NMR data processing & peak assignments nmrPipe nmrDraw nmrView Contents 1. nmrPipe 2. nmrDraw 3. nmrview nmrPipe nmrPipe: Spectral Processing as a UNIX Pipeline http://spin.niddk.nih.gov/NMRPipe/ ☺ Software system for processing, analyzing, and exploiting NMR spectroscopic data ☺ One of the most popular software packages for NMR Data Processing in part due to its efficiency ☺ NMRPipe consists of a series of "functions" which can be applied to a FID data file in any sequence, by using UNIX pipes ☺ Processed data can be used with well-known spectral analysis programs such as nmrview and sparky etc… F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293 (1995) nmrPipe stream Zero-filling Phase correction Zero-Filling Input data (ser file) SP ZF FT PS Transpose TP Window function Fourier Transformation Processed output stream FID (Free Induction Decay) Biological NMR lecture, Korea Magnetic resonance society Zero-Fill Jang sun bok Improve digital resolution by adding zero data points at end of FID raw data No zero-filling zero-fill zero-filling FT (Fourier Transform) Pulse Jang sun bok 1D Spectrum FID FT time frequency A pulse creates magnetization in the XY plane, which is ultimately detected by the coil in the NMR probe The RF signal detected by the coil, consisting of a superposition of many sinusoidal waves of differing frequencies, amplitudes and phases, is termed “free induction decay”, or FID FID dies out with time in an exponential manner and is converted to the frequency domain by a function called “Fourier transformation”, or FT: f(ω) = ∫f(t) eiωt dt from trigonometry eiωt = cosωt + isinωt FID thus consists of real and imaginary components: Re(f(ω)) = ∫f(t)cosωt dt and Im(f(ω)) = ∫f(t)sinωt dt Both the real and the imaginary components are Fourier transformed to generate a spectrum in the frequency domain Transpose ☺ Jang sun bok Ft.com file XYZ→X axis Processing→TP→ YXZ→Y axis Processing->ZTP → ZXY→Z축 Processing→TP → XZY-> result file # TP: Transpose 1 and 2 # ZTP: Transpose 1 and 3 C XYZ N → 측정 시 HNC H-N 2D plane을 C domain 축을 따라 가는 방식으로 분석 → N H XZY C H 측정 시 HCN H-C2D plane을 N domain축을 따라 가는 방식으로 분석 nmrPipe Jang sun bok Frank Delaglio www.nmrscience.com/embo nmrPipe ② ① ③ 2D experiment 3D experiment Jang sun bok nmrPipe Jang sun bok Conversion Script (Fid.com): nmrdata를 nmrPipe로 인식할 수 있게 하는 format conversion C-shell script #! /bin/csh Read raw file Digital filter Bruk2pipe –in ./ser \ -bad 0.0 –noswap -DMX -decim 16 -dspfvs 12 -grpdly 0 \ -xN -xT -xMODE -xSW -xOBS -xCAR -xLAB - ndim 2048 1024 DQD 8992.806 500.132 4.70 1H 2 - out ./test.fid –verb -ov -yN 256 -yT 128 -yMODE Echo-Antiecho -ySW -yOBS -yCAR -yLAB -aq2D 1875.293 50.684 117.359 15N States \ \ \ Data point Time domain Acquisition mode \ \ \ \ \ Sweep width (Spectral width) Base frequency Carrier frequency (O1/BF1) Label Dimension number , 2D plane acquisition mode Save the test.fid file in this directory NMR data size Jang sun bok NMR data size Increase in data points, resolution and acquisition time → Increase in the number of data points increase in resolution→ Increases acquisition time Protein NMR lecture , Amjad Farooq, University of Miami SW (Sweep Width) Jang sun bok Sweep Width (range of radio-frequencies monitored for nuclei absorptions) Ft.com (Fourier Transform script) #! /bin/csh nmrPipe –in test.fid │ │ │ │ │ │ │ │ │ │ │ │ │ │ nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -out \ SOL \ POLY time \ SP -off 0.3 -end 0.99 -pow 2 -c 0.5 \ ZF -size -auto \ FT -auto \ PS -p0 -31 -p1 0 -di \ EXT -left -sw -di \ TP \ SP -off 0.3 -end 0.99 -pow 1 -c 0.5 \ ZF -size -auto \ FT -auto \ PS -p0 -93 -p1 0 -di \ TP \ HSQC.ft -ov -verb \ nmrPipe –in HSQC.ft │ pipe2xyz -out SAV0816_HSQC.nv -nv -ov -verb Jang sun bok Solvent Removal Jang sun bok • Solvent Removal (SOL) PhD Jang Sun Bok protein NMR spectra are typical collected in water the large solvent signal can interfere with the interpretation of the NMR data Carrier frequency is usually centered on the water signal the signal associated with the water resonance can be filtered or subtracted from the time domain of the FID SOL Without Solvent Subtraction With Solvent Subtraction Linear Prediction Jang sun bok FID의 초기 감소 경향으로부터 예측하여 FID를 완전한 형태로 만들어 주는 조작 (apply complex linear prediction to predict or replace data at the head, tail, or interior of data vectors. Forward, backward, and mixed modes are supported along with mirror image modes) │ nmrPipe -fn LP LP전 Before LP -> 일반적인 LP를 가하는 함수를 적용하라 │ nmrPipe -fn LP -ps0-0 -> Mirror image processing. 32포인트 이하의 data에 효과적임 │ nmrPipe -fn LP –fb –auto -> Forward-back 양 방향으로 LP하여 나머지는 자동으로 처리하라 After LP후LP Linear Prediction Jang sun bok ☺ forward linear prediction - points immediately after each group are predicted ☺ backward linear prediction - points immediately before each group are predicted ☺ forward-backward linear prediction - combines results from separate forward- and backward-linear prediction calculations. LP Progress in Nuclear Magnetic Resonance Spectroscopy (1988), 20(6),515-626 Linear Prediction Jang sun bok Frank Delaglio www.nmrscience.com/embo Linear Prediction Jang sun bok LP Frank Delaglio www.nmrscience.com/embo Jang sun bok nmrDraw nmrDraw Ph.D Jang Sun Bok ☺ NMRDraw is the companion graphical interface for NMRPipe ☺ Real-time phasing of one or more vectors for any dimension nmrDraw (general example) Ph.D Jang Sun Bok Phase correction OK… nmrDraw nmrDraw (SAV0816) P0 Ph.D Jang Sun Bok P1 Vertical mode: Click ‘V’ P0,P1 값 조절 nmrDraw (SAV0816) P0 Ph.D Jang Sun Bok P1 Horizontal mode: Click ‘H’ P0,P1 값 조절 nmrDraw (SAV0816) Jang sun bok Phasing and Zero-Filling #! /bin/csh nmrPipe –in test.fid │ │ │ │ │ │ │ │ │ │ │ │ │ │ nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe nmrPipe -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -fn -out \ SOL \ Zerofilling POLY time \ SP -off 0.3 -end 0.99 -pow 2 -c 0.5 \ ZF -size -auto \ Phasing FT -auto \ PS -p0 -31 -p1 0 -di \ EXT -left -sw -di \ TP \ SP -off 0.3 -end 0.99 -pow 1 -c 0.5 \ ZF -size -auto \ FT -auto \ PS -p0 -93 -p1 0 -di \ TP \ HSQC.ft -ov -verb \ nmrPipe –in HSQC.ft │ pipe2xyz -out SAV0816_HSQC.nv -nv -ov -verb Jang sun bok Parameter Identifier in acqu file Jang sun bok Essential Parameters Identifier Time domain (data points) TD Sweep Width in ppm SW Sweep Width in Hertz SW_h Pulse program (Excitation sequence) PULPROG Type of Nucleus NUC Carrier Frequency O1, O2, O3 