Structure validation: Difference between revisions

Revision as of 09:19, 6 March 2020

Revision as of 07:15, 13 March 2020

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The first macromolecular validation software was developed around 1990, for proteins. It included Rfree [[cross-validation (statistics)|cross-validation]] for model-to-data match,<ref name="Rfree">{{cite journal | vauthors = Brünger AT | title = Free R value: a novel statistical quantity for assessing the accuracy of crystal structures | journal = Nature | volume = 355 | issue = 6359 | pages = 472–5 | date = January 1992 | pmid = 18481394 | doi = 10.1038/355472a0 | author-link = Axel T. Brunger | bibcode = 1992Natur.355..472B }}</ref> bond length and angle parameters for covalent geometry,<ref name="Engh">{{cite journal |vauthors=Engh RA, Huber R |year=1991 |title=Accurate bond and angle parameters for X-ray protein structure refinement |journal=Acta Crystallographica A |volume=47 |issue=4 |pages=392&ndash;400|doi=10.1107/s0108767391001071 }}</ref> and sidechain and backbone conformational criteria.<ref name="Ponder&Richards">{{cite journal |vauthors=Ponder JW, Richards FM |year=1987 |title=Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes |journal=Journal of Molecular Biology |volume=193 |issue=4 |pages=775–791 |doi=10.1016/0022-2836(87)90358-5|pmid=2441069 }}</ref><ref name="procheck">{{cite journal |vauthors=Laskowski RA, MacArthur MW, Moss DS, Thornton JM |author4-link=Janet Thornton |year=1993 |title=PROCHECK: a program to check the stereochemical quality of protein structures |journal=Journal of Applied Crystallography |volume=26 |issue=2 |pages=283–291 |doi=10.1107/s0021889892009944}}</ref><ref name="whatif">{{cite journal | vauthors = Hooft RW, Vriend G, Sander C, Abola EE | title = Errors in protein structures | journal = Nature | volume = 381 | issue = 6580 | pages = 272 | date = May 1996 | pmid = 8692262 | doi = 10.1038/381272a0 | bibcode = 1996Natur.381..272H }}</ref> For macromolecular structures, the atomic models are deposited in the [[Protein Data Bank]] (PDB), still the single archive of this data. The PDB was established in the 1970s at [[Brookhaven National Laboratory]],<ref>{{cite journal | vauthors = Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M | display-authors = 6 | title = The Protein Data Bank: a computer-based archival file for macromolecular structures | journal = Journal of Molecular Biology | volume = 112 | issue = 3 | pages = 535–42 | date = May 1977 | pmid = 875032 | doi = 10.1016/s0022-2836(77)80200-3 | author7-link = Olga Kennard }}</ref> moved in 2000 to the [http://www.rcsb.org/pdb RCSB] (Research Collaboration for Structural Biology) centered at [[Rutgers]],<ref>{{cite journal | vauthors = Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE | display-authors = 6 | title = The Protein Data Bank | journal = Nucleic Acids Research | volume = 28 | issue = 1 | pages = 235–42 | date = January 2000 | pmid = 10592235 | pmc = 102472 | doi = 10.1093/nar/28.1.235 | author8-link = Philip Bourne | author-link = Helen M. Berman }}</ref> and expanded in 2003 to become the [http://www.wwpdb.org/ wwPDB] (worldwide Protein Data Bank),<ref name="wwPDB">{{cite journal | vauthors = Berman H, Henrick K, Nakamura H | title = Announcing the worldwide Protein Data Bank | journal = Nature Structural Biology | volume = 10 | issue = 12 | pages = 980 | date = December 2003 | pmid = 14634627 | doi = 10.1038/nsb1203-980 | author-link = Helen M. Berman }}</ref> with access sites added in Europe ([http://pdbe.org|PDBe]) and Asia ([http://www.pdbj.org|PDBj]), and with NMR data handled at the [http://www.bmrb.wisc.edu BioMagResBank (BMRB)] in Wisconsin.

