The role of protein dynamics in allosteric effects—introduction

Roberts, Gordon C. K.

doi:10.1007/s12551-015-0174-6

Cited by 8 publications

(8 citation statements)

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“…Supporting our hypothesis, recent studies have proposed the existence of a new type of allostery that does not involve the propagation of a conformational change but that is rather based on altered protein dynamics or order-disorder transition [66,67,68,69]. We have indeed already noticed that some r-proteins display particular electrostatic properties that enable the allosteric coupling of their remote domains [70,71].…”

Section: Hypothesessupporting

confidence: 68%

Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives

Timsit

Bennequin

2019

IJMS

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In the past few decades, studies on translation have converged towards the metaphor of a “ribosome nanomachine”; they also revealed intriguing ribosome properties challenging this view. Many studies have shown that to perform an accurate protein synthesis in a fluctuating cellular environment, ribosomes sense, transfer information and even make decisions. This complex “behaviour” that goes far beyond the skills of a simple mechanical machine has suggested that the ribosomal protein networks could play a role equivalent to nervous circuits at a molecular scale to enable information transfer and processing during translation. We analyse here the significance of this analogy and establish a preliminary link between two fields: ribosome structure-function studies and the analysis of information processing systems. This cross-disciplinary analysis opens new perspectives about the mechanisms of information transfer and processing in ribosomes and may provide new conceptual frameworks for the understanding of the behaviours of unicellular organisms.

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Section: Hypothesessupporting

confidence: 68%

Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives

Timsit

Bennequin

2019

IJMS

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“…These rigidified methyl carbon atoms are shown in the right panel of Figure 5 (cf. Table S4 in SI: progressive # 5, 8, 9, 12, 15, 17, 18, 19, 24, 28, 42, 43, 50, 61, 62 of Figure 4F, corresponding to residues 11,18,20,22,26,28,30,39,40,41,66,78,89). Coordination decrease at the level of the side chains is only observed at isolated positions, such as the N terminal β strand containing residues 6, 11, 12, and around residue 61 before helix H2.…”

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains

et al. 2017

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With the aim of investigating the relationship between the fast fluctuations of proteins and their allosteric behavior, we perform molecular dynamics simulations of two model PDZ domains with differential allosteric responses. We focus on protein dynamics in the THz regime (0.1-3 THz) as opposed to lower frequencies. By characterizing the dynamic modulation of the protein backbone induced by ligand binding in terms of single residue and pairwise distance fluctuations, we identify a response nucleus modulated by the ligand that is visible only at THz frequencies. The residues of this nucleus undergo a significant stiffening and an increase in mutual coordination upon binding. Additionally, we find that the dynamic modulation is significantly more intense for the side chains, where it is also redistributed to distal regions not immediately in contact with the ligand allowing us to better define the response nucleus at THz frequencies. The overlap between the known allosterically responding residues of the investigated PDZ domains and the modulated region highlighted here suggests that fast THz dynamics could play a role in allosteric mechanisms.

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“…This issue focussed on the concept that a ligand interacting with one site on a protein can change the functional properties at another site without direct spatial proximity of the two binding sites (Roberts 2015 After that, other Special Issues are planned, one on Nanobiophysics and another on The Giant Protein Titin and its Binding Partners.…”

mentioning

confidence: 99%

The evolution of Biophysical Reviews

Remedios

2016

Biophys Rev

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The role of protein dynamics in allosteric effects—introduction

Cited by 8 publications

References 50 publications

Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives

Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives

Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains

The evolution of Biophysical Reviews

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