Structure validation: Difference between revisions

Revision as of 03:09, 6 May 2021

Revision as of 16:15, 5 July 2021

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

For globular proteins, interior atomic packing (arising from short-range, local interactions) of side-chains<ref>{{Cite journal| vauthors = Shen MY, Davis FP, Sali A |date= March 2005|title=The optimal size of a globular protein ___domain: A simple sphere-packing model|journal=Chemical Physics Letters|volume=405|issue=1–3|pages=224–228|doi=10.1016/j.cplett.2005.02.029|issn=0009-2614|bibcode= 2005CPL...405..224S}}</ref><ref>{{cite journal | vauthors = Misura KM, Morozov AV, Baker D | title = Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction | journal = Journal of Molecular Biology | volume = 342 | issue = 2 | pages = 651–64 | date = September 2004 | pmid = 15327962 | doi = 10.1016/j.jmb.2004.07.038 }}</ref><ref>{{cite journal | vauthors = Basu S, Bhattacharyya D, Banerjee R | title = Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs | journal = BMC Bioinformatics | volume = 12 | issue = 1 | pages = 195 | date = May 2011 | pmid = 21605466 | pmc = 3123238 | doi = 10.1186/1471-2105-12-195 }}</ref><ref name="The jigsaw puzzle model: search for">{{cite journal | vauthors = Banerjee R, Sen M, Bhattacharya D, Saha P | title = The jigsaw puzzle model: search for conformational specificity in protein interiors | journal = Journal of Molecular Biology | volume = 333 | issue = 1 | pages = 211–26 | date = October 2003 | pmid = 14516754 | doi = 10.1016/j.jmb.2003.08.013 }}</ref> has been shown to be pivotal in the structural stabilization of the protein-fold. On the other hand, the electrostatic harmony (non-local, long-range) of the overall fold<ref name=":2">{{cite journal | vauthors = Basu S, Bhattacharyya D, Banerjee R | title = Self-complementarity within proteins: bridging the gap between binding and folding | journal = Biophysical Journal | volume = 102 | issue = 11 | pages = 2605–14 | date = June 2012 | pmid = 22713576 | pmc = 3368132 | doi = 10.1016/j.bpj.2012.04.029 | bibcode = 2012BpJ...102.2605B }}</ref> has also been shown to be essential for its stabilization. Packing anomalies include steric clashes,<ref>{{cite journal | vauthors = Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC | display-authors = 6 | title = MolProbity: all-atom structure validation for macromolecular crystallography | journal = Acta Crystallographica Section D | volume = 66 | issue = Pt 1 | pages = 12–21 | date = January 2010 | pmid = 20057044 | pmc = 2803126 | doi = 10.1107/S0907444909042073 }}</ref> short contacts,<ref name="The jigsaw puzzle model: search for"/> holes<ref>{{cite journal | vauthors = Sheffler W, Baker D | title = RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation | journal = Protein Science | volume = 18 | issue = 1 | pages = 229–39 | date = January 2009 | pmid = 19177366 | pmc = 2708028 | doi = 10.1002/pro.8 }}</ref> and cavities<ref>{{cite journal | vauthors = Chakravarty S, Varadarajan R | title = Residue depth: a novel parameter for the analysis of protein structure and stability | journal = Structure | volume = 7 | issue = 7 | pages = 723–32 | date = July 1999 | pmid = 10425675 | doi = 10.1016/s0969-2126(99)80097-5 | doi-access = free }}</ref> while electrostatic disharmony<ref name=":2" /><ref>{{cite journal | vauthors = Basu S, Bhattacharyya D, Banerjee R | title = Applications of complementarity plot in error detection and structure validation of proteins | journal = Indian Journal of Biochemistry & Biophysics | volume = 51 | issue = 3 | pages = 188–200 | date = June 2014 | pmid = 25204080 }}</ref> refer to unbalanced partial charges in the protein core (particularly relevant for designed protein interiors). While the clash-score of [http://molprobity.biochem.duke.edu/ Molprobity] identifies steric clashes at a very high resolution, the [[Complementarity plot|Complementarity Plot]] combines packing anomalies with electrostatic imbalance of side-chains and signals for either or both.

====Carbohydrates====