Influence of Structural Symmetry on Protein Dynamics

Matsunaga, Yasuhiro; Koike, Ryotaro; Ota, Motonori; Tame, J.R.H.; Kidera, Akinori

doi:10.1371/journal.pone.0050011

Cited by 17 publications

(24 citation statements)

References 44 publications

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“…Proteins symmetry research continuous to be a central theme in structural biochemistry, and some recent examples are collected in Refs. . Understanding the abundance of this structural feature—symmetry—has received much attention, because at first glance it is not clear why this feature is important for proteins function, that is, why has symmetric clustering evolved at all.…”

Section: Introductionmentioning

confidence: 99%

The near‐symmetry of proteins

Bonjack-Shterengartz

Avnir

2015

Proteins

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The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.

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Section: Introductionmentioning

confidence: 99%

The near‐symmetry of proteins

Bonjack-Shterengartz

Avnir

2015

Proteins

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“…If we were to consider the co-occurrence of the functional dynamic classification states over time on any two sites of the protein, we can use mutual information to identify concerted dynamic functions between functional protein sites. This can potentially be very useful for the study of dynamics of proteins with bilateral binding symmetry (30,31) or allosteric regulation (32). If the dynamics of two neighboring sites or even two distant sites are locked together in time, they will exhibit higher degrees of mutual information.…”

Section: C) Mutual Information and Coordinated Dynamicsmentioning

confidence: 99%

Information theoretics for the machine learning detection of functionally conserved and coordinated protein motions

Babbitt

2020

Preprint

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The application of machine learning classification to the molecular dynamics of the functional states of protein allows for application of an information theoretic framework similar to traditional bioinformatics. The functional states of proteins involving binding interactions with partners comprised of protein, DNA or small molecules can first be defined in a binary fashion (i.e. bound vs unbound), subsequently simulated in molecular dynamics software, and then employed as a comparative training set for a binary machine learning classifier capable of discerning the complex dynamical consequences of binding interaction. This learner can subsequently be deployed on new simulations of the functionally bound state to validate its ability to recognize the molecular motions that are supporting binding function. Regions of proteins with functionally conserved dynamics will induce significant local correlations in learning performance across independent validation runs. Through case studies of Rbp subunit 4/7 interaction in RNA Pol II and DNA-protein interactions of TATA binding protein, we demonstrate this method of detecting functionally conserved protein dynamics. We also demonstrate how Shannon information, relative entropy and mutual information can be applied to these binary classification states of dynamic simulations in order to compare dynamics and identify coordinated motions involved in dynamic interactions across sites.

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“…One common motion patterns among all complexes with cyclic symmetry (C n ) is that all subunits have symmetric, identical motions, as given in Equation 22. They account for 1/n of the total number of modes.…”

Section: The Motion Patterns Of Complexes With Cyclic Symmetrymentioning

confidence: 99%

The finite number of global motion patterns available to symmetric protein complexes

Song

2017

Proteins

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In PDB, more than half of the entries are structure complexes and of these complexes, most are symmetric, composed of identical subunits. Complex formation is the way through which larger structures and even molecular machines are assembled and built in nature. In this work, we apply group theory and carry out a comprehensive study of the global motion patterns of protein complexes of various symmetries. The work presents for the first time a comprehensive list of all the symmetric, aesthetically pleasing, global motion patterns available to complexes of cyclic, dihedral, tetrahedral, or octahedral symmetry. Our results clearly demonstrate that complexes with the same symmetry will have the same global motion patterns and thus may function in a similar way, and that there are only a finite number of global motion patterns available to symmetric complexes as the number of protein symmetry groups is effectively finite. The work complements our current understanding of the principle of complex formation that has been mostly structure-based by providing novel dynamics-based insights. Furthermore, as dynamics is closely tied to function, these motion patterns can provide global insights into the general functional mechanisms of protein complexes.

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Influence of Structural Symmetry on Protein Dynamics

Cited by 17 publications

References 44 publications

The near‐symmetry of proteins

The near‐symmetry of proteins

Information theoretics for the machine learning detection of functionally conserved and coordinated protein motions

The finite number of global motion patterns available to symmetric protein complexes

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