Understanding on the residue contact network using the log‐normal cluster model and the multilevel wheel diagram

Sun, Weidong; He, Jing

doi:10.1002/bip.21494

“…Side-chain fluctuations are strongly correlated with the spatial arrangement of the residues, highlighting the fact that central amino acids (occurring on average on more shortest paths between other residues) display more restricted motion [Atilgan et al, 2004]. This is in agreement with the general notion that surface residues undergo larger fluctuations than core residues [Ruvinsky and Vakser, 2010], as well as normal mode analysis that shows that amino acid hubs have lower flexibility than sparsely connected amino acids [Sun and He, 2010]. Using elastic network model-inferred fluctuations, amino acids could be classified into 3 classes: the highly fluctuating Gly, Ala, Ser, Pro and Asp; PEST-sequences are keys in protein degradation and signaling.…”

supporting

confidence: 80%

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

Csermely¹,

Sandhu²,

Hazai³

et al. 2012

CPPS

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During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into 'cumulus-type', i.e., those similar to puffy (white) clouds, and 'stratus-type', i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an 'energy transfer' mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by 'multi-trajectories'; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach 'rarely visited' but functionally-related states. We also show the role of disorder in 'spatial games' of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks.

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“…network communities), which are often hierarchical, and usually correspond to domains. Proteins having less than 200 amino acids seldom display a modular structure [5,7,13,[15][16][17][18], however they consist of 'foldons' [19], which may form a distinct class of tighter structural networks, with fast folding kinetics.studies showing the effect of protein disorder to the small-worldness of protein structure networks are currently missing.…”

mentioning

confidence: 99%

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review

Csermely

¹

,

Sandhu

²

,

Hazai³

et al. 2011

View full text Add to dashboard Cite

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into 'cumulus-type', i.e., those similar to puffy (white) clouds, and 'stratus-type', i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an 'energy transfer' mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by 'multi-trajectories'; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach 'rarely visited' but functionally-related states. We also show the role of disorder in 'spatial games' of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks. # Mr. Zsolt Hoksza is a high school student of the Fazekas High School (www.fazekas.hu) in Budapest, Hungary, who started his research as a member of the EU Descartes Award winning High School Research Student organization (www.kutdiak.hu) founded by P.C. and offering research opportunities for several thousands of high school students since 1996. STRUCTURE AND DYNAMICS OF PROTEINS AS NETWORKS 2.A. Definition of protein structure networks.Protein structure networks (also called protein contact networks) form the basal layer of the cellular network hierarchy. At the residue level of coarse-graining, the nodes are amino acids, while links connect amino acids whose inter-distance is below a cut-off (usually 0.4 to 0.85 nm) in the native fold. Protein structure networks may have weighted links instead of distance cut-offs, and may discriminate between individual atoms (like αC or βC atoms). Covalent bonds may be included or excluded in the network representation [1-9].2.B. Key topological properties of protein structure networks. In the small world of protein structure networks any two amino acids are separated by only a few links, and the network diameter grows logarithmically with increasing number of amino acids. This smallworldness promotes the fast transmission of perturbations (conformational changes). Typically, protein structure networks have a Poisson degree distribution rather than the widely characteristic scale-free degree distribution. This means that they have fewer hubs than expected, and amino acid "mega-hubs", having an extremely large number of neighbors do not exist, whic...

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“…There are more interactions between these hub residues with other residues, so these hub residues play a vital role to the stability of whole protein structures [7, 8, 27]. In some other work, in order to embody the influence of the local environment, the distribution of residue clusters has been analyzed, and the outcome is a log-normal distribution [28]. …”

Section: Resultsmentioning

confidence: 99%

A Modified Amino Acid Network Model Contains Similar and Dissimilar Weight

Jiao

¹

,

Yang²,

Liu³

et al. 2013

Computational and Mathematical Methods in Medicine

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For a more detailed description of the interaction between residues, this paper proposes an amino acid network model, which contains two types of weight—similar weight and dissimilar weight. The weight of the link is based on a self-consistent statistical contact potential between different types of amino acids. In this model, we can get a more reasonable representation of the distance between residues. Furthermore, with the network parameter, average shortest path length, we can get a more accurate reflection of the molecular size. This amino acid network is a “small-world” network, and the network parameter is sensitive to the conformation change of protein. For some disease-related proteins, the highly central residues of the amino acid network are highly correlated with the hot spots. In the compound with the related drug, these residues either interacted directly with the drug or with the residue which is in contact with the drug.

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Understanding on the residue contact network using the log‐normal cluster model and the multilevel wheel diagram

Cited by 8 publications

References 92 publications

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review

A Modified Amino Acid Network Model Contains Similar and Dissimilar Weight

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