Validation rapidly became standard in the field,<ref name="Kleywegt2000">{{cite journal | vauthors = Kleywegt GJ |year= 2000 |title= Validation of protein crystal structures |journal=Acta Crystallographica D |volume=56 |pages=18–19|pmid= 10713511 }}</ref> with further developments described below. *Obviously needs expansion*

A large boost was given to the applicability of comprehensive validation for both x-ray and NMR as of February 1, 2008, when the worldwide [[Protein Data Bank]] (wwPDB) made mandatory the deposition of experimental data along with atomic coordinates. Since 2012 strong forms of validation have been in the process of being adopted for [http://www.wwpdb.org/validation.html wwPDB deposition] from recommendations of the wwPDB Validation Task Force committees for [[x-ray crystallography]],<ref name="xrayVTF">{{cite journal | vauthors = Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH | display-authors = 6 | title = A new generation of crystallographic validation tools for the protein data bank | journal = Structure | volume = 19 | issue = 10 | pages = 1395–412 | date = October 2011 | pmid = 22000512 | pmc = 3195755 | doi = 10.1016/j.str.2011.08.006 | author12-link = Jane Richardson (chemist) | author7-link = Gerard Kleywegt | author4-link = Axel Brunger }}</ref> for NMR,<ref name="nmrVTF">{{cite journal | vauthors = Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL | display-authors = 6 | title = Recommendations of the wwPDB NMR Validation Task Force | journal = Structure | volume = 21 | issue = 9 | pages = 1563–70 | date = September 2013 | pmid = 24010715 | pmc = 3884077 | doi = 10.1016/j.str.2013.07.021 | author12-link = Gerard Kleywegt | author11-link = Helen M. Berman | author3-link = Ad Bax | author6-link = Jane Richardson (chemist) }}</ref> for SAXS ([[SAXS|small-angle x-ray scattering]]), and for cryoEM (cryo-[[Electron Microscopy]]).<ref name="emVTF">{{cite journal | vauthors = Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL | display-authors = 6 | title = Outcome of the first electron microscopy validation task force meeting | journal = Structure | volume = 20 | issue = 2 | pages = 205–14 | date = February 2012 | pmid = 22325770 | pmc = 3328769 | doi = 10.1016/j.str.2011.12.014 | author16-link = Michael Rossmann | author-link = Richard Henderson (biologist) }}</ref>

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The backbone and side-chain [[dihedral angles]] of protein and RNA have been shown to have specific combinations of angles which are allowed (or forbidden). For protein backbone dihedrals (φ, ψ), this has been addressed by the legendary [[Ramachandran plot|Ramachandran Plot]] while for side-chain dihedrals (χ's), one should refer to the [http://dunbrack.fccc.edu/bbdep2010/Dataset.php Dunbrack's Rotamer library].

Though, mRNA structures are generally short-lived and single-stranded, there are an abundance of non-coding RNAs with different secondary and tertiary folding (tRNA, rRNA etc.) which contain a preponderance of the canonical [[Base pair|Watson-Crick]] (WC) base-pairs, together with significant number of non-Watson Crick (NWC) base-pairs - for which such RNA also qualify for regular structural validation that apply for nucleic acid helices. The standard practice is to analyse the intra- (Transnational: Shift, Slide, Rise; Rotational: Tilt, Roll, Twist) and inter-base-pair geometrical parameters (Transnational: Shear, Stagger, Stretch, Rotational: Buckle, Propeller, Opening) - whether in-range or out-of-range with respect to their suggested values.<ref>{{Cite journal|last=Dickerson|first=Richard E.|date=1989-02-01|title=Definitions and Nomenclature of Nucleic Acid Structure Parameters|url=https://doi.org/10.1080/07391102.1989.10507726|journal=Journal of Biomolecular Structure and Dynamics|volume=6|issue=4|pages=627–634|doi=10.1080/07391102.1989.10507726|issn=0739-1102|pmid=2619931|pmc=400765}}</ref><ref>{{Cite journal|last=Olson|first=Wilma K|last2=Bansal|first2=Manju|last3=Burley|first3=Stephen K|last4=Dickerson|first4=Richard E|last5=Gerstein|first5=Mark|last6=Harvey|first6=Stephen C|last7=Heinemann|first7=Udo|last8=Lu|first8=Xiang-Jun|last9=Neidle|first9=Stephen|last10=Shakked|first10=Zippora|last11=Sklenar|first11=Heinz|date=2001-10-12|title=A standard reference frame for the description of nucleic acid base-pair geometry11Edited by P. E. Wright22This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.|url=http://www.sciencedirect.com/science/article/pii/S0022283601949873|journal=Journal of Molecular Biology|language=en|volume=313|issue=1|pages=229–237|doi=10.1006/jmbi.2001.4987|issn=0022-2836|pmid=11601858}}</ref> These parameters describe the relative orientations of the two paired bases with respect to each other in two strands (intra) along with those of the two stacked base pairs (inter) with respect to each other, and, hence, together, they serve to validate nucleic acid structures in general. Since, RNA-helices are small in length (average: 10-20 bps), the use of electrostatic surface potential as a validation parameter <ref>{{Cite journal|last=Bhattacharyya|first=Dhananjay|last2=Halder|first2=Sukanya|last3=Basu|first3=Sankar|last4=Mukherjee|first4=Debasish|last5=Kumar|first5=Prasun|last6=Bansal|first6=Manju|date=2017-01-19|title=RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs|url=http://dx.doi.org/10.1007/s10822-016-0007-0|journal=Journal of Computer-Aided Molecular Design|volume=31|issue=2|pages=219–235|doi=10.1007/s10822-016-0007-0|pmid=28102461|issn=0920-654X}}</ref> has been found to be beneficial, particularly for modelling purposes.

