthefirstcaseoftRNAchargingwithanon-canonicalaminoacid.10.Trp,Tyr,andtoalesserextenPhe,absorbultravioletlight,whichaccountsforthecharacteristicstrongabsorbanceoflightbyproteinsatawavelengthof280nm.11.Nonstandardaminoacid:Derivedfromoneofthe20standardaminoacids,inamodificationreactionthatoccursafterthestandardaminoacidhasinsertedintoaprotein.12.Threewaystoobtainapeptide:1)Purificationfromtissue2)Geneticengineering3)Directchemicalsynthesis13.Solidphasepeptidesynthesis(SPPS):1)Pre-treatmentofaminoacids2)Formationofpeptidebond3)Deprotect,hydrolyzeandpurification14.Biologicalandchemicalsynthesisofpeptides:Commonpoints1)Activationofcarboxylgroup2)StepbystepDifferences1)Template2)Orientation:forbiologicalsynthesis,itisfrom“N”to“C”.Forchemicalways,itisfrom“C”to“N”.3)Efficiency4)Condition5)size15.Elucidationofantigenicpeptidesequencesinproteinsbyepitopemapping(表位作图).16.Edmandegradation1)Coupling:theN’oftheproteincoupleswithPITCunderbasicconditionstoformaPTC(phenylthiocarbamyl苯氨基硫甲酰)-polypeptide.2)Cleavage:thepeptidebondoftheN’PTC-residueundergoesacidcleavagefromthepolypeptidechain,releasinganunstableATZderivativeoftheaminoacid.3)Conversion:theunstableATZ-aminoacidisconvertedintothecorrespondingstablePTHderivative.17.Largeproteinssequencing:1)Breakingdisulfidebonds2)Cleavingthepolypeptidechain3)Sequencingofpeptides4)Orderingpeptidefragments5)Locatingdisulfidebonds18.Aproteinthatisrelatedtoanotherbycommonevolutionaryhistory(homologousproteins).19.Thefeaturesofanαhelix:1)Every3.6residuesmakeoneturn2)Thedistancebetweentwoturnsis0.54nm3)TheC=OofoneturnishydrogenbondedtoN-Hoftheneighboringturn4)Anαhelixcanbeeitherright-handedorleft-handed.20.β-turns:1)acommonstructuralelementusedtoredirectthechain.2)Aβ-turnismadeof4residues.ThecarbonylOfothefirstresidueishydrogenbondedtotheNofthefourthresidue.21.Fibrousproteins:1)α-keratin:coiled-coilofαhelices2)β-keratin:stackedβsheets.AlternatingAla-GlyallowsclosepackingofAla’smethylgroupinsilk.3)Collagen:usualsequenceisrepeatsofGly-X-(Hy)Pro.Threeleft-handedheliceswraparoundeachotherinaright-handedspiral.TheGlysareatcoreofbundles.22.Domains:thestableunitofproteinfoldingandtertiarystructure.Differentdomainsinaproteinmayhavedifferentfunction.23.Advantagesofmulti-domains1)Efficientfolding2)Largerfoldedproteins.3)Flexibilityandmotion4)Unionofnewfunction24.Theforcegoverningsubunitassociation:1)Ionicinteractions2)Hydrophobicinteractions3)Thesecondarystructure25.Reasonsforusingmultimerc(多聚体的)assembliesofprotomers(原体)：1)Allowslargerproteinwithoutincreasinggeneticinformationrequiredtocodeforit.2)Errorrateisnotsuchafactor3)Interactionsitescanbeatinterface26.Trytopredictstructuresbasedontheprimarysequences,using:1)Knownstructures2)Tendenciesofaminoacids3)Energyminimization27.Measure/monitorproteinfolding1)CD(circulardichroism圆二色性)canmeasurecontenofregularstructureslikeαhelixandβsheet.2)Trpfluorescenceincreasesinhydrophobicenvironment.28.Forcesactingonproteins1)Hydrogenbonding2)VanderWaalsinteractions3)Ionpairing4)Disulfidebonds5)Intrinsicproperties6)Hydrophobicity:thedominantforceinproteinfolding29.Therelationshipbetweenprimarystructureandconformation:1)Changeprimarystructure——changeconformation2)Changeprimarystructure——withoutchangeofconformation3)Changeconformation——withoutchangeofprimarystructureChapter2.Proteinfolding,misfoldinganddisease1.Proteinfoldingistheprocessbywhichaproteinassumesitsfunctionalshapeorconformation.2.Stringent(严格的)quality-controlsystemsensurethatthemisfoldedproductsaretargetedfordegradationbeforethecauseharm.3.Nativestatesofproteinsalmostalwayscorrespondtothestructuresthataremosthermodynamicallystableunderphysiologicalconditi