hem 43 - Experiment 4 MR & Mass pectroscopy and Biomolecular tructure Fall, 2 What does MR measure? Introduction What information does MR provide us about the structures of biological macromolecules - Will focus on the contributions of Kurt Wüthrich, the 22 obel Prize winner in hemistry. 2 istorical timeline Introduction 922 tern (obel Prize, 943) & Gerlach measure intrinsic angular momentum, I, of particles - beam is split in inhomogeneous field; spins (I) are quantized 924 Pauli (obel Prize, 94): two-valued quantum degree of freedom - spin quantum numbers and the Pauli Exclusion Principle 938 Rabi (obel Prize, 944) introduces the molecular-beam magnetic-resonance detection method - MR 946 Bloch (obel Prize, 92) and Purcell (obel Prize, 92) observed proton MR in liquids and solids 3 istorical timeline Introduction 922 tern (obel Prize, 943) & Gerlach measure intrinsic angular momentum, I, of particles - beam is split in inhomogeneous field; spins (I) are quantized 924 Pauli (obel Prize, 94): two-valued quantum degree of freedom - spin quantum numbers and the Pauli Exclusion Principle 938 Rabi (obel Prize, 944) introduces the molecular-beam magnetic-resonance detection method - MR 946 Bloch (obel Prize, 92) and Purcell (obel Prize, 92) observed proton MR in liquids and solids 3
istorical timeline Introduction 922 tern (obel Prize, 943) & Gerlach measure intrinsic angular momentum, I, of particles - beam is split in inhomogeneous field; spins (I) are quantized 924 Pauli (obel Prize, 94): two-valued quantum degree of freedom - spin quantum numbers and the Pauli Exclusion Principle 938 Rabi (obel Prize, 944) introduces the molecular-beam magnetic-resonance detection method - MR 946 Bloch (obel Prize, 92) and Purcell (obel Prize, 92) observed proton MR in liquids and solids 3 istorical timeline, con d Introduction 93 verhauser and others report E s and their correlation to internuclear distances - MR contains structural information 966 Ernst (obel Prize, 99) proposes Fourier transform MR - Greatly improved sensitivity and resolution 972 Lauterbur (obel Prize, 23) and others demonstrate imaging by MR 976 Ernst (obel Prize, 99) introduces 2 spectroscopy (ideas from Jeener) 98 Wüthrich (obel Prize, 22) presents a 3 structure of a protein, after complete assignment of 2 spectra 4 uclear - MR pectroscopy looks at the local environment of atomic nuclei, some of which have magnetic spins (I ). A Mass umber Z Atomic umber I uclear pin dd Even or dd /2, 3/2, /2,... Even Even Even dd, 2, 3,... uclear - MR pectroscopy looks at the local environment of atomic nuclei, some of which have magnetic spins (I ). A Mass umber Z Atomic umber I uclear pin dd Even or dd /2, 3/2, /2,... Even Even Even dd, 2, 3,...
