The effect of backbone on the small-world properties of protein contact maps

Bartoli, Lisa; Fariselli, Piero; Casadio, Rita

doi:10.1088/1478-3975/4/4/l01

Cited by 39 publications

(45 citation statements)

References 26 publications

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“…4.4, 4.7 and 4.8). This is in line with the results of [40], showing the main topological features of PCNs derive from the presence of a continuous backbone; as a matter of fact, the whole connectivity is lost as soon as L gets larger than 4,excluding the adjacent residues contacts, due to the peptide backbone. Relying on covalent, peptide bonds for network connectivity, allows for large motions of the proteins keeping alive the molecule integrity.…”

Section: Pictorial Sketch Of Graphssupporting

confidence: 91%

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Paci¹,

Paola²,

Santoni³

et al. 2012

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Long-range contacts in protein structures were demonstrated to be predictive of different physiological properties of hemoglobin and albumin proteins. Complex networks based approach was demonstrated to highlight basic principles of protein folding and activity. The presence of a natural scaling region ending at an approximate threshold of 120-150 residues shared by proteins of different size and quaternary structure was highlighted. This threshold is reminiscent of the typical size for a macromolecule to have a binding site sensible to environmental regulation.

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Section: Pictorial Sketch Of Graphssupporting

confidence: 91%

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Paci¹,

Paola²,

Santoni³

et al. 2012

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“…The centrality profile in the ATP-bound Hsp90 deviated from the random graph model, which was manifested by a sharper decay and a longer tail of the distribution. A similar effect was seen in proteins strongly affected by specific functional requirements such as thermal stability, ligand binding, and specificity of enzyme catalysis [116]. We then examined the network centrality profiles and the spatial distributions of mediating residues in different functional states of Hsp90.…”

Section: Resultsmentioning

confidence: 73%

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

Blacklock

Verkhivker

2014

PLoS Comput Biol

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A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple communication routes. This may be a universal requirement encoded in protein structures to balance the inherent tension between resilience and efficiency of the residue interaction networks.

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“…Long-range contacts occurring between residues that are close only in the tertiary structure contribute to a scale-free behavior [7,12]. In a scale-free network, central residues are more abundant than in a randomly connected network.…”

Section: Introductionmentioning

confidence: 99%

Protein thermal denaturation is modulated by central residues in the protein structure network

et al. 2016

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Network structural analysis, known as residue interaction networks or graphs (RIN or RIG, respectively) or protein structural networks or graphs (PSN or PSG, respectively), comprises a useful tool for detecting important residues for protein function, stability, folding and allostery. In RIN, the tertiary structure is represented by a network in which residues (nodes) are connected by interactions (edges). Such structural networks have consistently presented a few central residues that are important for shortening the pathways linking any two residues in a protein structure. To experimentally demonstrate that central residues effectively participate in protein properties, mutations were directed to seven central residues of the bglucosidase Sfbgly (b-D-glucoside glucohydrolase; EC 3.2.1.21). These mutations reduced the thermal stability of the enzyme, as evaluated by changes in transition temperature (T m ) and the denaturation rate at 45°C. Moreover, mutations directed to the vicinity of a central residue also caused significant decreases in the T m of Sfbgly and clearly increased the unfolding rate constant at 45°C. However, mutations at noncentral residues or at surrounding residues did not affect the thermal stability of Sfbgly. Therefore, the data reported in the present study suggest that the perturbation of the central residues reduced the stability of the native structure of Sfbgly. These results are in agreement with previous findings showing that networks are robust, whereas attacks on central nodes cause network failure. Finally, the present study demonstrates that central residues underlie the functional properties of proteins.

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The effect of backbone on the small-world properties of protein contact maps

Cited by 39 publications

References 26 publications

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

Protein thermal denaturation is modulated by central residues in the protein structure network

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