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PROTEIN NMR
Much space and discussion is devoted to practical aspects. The implementation of protein NMR assignment is described using the program CCPNmr Analysis. This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has theadvantage (a
HNCA | PROTEIN NMR
Dimensions: 3. Here the magnetisation is passed from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα and then back again to 15 N and 1 H hydrogen for detection. The chemical shift is evolved for 1 H N as well as the 15 N H and 13 Cα, resulting in a 3-dimensional spectrum. Since the amide nitrogen is coupled both to the Cα of its HN(CA)CO | PROTEIN NMR HN (CA)CO. R.T. Clubb, V. Thanabal and G. Wagner (1992) J. Magn. Reson. 97 213-217. ( Link to Article) The Magnetisation is transferred from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα. From there it is transferred to the 13 CO via the 13 Cα- 13 CO J-coupling. For detection the magnetisation is transferred back the same way TRIPLE RESONANCE BACKBONE ASSIGNMENT Triple Resonance Backbone Assignment. Standard triple resonance backbone assignment of proteins is based on the CBCANNH and CBCA (CO)NNH spectra. The idea is that the CBCANNH correlates each NH group with the Cα and Cβ chemical shifts of its own residue (strongly) and of the residue preceding (weakly). The CBCA (CO)NNH only correlatesthe NH
NCACX | PROTEIN NMR
Reference: J. Pauli, M. Baldus, B.-J. van Rossum, H. de Groot and H. Oschkinat (2001) Chem. Biochem. 2 272-281. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 (but often also recorded as an NcaCX 2D) Magnetisation is transferred from 1 H to 15 N via cross polarisation and then selectively to the 13 Cα using specific cross polarisation. A PDSD or DARR step is then used to CHEMICAL SHIFT MAPPING Chemical shift mapping is best suited to weak interactions in the mM range (giving rise to fast exchange ). In this situation the chemical shifts change continuously as the binding partner is added. Essentially, the interaction is so weak, that the complex only exists for part of the time it takes to record the NMR experiment. CC(CO)NH | PROTEIN NMR Reference: S. Grzesiek, J. Anglister and A. Bax (1993) J. Magn. Reson., Ser. B 101 114-119. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Then isotropic 13 C mixing is used to transfer magnetisation between the carbon nuclei. From here, magnetisation is transferred to the carbonyl CBCA(CO)NH / HN(CO)CACB CBCA (CO)NH / HN (CO)CACB. Reference: S. Grzesiek and A. Bax (1992) J. Am. Chem. Soc. 114 6291-6293. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from 1 Hα and 1 Hβ to 13 Cα and 13 Cβ, respectively, and then from 13 Cβ to 13 Cα. From here it is transferred first to 13 CO, then to 15 N H and HCCH-COSY | PROTEIN NMR NMR 1 299-304. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Magnetisation is then exchanged between neighbouring 13 C nuclei via the J-coupling and finally transferred back to the side-chain hydrogen atoms fordetection.
SEQUENCE-SPECIFIC ASSIGNMENT Sequence-Specific Assignment. By linking sequential spin systems you will have ended up with a number of long strings of spin systems in their correct sequential order. Now you need to work out which part of the sequence they match up to. In order to do this you need to identify the amino acid type of some of your spin systems.PROTEIN NMR
Much space and discussion is devoted to practical aspects. The implementation of protein NMR assignment is described using the program CCPNmr Analysis. This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has theadvantage (a
HNCA | PROTEIN NMR