uclear - MR pectroscopy looks at the local environment of atomic nuclei, some of which have magnetic spins (I ). A Mass umber Z Atomic umber I uclear pin dd Even or dd /2, 3/2, /2,... Even Even Even dd, 2, 3,... 6 uclear Magnetic - uclei with non-zero magnet spins, have a magnetic moment: h µ m = γ I 2π where: µm is the magnetic moment I is the spin angular momentum. γ is the gyromagnetic ratio (how fast the nucleus will precess in a magnetic field. h is Planck s constant MR stands for uclear Magnetic Resonance pectroscopy Νuclear Magnetic - When placed in a strong magnetic field (Βο), nuclei with non-zero magnetic spins will precess like a tops. 7 MR stands for uclear Magnetic Resonance pectroscopy Νuclear Magnetic - When placed in a strong magnetic field (Βο), nuclei with non-zero magnetic spins will precess like a tops. 7
uclear Magnetic - For nuclei with I = /2, the magnetic spin quantum number, mm, has one of two values mm = +/2 mm = -/2. - The energy of these two quantum states is given by E = µ m B o h = γ 2π m B o 8 uclear Magnetic - For nuclei with I = /2, the magnetic spin quantum number, mm, has one of two values - The energy difference between these two quantum states increases with the field strength of the magnet (Βο) mm = +/2 Energy - B (Field trength) mm = -/2 9 uclear Magnetic - For nuclei with I = /2, the magnetic spin quantum number, mm, has one of two values - The energy difference between these two quantum states increases with the field strength of the magnet (Βο) mm = +/2 Energy - B (Field trength) mm = -/2 9 uclear Magnetic - For nuclei with I = /2, the magnetic spin quantum number, mm, has one of two values - The energy difference between these two quantum states increases with the field strength of the magnet (Βο) mm = +/2 Energy - B (Field trength) mm = -/2 9
uclear Magnetic - When all the magnetic spins are added together, there is a net excess of spins aligned with the field (mm = -/2) compared to against the field (mm = +/2) a ue to thermal motions, the difference in populations is quite small For our magnet / 2 +/ 2 =.64 for uclear Magnetic - When all the magnetic spins are added The together, very weak there is a net excess of spins aligned with the field (mm sensitivity = -/2) of compared the to against the field (mm = +/2) MR signal is one of the driving forces ue to thermal a behind developing motions, the larger magnets. difference in The 9 Mz populations is magnet at the quite small University of For our magnet Wisconsin-Madison / 2 =.64 +/ 2 for uclear Magnetic - When all the magnetic spins are added together, there is a net excess of spins aligned with the field (mm = -/2) compared to against the field (mm = +/2) a ue to thermal motions, the difference in populations is quite small For our magnet / 2 +/ 2 =.64 for uclear Magnetic - The excess produces a net magnet moment (Μο) that is aligned with the field.
uclear Magnetic Resonance - If a sample in a strong magnet field is irradiated with electromagnetic radiation that is tuned to the precession (resonance) frequency of a nucleus. The nucleus will absorb the radiation and flip from the mm = -/2 state to the mm = +/2 state. 2 uclear Magnetic Resonance - epending on the local magnetic environment, different nuclei will resonate at different frequencies with the radiation. resonances Frequency 3 uclear Magnetic Resonance pectroscopy - In a bygone era, MR spectra were obtained by scanning through the frequencies and observing which frequencies were absorbed. These spectrometer were called continuous wave MR spectrometers. - Modern MR spectrometers use a method developed by Richard Ernst that involves Fourier transforms. These spectrometers are called FT-MR spectrometers. 4 FT-MR pectroscopy Instead of exciting the nuclei one frequency at a time, the magnetization (Mo) is rotated from the z-axis onto the the x-y plane by applying a strong magnetic pulse along the y-axis. This is called a 9 pulse.
