Protein Shape Determines Function Protein Structure
Protein Processing & FunctionProtein Shape Determines Function Post-translation modification– polypeptide Æ functional protein Specific 3-D shape Shape is critical to functionProtein StructureA protein’s specific function dependson its shape and distribution offunctional groups. Denaturation loss of shapeË loss of functionDNA polymerase: itsactive site fits DNALevels of Protein StructureÿPrimarylysozymePrimary structure of protein:the amino acid sequenceÿPolypeptide sequenceÿSecondaryÿFolding coils & pleatsÿTertiaryÿComplete 3-D shapePrimary structure is due to strongcovalent peptide bonds joining aminoacids together.ÿQuarternaryÿCombining polypeptideslysozymePrimary Structure & Protein TraffickingLeading sequence of amino acids in a polypeptide being synthesizeddetermines its fate: cytosolic, membrane-bound, nuclear, or secreted.1 Polypeptidesynthesis beginson a freeribosome inthe cytosol.2 An SRP bindsto the signalpeptide, haltingsynthesismomentarily.3 The SRP binds to areceptor protein in the ERmembrane. This receptoris part of a protein complex(a translocation complex)that has a membrane poreand a signal-cleaving enzyme.4 The SRP leaves, andthe polypeptide resumesgrowing, meanwhiletranslocating across themembrane. (The signalpeptide stays attachedto the membrane.)5 The signalcleavingenzymecuts off thesignal peptide.6 The rest ofthe completedpolypeptide leavesthe ribosome andfolds into its ecognitionparticle(SRP) SRPreceptorCYTOSOL cation of primary structure Chemical alteration of amino acid side groups– Methylation; hydroxylation; etc.– E.g.: N-terminal methyl-methionine fi protects peptide fromamino-peptidases. Collagen contains many hydroxy-prolines & hydroxylysines fi allows condensation with oligosaccharidesTranslocationcomplexFigure 17.21Heyer1
Protein Processing & FunctionModification of primary structure Cleavage of polypeptide chain–––Zymogens: inactive pre-enzyme minus fragment Æ active enzymeSecondary structure:group of amino acidsfolded repetitively tomake a discrete shape.Isolation of fragments within a protein: Insulin polypeptide folds over to be cross-linked withitself, and is then cleaved into two polypeptidesdue to hydrogenbonds betweenamino acids’backbones.Multiple products: Pro-opiomelanocortin (POMC) — translatedpolypeptide cleaved into fragments:1. Endorphin (opioid)2. Melanocyte stimulating hormone3. Corticotropin stimulating hormoneTertiarystructure:the overall 3-dconformation ofa polypeptide.lysozymeTertiary Structure(Salt bridge)Tertiary structureinvolves severalkinds of bondsbetween sidegroups of aminoacids at variouslocations alongthe polypeptidebackbone.Covalent disulfide bonds between cystineresidues are the strongest and most stable.Quaternary StructureMost proteins arehydrophilic outside,hydrophobic inside.Tertiary structure ismaintained by aminoacids interactingwith other aminoacids and withwater.HeyerMultiplepolypeptidesjoined to make asingle protein.(May be the sameor products ofseparate genes)2
Protein Processing & FunctionQuaternary StructureHemoglobin Genes and Gene Products2 b-chain polypeptides2 a-chain polypeptidescollagenhemoglobinHemoglobin Gene Product ProductionYolk sacLiverSpleenBone 530/DB Ch09/fig9 24.jpgProsthetic groupsNon-amino acid groups added to a polypeptide. Carbohydrate fi glycoproteinHbF: 2α and2γHbE: 2ζ and2εHbA1: 2α and2βHbA2: 2α and2δ Lipid fi lipoprotein Nucleic acid fi nucleoprotein Phosphate fi phosphoprotein “activated” protein Metal ion fi metalloproteinMehta, A. B., and A. V. Hoffbrand. 2000. Haematology at a glance, Blackwell Science, Malden, Mass.Hemoglobin MoleculeHeyer Heme (organic porphyrin ring with an ironcore) fi hemoproteinCytochrome CAn electroncarrier3
Protein Processing & FunctionProtein Shape Determines FunctionHow Proteins Foldv A protein’s function depends onits folding. How do proteins getfolded into the requiredconformation?DNA polymerase: itsactive site fits DNADNA polymerase: itsactive site fits DNAHbA – ß chainHbS – ß chainvalgluHemoglobin ElectrophoresishydrophobicHomozygous HbSSickle CellHemoglobin:foldingdepends onprimarystructureHow Proteins Foldv A protein’s function depends onits folding.v There may be more than 1 wayfor a big polypeptide to fold.HeyerHeterozygous n folding: Is it all downhill?Ribonucleasecan renatureitself. Thismakes it anunusuallytough protein.4
Protein Processing & FunctionDesigning a protein to foldStructure of an artificial proteinpredictedobserved—hydrophobic amino acid residuesUnderstanding protein structure isimportantNutlin, a tumorsuppressingdrug thatmimics theshape ofprotein p53(transcriptionfactor).How Proteins Foldv A protein’s function depends onits folding.v There may be more than 1 wayfor a big polypeptide to fold.v Some proteins can fold on theirown, but many require help.v Chaperonins are proteins thathelp fold other proteins.A ChaperoninunfoldedfoldedUnfolded orincompletelyfoldedproteins maybe destroyed.Provides a “safe folding environment”— Probably binds to polypeptide, to inducethe correct folding conformationHeyer5