Dimensions: 3. Here the magnetisation is passed from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα and then back again to 15 N and 1 H hydrogen for detection. The chemical shift is evolved for 1 H N as well as the 15 N H and 13 Cα, resulting in a 3-dimensional spectrum. Since the amide nitrogen is coupled both to the Cα of its HN(CA)CO | PROTEIN NMR HN (CA)CO. R.T. Clubb, V. Thanabal and G. Wagner (1992) J. Magn. Reson. 97 213-217. ( Link to Article) The Magnetisation is transferred from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα. From there it is transferred to the 13 CO via the 13 Cα- 13 CO J-coupling. For detection the magnetisation is transferred back the same way TRIPLE RESONANCE BACKBONE ASSIGNMENT Triple Resonance Backbone Assignment. Standard triple resonance backbone assignment of proteins is based on the CBCANNH and CBCA (CO)NNH spectra. The idea is that the CBCANNH correlates each NH group with the Cα and Cβ chemical shifts of its own residue (strongly) and of the residue preceding (weakly). The CBCA (CO)NNH only correlatesthe NH
NCACX | PROTEIN NMR
Reference: J. Pauli, M. Baldus, B.-J. van Rossum, H. de Groot and H. Oschkinat (2001) Chem. Biochem. 2 272-281. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 (but often also recorded as an NcaCX 2D) Magnetisation is transferred from 1 H to 15 N via cross polarisation and then selectively to the 13 Cα using specific cross polarisation. A PDSD or DARR step is then used to CHEMICAL SHIFT MAPPING Chemical shift mapping is best suited to weak interactions in the mM range (giving rise to fast exchange ). In this situation the chemical shifts change continuously as the binding partner is added. Essentially, the interaction is so weak, that the complex only exists for part of the time it takes to record the NMR experiment. CC(CO)NH | PROTEIN NMR Reference: S. Grzesiek, J. Anglister and A. Bax (1993) J. Magn. Reson., Ser. B 101 114-119. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Then isotropic 13 C mixing is used to transfer magnetisation between the carbon nuclei. From here, magnetisation is transferred to the carbonyl CBCA(CO)NH / HN(CO)CACB CBCA (CO)NH / HN (CO)CACB. Reference: S. Grzesiek and A. Bax (1992) J. Am. Chem. Soc. 114 6291-6293. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from 1 Hα and 1 Hβ to 13 Cα and 13 Cβ, respectively, and then from 13 Cβ to 13 Cα. From here it is transferred first to 13 CO, then to 15 N H and HCCH-COSY | PROTEIN NMR NMR 1 299-304. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Magnetisation is then exchanged between neighbouring 13 C nuclei via the J-coupling and finally transferred back to the side-chain hydrogen atoms fordetection.
SEQUENCE-SPECIFIC ASSIGNMENT Sequence-Specific Assignment. By linking sequential spin systems you will have ended up with a number of long strings of spin systems in their correct sequential order. Now you need to work out which part of the sequence they match up to. In order to do this you need to identify the amino acid type of some of your spin systems. BASICS | PROTEIN NMR The nuclei most commonly used in protein NMR ( 1 H, 15 N and 13 C) all have spin quantum number ½. The spin angular momentum is a vector quantity (i.e. it has a particular direction as well as a certain magnitude) and in spin-½ nuclei it is quantised into two states. Normally, these two states are of equal energy and are thus alsoequally
SOLUTION NMR
Solution NMR. This section provides information about the assignment process using solution NMR data as well as a list of commonly used solution NMR experiments.CHEMICAL EXCHANGE
Chemical Exchange. So-called chemical exchange occurs when microsecond to millisecond motions cause a modulation in the isotropic chemical shift. Chemical exchange is relevant both in the situation where a protein undergoes internal motions (e.g. a conformational change) or where it interacts with another molecule (e.g. complex formation). HCCH-COSY | PROTEIN NMR NMR 1 299-304. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Magnetisation is then exchanged between neighbouring 13 C nuclei via the J-coupling and finally transferred back to the side-chain hydrogen atoms fordetection.
