Re: [ccp4bb] Asn/Gln - pi-stacking prevalence
While working on PDB entries 1F0N and 1F0P, I aligned the side-chain dipoles of 4 asparagines with the side-chain dipoles of tryptophans (ring nitrogen is slightly negative, the rest of the 5-membered ring is slightly positive). Aligning dipoles simultaneously optimized hydrogen bonding for the 4 asparagines. So that could be a simultaneous pi-stack and dipole interaction (and hydrogen bonds). me, et al J. Molecular Biology (2001) 307, 671-681. On 11/10/18 1:45 AM, Michael Jarva wrote: Dear ccp4 community, I have recently been working with a structure that has an Asparagine that makes a planar stacking connection with a Tryptophan ring (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd like to find more examples of this. I've found a few other examples in the literature but they are mostly amide hydrogen-pi interactions (4PTI_ASN-TYR_v2.png and 1N4W_ASN-FAD_v2.png), which can be seen by the way the Asn is dipping down into the pi-cloud. One potential exception is of a DNA-binding protein where the orientation is more planar (3HXQ_GLN-DNA_v2.png). So, I'm looking for examples of Asparagine or Glutamine pi-stacking and am sure there are more of them out there and would greatly appreciate any examples. best regards Michael Michael Jarva, PhD ACRF Chemical Biology Division The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia Phone: +61 3 9345 2493 Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/ The ACRF Chemical Biology Division is supported by the Australian Cancer Research Foundation ___ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. ___ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Asn/Gln - pi-stacking prevalence
Thank you to Tomas, Bill, and Andrew for their tips and insights! It was really all I hoped for and more. The eLife paper with its downloadable text file of mined pi-pi stacking is really useful and is easily adapted into fast visual inspection with pymol. Problem now is having more examples to look at than I have time for! cheers michael From: Tomas Malinauskas Sent: Sunday, November 11, 2018 3:11 AM To: Michael Jarva Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Asn/Gln - pi-stacking prevalence Dear Michael, On Sat, Nov 10, 2018 at 9:56 AM Michael Jarva wrote: > > Dear ccp4 community, > > > I have recently been working with a structure that has an Asparagine that > makes a planar stacking connection with a Tryptophan ring > (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd > like to find more examples of this. You could check the following paper: https://elifesciences.org/articles/31486 Pi-Pi contacts are an overlooked protein feature relevant to phase separation They have a list of examples (including Asn-Trp pi-pi stacking) in PDB (Figure 1, data source): Pi-Pi contact annotations for the full PDB set. Text file listing the pi-pi contacts observed across our non-redundant PDB set, with contact types shown by residue annotations where single amino acid names refer to sidechains and pairs of amino acids refer to the backbone peptide bond between residue i and residue i + 1. https://doi.org/10.7554/eLife.31486.005 Best wishes, Tomas Dr. Tomas Malinauskas University of Oxford Wellcome Centre for Human Genetics Division of Structural Biology Roosevelt Drive Oxford OX3 7BN United Kingdom to...@strubi.ox.ac.uk tomas.malinaus...@gmail.com From: William G. Scott Sent: Sunday, November 11, 2018 1:54 AM To: Michael Jarva Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Asn/Gln - pi-stacking prevalence Hi Michael: It always makes me happy to see that there are people who care about this. 3.3 to 3.4 Å should be an ideal distance for this, and, as you note, the lone pair residing on the (sp^3-hybridized) nitrogen would have to be oriented for favorable overlap, which is a bit harder to deduce from your figure. The other rotomer would place oxygen at that position. Because it is double-bonded to the gamma carbon, the lone pairs are oriented differently, and the pi-bond would be approximately parallel to the plane containing the tryptophan, which would give a nice pi-stacking interaction similar to what is seen with adjacent base pairs in nucleic acids. Expectation bias, as well as having partial charges turned on during refinement, might influence the rotomeric state of examples from the PDB, so be careful of social consensus. With classical electostatics, N has a partial positive charge, and O has a partial negative charge. (If you think about it, all pi-stacking interactions, from the point of view of classical electrostatics, would be somewhat repulsive.) Good luck with this, and let us know of the outcome. Bill 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<http://scottlab.ucsc.edu/> > On Nov 10, 2018, at 1:45 AM, Michael Jarva wrote: > > Dear ccp4 community, > > I have recently been working with a structure that has an Asparagine that > makes a planar stacking connection with a Tryptophan ring > (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd > like to find more examples