Biotecnologie del farmaco: disegno e analisi di biofarmaci PER BIOTECNOLOGIE MEDICHE A.A. 2009-2010 Modulo Modulo analisi di biofarmaci (4 CFU) disegno di biofarmaci (2 CFU) Docente: Claudia Sissi Dip. Scienze Farmaceutiche, via Marzolo, 5; (Edificio B) Docente: Manlio Palumbo Dip. Scienze Farmaceutiche, via Marzolo, 5; (Edificio B) Ricevimento: tutte le mattine su accordi con il docente Ricevimento: tutte le mattine su accordi con il docente e-mail: claudia.sissi@unipd.it e-mail: manlio.palumbo@unipd.it Testi consigliati: - Appunti di lezione - Diapositive utilizzate durante le lezioni (copia fornita dal docente) - Articoli di letteratura indicati dal docente Utilizzo inglese scientifico Modalita’ d’esame: - relazione scritta preparata dallo studente su argomenti concordati con il docente che traggono spunto da recenti articoli scientifici riguardanti i biofarmaci - colloquio sulle tematiche teorico pratiche sviluppate nel corso ANALISI E DISEGNO DI BIOFARMACI BIOFARMACO farmaco basato sulla tecnologia del DNA ricombinante Biological tests design Test validation idea libreria Molecular biology Structural biology synthesis ADME preformulazione screening Identificazione lead compound Validazione librerie Structural analysis Phisico-chemical Analysis Drug design ottimizzazione Metabolismo farmacocinetica Chimica fisica Biologia molecolare Biologia cellulare METODOLOGIE ANALITICHE ¾Quantitative analysis of binding equilibria ¾Multiple binding sites ¾Mapping binding sites ¾Structural studies ¾Equilibrium measurements ¾Kinetics experiments ¾Experimental approaches: EXPERIMENTAL APPROACHES Electrophoresis Binding affinities Electrophoretic Mobility Shift Assay (EMSA) Footprinting Proteolysis Surface Plasmon Resonance (SPR) Calorimetric studies Structural informations IsoThermal Calorimetry (ITC) Differential Scanning Calorimetry (DSC) Spectrophotometry FRET CD Stopped flow The foundamental equation of binding - equilibrium A+B Ka [C] Ka = [A][B] C 0.30 [A] [B] Kd = [C] 12000 0.28 10000 8000 0.24 [A] SEGNALE 0.26 0.22 0.20 6000 4000 0.18 0.16 2000 0.14 0.00 0.02 0.04 0.06 [B] 0.08 0.10 0.12 0.14 0 0 2 4 6 8 10 12 [B] 0.850 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 A 0.40 0.35 0.30 0.25 0.20 0.15 0.10 0.05 0.000 350.0 360 370 380 390 400 410 420 nm 430 440 450 460 470 480.0 0.30 0.28 SEGNALE 0.26 [At ] = [A] + [C] 0.24 0.22 S = Slib([A] /[At]) + Sleg([C] /[At]) 0.20 0.18 0.16 0.14 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 [B] [C] [At] = ν= frazione di complessato 1.00 0.75 [A] [B] Kd = [C] 0.50 0.25 0.00 0.0 0.5 1.0 1.5 2.0 2.5 3.0 [B] mM 3.5 4.0 4.5 5.0 S - Slib Sleg - Slib A+B Ka C [A] [B] ([At]-[C]) ([Bt]-[C]) Kd = = [C] [C] se [B]>>[C] [B]=[B]tot [A] [B] Kd = [C] Kd [C] = ( [At]-[C]) [B] [A] = [At] – [C] [B] [At] [C] = [B] + Kd A+B Ka C [A] [B] Kd = [C] Se [B] ≈ [C] [B] = [B]tot – [C] Kd [C] = ( [At]-[C]) ([Btot]-[C]) [A] = [At] – [C] [C]2 – ([Atot]+[Btot]+Kd) [C] – [Atot][Btot] = 0 [C] = ½ { ([Atot]+[Btot]+Kd) - √([Atot]+[Btot]+Kd)2- 4[Atot][Btot] } The Scatchard plot Kd [C] = [A] [B] [B] [At] [C] = [B] + Kd [A] = [At] – [C] [C] = [At] – [C] [B] Kd 10 8 [C]/[B] ν = 1 - ν [B] Kd Kd 12 slope = -1/Kd 6 4 2 0.0 0.5 1.0 1.5 [C] 2.0 2.5 A+B A+S Ka Ka C C S = siti liberi S=B*s + + A+S Ka C S = siti liberi = B * s Kd [C] = [A] [S] [St] = [S] + [C] = [Bt] * s r/m [C] =r [Bt] slope = Ka [A] = m 1 r = (s - r) m Kd s r Multiple binding modes + A+S Ka C S = siti liberi = B * s r/m slope = Ka z z-1 r r = Ka (1-nr) m (2ω+1)(1 – nr)+r-R n-1 1 - (n – 1)r + R 2(ω-1) (1-nr) 2 2(1-nr) n-1 m = Ka (1-nr) 1 - nr 1 – (n-1)r Ka 3 2 r/m r r= [C]leg 1 [Bt] m = [A]lib 0 0.00 0.05 0.10 0.15 0.20 0.25 r 1/n 0.30 Hill Plot [A] [B] Kd = [C] [C] = ½ { ([Atot]+[Btot]+Kd) - √([Atot]+[Btot]+Kd)2- 4[Atot][Btot] } C B-C [A] C B-C [A] Stoichiometry - Job‘s methods aA + bB prodotto moli di A moli di B C 1.0 complex 0.8 0.6 0.4 0.2 0.0 0.00 0.25 0.50 molar fraction 0.75 1.00 The foundamental equation of binding - kinetics A+B Ka C A+B The rate of association is: The rate of dissociation is: [C] Ka = [A][B] [A] [B] Kd = [C] C Number of binding events per unit of time =[A]×[B]×kon. Number of dissociation events per unit time = [C]×koff. Equilibrium and Kinetic Constants are related A+B ka kd AB Saturation binding experiments: measure equilibrium binding of various concentrations of the ligand. Analyze the relationship between binding and ligand concentration to determine the number of sites, Bmax, and the ligand affinity, Kd. Competitive