Jang sun bok Assignment NMR Assignment Jang sun bok What is the NMR Assignment Issue? ☺ Each observable NMR resonance needs to be assigned or associated with the atom in the protein structure ☺ NMR spectra of proteins are complex, where the complexity increases with the size or number of residues of the protein ☺ Use 13C & 15N isotope enrichment to simplify the NMR spectra need to assign these NMR resonances ☺ A typical protein will have hundreds of 1H, 13C and 15N NMR resonance to assign NMR Assignment Jang sun bok ... Ala 70 Ser 71 O ... H2N CH O H N C CH CH3 Again, as illustrated here, the goal is to explicitly assign each H, C, & N in the protein’s primary sequence with its corresponding NMR resonance 119.3 ppm HN 7.76 ppm 13Ca 55.5 ppm Ha 3.76 ppm ... H2N CH 13CO CH3 13Cb 17.5 ppm Hb 1.45 ppm O H N C CH CH2 CH2 OH CH C OH ... CH3 CH3 ... Ala 70 15N Leu 72 ... Ser 71 O 15N 114.8 ppm HN 7.08 ppm C H N CH Leu 72 ... O C 13CO 171.9 ppm 125.6 ppm HN 8.20 ppm H N 178.1 ppm 64.8 ppm CH2 13Ca 59.9 ppm Ha 4.35 ppm Hb 3.73 ppm 13Cb OH O 15N CH CH 58.6 ppm Ha 4.09 ppm C 13CO CH2 13Ca ... 170.9 ppm 13Cb 42.9 ppm Hb 1.52 ppm CH3 13Cd CH3 OH 13Cg 27.9 ppm Hg 1.65 ppm 25.4 ppm; 25.7 ppm Hd 0.82 ppm; 0.98 ppm NMR Assignment Jang sun bok How Are NMR Assignments Made For a Protein? ☺ Requires the collection and analysis of multidimensional NMR data 2D, 3D, 4D NMR spectra ☺ This in turns requires software to assist in the processing and analysis of the data ongoing effort to develop software to automate NMR assignments not “100%” efficient but significantly aids in the manual assignment ☺ 1D NMR ~few mins. 2D ~few hours 3D ~ few days Kurt Wüthrich Jang sun bok NMR Assignment Protocol (peptide) ☺ 2D NMR Experiments Kurt Wüthrich Nobel prize in 2002 for developing NMR to determine 3D structures of proteins. Wüthrich “NMR of Proteins and Nucleic Acids” 1986, John Wiley & Sons 1. Applicable for proteins of <100 amino acids 2. Primarily dependent on three 2D experiments: NOESY, COSY, TOCSY 3. Sequence-Specific Resonance Assignments in Proteins (Backbone Assignemnts) H3C CiH O Takes advantage of short sequential distances between CaiH, CbiH and NHi+1 CH3 Ni Ci H H Ci Ni+1 H 3D NMR Experiments Jang sun bok Takes advantage of 13C and 15N labeling • Extends assignments to proteins in the 20-25 kDa range • Extends Connectivity by Scalar Coupling (J) into 3D dimensions 1 13 1 15 Primarily uses one-bond heteronuclear coupling ( H- C, H- N) 1 3 J generally stronger than J 2D 1H-15N HSQC is the root experiment of most of the standard tripleresonance (1H, 13C, 15N) NMR experiments • 3D NMR simplifies data and removes overlap by spreading information into third dimension • Requires multiple experiments (≥ 6) to “walk through” the backbone assignments similar to the 2D COSY & NOESY experiments • Requires a similar number of additional experiments to obtain the side-chain assignments Frank Delaglio www.nmrscience.com/embo Jang sun bok nmrview NMRView Jang sun bok ☺ NMRView version 1 was written by Bruce A. Johnson and Richard A ☺ NMRViewJ, released in the first useful version at the time of the NMRView 5 release, is written in the Java programming language. ☺ NMRView is a computer