CBCANH / HNCACB
CBCANH / HNCACB. S. Grzesiek and A. Bax (1992) J. Magn. Reson. 99 201-207. ( Link to Article) Magnetisation is transferred from 1 Hα and 1 Hβ to 13 Cα and 13 Cβ, respectively, and then from 13 Cβ to 13 Cα. From here it is transferred first to 15 N H and then to 1 H N for detection. Transfer form Cα i-1 can occur both to 15 N i-1 and 15N
1H-15N HSQC
Dimensions: 2. Magnetization is transferred from hydrogen to attached 15 N nuclei via the J-coupling. The chemical shift is evolved on the nitrogen and the magnetisation is then transferred back to the hydrogen for detection. This is the most standard experiment and shows all H-N correlations. Mainly these are the backbone amide groups, butTrp
HCCH-TOCSY | PROTEIN NMR References: A. Bax, G.M. Clore and A.M. Gronenborn (1990) J. Magn. Reson. 88 425-431. (Link to Article)E.T. Olejniczak, R.X. Xu and S.W. Fesik (1992) J. Biomol.NMR 2 655-659. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. This is followed by isotropic 13 C mixing and finally VISUALISING 3D SPECTRA Visualising 3D Spectra. 3D experiments are generally based upon 2D experiments and so the easiest way to think of a 3D is of a 2D which is then extended into a third dimension. Take, for instance, an HNCO. It is based upon a 2D HSQC (a), so the x and y axes are 1 H and 15 N, respectively. This is now extended into a third dimension which is aMANUAL ASSIGNMENT
Manual Assignment. The following flow diagram shows the different steps that need to be taken during the assignment process. 1. Find a peak in the HSQC to be used as a starting point. Begin by selecting a peak in the HSQC which looks nice and is not overlapped. 2.READING IN SPECTRA
Reading in Spectra. Go to the Experiment pull-down menu and choose Open Spectra. Make sure you select the correct data format at the top of the box – a large number are possible (Azara, Bruker, Felix, NMRPipe, NMRView, ucsf). Change the Experiment Name if you wish (you can always change it again at a later stage, if you want).PROTEIN NMR
Much space and discussion is devoted to practical aspects. The implementation of protein NMR assignment is described using the program CCPNmr Analysis. This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has theadvantage (a
HNCA | PROTEIN NMR
Dimensions: 3. Here the magnetisation is passed from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα and then back again to 15 N and 1 H hydrogen for detection. The chemical shift is evolved for 1 H N as well as the 15 N H and 13 Cα, resulting in a 3-dimensional spectrum. Since the amide nitrogen is coupled both to the Cα of its TRIPLE RESONANCE BACKBONE ASSIGNMENT Triple Resonance Backbone Assignment. Standard triple resonance backbone assignment of proteins is based on the CBCANNH and CBCA (CO)NNH spectra. The idea is that the CBCANNH correlates each NH group with the Cα and Cβ chemical shifts of its own residue (strongly) and of the residue preceding (weakly). The CBCA (CO)NNH only correlatesthe NH
NCACX | PROTEIN NMR
Reference: J. Pauli, M. Baldus, B.-J. van Rossum, H. de Groot and H. Oschkinat (2001) Chem. Biochem. 2 272-281. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 (but often also recorded as an NcaCX 2D) Magnetisation is transferred from 1 H to 15 N via cross polarisation and then selectively to the 13 Cα using specific cross polarisation. A PDSD or DARR step is then used to CHEMICAL SHIFT MAPPING Chemical shift mapping is best suited to weak interactions in the mM range (giving rise to fast exchange ). In this situation the chemical shifts change continuously as the binding partner is added. Essentially, the interaction is so weak, that the complex only exists for part of the time it takes to record the NMR experiment. VISUALISING 3D SPECTRA Visualising 3D Spectra. 3D experiments are generally based upon 2D experiments and so the easiest way to think of a 3D is of a 2D which is then extended into a third dimension. Take, for instance, an HNCO. It is based upon a 2D HSQC (a), so the x and y axes are 1 H and 15 N, respectively. This is now extended into a third dimension which is a1H-15N HSQC
Dimensions: 2. Magnetization is transferred from hydrogen to attached 15 N nuclei via the J-coupling. The chemical shift is evolved on the nitrogen and the magnetisation is then transferred back to the hydrogen for detection. This is the most standard experiment and shows all H-N correlations. Mainly these are the backbone amide groups, butTrp
HCCH-COSY | PROTEIN NMR NMR 1 299-304. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Magnetisation is then exchanged between neighbouring 13 C nuclei via the J-coupling and finally transferred back to the side-chain hydrogen atoms fordetection.
