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To follow up, This is what I use to teach to our undergrads: Current Opinion in Chemical Biology 2002, 6:736-741 Shows a nice representation (and justification) for edge to face interactions From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Savvas Savvides Sent: Thursday, 15 September 2016 5:20 AM To: [log in to unmask] Subject: Re: [ccp4bb] Tryptophan-Adenine interaction: T-shaped stacking? Dear Wenhe and colleagues, I would highly recommend the paper by Hunter, Singh, and Thornton in JMB. (doi:10.1016/0022-2836(91)90271-7<http://dx.doi.org/10.1016/0022-2836(91)90271-7>) In particular, Figure 5 is very informative with its 'Ramachandran-like' representation of repulsive vs attractive stacking combinations. best wishes Savvas ---- Savvas Savvides Professor of Structural Biology Ghent University & VIB Inflammation Research Center Technology Park 927, B-9052 Ghent (Zwijnaarde), Belgium +32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: savvas.savvides_skype http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx On 14 Sep 2016, at 16:57, Phoebe A. Rice <[log in to unmask]<mailto:[log in to unmask]>> wrote: Some dusty neurons in the back of my head recall a discussion as to if there was really anything particularly favorable about perpendicular aromatic stacking, or if it is just the most statistically likely arrangement. Might be worth looking up for your case. Phoebe ________________________________________ From: CCP4 bulletin board [[log in to unmask]<mailto:[log in to unmask]>] on behalf of William G. Scott [[log in to unmask]<mailto:[log in to unmask]>] Sent: Tuesday, September 13, 2016 6:05 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [ccp4bb] Tryptophan-Adenine interaction: T-shaped stacking? On Sep 6, 2016, at 8:07 PM, WENHE ZHONG <[log in to unmask]<mailto:[log in to unmask]>> wrote: I am not very familiar with the chemistry in terms of ð-stacking. So I am wondering whether it is a T-shaped stacking interaction between the aromatic rings? Any thought? Dear Wenhe: Please take a look at these references: Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization S. K. Burley and G. A. Petsko Science Vol. 229, No. 4708 (Jul. 5, 1985), pp. 23-28 Stable URL: http://www.jstor.org/stable/1695415 also, the basis in pi orbital stabilization interactions comes from this, I believe: Symmetry, Topology and Aromaticity, M. J. Goldstein and Roald Hoffmann. Journal of the American Chemical Society / 93:23 / November 17,1971 https://www.dropbox.com/s/y7blru2u37dsfiu/67s_0.pdf William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu