Structure validation: Difference between revisions

Revision as of 09:06, 6 May 2022

Revision as of 09:17, 7 April 2023

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====Conformation (dihedrals): protein & RNA====

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 Dunbrack [[Backbone-dependent rotamer library]].<ref>{{cite web |title=Smooth Backbone-Dependent Rotamer Library 2010 |url=http://dunbrack.fccc.edu/bbdep2010lab/Datasetbbdep2010 |website=dunbrack.phpfccc.edu Dunbrack's|access-date=7 RotamerApril library].2023}}</ref>

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|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|last1=Olson|first1=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.|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|last1=Bhattacharyya|first1=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|journal=Journal of Computer-Aided Molecular Design|volume=31|issue=2|pages=219–235|doi=10.1007/s10822-016-0007-0|pmid=28102461|bibcode=2017JCAMD..31..219B|s2cid=356097|issn=0920-654X}}</ref> has been found to be beneficial, particularly for modelling purposes.