binding experiments measure equilibrium binding of a single concentration of a ligand at various concentrations of a competitor. Analyze these data to learn the affinity of the receptor for the competitor. Kinetics experiments measure binding at various times to determine the rate constants for ligand association and dissociation. ELETTROFORESI Q + - d Migrazione di particelle cariche sotto l’azione di un campo elettrico. Tecnica soprattutto ANALITICA ma anche PREPARATIVA. E’ un mezzo di separazione molto potente, fra i piu’ usati in biochimica ELETTROFORESI Forza elettrica : Fel = Q · E Forza frizionale : Ffr = f ·v (E = ΔV/d) (f = 6π η r) Quando le forze si bilanciano: Q ·E = f ·v → Q v= —·E f mobilita’ elettroforetica : v Q μ = — = — = E f Q 6πηr v proporzionale al rapporto carica/massa a parita’ di tale rapporto dipende dall’ingombro sterico Migrazione di proteine e DNA in gel di varia porosita’ PROTEIN ELETTROPHORESYS SDS-PAGE (Sodium Dodecyl Sulfate Poly-Acrylamide Gel Electrophoresis) FOCALIZZAZIONE ISOELETTRICA Un’altra tecnica, oltre alla cromatografia a scambio ionico, che permette la separazione di macromolecole sulla base della loro carica. Estremamente potente. anodo pH3 ΔV catodo proteine pI acido proteine pI basico pH10 + - + pI, punto isoelettrico ´ Z=Ø ´ v= Ø 2D ELETTROFORESI 2D ELETTROFORESI - CATODO - + ΔV SDS-PAGE + ANODO 2D ELETTROFORESI pH 3-11 B pH 7-11 Elettroforesi di acidi nucleici Agarosio → 0.1 - 40 kb PFGE (Pulse Field Gel Electrophoresis) → 5 Mb poliacrilamide → 10-1000 nt Rivelazione : •UV shadowing •Coloranti :Bromuro di Etidio o Sybr Green •autoradiografia Recupero : •elettroeluizione •Eluizione •Sciogliendo l’agarosio. Separazione dei cromosomi di S. cerevisiae Size of fragments and distance traveled not linear when large fragments are analyzed Conventional agarose gel electrophoresis PFGE Periodically change the direction of the electric field. MODELLO A SETACCIO Le molecole di DNA piu’ grandi sono separate da quelle piu’ piccole dall’azione del setaccio dovuta alla miscela del gel MODELLO A SERPENTE Le molecole di DNA piu’ grandi dei pori del gel devono srotolarsi in modo da poter migrare. Il DNA si muove con un’estremita’ che conduce lo spostamento (TESTA) mentre il resto della molecola (CODA) segue lungo lo stesso percorso La PFGE permette di separare DNA fino a 5 Mb Capillary Electrophoresis (CE) silice Quando applico il voltaggio si forma un flusso laminare. I cationi che si trovano vicini alla parete hanno infatti un’elevata mobilita’ e migrando verso il catodo formano un flusso elettroendosmotico la cui velocita’ di migrazione e’ molto piu’ elevata della velocita’ di migrazione degli analiti. Cosi’, tutti gli analiti, indipendentemente dalla loro carica migrano verso il catodo. Capillary Electrophoresis (CE) Vantaggi dell’Elettroforesi Capillare - Alta efficienza di separazione (105 - 106 piatti teorici) N = 5.54 × (t/Δt1/2)2 - Piccola quantità di campione (1-10 ul) - Separazione veloce (1-45 min) - Selettività prevedibile - Automatizzabilità - Quantificabilità (lineare) - Riproducibilità - Accoppiamento alla spettrometria di massa Tipi di Molecole che possono essere separate con l’ Elettroforesi Capillare Proteine, Peptidi, Aminoacidi, Acidi nucleici, Ioni inorganici, Basi e Acidi organici, Cellule intere. METODOLOGIE IDRODINAMICHE Electrophoretic Mobility Shift Assay EMSA Q μ= 6πηr μ proporzionale al rapporto carica/massa a parita’ di tale rapporto dipende dall’ingombro sterico METODOLOGIE IDRODINAMICHE - EMSA gel shift assay PROTEIN 12000 10000 6000 4000 2000 0 0 2 4 6 8 10 12 [B] 12000 10000 8000 [A] [A] 8000 6000 4000 2000 0 0.1 1 10 [B] 100 Advantages : - Low reactive species concentration - Can separate different complexes Disadvantages : - Labelling - Complex stability and solubility - Not at the equilibrium TECNICHE DI SEQUENZIAMENTO DEL DNA CHE SEQUENZA? MAXAM AND GILBERT SEQUENCING (1977, Nobel prize 1980) There are four chemical cleavage reactions at the core of the Maxam and Gilbert sequencing system. The figure shows an example from these reactions, the reaction cleaving specifically at guanine. The other three reactions cleave at G+A, C+T, or C. MAXAM AND GILBERT SEQUENCING : C: Hydrazine in 0.6M NaCl; incubate at 25°C for 7-9 minutes. G: Dimethyl Sulfate (DMS) in 50mM sodium cacodylate, pH 8, 1mM EDTA; incubate at 25°C for 4-5 minutes. C+T: Hydrazine in H2O; incubate at 25°C for 7-9 minutes. G+A: formic acid; incubate at 25°C for 4-5 