program that is designed to be useful in visualizing and analyzing these data. NMRView works with various types of NMR datasets and can have multiple datasets and display windows opened simultaneously. Virtually all actions of the program can be controlled through the Tcl scripting language, and new graphical user interface components can be added with the Tk toolkit. NMR spectral peaks can be analyzed and assigned. A suite of tools exists within NMRView for assigning the data from triple-resonance experiments. http://www.onemoonscientific.com/index.html NMRView Jang sun bok NMRView is a program for the visualization and analysis of NMR datasets. Multiple views on one or more NMR spectra. Corresponding cursors in different windows track each other automatically. Spectral displays may be transferred from one window to another using a Copy/Paste protocol. Automatic peak picking. Peak searching. Facilitated peak analysis and interactive peak editing. Comprehensive NOE constraint generation and analysis. NMR Assignments Jang sun bok Correlates backbone amide 15N through one-bond coupling to amide In principal, each amino acid in the protein sequence will exhibit one peak in the 1H-15N 2D F2 (NH) ☺ side-chain NH2s (ASN,GLN) and NeH (Trp) ☺ position in HSQC depends on local structure and sequence ☺ no peaks for proline (no NH) 3D experiment as a collection of 2D experiments F1 (H) 2D-HSQC 3D The backbone assignments are then obtained by piecing together all the“jigsaw” puzzles pieces from the various NMR experiments to reassemble the backbone F2 (Ca) F1 (H) F3 (NH) 3D-HNCA HSQC (NMRView) Jang sun bok HSQC (NMRView) Jang sun bok HSQC (NMRView) Jang sun bok ① ③ 0827.Seq (file format) Met Arg Asn Ile Tyr Val ④ 1 2 3 4 5 6 ② Read Topology Sequence File HSQC (NMRView) ① ② ③ Add Ph.D Jang Sun Bok HSQC (NMRView) Ph.D Jang Sun Bok ① ② Open Datasets ③ HSQC (NMRView) Ph.D Jang Sun Bok File Misc Data Set Auto Lvl HSQC (NMRView) Ph.D Jang Sun Bok Level up Before After HSQC (NMRView) Jang sun bok ② ③ ① Before After HSQC (NMRView) Jang sun bok ① ② ⑥ Peaks ⑤ ③ hsqc ④ Write List ⑦ Navigator (nav.tcl) Jang sun bok Pulse sequence 90º Jang sun bok 180º Delay time t1 Delay time t2 A pulse sequence is a computer program, like a FPLC program, that runs the NMR spectrometer with pre-defined instructions to collect NMR data on a sample of interest It is essentially a serious of sequential and parallel pulses, separated by delays, which excite the specific nuclei and allow them to transfer their magnetization – a necessity for probing all the 3D information on the positioning of nuclei relative to each other Each pulse is denoted by a rectangular block, the width of the block corresponding to the size of the pulse – for example, a 180 pulse is twice the width of a 90 pulse The angle of the pulse dictates the tilt of the magnetization vector Why delays? The delays allow the evolution of resonances and allow spin-spin interactions before they can be further excited by a second or subsequent pulse Protein NMR lecture , Amjad Farooq, University of Miami 1H/15N-HSQC – the most popular NMR experiment Well-folded globular protein Jang sun bok Unfolded or unstructured protein NMR Titration 113 HA