==== Packing and Electrostatics: globular proteins ====

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[[File:(A)-ASN297.svg|thumb|A 2D diagram of an N-glycan linked to an antibody fragment in the structure with PDB accession code '4BYH'. This diagram, which has been generated with Privateer,<ref name=":0"/> follows the standard symbol nomenclature<ref name=":1"/> and includes, in its original svg format, annotations containing validation information, including ring conformation and detected monosaccharide types.]]

The branched and cyclic nature of carbohydrates poses particular problems to structure validation tools.<ref>{{cite journal | vauthors = Agirre J, Davies GJ, Wilson KS, Cowtan KD | title = Carbohydrate structure: the rocky road to automation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 39–47 | date = June 2017 | pmid = 27940408 | doi = 10.1016/j.sbi.2016.11.011 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf | series = Carbohydrates • Sequences and topology }}</ref> At higher resolutions, it is possible to determine the sequence/structure of oligo- and poly-saccharides, both as covalent modifications and as ligands. However, at lower resolutions (typically lower than 2.0Å), sequences/structures should either match known structures, or be supported by complementary techniques such as Mass Spectrometry.<ref>{{cite journal | vauthors = Crispin M, Stuart DI, Jones EY | title = Building meaningful models of glycoproteins | journal = Nature Structural & Molecular Biology | volume = 14 | issue = 5 | pages = 354; discussion 354–5 | date = May 2007 | pmid = 17473875 | doi = 10.1038/nsmb0507-354a }}</ref> Also, monosaccharides have clear conformational preferences (saturated rings are typically found in chair conformations),<ref>{{cite journal | vauthors = Davies GJ, Planas A, Rovira C | title = Conformational analyses of the reaction coordinate of glycosidases | journal = Accounts of Chemical Research | volume = 45 | issue = 2 | pages = 308–16 | date = February 2012 | pmid = 21923088 | doi = 10.1021/ar2001765 }}</ref> but errors introduced during model building and/or refinement (wrong linkage chirality or distance, or wrong choice of model - see<ref>{{cite journal | vauthors = Agirre J | title = Strategies for carbohydrate model building, refinement and validation | journal = Acta Crystallographica Section D | volume = 73 | issue = Pt 2 | pages = 171–186 | date = February 2017 | pmid = 28177313 | pmc = 5297920 | doi = 10.1107/S2059798316016910 | url = http://journals.iucr.org/d/issues/2017/02/00/ba5257/ }}</ref> for recommendations on carbohydrate model building and refinement and<ref>{{cite journal | vauthors = Lütteke T | title = Analysis and validation of carbohydrate three-dimensional structures | journal = Acta Crystallographica Section D | volume = 65 | issue = Pt 2 | pages = 156–68 | date = February 2009 | pmid = 19171971 | pmc = 2631634 | doi = 10.1107/S0907444909001905 }}</ref><ref>{{cite journal | vauthors = Lütteke T, von der Lieth CW | title = Data mining the PDB for glyco-related data | journal = Methods in Molecular Biology | volume = 534 | pages = 293–310 | date = 2009-01-01 | pmid = 19277543 | doi = 10.1007/978-1-59745-022-5_21 | isbn = 978-1-58829-774-7 }}</ref><ref>{{cite journal | vauthors = Joosten RP, Lütteke T | title = Carbohydrate 3D structure validation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 9–17 | date = June 2017 | pmid = 27816840 | doi = 10.1016/j.sbi.2016.10.010 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf }}</ref> for reviews on general errors in carbohydrate structures) can bring their atomic models out of their energy minima. Around 20% of the deposited carbohydrate structures are in unjustified energy minima.<ref>{{cite journal | vauthors = Agirre J, Davies G, Wilson K, Cowtan K | title = Carbohydrate anomalies in the PDB | journal = Nature Chemical Biology | volume = 11 | issue = 5 | pages = 303 | date = May 2015 | pmid = 25885951 | doi = 10.1038/nchembio.1798 | url = http://eprints.whiterose.ac.uk/95242/1/AgirreDaviesWIlsonCowtan_self_archived.pdf }}</ref>

