The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering

Zaccaı̈, Giuseppe; Natali, Francesca; Peters, Judith; Říhová, Martina; Zimmerman, Ella; Ollivier, Jacques; Combet, J.; Maurel, Marie‐Christine; Bashan, Anat; Yonath, Ada

doi:10.1038/srep37138

Cited by 12 publications

(9 citation statements)

References 57 publications

(67 reference statements)

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“…Zaccai et al . (2016) investigated both water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui , under high salt, stable conditions. Whereas no significant difference was observed for hydration water of the two subunits, the 30 S was found to have a softer force constant (0.016(1) and 0.018(2) N m −1 in 3 M NaCl and 3 M KCl, respectively) and larger MSD (17.9(9) and 16.3(8) Å 2 ) than the 50 S ( = 0.034(4) N m −1 , = 12.1(6) Å 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…The force constant was associated with the resilience of the protein, and was calculated in a number of studies to compare in a quantitative manner EINS results from different proteins in various conditions (Gabel et al, 2003). Zaccai et al (2016) investigated both water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Whereas no significant difference was observed for hydration water of the two subunits, the 30 S was found to have a softer force constant (0.016(1) and 0.018(2) N m −1 in 3 M NaCl and 3 M KCl, respectively) and larger MSD (17.9(9) and 16.3(8) Å 2 ) than the 50 S (〈k〉 = 0.034(4) N m −1 , 〈u 2 〉 = 12.1(6) Å 2 ).…”

Section: Dynamics Of Hydrated Protein Powdersmentioning

confidence: 99%

“…Whereas no significant difference was observed for hydration water of the two subunits, the 30 S was found to have a softer force constant (0.016(1) and 0.018(2) N m −1 in 3 M NaCl and 3 M KCl, respectively) and larger MSD (17.9(9) and 16.3(8) Å 2 ) than the 50 S (〈k〉 = 0.034(4) N m −1 , 〈u 2 〉 = 12.1(6) Å 2 ). The authors argued that the enhanced flexibility likely facilitates conformational adjustments required for messenger and transfer RNA binding (Zaccai et al, 2016). Fabiani et al (2009) combined circular dichroism (CD), neutron and X-ray scattering to study changes of MD of apomyoglobin (apoMb) as a function of temperature.…”

Section: Dynamics Of Hydrated Protein Powdersmentioning

confidence: 99%

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Dynamics of proteins in solution

Grimaldo

Roosen-Runge

Zhang

et al. 2019

Quart. Rev. Biophys.

107

164

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The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

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Section: Resultsmentioning

confidence: 99%

Section: Dynamics Of Hydrated Protein Powdersmentioning

confidence: 99%

Section: Dynamics Of Hydrated Protein Powdersmentioning

confidence: 99%

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Dynamics of proteins in solution

Grimaldo

Roosen-Runge

Zhang

et al. 2019

Quart. Rev. Biophys.

107

164

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“…To date, experimental techniques such as Nuclear Magnetic Resonance7, single molecule spectroscopy101314, time-resolved X-ray crystallography15, and Neutron Scattering1617 represent the principal means of investigation of protein dynamics and function. Particularly, elastic, quasielastic, and inelastic incoherent NS have been exploited not only to study the sub-nanosecond timescale local functional dynamics of model proteins1819 and their solvent2021, but also for in-vivo investigations of bacterial systems22.…”

mentioning

confidence: 99%

Thermal activation of ‘allosteric-like’ large-scale motions in a eukaryotic Lactate Dehydrogenase