CHEMICAL SHIFT ANISOTROPY For this reason, the chemical shift is also anisotropic and changes as the orientation of a molecule with respect to the magnetic field changes. In solution NMR, the anisotropy of the chemical shift is averaged out by fast molecular tumbling and only a single isotropic chemical shift value is observed. In solids, however, molecules will CBCA(CO)NH / HN(CO)CACB CBCA (CO)NH / HN (CO)CACB. Reference: S. Grzesiek and A. Bax (1992) J. Am. Chem. Soc. 114 6291-6293. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from 1 Hα and 1 Hβ to 13 Cα and 13 Cβ, respectively, and then from 13 Cβ to 13 Cα. From here it is transferred first to 13 CO, then to 15 N H andPROTEIN NMR
Much space and discussion is devoted to practical aspects. The implementation of protein NMR assignment is described using the program CCPNmr Analysis. This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has theadvantage (a
HNCA | PROTEIN NMR
Dimensions: 3. Here the magnetisation is passed from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα and then back again to 15 N and 1 H hydrogen for detection. The chemical shift is evolved for 1 H N as well as the 15 N H and 13 Cα, resulting in a 3-dimensional spectrum. Since the amide nitrogen is coupled both to the Cα of its TRIPLE RESONANCE BACKBONE ASSIGNMENT Triple Resonance Backbone Assignment. Standard triple resonance backbone assignment of proteins is based on the CBCANNH and CBCA (CO)NNH spectra. The idea is that the CBCANNH correlates each NH group with the Cα and Cβ chemical shifts of its own residue (strongly) and of the residue preceding (weakly). The CBCA (CO)NNH only correlatesthe NH
NCACX | PROTEIN NMR
Reference: J. Pauli, M. Baldus, B.-J. van Rossum, H. de Groot and H. Oschkinat (2001) Chem. Biochem. 2 272-281. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 (but often also recorded as an NcaCX 2D) Magnetisation is transferred from 1 H to 15 N via cross polarisation and then selectively to the 13 Cα using specific cross polarisation. A PDSD or DARR step is then used to CHEMICAL SHIFT MAPPING Chemical shift mapping is best suited to weak interactions in the mM range (giving rise to fast exchange ). In this situation the chemical shifts change continuously as the binding partner is added. Essentially, the interaction is so weak, that the complex only exists for part of the time it takes to record the NMR experiment. VISUALISING 3D SPECTRA Visualising 3D Spectra. 3D experiments are generally based upon 2D experiments and so the easiest way to think of a 3D is of a 2D which is then extended into a third dimension. Take, for instance, an HNCO. It is based upon a 2D HSQC (a), so the x and y axes are 1 H and 15 N, respectively. This is now extended into a third dimension which is a1H-15N HSQC
Dimensions: 2. Magnetization is transferred from hydrogen to attached 15 N nuclei via the J-coupling. The chemical shift is evolved on the nitrogen and the magnetisation is then transferred back to the hydrogen for detection. This is the most standard experiment and shows all H-N correlations. Mainly these are the backbone amide groups, butTrp
HCCH-COSY | PROTEIN NMR NMR 1 299-304. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Magnetisation is then exchanged between neighbouring 13 C nuclei via the J-coupling and finally transferred back to the side-chain hydrogen atoms fordetection.
CHEMICAL SHIFT ANISOTROPY For this reason, the chemical shift is also anisotropic and changes as the orientation of a molecule with respect to the magnetic field changes. In solution NMR, the anisotropy of the chemical shift is averaged out by fast molecular tumbling and only a single isotropic chemical shift value is observed. In solids, however, molecules will CBCA(CO)NH / HN(CO)CACB CBCA (CO)NH / HN (CO)CACB. Reference: S. Grzesiek and A. Bax (1992) J. Am. Chem. Soc. 114 6291-6293. ( Link to Article) Minimum labelling: 15 N, 13 C. Dimensions: 3. Magnetisation is transferred from 1 Hα and 1 Hβ to 13 Cα and 13 Cβ, respectively, and then from 13 Cβ to 13 Cα. From here it is transferred first to 13 CO, then to 15 N H and BASICS | PROTEIN NMR The nuclei most commonly used in protein NMR ( 1 H, 15 N and 13 C) all have spin quantum number ½. The spin angular momentum is a vector quantity (i.e. it has a particular direction as well as a certain magnitude) and in spin-½ nuclei it is quantised into two states. Normally, these two states are of equal energy and are thus alsoequally
