Coupled relaxations at the protein–water interface in the picosecond time scale

Paciaroni, Alessandro; Cornicchi, E.; Marconi, M.; Orecchini, A.; Petrillo, C.; Haertlein, Michael; Moulin, Martine; Sacchetti, F.

doi:10.1098/rsif.2009.0182.focus

Cited by 22 publications

(20 citation statements)

References 34 publications

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“…Instead, a subdiffusional model is required to account for the experimental observations. Subdiffusional behavior of certain aspects of polypeptide backbone dynamics has been reported on the pico-to nanosecond timescale from neutronscattering experiments (34) and molecular dynamics simulations (35), and on the millisecond to second timescale from singlemolecule electron transfer measurements (36). However, these results refer to small-scale equilibrium fluctuations, and it is not clear to what extent their conclusions can be extrapolated to largescale nonequilibrium conformational changes.…”

Section: Discussionmentioning

confidence: 47%

Measurement of energy landscape roughness of folded and unfolded proteins

Milanesi

Waltho

Hunter

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k B T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 k B T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues. photochemical trigger | subdiffusion M ajor advances have been made in recent years in understanding dynamic aspects of protein conformational changes, particularly protein folding; however, many issues remain to be solved (1). Among these are the properties of the unfolded protein ensemble and the role of residual structure of denatured proteins in promoting folding (2), the heterogeneity of microscopic folding pathways (3), and the existence of multiple distinct, but only transiently populated, intermediates (4). Particularly for fast-folding proteins, the idea of downhill folding, i.e., the absence of a significant barrier, has been suggested as an alternative mechanism (5, 6), but it is not clear to what extent fast-folding proteins make use of this mechanism. On the other hand, technical progress has made it possible to observe multiple folding and unfolding events in millisecond all-atom molecular dynamics simulations. Such simulations have shown that some proteins always follow the same folding pathway, whereas others have several different pathways (7). Moreover, individual folding events occur with submicrosecond transit times through a distinct transition state but are separated by long waiting times, which yield the experimentally observed folding times (8).The idea of motion on a rugged energy landscape (9-11) has been used widely to describe conformational changes in protei...

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Section: Discussionmentioning

confidence: 47%

Measurement of energy landscape roughness of folded and unfolded proteins

Milanesi

Waltho

Hunter

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Several features are shared by protein and PNIPAM dynamical transition: (i) T d does not depend on the concentration and the transition vanishes for dry conditions; (ii) the transition takes place at a temperature higher than that of the glass transition [2]; (iii) the strong coupling between water and PNIPAM dynamics, as shown in Fig. 3(a), is well established in hydrated proteins [10,[12][13][14]. It is then natural to ask whether water, through hydrogen bonding interactions with the involved macromolecule, drives the occurrence of this dynamical transition, that appears ubiquitous in proteins and in PNI-PAM microgels.…”

Section: B MD Simulationsmentioning

confidence: 97%

Evidence of a low-temperature dynamical transition in concentrated microgels

et al. 2018

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“…The slower relaxation appears due to the coupling with the protein motions. [19][20][21] Therefore several experiments show that hydration water appears not only slowed down by its interaction with the biosurface but also "bimodal" in the dynamics.…”

Section: Introductionmentioning

confidence: 99%

Two structural relaxations in protein hydration water and their dynamic crossovers

Camisasca

Marzio

Corradini

et al. 2016

The Journal of Chemical Physics

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We study the translational single particle dynamics of hydration water of lysozyme upon cooling by means of molecular dynamics simulations. We find that water close to the protein exhibits two distinct relaxations. By characterizing their behavior upon cooling, we are able to assign the first relaxation to the structural α-relaxation also present in bulk water and in other glass-forming liquids. The second, slower, relaxation can be ascribed to a dynamic coupling of hydration water motions to the fluctuations of the protein structure. Both relaxation times exhibit crossovers in the behavior upon cooling. For the α-process, we find upon cooling a crossover from a fragile behavior to a strong behavior at a temperature which is about five degrees higher than that of bulk water. The long-relaxation time appears strictly connected to the protein motion as it shows upon cooling a temperature crossover from a strong behavior with a lower activation energy to a strong behavior with a higher activation energy. The crossover temperature coincides with the temperature of the protein dynamical transition. These findings can help experimentalists to disentangle the different information coming from total correlators and to better characterize hydration water relaxations in different biomolecules.

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Coupled relaxations at the protein–water interface in the picosecond time scale

Cited by 22 publications

References 34 publications

Measurement of energy landscape roughness of folded and unfolded proteins

Measurement of energy landscape roughness of folded and unfolded proteins

Evidence of a low-temperature dynamical transition in concentrated microgels

Two structural relaxations in protein hydration water and their dynamic crossovers

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