Contribution of Non‐Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies

Stojanović, Srđan Đ.; Isenović, Esma R.; Zarić, Božidarka

doi:10.1002/minf.201000176

Cited by 5 publications

(3 citation statements)

References 73 publications

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“…The networks of hydrogen bonds between subunits are important for protein stability, functionality, and structural integrity . There are 903 hydrogen bonds across the 118 phycocyanin protein interfaces of our dataset.…”

Section: Resultsmentioning

confidence: 99%

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: 99%

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Breberina

Zlatović

Nikolić

et al. 2019

Molecular Informatics

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“…In general they are very stable and sometimes the presence of chaotropic agent is necessary for their disruption [14,17]. We have previously reported contribution of hydrogen bonds, salt bridges and non-canonical interactions to the stability of Sm oligomers [21,22]. In our work [23], we showed that the hot spots of Sm proteins are located within densely packed regions; these are highly conserved and have large energy contributions to the interface interactions.…”

Section: Introductionmentioning

confidence: 49%

“…In an effort to search for the factors that contribute to the affinity and specificity of protein-protein interactions, many previous studies were aimed at the analysis of the properties of protein-protein interfaces. This manuscript expands on our previous work on the non-canonical interactions of Sm/LSm proteins [21,22] by analyzing the same class of proteins with respect to ππ interactions. We have systematically analyzed the influence of π-π interactions to the stability of Sm/LSm proteins.…”

Section: Introductionmentioning

confidence: 81%

Aromatic π-networks in Sm/LSm protein interfaces

Breberina

Nikolić

Stojanović

2014

Facta Univ Phys Chem Technol

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In this work, we have analyzed the influence of ?-? interactions on stability and properties of Sm/LSm assemblies. Phe residues were found to be involved in ?-? interactions much more frequently than Tyr or His. Similarly, the Phe-Phe ?-? interacting pair had the highest frequency of occurrence. Furthermore, a significant number of ?-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 ?. 3? and 7?-networks were found to frequently have plane-plane angles less than 60?. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the ?-? interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins. [Projekat Ministarstva nauke Republike Srbije, br. 172001 i br. 172035]

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Contribution of cation–π interactions to the stability of Sm/LSm oligomeric assemblies

2014

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In this work, we have analyzed the influence of cation-π interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the π group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-π interactions is much higher than that of single cation-π interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-π interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the ΔΔG of binding for residues in the core and also for hot spot residues cation-π bonded across the interface. Secondary structure of the cation-π residues shows that Arg and Lys preferred to be in strand. Among the π residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-π interactions are important in locating one or more of such centers. More than 50 % of the cation-π interacting residues are highly conserved. It is likely that the cation-π interactions contribute significantly to the overall stability of Sm/LSm proteins.

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Contribution of Non‐Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies

Cited by 5 publications

References 73 publications

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Aromatic π-networks in Sm/LSm protein interfaces

Contribution of cation–π interactions to the stability of Sm/LSm oligomeric assemblies

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