minutes. SANGER SEQUENCING (1977, Nobel prize 1980) SANGER SEQUENCING In Sanger dideoxy terminator sequencing, the sample DNA is used as a template for a DNA polymerase. Four polymerase reactions are carried out involving enzyme, primer and sample DNA, along with dNTP's. Each reaction also contains one of the four dideoxy NTP's. When a dideoxy NTP is added, chain lengthening terminates because ddNTP nucleotides lack 3' hydroxyl groups by which to form the next phosphodiester bond. Each reaction contains one of the four bases as a dideoxy NTP, thus each reaction results in fragments terminating at that base. The four reactions produce four collections of fragments with lengths reflecting the sequence positions of each of the four respective bases. DYE TERMINATOR SENQUECING FOOTPRINTING FOOTPRINTING 60 40 20 •Localizzazione •Efficienza di protezione MX 100 80 0 GG C/ GT GC C C/ CA GA C C/ C G T G G C/ CT GC G C/ CT GA G G / AA CA G C/ G AA T T G / AC CTT G/ C A G GT G/ A CC GT T / AT A CT C/ AT GA G/ T AT CA T T/ AA T T A C/ GT T A A G/ T A CT A T/ A T T C C/ A T C GG A G/ T C C GA T / T G AG G/ A CC T GA A /T T G CA T/ TT A CA C/ GA A QUANTITATIVE FOOTPRINTING DNA TRIPLE HELIX + DNA CLEAVING AGENTS Enzymes : DNAse I DNAse II Micrococcal Nuclease Chemical : [Fe-EDTA]2KMnO4 OsO4 DMS Br2 DNase I–DNA complex. Tight interactions in the minor groove formed by Y76 and R41 (shown in purple) and contacts to the sugar–phosphate backbone of both strands (represented by large yellow spheres centered at the phosphate positions) cause a widening of the minor groove and bending of the DNA. The scissile phosphate is shown as a red sphere Hydroxil radical footprinting Hydroxil radical footprinting Method to probe DNA structure Cleavage by .OH Separate products on gel HUMAN TELOMERIC SEQUENCE BCL2 TTAGGG-TTAGGG-TTAGGG-TTAGGG AGGGGCGGGCCGGGAGGAAGGGGGCGGGAGCGGGGCTG Proteolysis •Identificazione domini strutturali •Identificazione cambi conformazionali •Proteomica Pulse proteolysis F Kunf U (a) (b) b Time Lower limit: Upper limit: long enough to completely digest unfolded protein but short enough to not digest folded protein short enough to not digest folded protein F Kunf U [U] Kunf = [F] ΔGunf = -RT ln Kunf 1.2 without ligand with ligand 1.0 f fold 0.8 0.6 0.4 0.2 0.0 0 2 4 [Urea ] 6 8 CIRCULAR DICHROISM SPECTROSCOPY L’ATTIVITA’ OTTICA Una sostanza capace di ruotare il piano di polarizzazione di un fascio di luce planarmente polarizzata viene definita otticamente attiva Per essere otticamente attiva una sostanza non deve possedere dei piani di simmetria isomers: different compounds which have the same molecular formula Constitutional Isomers: Isomers which differ in "connectivity". Stereoisomers: Isomers which have the same connectivity L’ATTIVITA’ OTTICA- GLI ENANTIOMERI Isomeric molecules that are non-superimposable mirror images are enantiomers. Enantiomers are known as chiral molecules (derived from the Greek meaning hand). Chiral enantiomers of a molecule have identical physical properties - melting point, vapor pressure, etc. – with one exception: they scatter polarized light differently. For example, if linearly polarized light passes through a solution of chiral molecules (all of the same enantiomer), the plane of polarization will rotate. Most importantly, the two enantiomers of a molecule will rotate the plane of polarization in opposite directions. This phenomenon is called optical rotation. LA LUCE LUCE LINEARMANTE POLARIZZATA LUCE CIRCOLARMANTE POLARIZZATA sx dx tg Θ = a/b B A Θ = arctg (a/b) Θ = k * (εL-εR) * c* d gradi [Θ] = 3300 * (εL-εR) gradi*cm2*decimole R = K * μ * m * cosγ Cromofori nelle proteine: FAR UV n -> π* involves non-bonding electrons of O of the carbonyl It is centered around 220 nm. It is weak as it is symmetry forbidden (εmax 100) π-> π* involves the π-electrons of the carbonyl It is centered around 190 nm. It is very intense (εmax 7000) The intensity and energy of these transitions depends on φ and ψ (i.e., secondary structure) Effetto della struttura proteica Spettro di assorbimento UV di una catena di poli-L-lisina in differenti conformazioni. 