Title: Using the CCHMC BMI cluster for NMR structure and dynamics calculations
1Using the CCHMC BMI cluster forNMR structure and
dynamics calculations
- Douglas Kojetin, Ph.D.
- UC College of Medicine
2Biomacromolecular Structure
- Two principal methods (high-resolution)
- X-ray crystallography
- Solid-state
- NMR spectroscopy
- Solid-state
- Solution-state
- Different from MRI both use magnets
- MRI bulk density
- NMR atomic-level applications
- Others (Small Angle X-ray Scattering solution)
3NMR Studies of
- 3D structure determination (structure ensemble
vs. static crystal representative) - NMR is limited (size, solubility)
- Dynamics (time-scale movements)
- Certain time-scale motions are important for
protein function (interactions, catalysis, etc.) - Sample quality (folded? domains?)
- Titrations/conditions (ligand, pH, temp)
4Protein NMR Spectroscopy
ubiquitin
5Protein NMR Spectroscopy
2D 1H-15N HSQC
Each point is sensitiveto chemical
environment Ligands, temp, pH, etc.
6Data Analysis Step 1
- Unambiguously assign all atoms in the protein
- Backbone (HN, N, Ca, Cb, C)
- Side-chain
HNCACB, (2) HNCO/HN(CO)CA, (3) HNCA/HN(CO)CA
7Structure determination
- Start from an extended polypeptide chain
- Constraints for structure calculation
- through-space 1H-1H connectivities (NOEs)
- Dihedral angles (predicted chemical shifts vs.
random coil database) - Hydrogen bonds
- Residual dipolar couplings (orientation)
8Structure determination
- Automated software iteratively assign and remove
bad assignments (CNS ARIA) - Iteration 0-7 20 structures per iteration
- Last iteration 100-200 structures
- Entire process is iterated (nested) 1 day over
20 desktop CPUs ethernet, NFS farm out calcs
9Structure determination
- Solvent refinement
- Fine tune NOE automated assignments
- Better Ramachandran (stereochemical) quality
fewer atom clashes - AMBER MPI capable, but calculations take 3 hrs
per structure 100 separate, independent
calculations - shell scripts to setup files, submit 100 jobs to
queue write working files to /tmp/XXX on node
copy important files to home dir delete /tmp/XXX
when finished) - Future MD calculations will take advantage of MPI
10Dynamics calculations (time-scale motions)
- Measure 15N backbone relaxation rates (measures
motions on ps-ns time-scale) - Fit rates to motional models use statistical
model selection to choose best fit - Motional model type of tensor describing system
- Important motional parameters S2 (order
parameter) and Rex (ms time-scale motions data
cannot be described by ps-ns motions only)
11Dynamics calculations (time-scale motions)
- Nested, single calculations
1
1. Initial calculation
2. Analyze data vs. 4 tensor types sphere,
prolate, oblate, ellipsoid
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2
2
2
3. Final selection of tensor monte carlo
error estimation
3
4. Extract statistical information into csv
table
Repeated using different initial parameter
estimates describing system (NH bond length,
corr. Timr tensor params)
4
12Dynamics calculations (time-scale motions)
1
PBS -S /bin/csh PBS -l walltime240000 PBS
-l nodes1ppn1opteron ...
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2
2
2
PBS -S /bin/csh PBS -l walltime240000 PBS
-l nodes1ppn1opteron ... PBS -W
dependafterokCLUSTER_JOB
x4
3
4
13Dynamics calculations (time-scale motions)
!/bin/sh 1 QUEUE INITIAL RUN local_tmqsub
JOB_DIR/local_tm local_tmidecho local_tm
gawk -F '.' 'print 1' sleep 2 2a SETUP
TENSOR RUNS sed "s/CLUSTER_JOB/local_tmid/g"
JOB_DIR/sphere \ gt JOB_DIR/sphere.mod ...
prolate, oblate, ellipsoid (4 total) 2b QURUE
TENSOR RUNS sphereqsub JOB_DIR/sphere.mod sphe
reidecho sphere awk -F '.' 'print 1 ...
prolate, oblate, ellipsoid (4 total) 3 QUEUE
FINAL RUN sed "s/FINAL_JOB/sphereidprolateido
blateidellipsoidid/g \ JOB_DIR/final gt
JOB_DIR/final.mod finalqsub JOB_DIR/final.mod
finalidecho final awk -F '.' 'print
1' 4 QUEUE FINAL STATS EXTRACTION sed
"s/STATS_JOB/finalid/g" JOB_DIR/stats \ gt
JOB_DIR/stats.mod statsqsub JOB_DIR/stats.mod
PBS -S /bin/csh PBS -l walltime240000 PBS
-l nodes1ppn1opteron ... PBS -W
dependafterokCLUSTER_JOB
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2
2
2
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14Example Map S2 on structure
15Thanks!
- CCHMC BMI
- Prakash
- Those who provide
- Good Samaritan ER