S154 S154 N CA C 115 HN R Q148 O Q148 T123 117 9.5 9.3 9.1 ☺The quality of HSQC spectrum provides a footprint for the state of protein: Well-folded globular protein Good chemical shift dispersion & sharp peaks Unfolded or unstructured protein Poor chemical shift dispersion & peak broadening ☺The quality of HSQC spectrum dictates whether structural studies would be feasible 3D HNCA Experiment Jang sun bok HNCA Pulse name derives from magnetization transfer…. Amide proton (H) → Amide Notrogen (N) → α carbon (Cα) both the starting residue(i) and the previous residue(i-1) in the protein's amino acid sequence 1. correlates NHi to Cαi-1 and Cαi 2. typically the intensity of NHi-Cai > NHi-Cai-1, 1JNCa > 2JNCa 3. Provides a means to sequential connect NH and Ca chemical shifts 4. No peaks for proline (no NH) breaks assignment chain HNCACB similar to HNCA : correlates NHi to Cβi-1 and Cβi Bruker AVANCE 3D / Triple resonance Manual 3D HNCA Experiment Jang sun bok HN(CO)CA Pulse name derives from magnetization transfer…. Amide proton (H) → Amide Notrogen (N) → α carbon (Cα) alpha carbon of the previous residue(i-1) in the protein's amino acid sequence 1. correlates NHi to Cai-1 2. Companion experiment to HNCA 3. No peaks for proline (no NH) breaks assignment chain HN(CO)CACB similar to HN(CO)CA : correlates NHi to Cβi-1 Bruker AVANCE 3D / Triple resonance Manual 3D HN(CA)CO Experiment Jang sun bok HN(CA)CO Amide proton (H) → Amide Notrogen (N) → Carbonyl carbon (CO) both the starting residue(i) and the previous residue(i-1) in the protein's amino acid sequence 1. correlates NHi to Coi 2. provides a means to sequential connect NH and CO chemical shift → match NHi-COi [(HN(CA)CO with NHi-COi-1 (HNCO)] 3. No peaks for proline (no NH) breaks assignment chain Bruker AVANCE 3D / Triple resonance Manual 3D HNCO Experiment Jang sun bok HNCO Amide proton (H) → Amide Notrogen (N) → Carbonyl carbon (CO) alpha carbon of the previous residue(i-1) in the protein's amino acid sequence 1. correlates NHi to Ci-1 (carbonyl carbon, CO or C’) HN(CA)CO 2. Most sensitive 3D triple resonsnce experiment 3. Identifies potential overlap in 2D 1H-15N HSQC spectra, especially for larger MW proteins HNCO Bruker AVANCE 3D / Triple resonance Manual Backbone Assignment — HNCA and HN(CO)CA experiments HA Jang sun bok HA N CA C N CA C HN R O HN R O HNCA CAi CAj CAi-1 i i-1 CAj-1 13C 15N i HNCA correlates HN and N of residue i to CA of residues i and i-1 HA j HA N CA C N CA C HN R O HN R O i-1 1HN HN(CO)CA CAj-1 13C CAi-1 i 15N i j 1HN HN(CO)CA correlates HN and N of residue i to CA of residue i-1 Protein NMR lecture , Amjad Farooq, University of Miami Backbone assignments Jang sun bok Backbone assignments i-1 Jang sun bok i-1 HN(CO)CA HNCA i HNCACB i-1 i i-1 HN(CO)CACB HNCA and HN(CO)CA exercise HNCA Jang sun bok HN(CO)CA 15N 15N i-1 i-1 15N i 15N i 15N 15N i+1 i+1 13CA i+1 13CA i 13CA i-1 13CA i-2 1HN 1 i-1 HNi-1 Scan through 15N 1HN i 1HN i 1HN 1 i+1 HNi+1 dimension of HNCA until a peak matching the resonance of CAi-1 is detected Strip plotting (HNCA) Jang sun bok Strip Plot Strip plot of HP0827 Jang sun bok HNCA HNCACB The top is 3D HNCA and bottom is 3D HNCACB using NMRView HP0827 Jang sun bok S.B