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dc.contributor.authorPinheiro, Silvana
dc.contributor.authorSoteras, Ignacio
dc.contributor.authorGelpí, Josep Lluís
dc.contributor.authorDehez, François
dc.contributor.authorChipot, Christophe
dc.contributor.authorLuque, F. Javier
dc.contributor.authorCurutchet, Carles
dc.date.accessioned2015-06-03T10:41:19Z
dc.date.available2015-06-03T10:41:19Z
dc.date.issued2015-05-05
dc.identifier.citationPinheiro, Silvana [et al.]. Cation–π–cation interactions in structural biology. A: "BSC Doctoral Symposium (2nd: 2015: Barcelona)". 2nd ed. Barcelona: Barcelona Supercomputing Center, 2015, p. 103-105.
dc.identifier.urihttp://hdl.handle.net/2099/16566
dc.description.abstractBiological structures are stabilized by a variety of noncovalent interactions, such as hydrogen bonds, π –stacking, salt bridges or hydrophobic interactions. Besides hydrogen bonds and π– stacking, cation–π interactions between aromatic rings and positively charged groups have emerged as one of the most important interactions in structural biology. Although the role and energetic characteristics of these interactions is well established, a special case involving three molecular species, termed cation–π–cation interaction, is still poorly understood. In this contribution, we aim at advancing in the understanding of cation–π–cation interactions and their role in the structure and stability of biosystems via two complementary approaches. The first one consists of a statistical study of the occurrence, composition and geometry of cation–π– cation interactions identified on a non-redundant set of protein structures from the PDB (Protein Data Bank), which demonstrates that cation–π–cation interactions are indeed common in proteins. We also analyze the degree of conservation of the interactions by inspection of similar sequences obtained through the sequence alignment tool BLAST. The second part of the study consists of an energetic analysis of the most relevant interactions at the SCSMP2/ CBS level of theory, as well as an energy decomposition analysis for representative cases performed at the SAPT2 level. Besides the well-known deficiency of standard additive force fields to describe the relevant polarization contribution to cation–π interactions, our results indicate that non-additive three-body contributions are significant in this case, implying that cation–π– cation interactions constitute an even more challenging case expected to be dramatically misrepresented by standard additive force fields. In vacuum, the interactions identified are strongly repulsive. Further work is being carried out in order to understand the strength of cation–π–cation interactions in a protein environment, where the cation–cation repulsion will be strongly screened.
dc.format.extent3 p.
dc.language.isoeng
dc.publisherBarcelona Supercomputing Center
dc.relation.ispartofBSC Doctoral Symposium (2nd: 2015: Barcelona)
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.subjectÀrees temàtiques de la UPC::Informàtica::Arquitectura de computadors
dc.subjectÀrees temàtiques de la UPC::Enginyeria química::Química orgànica
dc.subject.lcshHigh performance computing
dc.subject.lcshSupercomputers
dc.subject.lcshCations
dc.subject.lcshMolecular biology
dc.subject.otherCation–π interaction
dc.subject.otherThree-body
dc.subject.otherInteraction energy
dc.subject.otherCation-cation– π interactions
dc.subject.otherNon-polarizable FFs
dc.titleCation–π–cation interactions in structural biology
dc.typeConference report
dc.subject.lemacCàlcul intensiu (Informàtica)
dc.subject.lemacSupercomputadors
dc.subject.lemacCations
dc.subject.lemacBiologia molecular
dc.rights.accessOpen Access
local.citation.authorPinheiro, Silvana; Soteras, Ignacio; Gelpí, José Luis; Dehez, François; Chipot, Christophe; Luque, F. Javier; Curutchet, Carles
local.citation.pubplaceBarcelona
local.citation.publicationNameBSC Doctoral Symposium (2nd: 2015: Barcelona)
local.citation.startingPage103
local.citation.endingPage105
local.citation.edition2nd


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