Anion–π interactions in active centers of superoxide dismutases

Ribić, Vesna; Stojanović, Srđan Đ.; Zlatović, Mario

doi:10.1016/j.ijbiomac.2017.08.050

Cited by 20 publications

(17 citation statements)

References 68 publications

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“…The repulsive nature of those interactions emerges from the unfavorable geometries of interacting pairs in the crystal structures and usually is counterbalanced by other interactions. Namely, when examined under isolated conditions, this type of interaction is considered unfavorable, but similar to other potentially unfavorable interactions, their influence can be compensated by other interactions from the rest of the polypeptide chain . This observation indicates that hydrogen bonding free energy is important for maintaining the stability of phycocyanin proteins.…”

Section: Resultsmentioning

confidence: 96%

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Breberina

Zlatović

Nikolić

et al. 2019

Molecular Informatics

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Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call "standard-size" interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 % � 1.7 % on average in these complexes. Moreover, there is about 1.9 % � 1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than À 16 kJ mol À 1 , while most of them have energy in the range from À 6 to À 14 kJ mol À 1 . The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.

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Section: Resultsmentioning

confidence: 96%

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Breberina

Zlatović

Nikolić

et al. 2019

Molecular Informatics

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“…Earlier publications confirmed π interactions as long-range interactions, having notable binding forces even at intermolecular distances of 7 Å. [27][28][29] Fig. 1.…”

Section: Amide- Interaction Analysismentioning

confidence: 76%

“…calculations were performed on structurally reduced model systems. 29 We used formamide (1) as mimics for amide groups. Phenylalanine was simplified to methylbenzene (2), histidine to 5-methyl-1H-imidazole (3), while tryptophan and tyrosine were reduced to 3-methyl-1H--indole ( 4) and 4-methyphenol (5), respectively (Fig.…”

Section: O N L I N E F I R S Tmentioning

confidence: 99%

“…This might be because, of all the aromatic amino acids, His occurs most frequently in both coordination spheres of active centers. 29 The number of times a particular amino acid occurs in an appropriate interaction; b Percent of amino acid occurs in an appropriate interaction A typical interface with some of the amide- interactions involving backbone planar residues (A:Ile36:C,O;Met37:N-A:His40) and side-chain residues (A:Gln14:N-A:Tyr16) is shown in Fig. 3a and 3b respectively.…”

Section: O N L I N E F I R S Tmentioning

confidence: 99%

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Amide-π interactions in active centers of superoxide dismutase

2021

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In this work, we have analyzed the influence of amide-? interactions on stability and properties of superoxide dismutase (SOD) active centers. In the data set of 43 proteins, 5017 amide-? interactions were observed, and every active center forms 117 interactions, on the average. Most of the interactions belong to the backbone of proteins. The analysis of the geometry of the amide-? interactions revealed two preferred structures, parallel-displaced and T-shaped structure. The aim of this study was to investigate the energy contribution resulting from amide-? interactions, which were in the lower range of strong hydrogen bonds. The conservation patterns in the present study indicate that more than half of the residues involved in these interactions are evolutionarily conserved. Stabilization centers for these proteins showed that all residues involved in amide-? interactions were important in locating one or more of such centers. The results presented in this work can be very useful for understanding the contribution of amide-? interaction to the stability of SOD active centers.

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“…In some cases, the water molecule had two short contacts to hydrogen‐bond acceptors, and the authors concluded by inference that one of the lone‐pairs of the water molecule must be oriented along a normal to the indole plane. Since then, such interactions, baptized “lone‐pair–π (lp–π) interactions”, became widely recognized as a force stabilizing biomolecules …”

Section: Introductionmentioning

confidence: 99%

Water–Tryptophan Interactions: Lone‐pair⋅⋅⋅π or O−H⋅⋅⋅π? Molecular Dynamics Simulations of β‐Galactosidase Suggest that Both Modes Can Co‐exist

Durec

Marek

Kozelka

2018

Chemistry A European J

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In proteins, the indole side chain of tryptophan can interact with water molecules either in-plane, forming hydrogen bonds, or out-of-plane, with the water molecule contacting the aromatic π face. The latter interaction can be either of the lone pair⋅⋅⋅π (lp⋅⋅⋅π) type or corresponds to the O-H⋅⋅⋅π binding mode, an ambiguity that X-ray structures usually do not resolve. Here, we report molecular dynamics (MD) simulations of a solvated β-galactosidase monomer, which illustrate how a water molecule located at the π face of an indole side chain of tryptophan can adapt to the position of proximate residues and "select" its binding mode. In one such site, the water molecule is predicted to rapidly oscillate between the O-H⋅⋅⋅π and lp⋅⋅⋅π binding modes, thus gaining entropic advantage. Our MD simulations provide support for the role of lp⋅⋅⋅π interactions in the stabilization of protein structures.

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Anion–π interactions in active centers of superoxide dismutases

Cited by 20 publications

References 68 publications

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Amide-π interactions in active centers of superoxide dismutase

Water–Tryptophan Interactions: Lone‐pair⋅⋅⋅π or O−H⋅⋅⋅π? Molecular Dynamics Simulations of β‐Galactosidase Suggest that Both Modes Can Co‐exist

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