Jang et al .J. Biochem 2009;146(5)667-674 15N-TOCSY experiment Jang sun bok CE HE1 15N-TOCSY CD HD1 CG HG1 CB HA CA R C O N HB1 CA HA HN C O i N HN HB1j HB1i 1H HA1i HA1j HNi HNj 15N j i 1HN i-1 15N-TOCSY correlates HN and N resonances to sidechain protons within the same residue Experiment is run on 15N-labeled protein in H2O In combination with HNCA/HN(CO)CA and HN(CA)CB/HN(CO)CACB, resonance assignments of backbone and sidechain H atoms can be made Assignment for sidechain H atoms for aromatic residues cannot be obtained from the above experiments but alternative experiments are available Protein NMR lecture , Amjad Farooq, University of Miami HBHA(CO)NH experiment Jang sun bok HBHA(CO)NH R HB1 CB HA CA C N N O HN i-1 CA C O i HB1j-1 HB1i-1 1H HA1i-1 HA1j-1 15N j i 1HN HBHA(CO)NH correlates HN and N resonances to sidechain protons at previous residue Protein NMR lecture , Amjad Farooq, University of Miami 15N-TOCSY, HBHA(CO)NH (HP0827) 15N-TOCSY (i) Jang sun bok HBHA(CO)NH (i-1) Sidechain Assignment (HP0827) Jang sun bok 7 Gly 7Gly-8Asn 8 Asn 15N-TOCSY HBHA(CO)NH 15N-TOCSY HBHA(CO)NH 15N-TOCSY HBHA(CO)NH N:113.062 HN:9.20 N:116.453 HN:8.24 Ha: 4.75 Ha: 3.65 N:116.453 HN:8.21 N:116.234 HN:7.90 Hα: 4.50 Hα: 3.83 N:116.234 HN:7.92 N:113.062 HN:9.20 Hα: 4.31 Hα: 1.24 Hα: 4.77 Hα: 3.66 Hα: 4.50 Hα: 3.80 8Asn-9Leu 9 Leu Hα: 4.32 Hα: 1.25 9Leu-10Val CCCONH Jang sun bok ☺ confirm the previous sequential assignment specifically designed to correlate the 1H and 15N amide resonances of one residue with and all other 13C side-chain resonances of its preceding residue via the intervening 13CO spin (i-1) (i) 13CA CCCONH Jang sun bok 6Cγ2 6Cγ1 19Cγ 19Cδ 19Cβ 6Cβ (weak) C C 7Cα C 19Cε 6Cα 6Val 19Cα (weak) 19Lys ←20Glu ←7Gly N:112.753 HN:9.20 HN N:120.750 HN:8.26 HN HN 7Gly ←8Asn N:116.463 HN:8.28 Sidechain Assignment — HCCH-TOCSY experiment CE CD HA CA R C O N HE1 Experimen Acceptor t Donor HD1 3D H(C)CH C-H -TOCSY H 3D (H)CCH C-H -TOCSY C CG HG1 CB HB1 CA HA HN C i 1H j Jang sun bok HCCH-TOCSY HAi HB1i HAj HB1j HG1j HG1i HD1j 13C N 1H O HN i i-1 HCCH-TOCSY correlates H and C resonances within the same residue Experiment is run on 15N/13C-labeled protein in D2O In combination with HNCA/HN(CO)CA & HN(CA)CB/HN(CO)CACB and C(CO)NH & resonance assignments of backbone and sidechain H atoms can be made 15N-TCOSY, Assignment for sidechain H and C atoms for aromatic residues can also be obtained from the above experiment run in the aromatic region Protein NMR lecture , Amjad Farooq, University of Miami Sidechain Assignment — HCCH-TOCSY exercise Jang sun bok Diagonal Peak Cross Peak Open up 3-5 windows aligned up vertically above each other in NMRView Scan through 13C dimension of HCCH-TOCSY to display the CA-plane of a spin system Repeat the above step for other C atoms, such as CB and CG, in other planes Match up all the spin systems across all C planes Protein NMR lecture , Amjad Farooq, University of Miami HCCH-TOCSY exercise 1(HP0827) Hβ1 Hβ2 2.12 2.01 Jang sun bok Cβ 30.06 Cγ 34.75 Cx Cx Cx Ca 52.91 Hγ1 Hγ2 2.13 2.02 Ha 5.24 1H 49Glu (Ca:52.91) 1H 49Glu (Cβ: 30.06) 1H 49Glu (Cγ:34.75) HCCH-TOCSY exercise 2(HP0827) Jang sun bok Cγ2 20.23 Cγ1 21.07 Cβ 29.31 Hγ1 Hβ1 Cx Cx Cx Cx Hγ21 Hγ22 Ca 64.47 Ha 1H 55Val (Ca:64.47) 1H 55Val (Cβ:29.31) 1H 55Val (Cγ1:21.07) 1H 55Val (Cγ2:20.23) NOE Assignment — 15N-NOESY experiment CE HE1 Jang sun bok 15N-NOESY CD HD1 CG HG1 CB HA CA HA N CA C N HN R O HN C i-1 HB1 i N 1H HB1i HB1i-1 HA1i-1 HA1i-1 HNi-1 HNi HNi-1 HNi HA1i i-1 i 15N 1HN HN Protein NMR lecture , Amjad Farooq, University of Miami What is NOE?