1. Alpha helix (pH 11, 25°C) 2. Disordered (pH 6, 25°C) 3. Beta sheet (pH 11, 52°C) a+b+t+r=1 s=(a*x)+(b*y)+(t*z)+(r*n) K2D : neural network Cromofori nel DNA NH O H3C N N N H O N H TIMINA NH N N H 2 O CITOSINA O 2 N N ADENINA N N H NH N GUANINA NH 2 ssDNA dsDNA 13 10 CD[m de g] 0 -11 230 240 260 280 W a ve le ngth[nm ] 300 320 For nucleic acids, unlike proteins, one cannot ignore spectral differences between different monomeric residues. The bases themselves are directly involved in close interactions in all common secondary structures. Even some actual sequence information must be taken into account to explain CD spectra. For example the CD spectrum of the dinucleoside phosphate ApG is different from the sum of the CD spectra of A and G monomers. The CD spectra of ApG and GpU are the sum of the two monomers plus and an additional term to account for the base-base interactions: 2[qApG(l)] = [qA(l)] + [qG(l)] + IAG(l) 2[qGpU(l)] = [qG(l)] + [qU(l)] + IGU(l) The spectrum of a random coil can be estimated as simply the average of the properties of the four monomers. The spectrum of a single-strand stacked helix would contain optical contributions from each of the 16 possible dinucleoside phosphates, weighted by their frequencies of occurrence. The spectrum of a double-strand is accounted for in an analogous way, by adding the contributions of each of the 10 possible double-strand dimers (ApG base paired with CpU, and so on). In practice, a total of up to 30 different spectral contributions must be combined o compute the CD of a molecule such as tRNA that has both single-strand and double-strand regions. This approach is very complex! B-Z A-Z Induced Circular Dichroism ETBr Induced Circular Dichroism BBR3387 BBR3388 1000 200 Mol. Ellip. Mol. Ellip. poly(dAdT) poly(dGdC) -4000 400 Wavelength[nm] 560 -2000 400 poly(dAdT) poly(dGdC) Wavelength[nm] 560 Linear Dichroism (5) Epar Perfectly oriented DNA Epar Eperp Eperp ΔA = Az − Ax LDr = ( Az − Ax ) 3 Aiso = cos 2 θ z − cos 2 θ x Linear Dichroism (6) The α-helix Fluorescence Fluorescence Resonance Energy Transfert (FRET) Fluorescence Quencing FLUORESCENZA n fotoni emessi Resa quantica = Q = n fotoni assorbiti F = k q Io (εlc) Fluorescence Resonance Energy Transfert (FRET) Cyan Fluorescent Proteins The first fluorescent protein emitting in the bluish-green cyan spectral region (CFP) was discovered during mutagenesis studies that converted the tyrosine residue in the GFP chromophore to tryptophan (Y66W). This single mutation yielded a chromophore that displays an absorption maximum at 436 nanometers with a very broad fluorescence emission spectral profile centered at 485 nanometers. Subsequent refinements, including F64L and S65T, resulted in the production of an enhanced version (ECFP) with greater brightness and photostability. Other than providing an additional hue for multicolor imaging, initially the most promising aspect of ECFP was the potential for utility as a biosensor FRET partner with yellow fluorescent proteins. Yellow Fluorescent Proteins Yellow fluorescent proteins, as a spectral class, are among the most versatile genetically-encoded probes yet developed. Ranging in emission wavelength maxima from approximately 525 to 555 nanometers, those proteins residing in the shorter wavelength region actually appear green, rather than yellow, when viewed in a widefield fluorescence microscope. The first member in what has become a rather large family of probes was rationally engineered after the high resolution crystal structure of green fluorescent protein revealed that threonine residue 203 (Thr203) was positioned near the chromophore and potentially able to alter the spectral characteristics upon substitution. Mutations of this aliphatic amino acid to several aromatic moieties were introduced in order to induce pi-orbital stacking and attempt stabilization of the excited state dipole moment of the chromophore. The most successful mutant proved to be tyrosine (T203Y; termed mutant 10C, the original YFP), which resulted in almost a 20-nanometer shift to longer wavelengths for both the excitation and emission spectra. Several YFP variants were initially constructed in attempts to maximize brightness as well as to increase the speed of maturation and optimize expression at 37 degrees Celsius. a | An intermolecular fluorescence resonance energy transfer (FRET)-based probe consists of two different proteins (X and Y) that are labelled with cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), respectively, which interact and bring the fluorophores into close proximity, thereby increasing the FRET efficiency. b | An intramolecular FRET-based probe consists of either a cleavable linker or a conformationally responsive region sandwiched between a FRET pair. c | Cameleon is an intramolecular FRET-based probe that