Protein Processing & FunctionProteinsthe Molecular Machinesv Incorrectly folded proteins don’t work,and they clump together (they becomeinsoluble).v If not refolded or destroyed, they canaccumulate and cause problems.ß Eg., excess accumulated misfoldedproteins (plaques) in neural tissue ÆßParkinson diseaseßAlzheimers diseaseßMad cow diseasePrion Basicsv Prions are an unusual kind ofmisfolded protein.Prionsinfectiousproteinagentsv Prions can cause CNS diseases likemad cow, scrapie, kuru, andCreutzfeldt-Jakob disease.v Prions can be transmittedfrom one individual to another.Prion BasicsPrion Basicsv Everybody has prion proteins (PrP).v Everybody has prion proteins (PrP).v PrP comes in 2 forms: good and bad.Prion proteinstructure isconserved.Heyernormal& prionversionsof P r P6
Protein Processing & FunctionPrion Basicsv Everybody has prion proteins (PrP).v PrP comes in 2 forms: good and bad.v Bad PrP catalyzes the misfolding ofgood PrP, changing good PrP to bad.PrionOriginalprionMany prionsNormalproteinNewprionMisfolded badPrP catalyzesthe misfoldingof good PrP.Figure 18.13Prion BasicsPrion Disease: Open Questionsv Everybody has prion proteins (PrP).v What does good PrP normally do?v PrP comes in 2 forms: good and bad.v How specifically does bad PrPconvert good PrP?v Bad PrP catalyzes the misfolding ofgood PrP, changing good PrP to bad.v Consuming bad PrP can turn allyour good PrP bad (chain reaction). Transmitted by food, transfusions,transplants, brain extracts.Other Protein Folding Researchv Why isn’t PrP digested/destroyedwhen eaten?v How does bad PrP get to the brain?v How does bad PrP cause disease?Accumulations of misfolded proteinsv Alzheimer’s disease is completelydifferent from prion diseases.v Prion disease: misfolded proteincatalyzes more misfolding.v However, both are caused byaccumulations of misfoldedproteins.v Alzheimer’s: cause of misfoldingunknown, but failure of “unfoldedprotein response” pathway is key.Alzheimer’sHeyerv Can conversion be Jakob7
Protein Shape Determines Function A protein’s specific function depends on its shape and distribution of functional groups. lysozyme Protein Structure ÿPrimary ÿPolypeptide sequence ÿSecondary ÿFolding coils & pleats ÿTertiary ÿComplete 3-D shape ÿQuarternary ÿCombining polypeptides Levels of Protein Structure Primary structure is due .
Protein Structure and Function Functional protein has one or more polypeptides precisely twisted, folded, and coiled into a unique shape The sequence of amino acids determines the protein’s three-dimensional structure and the structure determines the function (a) A ribbon model (b) A space-filling model Groove Groove
Slide 36 Fig. 5-19 A ribbon model of lysozyme (a) (b) A space-filling model of lysozyme Groove Groove A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape. The sequence of amino acids determines a protein's three-dimensional structure A protein's structure determines its function
Sep 24, 2018 · function—genetic information storage—for which it assumes a single shape. The sequence of amino acids in a protein determines its folded structure The specific order of amino acids in a protein is known as its primary structure. It is this sequence that determines the three-dimensional architecture of a protein.
How Big Is a Protein Molecule? Assuming this partial specific volume (v 2 0.73 cm . 825 V (nm3). Size and Shape of Protein Molecules at the Nanometer Level 33. What we really want is a physically intuitive parameter for the size of the protein. If we assume the protein has the simplest shape, a sphere, we can calculate its radius. We will .
protein:ligand, K eq [protein:ligand] [protein][ligand] (1) can be restated as, K eq 1 [ligand] p 1 p 0 (2) where p 0 is the fraction of free protein and p 1, the fraction of protein binding the ligand. Assuming low protein concentration, one can imagine an isolated protein in a solution of Nindistinguishable ligands. Under these premises .
Part I- Protein Purification Each protein folds into a specific shape and has a unique 3-D conformation. Objectives of Protein Purification Step: To separate one protein from a complex mixture of proteins (such as a tissue extract), while maintaining Biological Function. One can maintain biological function by controlling the
Of the 190 billion cells in the human brain , about half of them neurons while the other half is comprised of glia, ependymal, and endothelial cells (Azevedo et al., 2009). Neurons vary enormously in size, shape, and function. The shape of a neuron determines its connections with other cells and thereby determines its function.
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