SOLUTION NMR
Solution NMR. This section provides information about the assignment process using solution NMR data as well as a list of commonly used solution NMR experiments.HNCA | PROTEIN NMR
Dimensions: 3. Here the magnetisation is passed from 1 H to 15 N and then via the N-Cα J-coupling to the 13 Cα and then back again to 15 N and 1 H hydrogen for detection. The chemical shift is evolved for 1 H N as well as the 15 N H and 13 Cα, resulting in a 3-dimensional spectrum. Since the amide nitrogen is coupled both to the Cα of itsCHEMICAL EXCHANGE
Chemical Exchange. So-called chemical exchange occurs when microsecond to millisecond motions cause a modulation in the isotropic chemical shift. Chemical exchange is relevant both in the situation where a protein undergoes internal motions (e.g. a conformational change) or where it interacts with another molecule (e.g. complex formation).ASSIGNMENT PRACTICE
Assignment Practice. This section describes how the assignment principles described under Assignment Theory can be but put into practice using the CCCPNmr Analysis software. There are several ways in which triple resonance backbone assignment, in particular, can be approached in CCPNmr Analysis using more or less automated methods. VISUALISING 3D SPECTRA Visualising 3D Spectra. 3D experiments are generally based upon 2D experiments and so the easiest way to think of a 3D is of a 2D which is then extended into a third dimension. Take, for instance, an HNCO. It is based upon a 2D HSQC (a), so the x and y axes are 1 H and 15 N, respectively. This is now extended into a third dimension which is a CHEMICAL SHIFT ANALYSIS Chemical Shift Analysis. Talos+ uses a database of chemical shifts of proteins for which high resolution crystal structures are available. By matching amino acid type and chemical shifts (N, HN, Cα, Cβ, CO) to triplets of amino acids from the database, it predicts the average φ and ψ angles for your protein. Also available via the WeNMRCBCANH / HNCACB
CBCANH / HNCACB. S. Grzesiek and A. Bax (1992) J. Magn. Reson. 99 201-207. ( Link to Article) Magnetisation is transferred from 1 Hα and 1 Hβ to 13 Cα and 13 Cβ, respectively, and then from 13 Cβ to 13 Cα. From here it is transferred first to 15 N H and then to 1 H N for detection. Transfer form Cα i-1 can occur both to 15 N i-1 and 15N
CC(CO)NH | PROTEIN NMR Reference: S. Grzesiek, J. Anglister and A. Bax (1993) J. Magn. Reson., Ser. B 101 114-119. (Link to Article)Minimum labelling: 15 N, 13 C Dimensions: 3 Magnetisation is transferred from the side-chain hydrogen nuclei to their attached 13 C nuclei. Then isotropic 13 C mixing is used to transfer magnetisation between the carbon nuclei. From here, magnetisation is transferred to the carbonyl SEQUENCE-SPECIFIC ASSIGNMENT Sequence-Specific Assignment. By linking sequential spin systems you will have ended up with a number of long strings of spin systems in their correct sequential order. Now you need to work out which part of the sequence they match up to. In order to do this you need to identify the amino acid type of some of your spin systems.PROTEIN NMR
A PRACTICAL GUIDE
Menu Skip to content* Introduction
* Solution NMR
* Assignment Theory
* Visualising 3D Spectra * Triple Resonance Backbone Assignment * Triple Resonance Side-chain Assignment * Double Resonance Backbone Assignment * Double Resonance Side-chain Assignment * Assignment Practice * Initialising the HSQC * Peakpicking the 3D Spectra * Triple Resonance Backbone Assignment* Manual Assignment
* Semi-automated Assignment * Sequence-Specific Assignment * Using HNCA/HNCO Spectra * Double Resonance Backbone Assignment * Neighbouring Residues* Directionality
* Matching Peaks
* Lining Up Strips
* Sequence-Specific Assignment* Hints and Tips
* Spectrum Descriptions* 1H-15N HSQC
* HNCO
* HN(CA)CO
* HNCA
* HN(CO)CA
* CBCA(CO)NH / HN(CO)CACB* CBCANH / HNCACB
* CC(CO)NH
* H(CCO)NH
* HBHA(CO)NH
* HCCH-TOCSY
* HCCH-COSY
* 15N-TOCSY-HSQC
* 13C-HMQC
* H-H NOESY
* 15N-NOESY-HSQC
* 13C-NOESY-HSQC
* 13C-HMQC-NOESY
