Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion

Braun, Michal K.; Grimaldo, Marco; Roosen-Runge, Felix; Hoffmann, Ingo; Czakkel, Orsolya; Sztucki, Michael; Zhang, Fajun; Schreiber, Frank; Seydel, Tilo

doi:10.1021/acs.jpclett.7b00658

Cited by 41 publications

(69 citation statements)

References 51 publications

(101 reference statements)

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“…The presented lifetimes are also not in contradiction with reports for solutions of bovine β-lactoglobulin (BLG) that indicate that BLG clusters are static on NSE observation time scale, i.e. up to 50 ns 33 , but have a limited lifetime on the microsecond observation time scale of dynamic light scattering 33 .…”

Section: Resultssupporting

confidence: 55%

“…increasing the concentration, decreasing temperature, or screening the repulsive electrostatic by high ionic strength or pH, enhances cluster formation and the possibility of liquid-liquid phase separations. 29, 30, 33–37 Studies of colloids, furthermore, show that as clusters grow, a transition to glass and gel phases occurs where dynamically arrested states are formed before crystallization occurs. 38 Experiments, theory and simulations of colloid systems generally assume that besides the attraction-dominated states, where particles move together, a repulsion-dominated state exists, where particles are trapped in a cage formed by surrounding particles.…”

Section: Introductionmentioning

confidence: 99%

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Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

et al. 2017

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For a long time the effect of crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse much slower in a living cell than in a diluted solution and further studies suggest that the diffusion depends on the local surrounding. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin head piece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. While internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

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Section: Resultssupporting

confidence: 55%

Section: Introductionmentioning

confidence: 99%

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

et al. 2017

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“…Da Vela et al (2017) for γ-globulin). For instance, clusters of bovine beta-lactoglobulin (BLG) were investigated with SAXS as well as NSE and NBS spectroscopy by Braun et al (2017), and a monotonous increase of the average hydrodynamic cluster radius was observed over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The combination of static and dynamic measurements suggested that the clusters are compact and have a lifetime that is larger than both the NSE and NBS observation timescales, that is up to ∼50 ns (Braun et al, 2017).…”

Section: Dynamics Of Protein Clusters Aggregates and Glassesmentioning

confidence: 99%

“…For instance, clusters of bovine beta-lactoglobulin (BLG) were investigated with SAXS as well as NSE and NBS spectroscopy by Braun et al (2017), and a monotonous increase of the average hydrodynamic cluster radius was observed over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The combination of static and dynamic measurements suggested that the clusters are compact and have a lifetime that is larger than both the NSE and NBS observation timescales, that is up to ∼50 ns (Braun et al, 2017). The authors further reported that an SLS/DLS study by Piazza and Iacopini (2002) on a specific type of BLG (bovine β-lactalbumin A) indicated the formation of oligomer-type 'transient' clusters with a limited lifetime on the microsecond observation timescale, consistent with PFG-NMR results on millisecond timescales by Le Bon et al (1999), indicating that BLG self-diffusion in concentrated solutions is in agreement with that of dimers.…”

Section: Dynamics Of Protein Clusters Aggregates and Glassesmentioning

confidence: 99%

Dynamics of proteins in solution

Grimaldo

Roosen-Runge

Zhang

et al. 2019

Quart. Rev. Biophys.

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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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“…The dynamics of complex soft matter, including polymers [1][2][3][4], biological matter [5][6][7], colloids [8,9] and various liquids [10,11], is frequently measured by scattering experiments, such as quasi-elastic neutron scattering (QENS), x-ray photon correlation spectroscopy (XPCS) and neutron spin echo (NSE).…”

mentioning

confidence: 99%

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

Iwashita

Egami

2018

Phys. Rev. Lett.

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The de Gennes narrowing phenomenon is frequently observed by neutron or x-ray scattering measurements of the dynamics of complex systems, such as liquids, proteins, colloids, and polymers. The characteristic slowing down of dynamics in the vicinity of the maximum of the total scattering intensity is commonly attributed to enhanced cooperativity. In this Letter, we present an alternative view on its origin through the examination of the time-dependent pair correlation function, the van Hove correlation function, for a model liquid in two, three, and four dimensions. We find that the relaxation time increases monotonically with distance and the dependence on distance varies with dimension. We propose a heuristic explanation of this dependence based on a simple geometrical model. This finding sheds new light on the interpretation of the de Gennes narrowing phenomenon and the α-relaxation time.

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Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion

Cited by 41 publications

References 51 publications

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Dynamics of proteins in solution

Atomic Dynamics in Simple Liquid: de Gennes Narrowing Revisited

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