Wiki Tree Layout

This outline of the NESG NMR Wiki is designed to expand on the existing "Master Recipe" and should serve as an experience harvesting tool.

• It has a rather broad coverage to facilitate long-tewrm growth and development. Aditional compact aggregator pages may be needed to pesent specific information concisely.
• There would be separate webs within the wiki: Public(or Main), NESG, and member lab webs. Most common knowlege topics should be public, unless they are specific to NESG
• We assume that the target audience has some knowledge about NMR and protein structure determination, but make the content useful for training
• "Resonance Assignment" and "Structure Determination" chaptes would focus on individual software packages. The XEASY resonance assignment tree, as the most complete, would serve as a template for other software.
• Most chapters should include a "general principles" section.

Please leave your comments/suggestion at the bottom of this page

HTP NMR structure determination

Protein Target Selection, Sample Preparation, and Initial Screening

1. NESG target selection - overview of target selection in PSI III
2. Bioinformatics - protein sequence
3. DNA cloning protocols - standard protocols from Rutgers and Toronto
4. Protein expression and purification protocols - standard protocols from Rutgers and Toronto
5. Specialized protein production protocols
   1. SPP
   2. Wheat germ
   3. Mammalian cell culture - Macrcotrigiano vinette?
6. Sample Optimization
   1. construct optimization
   2. buffer optimization
   3. cofactor optimization
7. Initial protein analysis
   1. SDS page gel
   2. Protein concentration measurement
   3. Assessment of Oligomerization Status
      1. gel-filtration and light scattering
      2. Rotational correlation time
         1. Bruker Protocol
   4. Mass spectrum
   5. Initial 15N,1H HSQC - expected peaks, peak picking

NMR Data Collection

1. Routine operation
   1. NMR sample tubes
   2. NMR Sample Preparation
   3. Inserting NMR Sample
   4. Tuning and matching
   5. Deuterium Lock
   6. Shimming
   7. Pulse width calibration
   8. Temperature calibration
   9. Chemical shift referencing
2. Advanced operation
   1. Deuterium pulse width calibration and decoupling
3. NMR data acquisition for protein structure determination
   1. Common NMR experiment sets
   2. Custom NMR experiment setup scripts for VNMRJ
   3. 1D 1H NMR spectra and 2D [15N, 1H]-HSQC
   4. Estimation of rotational correlation time
   5. Estimation of measurement time
   6. NMR experiments for spin system identification
   7. 2D and 3D NOESY
   8. Double and triple NMR experiments
      1. 3D CBCA(CO)NH and HNCACB
      2. 3D HNCA and HN(CO)CA
      3. 3D HAHB(CO)NH
      4. (4,3)D CABCA(CO)NH and HNCACB
      5. (4,3)D HABCAB(CO)NH
      6. (H)CCH
      7. (H)CCH-TOCSY
      8. H(C)CH
      9. H(C)CH-TOCSY
      10. (4,3)D HCCH
   9. Other NMR experiments
      1. 2D [13C, 1H]-HSQC for 5% 13C-labeled samples
      2. 2D [15N, 1H]-long-range-HSQC for determination of histidine protomer state
      3. MEXICO
      4. CLEANEX
      5. H-D exchange experiment
      6. 15N spin relaxation parameters
4. Advanced problems for data collection
   1. Setting up non-uniformly sampled spectra
      1. Guide for Varian/BioPack
      2. Guide for Bruker according to Arrowsmith group
5. Maintenance
   1. VARIAN
      1. Installing and updating BioPack
      2. Full Probefile calibration
      3. Rebooting the console
      4. Cryoprobe conditioning
   2. BRUKER

NMR Data Processing

1. General Priciples and Concepts
   1. Fourier transformation
      1. Zero-filling
      2. Apodization
      3. Phasing
      4. Linear prediction
      5. G-matrix Fourier transformation (GFT)
   2. Alternatives to Fourier transformation
      1. Maximum entropy reconstruction
      2. MDD reconstruction
      3. ...
2. Practical Aspects
   1. NMRPIPE
      1. General information
      2. Buffalo's Processing Protocol using NMRpipe
   2. PROSA
   3. TOPSPIN
   4. AGNUS/AUTOPROC
   5. UBNMR
   6. Spectral format conversion

Resonance Assignment

This chapter would focus on individual data analysis and resonance assignment packages, as most people stick to a particular software for entire structure determination projects.