~~~ Jang sun bok Frank Delaglio www.nmrscience.com/embo NOE Assignment — 15N-NOESY experiment Jang sun bok 15N-NOESY correlates through-space HN and N resonances of residue i to any protons < 5Å of backbone HN of residue i Experiment is run on 15N-labeled protein in H2O 15N-NOESY provides information on NOEs between HN and all other protons in the protein but, in practice, only local short range NOEs can be assigned with certainty (due to lack of asymmetry) 15N-NOESY is particularly useful for identification of local secondary structure elements: -helices strong dHN,HN(i, i+1) and dHA,HN(i, i+3) -strands strong dHA,HN(i, i+1) NOE Assignment — 13C-NOESY experiment CE HE1 Jang sun bok 13C-NOESY CD HD1 CG HG1 CB HA HB1i HB1 HA CA HA CA C N R O HN C i-1 1H O i N N CA HN R j HAj C HAi HB1i HAj HB1j HG1i HG1j HD1j 13C 1H O Protein NMR lecture , Amjad Farooq, University of Miami NOE Assignment — 13C-NOESY experiment Jang sun bok 13C-NOESY correlates through-space C and H resonances of residue i to any protons < 5Å of HC, not HN, of residue i Experiment is run on 13C-labeled protein in D2O 13C-NOESY provides information on NOEs between i and j pairs of protons in the protein and, because of its symmetrical nature, it is the only means with which long range NOEs can be assigned with certainty 13C-NOESY is also useful for identification of local secondary structure elements: -helices strong dHA,HB(i, i+3) NOE Assignment — 13C-NOESY exercise Jang sun bok In 13C-NOESY, NOEs appear as cross-peaks with a symmetrical relationship The symmetry of NOE cross-peaks avoids ambiguity in assignment and thus plays a crucial role in the assignment of long-range NOEs Protein NMR lecture , Amjad Farooq, University of Miami characteristic chemical shifts Jang sun bok Knowledge of protein sequence coupled with characteristic chemical shifts of specific spin systems (specific atoms within amino acids) is sufficient to provide near-complete backbone connectivities for small to medium-sized proteins (< 300 residues) Chemical shift table Jang sun bok Random coil 1H and 13C chemical shifts in the natural amino acids Ph.D Jang Sun Bok 10 Aβ Carbon-13 Chemical Shift 20 Hβ Q,Eβ Cβ Rβ Wβ 30 Kβ F,Yβ 40 Gα Nβ Dβ Iβ N,D,Hα Lβ Aα 50 M,R,Q,E,K,Lα 60 C,F,W,Yα 70 P,M,Vβ 5 T,Iα Sα Pα Vα Tβ 4 Sβ 3 2 1 0 Proton Chemical Shift Bruker AVANCE 3D / Triple resonance Manual Random coil 1H and 13C chemical shifts in the natural amino acids 10 Mε Carbon-13 Chemical Shift 20 Pγ Mγ 30 Qγ Eγ 40 Rδ Lγ Rγ Kδ Ph.D Jang Sun Bok Iδ IγCH3 Tγ Vγ Kγ Lδ IγCH2 Kε Pδ 50 60 70 5 4 3 2 1 0 Proton Chemical Shift Bruker AVANCE 3D / Triple resonance Manual NOE Jang sun bok 1H-1H Distances From NOEs Long-range (tertiary structure) Sequential Intraresidue A B C D •••• Z Medium-range (helices) Challenge is to assign all peaks in NOESY spectra Good luck to you~~^^*