Katava

Maccarini

Villain

et al. 2017

Sci Rep

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Conformational changes occurring during the enzymatic turnover are essential for the regulation of protein functionality. Individuating the protein regions involved in these changes and the associated mechanical modes is still a challenge at both experimental and theoretical levels. We present here a detailed investigation of the thermal activation of the functional modes and conformational changes in a eukaryotic Lactate Dehydrogenase enzyme (LDH). Neutron Spin Echo spectroscopy and Molecular Dynamics simulations were used to uncover the characteristic length-and timescales of the LDH nanoscale motions in the apo state. The modes involving the catalytic loop and the mobile region around the binding site are activated at room temperature, and match the allosteric reorganisation of bacterial LDHs. In a temperature window of about 15 degrees, these modes render the protein flexible enough and capable of reorganising the active site toward reactive configurations. On the other hand an excess of thermal excitation leads to the distortion of the protein matrix with a possible anti-catalytic effect. Thus, the temperature activates eukaryotic LDHs via the same conformational changes observed in the allosteric bacterial LDHs. Our investigation provides an extended molecular picture of eukaryotic LDH's conformational landscape that enriches the static view based on crystallographic studies alone.Protein dynamics and functionality are intimately related. Nevertheless, the fine details of how the conformational changes of proteins modulate and regulate their activity are still to be defined [1][2][3][4] . It is now accepted that protein dynamics is characterized by a hierarchy of timescales, from picoseconds to microseconds, reflecting a rough manifold conformational landscape [5][6][7] . There have been numerous studies on the relationship between this wide range of dynamical processes and protein functionality. These include substrate binding/unbinding kinetics 8 , catalysis 9,10 , and allosteric relaxation 11,12 . To date, experimental techniques such as Nuclear Magnetic Resonance 7 , single molecule spectroscopy 10,13,14 , time-resolved X-ray crystallography 15 , and Neutron Scattering 16,17 represent the principal means of investigation of protein dynamics and function. Particularly, elastic, quasielastic, and inelastic incoherent NS have been exploited not only to study the sub-nanosecond timescale local functional dynamics of model proteins 18,19 and their solvent 20,21 , but also for in-vivo investigations of bacterial systems 22 . On the other hand, Neutron Spin Echo spectroscopy (NSE) has been shown to be an invaluable tool to explore the dynamics of biomolecules on larger spatial scales, of the order of nanometer, for times up to hundreds of nanoseconds [23][24][25][26][27] . NSE has been successfully applied to systems that exhibit long-range signaling modes via domain displacement, as in the case of the NHERF1 , as well as to Alcohol Dehydrogenase, a more compact multimeric protein 24 . Because the investigate...

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“…To date, the QENS method has been used in many studies to characterize the overall picture of protein dynamics 29 . The scope of QENS research is expanding from small single-domain proteins 41,42 to larger and more complex molecular systems 43,44,45 , as well as to large-scale conformational changes such as those that occur upon ligand binding 33,46,47 , pressurization 48,49,50 , unfolding 35, 51, 52, 53, 54, , and fibrillization 34,56 .…”

Section: Discussionmentioning

confidence: 99%

Cross-scale Analysis of Temperature Compensation in the Cyanobacterial Circadian Clock System

Furuike

Ouyang²,

Tominaga

et al. 2021

Preprint

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Clock proteins maintain constant enzymatic activity regardless of temperature, even though thermal fluctuation is accelerated as temperature increases. We investigated temperature influences on the dynamics of KaiC, a temperature-compensated ATPase in the cyanobacterial circadian clock system, using quasielastic neutron scattering. The frequency of picosecond to sub-nanosecond incoherent local motions in KaiC was accelerated very slightly in a temperature-dependent manner. Our mutation studies revealed that internal motions of KaiC include several contributions of opposing temperature sensitivities. To take advantage of this balancing effect, the motional frequency of local dynamics in KaiC needs to exceed ∼0.3 ps-1. Some of the mutation sites may be in a pathway through which the motional frequency in the C-terminal domain of KaiC is fed back to the active site of ATPase in its N-terminal domain. The temperature-compensating ability at the dynamics level is likely crucial for circadian clock systems, into which the clock proteins are incorporated, to achieve reaction- or even system-level temperature compensation of the oscillation frequency.

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The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering

Cited by 12 publications

References 57 publications

Dynamics of proteins in solution

Dynamics of proteins in solution

Thermal activation of ‘allosteric-like’ large-scale motions in a eukaryotic Lactate Dehydrogenase

Cross-scale Analysis of Temperature Compensation in the Cyanobacterial Circadian Clock System

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