HI Pavel and all, I’m not sure if this is what you were thinking of, but we published in 2016 a rather dramatic example showing how a series of reliably determined extreme phi,psi outliers document how the strain-energy associated with adopting the phi,psi angles is distributed between an extreme close approach of atoms and a coordinated set of bond angle changes involving their increasing distortion from their “standard” values in ways that make sense. The paper is here<https://www.science.org/doi/10.1126/sciadv.1501188>.
While that is a particularly extreme example, it is actually just one example of the systematic variations in observed bond angles from their classical standard “ideal” values that are occurring throughout phi,psi space. Building on earlier work, our main paper documenting the conformation dependence of “ideal” geometry using a fairly large set of ultra-high resolution structures is here<https://www.sciencedirect.com/science/article/pii/S0969212609003359>. Figure 6 in that paper provides some specific examples of how the bond angle variations seen near the edges of “classically allowed” regions make sense in terms of the bond angles incurring strain energy as part of relieving what would have been a much worse collisional strain energy. In documenting those trends, we sought to shift our community away from thinking that there is a single set of ideal geometry values and instead recognize that the expected (or “ideal”) geometry values are strongly conformation dependent. While many users may not be aware of it, a restraint library based on that concept is now the default library in Phenix (see here<https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.12860>). We’ve similarly shown (also building on earlier work) that reliable outliers also exist with regard to peptide bond planarity (as measured by the omega torsion angle), and that the expected omega torsion angle also has conformation-dependent trends such that the its expected value deviates by up to 7 or 8 degrees from planarity even in phi,psi regions that are reasonably well populated (see here<https://www.pnas.org/doi/pdf/10.1073/pnas.1107115108>). Ultra-high resolution protein structures can achieve a level of precision and accuracy that is tremendously valuable for revealing deviations from standard geometry that are quite real and helpful for our understanding of fundamental principles. HTH, Andy [Black Lives Matter] Dr. P. Andrew Karplus (he, him, his) Distinguished Professor of Biochemistry and Biophysics NIGMS GCE4All Research Center<http://gce4all.oregonstate.edu/> Director of Communications 2133 ALS Building Oregon State University Corvallis, OR 97331 ph. 541-737-3200 andy.karp...@oregonstate.edu<mailto:andy.karp...@oregonstate.edu> “Revealing how life works for the benefit of all!” http://biochem.oregonstate.edu/ https://www.facebook.com/OSUBB From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Pavel Afonine <pafon...@gmail.com> Date: Wednesday, November 9, 2022 at 6:20 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] outliers [This email originated from outside of OSU. Use caution with links and attachments.] This is best illustrated by Ramachandran "outliers", which are perfectly supported by electron density. Indeed, and 3NOQ is one of my favorite examples of that, an outlier isn't necessarily equates to wrong! However, I think torsion angles (eg, phi/psi) are much more flexible than covalent angles/bonds and so they can possibly afford larger deviations compared to covalent bonds/angles. The strain caused by any one of them will distribute itself over all neighbouring bond lengths and angles as well as over the torsion angles. I wonder if there is a documented study that actually shows this happening? Clearly this must take place one way or another, but I wonder if anyone "measured" the effect and documented it.. Pavel ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7Ca4a429415c2f4239dec608dac2c22f0a%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638036436516161568%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IR%2F9q%2BcIuCD29HOoWKNTs7WxXK4YMPoyha%2FiU089Z7Q%3D&reserved=0> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