A number of carbohydrate validation web services are available at [http://ww.glycosciences.de glycosciences.de] (including nomenclature checks and linkage checks by [http://www.glycosciences.de/tools/pdb-care/ pdb-care],<ref>{{cite journal | vauthors = Lütteke T, von der Lieth CW | title = pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files | journal = BMC Bioinformatics | volume = 5 | pages = 69 | date = June 2004 | pmid = 15180909 | pmc = 441419 | doi = 10.1186/1471-2105-5-69 }}</ref> and cross-validation with Mass Spectrometry data through the use of GlycanBuilder), whereas the [http://www.ccp4.ac.uk CCP4] suite currently distributes [http://www.ccp4.ac.uk/html/privateer.html Privateer],<ref name=":0">{{cite journal | vauthors = Agirre J, Iglesias-Fernández J, Rovira C, Davies GJ, Wilson KS, Cowtan KD | title = Privateer: software for the conformational validation of carbohydrate structures | journal = Nature Structural & Molecular Biology | volume = 22 | issue = 11 | pages = 833–4 | date = November 2015 | pmid = 26581513 | doi = 10.1038/nsmb.3115 | url = http://eprints.whiterose.ac.uk/95794/1/Privateer_selfarchived.pdf }}</ref> which is a tool that is integrated into the model building and refinement process itself. Privateer is able to check stereo- and regio-chemistry, ring conformation and puckering, linkage torsions, and real-space correlation against positive omit density, generating aperiodic torsion restraints on ring bonds, which can be used by any refinement software in order to maintain the monosaccharide's minimal energy conformation.<ref name=":0" />

Privateer also generates scalable two-dimensional SVG diagrams according to the Essentials of Glycobiology<ref name=":1">{{cite journal | vauthors = Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, Prestegard JJ, Schnaar RL, Freeze HH, Marth JD, Bertozzi CR, Etzler ME, Frank M, Vliegenthart JF, Lütteke T, Perez S, Bolton E, Rudd P, Paulson J, Kanehisa M, Toukach P, Aoki-Kinoshita KF, Dell A, Narimatsu H, York W, Taniguchi N, Kornfeld S | display-authors = 6 | title = Symbol Nomenclature for Graphical Representations of Glycans | journal = Glycobiology | volume = 25 | issue = 12 | pages = 1323–4 | date = December 2015 | pmid = 26543186 | pmc = 4643639 | doi = 10.1093/glycob/cwv091 }}</ref> standard symbol nomenclature containing all the validation information as tooltip annotations (see figure). This functionality is currently integrated into other CCP4 programs, such as the molecular graphics program CCP4mg (through the ''Glycoblocks'' 3D representation,<ref>{{cite journal | vauthors = McNicholas S, Agirre J | title = Glycoblocks: a schematic three-dimensional representation for glycans and their interactions | journal = Acta Crystallographica Section D | volume = 73 | issue = Pt 2 | pages = 187–194 | date = February 2017 | pmid = 28177314 | pmc = 5297921 | doi = 10.1107/S2059798316013553 }}</ref> which conforms to the standard symbol nomenclature<ref name=":1" />) and the suite's graphical interface, CCP4i2.