Lab Meeting 06/05/20051 NMRQ: Quality Assessment and Validation for Protein Structures Generated by NMR Spectroscopy Gary Van Domselaar May 06, 2005

Lab Meeting 06/05/20052 Introduction Protein structure determination is important for: –Protein functional characterization –Rational drug design –Biological understanding Protein structures must be reliable and accurate to be useful. Protein structures can be determined by X-ray crystallography and by NMR spectroscopy

Lab Meeting 06/05/20053 Introduction Protein structure generation by either method is prone to experimental and interpretation error. Protein structure analysis programs are available to assess protein structure quality: –WHATCHECK –PROCHECK & PROCHECK-NMR –PROVE –SQUID –VADAR –MOLPROBITY –Coming Soon: NMRQ!

Lab Meeting 06/05/20054 Introduction Protein Structure Validation Packages: –Verify the structure file syntax –Check the consistency of the structure against a library of high-quality structures and identify outliers –Detect gross errors in the model –Check for local stereochemical abnormalities –Produce a score to describe the quality of the structure

Lab Meeting 06/05/20055 WHAT CHECK Stereochemical Analysis Postscript/Text/HTML “Z” Scores Crude Graphics Does not perform “ensemble analysis”

Lab Meeting 06/05/20056 PROCHECK-NMR Sterochemical Analysis Restraint Analysis via AQUA Ensemble Analysis Postscript Good Graphics Times Cited: 6390

Lab Meeting 06/05/20057 NMRQ Sterochemical Analysis Restraint Analysis Ensemble Analysis Chemical Shift Analysis Superposition and RMSD HTML Reports

Lab Meeting 06/05/20058 NMRQ

Lab Meeting 06/05/20059 NMRQ

Lab Meeting 06/05/ NMRQ: Superposition

Lab Meeting 06/05/ NMRQ: Superposition

Lab Meeting 06/05/ NMRQ: Superposition

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Torsion Angle Analysis Favorable Allowed Generously Allowed Disallowed

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Torsion Angle Analysis

Lab Meeting 06/05/ Chi Angle Analysis

Lab Meeting 06/05/ Relation Between  and 

Lab Meeting 06/05/ SCWRL The SCWRL rotamer library is a backbone dependant rotamer library aa phi psi prob. chi1 chi2 chi3 chi4 sd1 sd2 sd3 sd4 ARG ARG ARG

Lab Meeting 06/05/ NMRQ: Chi Angle Analysis Adds the probability values for all chi angle distributions within +/- 20 degrees, for a given phi, psi. #Sequence Chi1 Probability Secondary Structure Y C K C C C G C L C

Lab Meeting 06/05/ Aside: Parsing the SCWRL Library -rw-rw-r-- 1 gvd gvd 4.0K Dec 13 16:57 RotamerLibrary.index.dir -rw-rw-r-- 1 gvd gvd 2.0M Dec 13 16:57 RotamerLibrary.index.pag -rw-r--r-- 1 gvd gvd 48M Dec 13 11:28 RotamerLibrary.txt unless ($self->{_ROTAMER_LIBRARY}{"$res $phi $psi"}) { tie (%rotLib, 'SDBM_File', $dbPath, O_RDONLY,0666) || throw Error::Simple("CreateRotamerLibrary: Could not create the DB: $!"); my $key = "$res $phi $psi"; my $val = $rotLib{$key}; # get the info from file. my ($start,$offset) = split(/\,/,$val); seek(LIBRARY, $start,0); my $buffer; read(LIBRARY,$buffer,$offset);... $phi $psi"}}, \%row; }

Lab Meeting 06/05/ Chi-Angle Dispersion Correlates With Accessible Surface Area Fractional ASA

Lab Meeting 06/05/ Chi Angle Analysis

Lab Meeting 06/05/ Chi Angle Analysis

Lab Meeting 06/05/ Volume and Area Loose Packing Dense Packing Protein Proteins are Densely Packed

Lab Meeting 06/05/ Volume and Area

Lab Meeting 06/05/ Volume and Area

Lab Meeting 06/05/ Volume and Area

Lab Meeting 06/05/ Volume and Area

Lab Meeting 06/05/ Volume and Area Solvent Probe Accessible Surface Van der Waals Surface Reentrant Surface

Lab Meeting 06/05/ Volume and Area

Lab Meeting 06/05/ Chemical Shift Analysis

Lab Meeting 06/05/ Chemical Shift Analysis

Lab Meeting 06/05/ Chemical Shift Analysis

Lab Meeting 06/05/ Chemical Shift Analysis

Lab Meeting 06/05/ Chemical Shift Analysis

Lab Meeting 06/05/ Other Statistics

Lab Meeting 06/05/ Other Statistics

Lab Meeting 06/05/ Other Statistics

Lab Meeting 06/05/ Other Statistics

Lab Meeting 06/05/ Other Statistics

Lab Meeting 06/05/ Summary Reports

Lab Meeting 06/05/ Summary Reports

Lab Meeting 06/05/ Summary Reports

Lab Meeting 06/05/ Restraint Analysis

Lab Meeting 06/05/ Restraint Analysis Coming Soon... PROCHECK-NMR + AQUA: –Distance restraints plot –Restraint differences plot –Numbers of distance restraints –Actual distance - restraint summary –Violation frequency summary –Restraint statistics –Residue-by-residue restraint violations –Model-by-model violations

Lab Meeting 06/05/ NMRQ TODO List Chi angle plots, and cumulative plots Restraint analysis Model and ensemble scoring statistics Syntax Validation

Lab Meeting 06/05/ NMRQ Limitations NO Chi1-Chi2 Torsion Angle Distribution PDB parsing not robust, no validation Hydrogen bond analysis available, not implemented. Insert your comments here.

Lab Meeting 06/05/ Acknowledgements Dr. Paul Stothard Trent Bjorndahl Steve Neal Prof. David Wishart