FT-MR pectroscopy As the magnetization will rotate in the x-y plane at the precession (resonance) frequency. As it sweeps past the receiver coil located on the x-axis, it will induce an electrical current in the coil that oscillates at the resonance frequency (ωο in radians, νo in hertz). ω o = γ B o ν o = γ B o 2π This signal will decay with time to produce what is called a free induction decay, or FI. 6 FT-MR pectroscopy As the magnetization will rotate in the x-y plane at the precession (resonance) frequency. As it sweeps past the receiver coil located on the x-axis, it will induce an electrical current in the coil that oscillates at the resonance frequency (ωο in radians, νo in hertz). ω o = γ B o ν o = γ B o 2π This signal will decay with time to produce what is called a free induction decay, or FI. 6 FT-MR pectroscopy As the magnetization will rotate in the x-y plane at the precession (resonance) frequency. As it sweeps past the receiver coil located on the x-axis, it will induce an electrical current in the coil that oscillates at the resonance frequency (ωο in radians, νo in hertz). ω o = γ B o ν o = γ B o 2π This signal will decay with time to produce what is called a free induction decay, or FI. 6 FT-MR pectroscopy The MR spectrum is obtained by carrying out a Fourier transform on the FI to extract the frequency components of the FI Richard Ernst was awarded his obel Prize in 99, in part, for his work in developing FT- MR. 7
FT-MR pectroscopy 8 pin-pin oupling Resonance peaks can be split by the presence of other magnetic nuclei, which are located to 3 bonds away in the structure. This phenomenon is called spin-spin, scaler, or J coupling 9 pin-pin oupling Resonance peaks can be split by the presence of other magnetic nuclei, which are located to 3 bonds away in the structure. This phenomenon is called spin-spin, scaler, or J coupling 2 pin-pin oupling Resonance peaks can be split by the presence of other magnetic nuclei, which are located to 3 bonds away in the structure. This phenomenon is called spin-spin, scaler, or J coupling 2
pin-pin oupling The frequency difference for the split peaks is called the coupling constant, J. 3-bond coupling constants contain information about the dihedral angle between the two nuclei. 22 In 22, Kurt Wüthrich shared the obel Prize in hemistry for his contributions in applying MR spectroscopy to the study of biological macromolecules Like Richard Ernst, Wüthrich work at the ET Institute in Zurich, witzerland is obel Prize winning contributions span a 3- year period. 23 The MR pectra of proteins contains structural information. The thermal denaturation of lysozyme (96 s). 24 The MR pectra of proteins contains structural information. omparison of spectrum for bovine pancreatic trypsin inhibitor (BPTI) with that expected for the unfolded form of the protein (97 s). 2
The MR pectra of proteins contains structural information. Ring current shifts. 26 The MR pectra of proteins contains structural information. A lot of the early MR studies on proteins were done on heme-containing proteins. - The ring current shifts arising from the heme groups would shift some of the resonances out from under the envelope, where they could be studied 27 Advances in MR technologies in the 97 s opened up new avenues for study. Fourier Transform MR uperconducting magnets with higher, more stable fields 28 968 22 Mz continuous-wave MR 98 36 Mz FT-MR Recognized that the uclear verhauser effect (E) contained information that could be used to solve for the solution structure of biomacromolecules. E An E is observed as change in intensity that occurs in one resonance peak when another resonance peak is irradiated. It arrises from through-space dipole-dipole interactions between different nuclei. ( ) r 6 f τ 29
The emergence of FT-MR spectrometers led to the development of multi-pulse, 2-dimensional MR experiments. Richard Ernst also contributed to the development of 2experiments These experiments greatly expanded the resolution and efficiency of collecting spin-spin (J) and dipole-dipole (E) data on large molecules - For example: 2-Y (spin-spin, through bond, coupling) 2-EY (dipole-dipole, through space, coupling) 3 The emergence of FT-MR spectrometers led to the development of multi-pulse, 2-dimensional MR experiments. 2-EY spectrum of BUI IIA at Mz 3 The emergence of FT-MR spectrometers led to the development of multi-pulse, 2-dimensional MR experiments. 2-EY spectrum of BUI IIA at Mz 3 The emergence of FT-MR spectrometers led to the development of multi-pulse, 2-dimensional MR experiments. 2-EY spectrum of BUI IIA at Mz 3
-MR spectrum of the amino acid leucine 2 3 3 32 -MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 33 -MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 33 -MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 33
-MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 33 -MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 33 -MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 33 -MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 7 9 6 8 7 6 4 PPM PPM 4 3 2 3 2 34
-MR spectrum of the amino acid leucine 4.3 2.76 8.3.49 3.9 3.9 9 8 7 6 PPM 4 3 2 34 Y 3 Y By moving to 2-dimensions, we can map out correlations between different protons ( ). 3 Y 3
36 Y Y 37 Y 38 Y 39
4 Y Y TY experiments allow us to map out entire spin systems in one step. 4 Y TY experiments allow us to map out entire spin systems in one step. 4 Y TY experiments allow us to map out entire spin systems in one step. 2 3 3 4
4 TY TY 42 TY 43 TY 44
44 TY Applying this now to methanobactin spectrum for Methanobactin 44 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 TY 3 4 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 3 TY 4
TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 3 TY glycine 4 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 3 TY 46 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 TY 3 serine 46 TI or Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 3 TY serine 46
TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 3 TY 47 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 or 3 TY serine 47 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 u + 3 3 2 2 2 2 2 2 2 2 2 2 REY 3 48 TI u + Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 3 3 2 2 2 2 2 2 2 2 2 2 REY experiments allow us to connect spin systems. 3 48
TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 u + 3 3 2 2 2 2 2 2 2 2 2 2 3 REY 48 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 u + 3 3 2 2 2 2 2 2 2 2 2 2 3 REY 49 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 u + 3 3 2 2 2 2 2 2 2 2 2 2 REY 3 TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 u + 3 3 2 2 2 2 2 2 2 2 2 2 3 REY
TI Gly er 2 ys 3 Tyr 4 TI er ys 6 Met 7 u + 3 3 2 2 2 2 2 2 2 2 2 2 3 REY 2 Wüthrich and coworkers developed methods of making sequencial resonance assignments for all of resonances in a protein. 3 Wüthrich and coworkers developed methods of making sequencial resonance assignments for all of resonances in a protein. 4 With the assignments in hand, they could then go on and use the Y and EY data to determine the local structure of a polypeptide backbone α-helices β-sheets
The EY data can also be used find long range interactions, which can be used to predict the tertiary structure of biomacromolecules. 6 In 98, Wüthrich and coworkers published the first 3- dimensional solution structure of a protein that was determined using MR spectroscopy. olution structure of bull seminal proteinase inhibitor (BUI) IIA 7 There protocol has since been used to solve the solution structures of numerous proteins. 8 9
In 98, Wüthrich and coworkers published the first 3- dimensional solution structure of a protein that was determined using MR spectroscopy. olution structure of bovine pancreatic tripsin inhibitor 6 Modern higher dimensional and indirect detection experiments are further stream-lining the protocol. With one day the goal being to fully automate the process. 6 Wüthrich and coworkers have gone on to develop experiments that can greatly expand the size of macromolecule whose structure can be determined. 62 In 997 they published and MR experiment called TRY (Transverse Relaxation ptimization pectroscopy), which has be used to study systems as large as 87, a. 63
In 997 they published and MR experiment called TRY (Transverse Relaxation ptimization pectroscopy), which has be used to study systems as large as 87, a. 64 Mass pectroscopy Accurate mass determination on mb using our Agilent 62 EI-TF mass spectrometer 6 Mass pectroscopy The isotope pattern reflects the relative distribution for each isotope in a sample m/z = 2.2 (M - 2 + + 63 u + ) - 66 Mass pectroscopy The isotope pattern reflects the relative distribution for each isotope in a sample 67
8x 3 Mass pectroscopy 6 The isotope pattern reflects the relative distribution for each 4 isotope in a sample TI 2 67.3 2.8 m/z 2 2 8x 3 TI 6 4 2 2.8 26.8 27.8 28.8 29.9 22 24 26 28 m/z 22 222 224 2x 3 2 TI 67.3 67.44 68.3 68.33 69.43 67 64 66 68 6 m/z 62 64 Mass pectroscopy Even though the highest m/z accessible on our instrument is 3, the molecular weights of large proteins can still be determined. 68 Mass pectroscopy Even though the highest m/z accessible on our instrument is 3, the molecular weights of large proteins can still be determined. 68 Mass pectroscopy Even though the highest m/z accessible on our instrument is 3, the molecular weights of large proteins can still be determined. 68
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