* Solid-State MAS NMR * Solid-state Assignment Tutorial * CCPNmr Analysis Solid-state Tips * Spectrum Descriptions* PDSD
* DARR
* NCA
* NCO
* NCACX
* NCOCX
* NCACB
* CANCO
* CANCOCX
* CHHC
* NHHC
* General NMR
* Chemical Shifts
* Basics
* Chemical Shift Anisotropy* Chemical Exchange
* Chemical Shift Mapping * Random Coil Chemical Shifts * Secondary Structure * Structure Calculation * Chemical Shift Prediction * Isotopic Labelling* 15N
* 15N,13C
* 15N,13C,2H
* IVL side-chain methyl groups * SAIL (Stereo-Array Isotope Labelling) * 1,3-13C- and 2-13C-Glycerol * Amino Acid Specific* Cell-free
* Segmental
* Other Labelling Schemes* Literature
* Software
* Processing
* Assignment
* Automatic Assignment * Structure Calculation* Molecular Viewers
* Validation
* Chemical Shift Analysis* RDC Analysis
* Analysis of Dynamics Data * Pulse Sequence Simulation * Lab Software Pages* NMR Links
* Glossary / Abbreviations* CCPNmr Analysis
* Version 1.0 Basics* New Project
* Molecules
* Reading in Spectra* Windows and Axes
* Spectrum Attributes* Navigation
* Mouse Usage
* Marks and Rulers
* Peakpicking
* Resonances and Spin Systems * Assignment of Peaks* Peak Lists
* Strips
* Tables
* Keyboard Shortcuts * Version 2.x Basics* New Project
* Molecules
* Reading in Spectra* Windows and Axes
* Spectrum Attributes* Navigation
* Mouse Usage
* Marks and Rulers
* Peakpicking
* Resonances and Spin Systems * Assignment of Peaks* Peak Lists
* Strips
* Tables
* Keyboard Shortcuts * CCPNmr Analysis Solid-state Tips* Experiment Types
* Overlaying Spectra * Double Cross-hair Mouse * Organising Windows and Spectra * Strips and Separators * Making Strip Plots* Tolerances
* 1D Spectra
* Assignments
* Tentative Assignments * Identifying Side-band Peaks * Marking Side-band Peaks * Double-Quantum Axes* Labelling Schemes
* Editing Labelling Schemes * Distance Restraints * Figures with CCPNmr Analysis* Contact
Search for:
INTRODUCTION
Most books on Protein NMR focus on theoretical aspects and pulse sequences with only little space devoted to resonance assignment and structure calculations. At the same time many software manuals provide detailed information on how to use the software, but assume prior knowledge of the concepts of assignment and structure calculation. This has produced a gap in this area which these webpages aim to bridge by describing the concepts of assignment in detail with the help of many illustrations. Much space and discussion is devoted topractical aspects.
The implementation of protein NMR assignment is described using the program CCPNmr Analysis . This program has been developed by CCPN and actively seeks input from the NMR community. CCPNmr Analysis is based on the detailed and well thought-out CCPN Data Model which has the advantage (a) that it feeds directly into the CCPN Format Converter thus simplifying the import from and export to other programs, and (b) that as more and more NMR-related programs adopt the CCPN Data Model it is likely to take on a key role in NMR data management – in a similar way to CCP4 for protein X-ray crystallography. CCPNmr Analysis is already one of the best assignment programs available while still being developed and provides excellent support via the CCPN Mailing List(a manual
is also available). (Although I now work for the CCPN group, these webpages and my recommendation to use this program far predate this!)Webpages include:
* description of several resonance assignment strategies * simple descriptions and discussions of many multidimensional NMRexperiments
commonly used in protein NMR * basic usage of CCPNmr Analysis (versions 1and 2
)
* how to make publication quality figures using CCPNmr Analysis * advice for using CCPNmr Analysis with solid-state MAS NMRdata
* tutorial
on protein assignment using solid-state MAS NMR data * description of isotopic labelling strategiescommonly
used in protein NMR
* links to a large number of protein NMR software packages * suggested literaturefor further
reading
* links to other
useful NMR webpages
* Glossary
CONTENT
* Introduction
* Solution NMR
* Solid-State MAS NMR* General NMR
* CCPNmr Analysis
* Contact
by Victoria A. Higman, last modified on 10 April 2019Details
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