Analysis of the Quality of NMR Protein Structures

Analysis of the Quality of NMR Protein Structures With A Structure Calculated From Your NMR Data, How Do You Determine the Accuracy and Quality of the Structure?

• Consistency with Known Protein Structural Parameters bond lengths, bond angles, dihedral angles, VDW interactions, etc

all the structural details discussed at length in the beginning• Consistency with the Experimental DATA

distance constraints, dihedral constraints, RDCs, chemical shifts, coupling constants all the data used to calculate the structure

• Consistency Between Multiple Structures Calculated with the Same Experimental DATA

Overlay of 30 NMR Structures

Analysis of the Quality of NMR Protein Structures

As We have seen before, the Quality of X-ray Structures can be monitored by an R-factor

• No comparable function for NMR • Requires a more exhaustive analysis of NMR structures

Analysis of the Quality of NMR Protein Structures Root-Mean Square Distance (RMSD) Analysis of Protein Structures

• A very common approach to asses the quality of NMR structures and to determine the relative difference between structures is to calculate an rmsd

an rmsd is a measure of the distance separation between equivalent atoms

two identical structures will have an rmsd of 0Å the larger the rmsd the more dissimilar the structures

0.43 ± 0.06 Å for the backbone atoms 0.81 ± 0.09 Å for all atoms

Analysis of the Quality of NMR Protein Structures Root-Mean Square Distance (RMSD) Analysis of Protein Structures

• A variety of approaches can be used to measure an RMSD only backbone atoms exclude disordered regions only regions with defined secondary structure only the protein’s active-site region on a per-atom or per-residue basis

rmsd difference between NMR and X-ray structure


Root-Mean Square Distance (RMSD) Analysis of Protein Structures• Using XPLOR to measure an RMSD

only one PSF file can be used the structures being compared have to be consistent with the PSF file

can only compare similar structures/sequence can not compare structural homologs

structure @PROTEIN.psf endset precision 3 endevaluate ($1= “PROTEIN_ave.min") set display=all_all.rms enddisplay $1 set display=back_all.rms enddisplay $1 coor disp=comp @@$1

for $2 in(“PROTEIN_dg_103.sam"“PROTEIN_dg_3.sam“...“PROTEIN_dg_18.sam"“PROTEIN_dg_84.sam")

Read in the PSF file and identify the reference structure

Name the files to contain the rmsd data

Compare the coordinates

Loop through a list of files to compare against PROTEIN_ave.min


loop fil2 coor @@$2 coor select ((not hydro) and (resid 4:81 or resid 90:111)) fit end coor select ((not hydro) and (resid 4:81 or resid 90:111)) rms end evaluate ($20=$result) set display all_all.rms end display $2 $20 coor select ((name ca or name c or name n) and (resid 4:81 or resid 90:111)) fit end coor select ((name ca or name c or name n) and (resid 4:81 or resid 90:111)) rms end set display back_all.rms end evaluate ($20=$result) display $2 $20end loop fil2stop

Continuation of XPLOR ScriptThe following set of commands are executed for each protein in the list

First, the structures are aligned based on the selected atoms

Then, an rmsd is calculated based on the selected atoms and written to the specified file

Selection tool is very flexible and you can choose a variety of atom names, types, residue names and types and chains


Some Caveats About (RMSD) Analysis of Protein Structures

• rmsd is a global measure an unexpected high or low value may reflect only a region of the protein that is ordered/disordered or similar/dissimilar

• For an ensemble of NMR structures, rmsd implies precision

accuracy can be inferred by comparing structures determined by multiple methods and groups

• High rmsd is an indicator of protein dynamics This is generally true, but it strongly depends on the completeness and accuracy of analyzing the NOESY data. regions of mobility need to be confirmed by experimental measurments high rmsd is directly related to the number of distance constraints

Literature Reports of NMR Protein Structures• RMSD provides a means to evaluate the quality of the structures

Always calculate multiple structures (10-100) with a single experimental data set identify the lowest energy structures (10-30) <SA> calculate an “average” structure (SA) minimize the “average” structure (SA)r against the NMR experimental constrains calculate rmsd between the ensemble of structures (<SA>), (SA), (SA)r and x-ray structure (if available)



What is an “Average” NMR Structure?• Average the x,y,z-coordinate positions for each atom over the entire ensemble of structures

Structure 1: ATOM 1 N MET 1 0.825 20.945 0.300

Structure 2: ATOM 1 N MET 1 3.524 22.037 -0.733Structure 3: ATOM 1 N MET 1 -0.813 21.297 -1.463...

Average Structure: ATOM 1 N MET 1 2.888 21.188 -0.390

Align the structures and calculate an average

n

X

X

n

jj

ave

1

Analysis of the Quality of NMR Protein Structures Is the “Average” NMR Structure a Real Structure?

• No-it is a distorted structure level of distortions depends on the similarity between the structures in the ensemble provides a means to measure the variability in atom positions between an ensemble of structures

Expanded View of an “Average” Structure

Some very long, stretched bonds

Position of atoms are so scrambled the graphics program does not know which atoms to draw bonds between Some regions of the structure

can appear relatively normal


Refine or Minimize the “Average” NMR Structure• Remove “bad” bond lengths, angles, etc• Minimize against the experimental NMR data• Is this structure a “true” representation of the average of the ensemble of structures?

A point of discussion in the NMR community an overlay of the refined average structure with the ensemble of structures will place the average in the center of the structures

• Alternative view is to select one structure from the ensemble Does this represent the average of the ensemble?