is used to measure intracellular Ca2+. d | Intramolecular phosphorylation-sensitive FRET probes have been constructed with specificities for various different kinases. Arg, arginine; CaM, calmodulin; Lys, lysine; pS, phosphoserine; pT, phosphothreonine; pY, phosphotyrosine. Figure 5, part c is reprinted with permission from Ref. 105Nature © (1997) Macmillan Magazines Ltd. Figure 5, part d is reproduced with permission from Refs 116, 118 © 2002, National Academy of Sciences. Fluorescence Quencing Some of the processes which reduce the quantum yield are: - collisional quenching - static quenching -energy transfer Dependent upon distance require contact between the fluorophore and the quencher useful to measure rates of diffusion and exposure of fluorescent species to the quencher. molecular oxygen, amides, BrO4-, xenon, I-, peroxides, nitroxides, acrylamide FLUOROPHORE/QUENCHER COMBINATIONS (*) Recommend Maximum (nm) ed Quencher Fluorophore Excitation Emission Dabcyl Coumarin 434 475 Dabcyl 6-Fam (Fluorescein) 494 521 Dabcyl TET 519 537 Dabcyl Eosin 524 544 Dabcyl HEX 535 556 Black-Hole 2 Tetramethylr hodamine 558 580 Black-Hole 2 Texas Red 592 615 T A T G G G G G G G G G G G A GG T G T G GG T TA G GG G G G T TA T G A T T A T 1.2 0.2 1.1 0.1 -d(F)/d(T) 1.0 0.9 F 0.8 0.0 -0.1 0.7 -0.2 0.6 -0.3 0.5 40 50 60 70 Temperature (°C)(°C) 80 90 -0.4 100 50 Tm 60 70 80 Temperature (°C) 90 100 1.4 Oligonucleotide da solo 1.2 1.0 0.8 F 0.6 Oligonucleotide complessato con un legante 0.4 0.2 0.0 20 30 40 50 60 70 80 90 TEMP CSA32 K 5-50 mM (COOPERATIVE BINDING) CSA7 IN K 5 mM 50 mM (ONE BINDING SITE) 35 35 30 30 25 25 20 DTm 20 DTm 100 15 15 10 10 5 5 0 0 0 10 20 CONC 30 0 2 CONC. (μM) 4 6 APPLICATIONS: - macromolecule structure: folding distances stability accessibility -macromolecule-ligand interactions - real time PCR : identification of specific sequence quantification of PCR reaction products quantification of PCR reaction substrate -single molecule fluorescence Single molecule (a) guarantee that only one molecule is in resonance in the volume probed by the laser, (b) provide that the signal-to noise ratio (SNR) for the single-molecule signal is greater than the background for reasonable averaging time. Guaranteeing that only one molecule is present in the detection volume is generally achieved by dilution. For example, at room temperature one needs to work with roughly 10-10 mole/liter concentration with a probed volume of about 10mm3. optics and detector are systems that will simultaneously collect up to four types of correlated information from each photon: 1) the time at which the photon was collected, 2) the polarization of the photon, 3) the wavelength region (above or below some cutoff) of the photon and 4) the lifetime of the excited state that gave rise to the photon. REQUIREMENTS: •severe background reduction •high detection efficiency •spatially selective imaging near-field microscopy confocal microscopy wide-field microscopy total internal reflection (dark-field) microscopy Immobilized molecules Flowing or diffusing single molecules Immobilized molecules Flowing or diffusing single molecules Population distribution Diffusion coefficient Concentration Calorimetric methods endothermic A+B C Q exothermic Q is proportional to C formation ITC Isothermal Titration Calorimetry DSC Differential Scanning Calorimetry - Binding Constants - Reaction Stoichiometry - Thermodynamic Profile of the reaction A+B Ka ΔG = ΔH -TΔS Q C ΔG = -RT ln Ka ΔCp = d(ΔH)/dT = T d(ΔS)/dT Energia libera di Gibbs ΔG ΔG < 0, a reaction/process will occur spontaneously ΔG > 0, it won’t Ka Entalpia ΔH Entropia ΔS Capacita’ termica ΔCp HEAT CAPACITY Heat _______ time = q ____ t = heat flow Temp. increase ΔT = = heating rate time t q __ t ______ ΔT ____ t = q ____ ΔT = Cp = Heat capacity Microcalorimetry Isothermal Titration Calorimetry (ITC) Measures the heat developed/absorbed during a (binding) reaction between molecules in the sample cell and molecules injected Differential Scanning Calorimetry (DSC) Measures differences in heat capacity between reference and sample cell due to dissociation or melting of macromolecules in solution •Ka and enthalpy (ΔH) can be determined directly. •Entropy (ΔS) can be calculated from these values. •Heat capacity, ΔCp, can also be obtained by varying the temperature of the experiment. ITC A+B Ka Kcal/mol mol I Kcal/ ITC C [B] tot ITC B A Adiabatic jacket ITC Measurements • When an injection is made, heat will