Cation–π–cation interactions in structural biology
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hdl:2099/16566
Tipus de documentText en actes de congrés
Data publicació2015-05-05
EditorBarcelona Supercomputing Center
Condicions d'accésAccés obert
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Reconeixement-NoComercial-SenseObraDerivada 3.0 Espanya
Abstract
Biological 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.
CitacióPinheiro, 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.
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