Overlay of backbone atoms for the refined minimized structure (blue) and ensemble of 30 structures (yellow)

Analysis of the Quality of NMR Protein Structures Structural Statistics Provide Another Approach to Quantify the Quality of an NMR Structure

• r.m.s deviations from experimental restraints• energies

NOE violations, torsional angle violations, repulsive forces, Lennard-Jones electrostatics (not a target function in refinement)

• deviations from idealized covalent geometry• PROCHECK

G-factor, Ramachandran, bad contacts hydrogen bond energy

REMARK FILENAME=“PROTEIN.sam"REMARK =============================================================== REMARK overall, bonds, angles, improper,vdw,REMARK energies: -580.981, 51.7637, 218.963, 42.2728, 177.029, REMARK cdih, noe, coup, shift, rama, collREMARK energies: 19.8689, 104.49, 18.5721, 62.6244, -1404.57, 128.003REMARK =============================================================== REMARK bonds, angles, impropers, cdih, noe, coupREMARK RMS: 5.096347E-03, 0.616985, 0.51284, 1.21754, 3.558853E-02, 0.591961REMARK shifts RMS a, b: 0.883305, 0.89601REMARK =============================================================== REMARK cdih coup noe REMARK violations : 3 7 3 REMARK shifts: 55REMARK =============================================================== REMARK REMARK jcoup rms-d: 0.591961REMARK ===============================================================REMARK ===============================================================REMARK ===============================================================REMARK DATE:16-Feb-04 17:50:26 created by user:


Energies, violations and rms deviations are routinely printed as headers in XPLOR Structure files


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.cons inter (all) (all) endprint threshold = 0.01000 collapseevaluate ($rms_col=$result)evaluate ($violations_col=$violations)print threshold = 0.10000 noeevaluate ($rms_noe=$result)evaluate ($violations_noe=$violations)print threshold = 1.0000 cdihevaluate ($rms_cdih=$result)evaluate ($violations_cdih=$violations)print threshold = 0.0500 bondsevaluate ($rms_bonds=$result)print threshold = 10.0000 anglesevaluate ($rms_angles=$result)evaluate ($violations_angles=$violations)print threshold = 3.0000 impropersevaluate ($rms_impropers=$result)evaluate ($violations_improp=$violations)...

Obtaining rms deviations of experimental restraints, energies and deviations from idealized geometry by simply printing the values from XPLOR

Structural Statistics Provide Another Approach to Quantify the Quality of an NMR Structure

Sets the thresholds for which violations will be reported


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. ========== spectrum 1 restraint 2745 ========== set-i-atoms 93 ALA HN set-j-atoms 78 VAL O R<average>= 2.469 NOE= 1.80 (- 0.30/+ 0.50) Delta= -0.169 E(NOE)= 1.432 ========== spectrum 1 restraint 2747 ========== set-i-atoms 76 GLY HN set-j-atoms 95 VAL O R<average>= 2.457 NOE= 1.80 (- 0.30/+ 0.50) Delta= -0.157 E(NOE)= 1.230

NOEPRI: RMS diff. = 0.040, #(violat.> 0.1)= 69 of 2750 NOEs NOEPRI: RMS diff. class INTR = 0.004, #(viol.> 0.1)= 0 of 483 NOEs NOEPRI: RMS diff. class SHOR = 0.035, #(viol.> 0.1)= 22 of 825 NOEs NOEPRI: RMS diff. class LONG = 0.040, #(viol.> 0.1)= 20 of 651 NOEs NOEPRI: RMS diff. class SEQ = 0.046, #(viol.> 0.1)= 10 of 719 NOEs NOEPRI: RMS diff. class H-BO = 0.104, #(viol.> 0.1)= 17 of 72 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.399183E-01 (real) X-PLOR>evaluate ($violations_noe=$violations) EVALUATE: symbol $VIOLATIONS_NOE set to 69.0000 (real)...

Typical Output of an XPLOR restraint analysis where violated restraints are listed followed by a summary

Violated NOE restraint, average distance, error and energy

RMS summary and number of violated restraints


As We Discussed Before, PROCHECK is a Very Valuable Tool For Accessing The Quality of a Protein Structure

► Correct , distribution► Comparison of main chain and side-chain parameters to standard values


Predict NOEs from the Experimental Structure and Compare to the NOESY Data

• short distances observed in the structure should correlate with NOE cross-peaks• missing NOE peaks may arise because of:

degeneracy too close to diagonal overlap with noise disordered region of the structure while ($3 < 113) loop select

evaluate ($4 = $3 + 1)

noe

set display $2 end

set print $2 end

predict

from=(resid $3 and name h*)

to=(resid $4:113 and name h* )

cutoff=4.5

end

end

evaluate ($3=$3+1)

end loop select

end loop dist

Lists all the predicted NOEs between the selected atom pairs within the given distance cut-off

======================================== set-i-atoms 2 THR HN set-j-atoms 1 MET HT1 1 MET HT2 1 MET HT3 ( ( <R^-6> )^-1/6 ) = 1.684 ======================================== set-i-atoms 2 THR HN set-j-atoms 1 MET HA ( ( <R^-6> )^-1/6 ) = 3.404 ======================================== set-i-atoms 2 THR HN set-j-atoms 1 MET HB1 1 MET HB2 ( ( <R^-6> )^-1/6 ) = 4.137 ========================================

Analysis of the Quality of NMR Protein Structures NMR R-factor

• difference between expected and observed NOEs expected NOEs structure observed NOEs NMR spectra also includes unassigned NOEs perfect fit would yield R = 0

• R-factors have not been readily adapted in NMR community

affected by completeness of assignments, peak overlap, sensitivity, noise, extent of data (RDCs, coupling constants, etc trends with rmsd without complications

Journal of Biomolecular NMR, 17: 137–151, 2000.

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Analysis of the Quality of NMR Protein Structures