1. Principles and concepts
   1. Stable isotope labeling schemes
   2. NMR experiments
      1. Through-bond
      2. Through space
   3. Spin systems
      1. Definitions
      2. Identification
      3. Linking spin systems
      4. Matching onto covalent structure
2. Practical aspects
   1. Semi-automated protocols
      1. CARA
         1. Spin System Identification in 2D 15N-HSQC and 3D HNNCO
         2. Backbone Resonance Assignment
         3. Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN
         4. Side Chain Assignment
            1. Aliphatic side-chain assignment
            2. Aromatic side-chain assignment
            3. Amide side-chain assignment
      2. Sparky
      3. XEASY
         1. Spin system identification
         2. Backbone resonance assignment
            
            1. GFT-based spectra
               1. HNCACAB/CABCA(CO)NH
            2. Conventional spectra
               1. HNCACB/CBCA(CO)NH
               2. HNCA/HN(CO)CA
               3. HNCO/HN(CA)CO
               4. NOESY/TOCSY
         3. Side chain resonance assignment
            1. Aliphatic
               1. GFT NMR spectra
                  1. (4,3)D GFT HABCAB(CO)NHN
                  2. (4,3)D GFT HCCH
               2. Conventional spectra
                  1. HAHB(CO)NH
                  2. HCCH-COSY
                  3. HCCH-TOCSY
                  4. Simultaneous NOESY
                  5. (H)CC-TOCSY-(CO)NH
                  6. H(CC-TOCSY-CO)NH
            2. Aromatic
               1. GFT-based spectra
               2. Conventional spectra
            3. Other
               1. Trp e1 NH and d1 CH
               2. Met e CH3
               3. Asn d2 and Gln e2 NH2
            4. NOESY peak integration
   2. Automated protocols
      1. AutoAssign
      2. AutoAssign server
      3. CLOUDS/ABACUS
      4. PINE server
   3. Validation of resonance assignment
   4. AVS
   5. LACS
   6. Depositing chemical shifts

Structure Calculation and Validation

1. Principles and concepts
   1. Constraints
      1. Distance (NOE, H-bond, distance calibration, NOE averaging, stereospecific assignments, PRE)
      2. Dihedral angle (J-coupling, chemical shifts)
      3. Orientational constraints (RDC, PRE)
   2. Advanced approaches to derive structural information
      1. SAXS
   3. Computational methods
   4. Assignment of NOESY peaklists and structure calculation
   5. Structure validation and quality assessment
2. Practical aspects
   1. Structure calculation
      1. CYANA
         1. Getting started (init.cya, sequence, chemical shifts, peaks, macros/scripts, homodimers, cis-PRO, HIS protomer)
         2. Dihedral angle constraints (link to FOUND, CASHIFT, link to TALOS tutorial, J-couplings, converting TALOS to CYANA)
         3. Distance constraints (link to FOUND, various methods for NOE -> distance conversion, sum/average, stereospecific assignments, distance modification)
         4. Orientational restraints (RDCs) (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file)
         5. FOUND
         6. TALOS
         7. GLOMSA
         8. Automated NOESY assignment and structure calculation
         9. Manual structure calculation
         10. Homodimer structure calculations
      2. AutoStructure
         1. Theory
         2. Getting started
         3. CYANA run
         4. XPLOR run
         5. Analyzing the Output
         6. RPF/DP scores
         7. Structure calculation using AS-DP
      3. "Consensus" Approaches
         1. Overview of Consensus runs
         2. Finding Consensus NOE assignments
         3. Validation of Consensus runs
      4. CS-ROSETTA
      5. CS-DP ROSETTA
      6. RDC-ROSETTA
      7. RDC-assisted dimer structure calculation
         
      8. Special topics
         1. Protein-Ligand Complexes
         2. Metal Ions
         3. Dimers
         4. PRE constraints
   2. Structure Refinement
      1. CNS Refinement
      2. XPLOR Refinement
      3. ROSETTA Refinement
   3. Validation and deposition
      1. PdbStat
      2. PSVS
      3. RPF Analysis
      4. MolProbity server
      5. PDB and BMRB deposition
      6. ADIT-NMR
      7. HarvestDB
      8. SPINS

-- JeffMills - 28 May 2009

Here are two comments from Guy:

- need to have centralized site for downloading all software that NESG has developed or licensed; this would be a central site for NESG scientists to use to access the latest version of all software

- need to allow outside users to access links to all software (they will need licenses to download) and also to download software from NESG

-- AlexEletski - 13 Jul 2009