Comparing local search paths with global search paths on protein residue networks: allosteric communication

Khor, Susan

doi:10.1093/comnet/cnw020

Cited by 3 publications

(4 citation statements)

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“…The network of shortcut edges present in a native-state protein (SCN0) is proposed as an effective structural abstraction of protein molecules for folding purposes. Shortcut edges are identified by the EDS algorithm on a Protein Residue Network of a native-state protein (PRN0) [16,24]. The EDS algorithm is based on an intuitive message passing algorithm on a social network [27,28].…”

Section: Resultsmentioning

confidence: 99%

“…Despite this, the modular structure of proteins is preserved in PRN0s . Besides, distant contacts (≈10 Å) can be functional . The maximum Cα‐Cα Euclidean distance of edges in SCN0s is smaller (≈9 Å).…”

Section: Methodsmentioning

confidence: 99%

“…This design choice was inherited from [18], and has so far shown itself to be a fortuitous one. It has allowed investigation of allosteric communication in proteins [24], and provided this research is successful, it potentially equips the PRN model to facilitate an integrated investigation into protein folding and dynamics [25]. We note that peptide bond effects, i.e.…”

Section: The Native Shortcut Networkmentioning

confidence: 96%

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Folding with a protein's native shortcut network

Khor

2018

Proteins

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A complex network approach to protein folding is proposed, wherein a protein's contact map is reconceptualized as a network of shortcut edges, and folding is steered by a structural characteristic of this network. Shortcut networks are generated by a known message passing algorithm operating on protein residue networks. It is found that the shortcut networks of native structures (SCN0s) are relevant graph objects with which to study protein folding at a formal level. The logarithm form of their contact order (SCN0_lnCO) correlates significantly with folding rate of two-state and nontwo-state proteins. The clustering coefficient of SCN0s (C ) correlates significantly with folding rate, transition-state placement and stability of two-state folders. Reasonable folding pathways for several model proteins are produced when C is used to combine protein segments incrementally to form the native structure. The folding bias captured by C is detectable in non-native structures, as evidenced by Molecular Dynamics simulation generated configurations for the fast folding Villin-headpiece peptide. These results support the use of shortcut networks to investigate the role protein geometry plays in the folding of both small and large globular proteins, and have implications for the design of multibody interaction schemes in folding models. One facet of this geometry is the set of native shortcut triangles, whose attributes are found to be well-suited to identify dehydrated intraprotein areas in tight turns, or at the interface of different secondary structure elements.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: The Native Shortcut Networkmentioning

confidence: 96%

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Folding with a protein's native shortcut network

Khor

2018

Proteins

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“…The focus on dynamical network models, or rather the dynamics of PRN was explored as well [22]. VanWarth et al [23] examined dynamic models of allostery, see also [24]. Conformational changes in PRNs were elucidated in several works [25][26][27] The field of protein folding also adopted ideas from PRN models [28,29].…”

Section: Introductionmentioning

confidence: 99%

pyProGA—A PyMOL plugin for protein residue network analysis

et al. 2021

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The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be used by the proteomics community outside of the PRN specialists. In this paper we present software which collects an ensemble of (network) methods tailored towards the analysis of protein-protein interactions (PPI) and/or interactions of proteins with ligands of other type, e.g. nucleic acids, oligosaccharides etc. In parallel, we propose the use of the network differential analysis as a method to identify residues mediating key interactions between proteins. We use a model system, to show that in combination with other, already published methods, also included in pyProGA, it can be used to make such predictions. Such extended repertoire of methods allows to cross-check predictions with other methods as well, as we show here. In addition, the possibility to construct PRN models from various kinds of input is so far a unique asset of our code. One can use structural data as defined in PDB files and/or from data on residue pair interaction energies, either from force-field parameters or fragment molecular orbital (FMO) calculations. pyProGA is a free open-source software available from https://gitlab.com/Vlado_S/pyproga.

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Thermostability of Lipase A and Dynamic Communication Based on Residue Interaction Network

Xia

Ding

2019

PPL

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Objective: Dynamic communication caused by mutation affects protein stability. The main objective of this study is to explore how mutations affect communication and to provide further insight into the relationship between heat resistance and signal propagation of Bacillus subtilis lipase (Lip A). Methods: The relationship between dynamic communication and Lip A thermostability is studied by long-time MD simulation and residue interaction network. The Dijkstra algorithm is used to get the shortest path of each residue pair. Subsequently, time-series frequent paths and spatio-temporal frequent paths are mined through an Apriori-like algorithm. Results: Time-series frequent paths show that the communication between residue pairs, both in wild-type lipase (WTL) and mutant 6B, becomes chaotic with an increase in temperature; however, more residues in 6B can maintain stable communication at high temperature, which may be associated with the structural rigidity. Furthermore, spatio-temporal frequent paths reflect the interactions among secondary structures. For WTL at 300K, β7, αC, αB, the longest loop, αA and αF contact frequently. The 310-helix between β3 and αA is penetrated by spatio-temporal frequent paths. At 400K, only αC can be frequently transmitted. For 6B, when at 300K, αA and αF are in more tight contact by spatio-temporal frequent paths though I157M and N166Y. Moreover, the rigidity of the active site His156 and the C-terminal of Lip A are increased, as reflected by the spatio-temporal frequent paths. At 400K, αA and αF, 310-helix between β3 and αA, the longest loop, and the loop where the active site Asp133 is located can still maintain stable communication. Conclusion: From the perspective of residue dynamic communication, it is obviously found that mutations cause changes in interactions between secondary structures and enhance the rigidity of the structure, contributing to the thermal stability and functional activity of 6B.

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Comparing local search paths with global search paths on protein residue networks: allosteric communication

Cited by 3 publications

References 48 publications

Folding with a protein's native shortcut network

Folding with a protein's native shortcut network

pyProGA—A PyMOL plugin for protein residue network analysis

Thermostability of Lipase A and Dynamic Communication Based on Residue Interaction Network

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