of this. > > I've found a few other examples in the literature but they are mostly amide > hydrogen-pi interactions (4PTI_ASN-TYR_v2.png and 1N4W_ASN-FAD_v2.png), which > can be seen by the way the Asn is dipping down into the pi-cloud. One > potential exception is of a DNA-binding protein where the orientation is more > planar (3HXQ_GLN-DNA_v2.png). > > So, I'm looking for examples of Asparagine or Glutamine pi-stacking and am > sure there are more of them out there and would greatly appreciate any > examples. > > best regards > Michael > > Michael Jarva, PhD > ACRF Chemical Biology Division > The Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade > Parkville Victoria 3052 > Australia > Phone: +61 3 9345 2493 > Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/ > The ACRF Chemical Biology Division is supported by the > Australian Cancer Research Foundation > > ___ > > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission
Re: [ccp4bb] Asn/Gln - pi-stacking prevalence
Dear Michael, On Sat, Nov 10, 2018 at 9:56 AM Michael Jarva wrote: > > Dear ccp4 community, > > > I have recently been working with a structure that has an Asparagine that > makes a planar stacking connection with a Tryptophan ring > (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd > like to find more examples of this. You could check the following paper: https://elifesciences.org/articles/31486 Pi-Pi contacts are an overlooked protein feature relevant to phase separation They have a list of examples (including Asn-Trp pi-pi stacking) in PDB (Figure 1, data source): Pi-Pi contact annotations for the full PDB set. Text file listing the pi-pi contacts observed across our non-redundant PDB set, with contact types shown by residue annotations where single amino acid names refer to sidechains and pairs of amino acids refer to the backbone peptide bond between residue i and residue i + 1. https://doi.org/10.7554/eLife.31486.005 Best wishes, Tomas Dr. Tomas Malinauskas University of Oxford Wellcome Centre for Human Genetics Division of Structural Biology Roosevelt Drive Oxford OX3 7BN United Kingdom to...@strubi.ox.ac.uk tomas.malinaus...@gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Asn/Gln - pi-stacking prevalence
Hi Michael: It always makes me happy to see that there are people who care about this. 3.3 to 3.4 Å should be an ideal distance for this, and, as you note, the lone pair residing on the (sp^3-hybridized) nitrogen would have to be oriented for favorable overlap, which is a bit harder to deduce from your figure. The other rotomer would place oxygen at that position. Because it is double-bonded to the gamma carbon, the lone pairs are oriented differently, and the pi-bond would be approximately parallel to the plane containing the tryptophan, which would give a nice pi-stacking interaction similar to what is seen with adjacent base pairs in nucleic acids. Expectation bias, as well as having partial charges turned on during refinement, might influence the rotomeric state of examples from the PDB, so be careful of social consensus. With classical electostatics, N has a partial positive charge, and O has a partial negative charge. (If you think about it, all pi-stacking interactions, from the point of view of classical electrostatics, would be somewhat repulsive.) Good luck with this, and let us know of the outcome. Bill 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 > On Nov 10, 2018, at 1:45 AM, Michael Jarva wrote: > > Dear ccp4 community, > > I have recently been working with a structure that has an Asparagine that > makes a planar stacking connection with a Tryptophan ring > (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd > like to find more examples of this. > > I've found a few other examples in the literature but they are mostly amide > hydrogen-pi interactions (4PTI_ASN-TYR_v2.png and 1N4W_ASN-FAD_v2.png), which > can be seen by the way the Asn is dipping down into the pi-cloud. One > potential exception is of a DNA-binding protein where the orientation is more > planar (3HXQ_GLN-DNA_v2.png). > > So, I'm looking for examples of Asparagine or Glutamine pi-stacking and am > sure there are more of them out there and would greatly appreciate any > examples. > > best regards > Michael > > Michael Jarva, PhD > ACRF Chemical Biology Division > The Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade > Parkville Victoria 3052 > Australia > Phone: +61 3 9345 2493 > Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/ > The ACRF Chemical Biology Division is supported by the > Australian Cancer Research Foundation > > ___ > > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of the > sender. > > The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the > Kulin > Nation as the traditional owners of the land where our campuses are located > and > the continuing connection to country and community. > ___ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <4PTI_ASN-TYR_v2.png><3HXQ_GLN-DNA_v2.png><1N4W_ASN-FAD_v2.png> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