be generated or absorbed by the molecules reacting (exothermic or endothermic reactions) • Heat input in sample cell adjusted to keep ΔT constant • Exothermic reaction will result in negative peaks (less heat is needed while the reaction proceeds) • Endothermic reactions will result in positive peaks (more heat is needed while the reaction proceeds) ITC Measurements II • The heat input is integrated over time until the it returns to the baseline value • The heat generated/absorbed after any given injection is a function of amount of ligand in that injection, total amount of ligand injected until that point of the experiment, concentration of the molecule in the cell, number of binding sites, binding constant and ΔH of the reaction ITC Measurements III • The observed heat change per injection (dq/dLT) is fitted to the theoretical binding curve, rather than the “standard” binding curve that plots total change versus total added ligand. The ITC experiment • The sample cell holds approx. 1.4 ml, but must be overfilled, so each experiment uses 1.8-2.0 ml of sample • The contents of both cells and of the syringe must be degassed to avoid bubbles forming • The cells must be filled carefully, as bubbles caught on the side of the cell will ruin the experiment • Buffer blanks must be recorded to correct for dilution effects The ITC experiment II • Certain things must be taken into consideration when setting up an ITC experiment: – The ligand and the molecule in the cell MUST be in the exact same buffer to avoid large injection peaks due to dilution – If protonation/deprotonation is expected to be part of the reaction, a buffer with a low ΔHion must be chosen, as ΔHobs= ΔHbind + ΔHion – No other reactions should be taking place on the timescale of the experiment ITC BINDING CURVES • From Andersen et al. (2001), Biochem. 40; 15408-17 ITC Q = V0 ΔH [M]t Ka [L] / (1 + Ka [L]) ITC Isothermal Titration Calorimetry Contro ¾ Requires ΔH > ± 3-5 ¾ Works in solution kcal/mol for precise ¾ Measures equilibrium data determinations ¾ Determines the ¾ Most often requires thermodynamics the of macromolecule concentrations in the binding reaction range 1 µM – 1 mM ¾ Automatic titration – setup ¾ Consumes “large” and leave amounts of purified ¾ No labelling/immobilization material ¾ Tight or very weak binding ¾ Slow – 2-3 Insensitive to very hours per run Pro Measuring very tight binding • ITC is not good for measuring very tight binding directly, although DH can be determined accurately • From Leavitt and Freire, (2001), Curr. Op. Struct. Biol. 11; 560-6 ITC Very tight binding II • But one can do a competition assay: – First we make a complex with a weak-binding ligand – We then compete with a stronger binding ligand – Kapp= Ka,s/(1+Ka,w[X]) ITC • Very tight binding III From Velazquez-Campoy et al. (2001), ABB 390; 169-75 ITC Alternatives • Surface Plasmon Resonance • Requires attachment of molecules to chip • Can give on and off rates • Intrinsic Fluorescence • Requires sensitive* Trp or Tyr residue(s) close to binding site • Interfering agents such as BSA must be absent • Titrating in the ligand can give an increased signal by itself • Works in solution • Potentially much more sensitive ITC Alternatives II • Extrinsic Fluorescence • Requires labeling of macromolecule – most often by introducing single cysteines in select locations • Bulky fluorophores on surface of molecule may interfere with binding • Works in solution • Much more sensitive (depending on fluorophore) • Can give additional information about internal distances using two defined fluorophores and FRET DSC Folded (N) Unfolded (U) N ΔG = ΔH -TΔS Kunf U ΔG = -RT ln Kunf Protein stability : General Observations ΔG = ΔH -TΔS ΔG = 0 equilibrio tra stato nativo e denaturato ΔG > 0 stato nativo piu’ stabile di quello denaturato ΔH is positive for unfolding: favorable interactions in the folded state are disrupted ΔS is often positive, but: disorder increases due to increased freedom of bond rotation disorder decreases due to the hydrophobic effect Denaturazione avviene quando TΔS > ΔH Apparecchiatura DSC Differential Scanning Calorimetry (DSC) • The reference cell contains buffer (exactly the same as the sample is dissolved in) • The two cells are heated at a constant rate • The cells are pressurized, allowing a range of 2-130º C to be measured (-10-130º C if one dare to unlock the protection of the system) • Differences in energy required to heat the two cells is a measure of the heat capacity Cp of the dissolved sample • Dissociation or denaturation of a macromolecule will result in a peak at the transition (melting) temperature Tm • If reversible, a negative peak should be seen on the down scan as the molecule readopts the folded structure DSC setup • DSC cells are filled with buffer and started scanning 8-10 times before doing the real experiment to establish a baseline • When the instrument has almost cooled down to the starting temperature, the sample cell is loaded with the macromolecule • If the molecule does not survive being cooked, this is repeated for each run DSC setup II • Reactive buffer components should be avoided to keep the baseline heat capacity stable between runs • The sample must be pure to avoid additional unfolding event during the experiment • The cells hold less than 0.6 ml, but loading the cells require 0.8-1.0 ml Cp (kcal/mol•˚C) Tm DSC Temp (˚C) Tm is the temp. at which ∆Gunfolding = 0.. ΔCp Area under the curve reflects ∆Hcal DSC APPLICATIONS • Measuring the stability of macromolecules – Testing that functional mutations are representative for the molecule looked at, rather than just being misfolded • Determining the number of domains in a protein • Determining the oligomeric state of a protein Tm, ΔH and ΔCp of the transition are calculated by fitting the data to a two-state transition model using non-linear least squares regression analysis Ligand-Induced Stabilization U N+Q X Any thermodynamically favorable modification of the native structure that takes place will enhance the stability of the folded state (N) vs. the denatured state (U). DSC Ligand-Induced Stabilization Tm increases from 57˚C to 96˚C ∆Gunf at 25˚C increases from 20.5 kcal/mol to 40.5 kcal/mol Tm is function of : •Enthalpy of DNA melting •Drug binding constant DSC Alternatives • Circular dichroism (CD) – Follows the circular polarization of light at a wavelength sensitive to secondary structure elements while the sample is heated – Not all proteins have enough secondary structure for this approach to work – Glass cells and the use of waterbaths to control the temperature limits the range to 0-100º C • Intrinsic fluorescence – Follow changes in Trp or Tyr fluorescence as the sidechains changes environment upon protein denaturation – Heated in same manner as CD sample Surface Plasmon Resonance SPR analyte ligand n2 < n1 n1 Θ ΘC Total Internal Reflection Cella : 20-60 nl Flusso : 1-100 μl/min Ligando : 50 pg/mm2 What SPR Biosensors Measures Kinetics Kinetics Affinity Affinity Specificity Specificity Active Active Concentration Concentration Thermodynamics Thermodynamics How fast and strong … How specific & selective... Is the binding of a lead compound Is this drug binding to its receptor? How much... Biologically active compound is in a production batch? Rate Constants Association rate constant kon Definition Unit Describes Typical range A+B kon AB Dissociation rate constant koff AB koff A+B [M-1s-1] [s-1] Rate of complex formation, i.e. the number of AB formed per second in a 1 molar solution of A and B Stability of the complex i.e. the fraction of complexes that decays per second. 1x10-3 – 1x107 1x10-1 – 5x10-6 Time (sec) Association : dR/dt = KonCRmax – (KonC + Koff) R Dissociation : ln(Ro/Rt) = Koff (t-t0) Binding constant : Ka = Kon / Koff Req/C = KaRmax - KaReq Equilibrium Constants Equilibrium dissociation constant KD Definition Unit Describes Typical range Equilibrium association constant KA (A).(B) koff =k on (AB) k (AB) = kon (A).(B) off [M] [M-1] Dissociation tendency High KD = low affinity Association tendency High KA = high affinity 1x10-5 – 1x10-12 1x105 – 1x1012 Affinity and Equilibrium Signal [RU] 20 15 10 5 0 Time [s] 0 60 120 Same Affinity but different Kinetics • All four compounds have the same affinity KD = 10 nM = 10-8M • The same affinity can be the result from different kinetics kon koff [M-1s-1] [s-1] All target sites occupied 100 nM 30 min 106 10-2 105 10-3 104 10-4 103 10-5 60 min KD 10 nM 1 µM 30 min 60 min Concentration • Signal proportional to mass • Same specific response for different proteins Applications : -Kinetic measurements -Kon (<106 M-1s-1) -Koff (10-5 -1 s-1) -Equilibrium measurements -Binding affinity -enthalpy -Ligands evaluation Not suitable for : Small analytes (100 Da) - High affinity interactions (Kd<10nM) Advantages : -Weak interactions Kd>100μM - Small sample volume Problems : - Cost of the apparatus - Ligand immobilization Immobilization Immobilization DIRECT (covalent) INDIRECT amine – Lys thiol – Cys aldehyde - carbohydrate suitable binding site tag Experimental Design – Direct coupling of Ligand to Surface. – Indirect, via a capture molecule (eg a specific IgG). – Membrane anchoring, where the interacting ligand is on the surface of a captured liposome. Immobilization : Problems Heterogeneug coupling Interference with analyte binding Interference with ligand structure/activity NEW DEVELOPMENTS: Calorimetric data Recovery SPR-MS Arrays SPR microscopy or imaging MICRORECOVERY SPR-MS MICROFLUIDIC in SPR F1 F1 & 2 F2 F3 & 4 F3 F1 - 3 F4 F1 - 4 Spot 1 ot 2 Spot 3 Spot 4 (Reference) Spot 5 SPR Microscopy (SPRM or SPRI) Spatial resolution 4 μm SPR imaging SPR spectroscopy Principle of SPR microscopy. SPR reflectivity curves versus the light's incident angle (at fixed wavelength) for samples of two different effective refractive indices in contact with the gold surface. There is a linear region on the left where the light intensity increases almost proportionally with the change in effective refractive index. If the microscope is set up at an angle in this so-called high-contrast region, the intensity change measured at fixed angle is proportional to the change in effective refractive index, which in turn is proportional to adsorbate coverage. Advantages of SPRM for high-throughput bioaffinity assays • Simultaneous monitoring of rates of >1000 different interactions • Label-free detection • Absolute quantification of binding amounts and ratios • Kinetic measurements with 1 s time resolution • Detection limit: 80 fg, or 1 attomole (<1 million molecules) for 60-kDa proteins • Can detect small ligands (<300 Da) • Near perfect referencing for removing spurious signals due to changes in index of refraction of buffer solutions, temperature, etc. • Requires much less of the precious biomolecules than normal SPR: ○ On-chip receptors: requires only enough of each for spotting 1 nL droplet onto microarray ○ Solution-phase biomolecules in the flow cell: requires 1000-fold less, since >1000 interactions probed with every injection to cell • SPR-active chips typically compatible with inexpensive but reliable robotic spotters • Timely: many new methods for spotting protein arrays and arrays of other receptors on gold have recently been developed Example potential applications of SPRM for high-throughput bioaffinity analyses • Analyses of protein and ligand concentrations with protein or antibody arrays • Analysis of concentrations of DNA-binding proteins from small cell colonies with dsDNA arrays • Screening for ligands that bind to proteins: drug discovery • Screening for substrates (peptides) for catalysis by proteases or kinases, and the relative reaction rates of different peptides • Searches for cofactors in all sorts of protein binding events • Fundamental research in proteomics, neurobiology, cell biology, … • Arrays designed for early disease diagnostics, other clinical applications, … 1020 spot protein microarray Coupling SPRi and ProteinChip based mass spectrometry SPR image and mass spectra obtained from a single 10 × 10 antibody array containing all five antibodies, incubated with a solution containing the five proteins Rapid kinetic experiments stopped flow Cinetica enzimatica 0.630 0.60 0.55 0.50 0.45 0.40 0.35 0.30 0.25 0.20 0.15 0.10 0.05 0.000 0.0 10 20 30 40 50 60 min 70 80 90 100 110 1.1 1.0 0.9 0.8 0.7 Vi / Vo A 0.6 0.5 0.4 0.3 0.2 0.1 0.0 -0.1 0 200 400 concentrazione C 4 (nM ) 600 800 E+S E+S E+P ES E+P Rapid kinetic experiments stopped flow 0,06 0,05 0,04 dA243 0,03 0,02 0,01 0,00 -0,01 0 2 4 6 t/s 8 10 12 Transient Kinetics Recordings (Fluorescence and CD) Refolding kinetics of Lysozyme Followed by CD at 225 nm and simultaneous recording of fluorescence at >305 nm Traces correspond to 5 accumulated shots. Folding was initiated by 10 fold dilution of 3 mg/mL lysozyme denaturated in 6 M guanidine-cl (final concentration 0.3 mg/mL) Cuvette light path = 1.5 mm (FC-15 model) Experiment dead time = 2 ms Sampling rates from 50 µs/point (20kHz) to 100 s/point (0.1 Hz) can be used Applications Measured by: Stopped-Flow Experiments Protein Folding Conformational Changes Substrate Binding Enzyme Kinetics Substrate Transport in Vesicles UV/VIS Absorbance Light Scattering Fluorescence Circular Dichroism Fluorescence Anisotropy FTIR X-ray scattering Conductivity Mass Spectrometry
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