What Is the Time Scale for α-Helix Nucleation?

2011 ◽  
Vol 133 (17) ◽  
pp. 6809-6816 ◽  
Author(s):  
David De Sancho ◽  
Robert B. Best
Keyword(s):  
Time Scale ◽  
Helix Nucleation ◽  
Α Helix

scholarly journals Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics

2019 ◽  
Vol 116 (12) ◽  
pp. 5356-5361 ◽  
Author(s):  
Maxim B. Prigozhin ◽  
Yi Zhang ◽  
Klaus Schulten ◽  
Martin Gruebele ◽  
Taras V. Pogorelov
Keyword(s):  
Pressure Drop ◽  
Time Scale ◽  
Tertiary Structure ◽  
Specific Protein ◽  
Pressure Jump ◽  
Characteristic Time Scale ◽  
Hydrophobic Core ◽  
Pressure Drops ◽  
Contact Formation ◽  
Α Helix

As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ6–85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α3D)], whose drying and core formation proceed in concert, λ6–85repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

scholarly journals Helix Nucleation by the Smallest Known α-Helix in Water

2016 ◽  
Vol 55 (29) ◽  
pp. 8275-8279 ◽  
Author(s):  
Huy N. Hoang ◽  
Russell W. Driver ◽  
Renée L. Beyer ◽  
Timothy A. Hill ◽  
Aline D. de Araujo ◽  
...  
Keyword(s):  
Helix Nucleation ◽  
Α Helix

α-Helix Nucleation Constant in Copolypeptides of Alanine and Ornithine or Lysine

1998 ◽  
Vol 120 (41) ◽  
pp. 10646-10652 ◽  
Author(s):  
Jianxin Yang ◽  
Kang Zhao ◽  
Youxiang Gong ◽  
Alexander Vologodskii ◽  
Neville R. Kallenbach
Keyword(s):  
Helix Nucleation ◽  
Α Helix

Conformational Exchange on the Microsecond Time Scale in α-Helix and β-Hairpin Peptides Measured by13C NMR Transverse Relaxation†

Biochemistry ◽  
2001 ◽  
Vol 40 (9) ◽  
pp. 2844-2853 ◽  
Author(s):  
Irina Nesmelova ◽  
Alexei Krushelnitsky ◽  
Djaudat Idiyatullin ◽  
Francesco Blanco ◽  
Marina Ramirez-Alvarado ◽  
...  
Keyword(s):  
Time Scale ◽  
Conformational Exchange ◽  
Transverse Relaxation ◽  
Hairpin Peptides ◽  
Α Helix

Mechanism of Helix Nucleation and Propagation:  Microscopic View from Microsecond Time Scale MD Simulations

2005 ◽  
Vol 109 (43) ◽  
pp. 20064-20067 ◽  
Author(s):  
Luca Monticelli ◽  
D. Peter Tieleman ◽  
Giorgio Colombo
Keyword(s):  
Time Scale ◽  
Md Simulations ◽  
Helix Nucleation

scholarly journals Direct Assessment of the α-Helix Nucleation Time

2011 ◽  
Vol 115 (22) ◽  
pp. 7472-7478 ◽  
Author(s):  
Arnaldo L. Serrano ◽  
Matthew J. Tucker ◽  
Feng Gai
Keyword(s):  
Nucleation Time ◽  
Direct Assessment ◽  
Helix Nucleation ◽  
Α Helix

scholarly journals Helix Nucleation by the Smallest Known α-Helix in Water

2016 ◽  
Vol 128 (29) ◽  
pp. 8415-8419 ◽  
Author(s):  
Huy N. Hoang ◽  
Russell W. Driver ◽  
Renée L. Beyer ◽  
Timothy A. Hill ◽  
Aline D. de Araujo ◽  
...  
Keyword(s):  
Helix Nucleation ◽  
Α Helix

Large-scale Motion of Solar Filaments

2000 ◽  
Vol 179 ◽  
pp. 205-208
Author(s):  
Pavel Ambrož ◽  
Alfred Schroll
Keyword(s):  
Magnetic Flux ◽  
Proper Motion ◽  
Time Scale ◽  
Large Scale ◽  
Accuracy Of Measurements ◽  
Solar Filaments ◽  
General Movement ◽  
Scale Motion ◽  
Velocity Scatter

AbstractPrecise measurements of heliographic position of solar filaments were used for determination of the proper motion of solar filaments on the time-scale of days. The filaments have a tendency to make a shaking or waving of the external structure and to make a general movement of whole filament body, coinciding with the transport of the magnetic flux in the photosphere. The velocity scatter of individual measured points is about one order higher than the accuracy of measurements.

The E-ring: interactions with plasma and implications for its evolution

1984 ◽  
Vol 75 ◽  
pp. 599-602
Author(s):  
T.V. Johnson ◽  
G.E. Morfill ◽  
E. Grun
Keyword(s):  
Time Scale ◽  
Particle Density ◽  
High Energy ◽  
Particle Removal ◽  
Density Region ◽  
Drag Forces ◽  
Orbit Evolution ◽  
History Of ◽  
Ring Particle ◽  
Ring Material

A number of lines of evidence suggest that the particles making up the E-ring are small, on the order of a few microns or less in size (Terrile and Tokunaga, 1980, BAAS; Pang et al., 1982 Saturn meeting; Tucson, AZ). This suggests that a variety of electromagnetic and plasma affects may be important in considering the history of such particles. We have shown (Morfill et al., 1982, J. Geophys. Res., in press) that plasma drags forces from the corotating plasma will rapidly evolve E-ring particle orbits to increasing distance from Saturn until a point is reached where radiation drag forces acting to decrease orbital radius balance this outward acceleration. This occurs at approximately Rhea's orbit, although the exact value is subject to many uncertainties. The time scale for plasma drag to move particles from Enceladus' orbit to the outer E-ring is ~104yr. A variety of effects also act to remove particles, primarily sputtering by both high energy charged particles (Cheng et al., 1982, J. Geophys. Res., in press) and corotating plasma (Morfill et al., 1982). The time scale for sputtering away one micron particles is also short, 102 - 10 yrs. Thus the detailed particle density profile in the E-ring is set by a competition between orbit evolution and particle removal. The high density region near Enceladus' orbit may result from the sputtering yeild of corotating ions being less than unity at this radius (e.g. Eviatar et al., 1982, Saturn meeting). In any case, an active source of E-ring material is required if the feature is not very ephemeral - Enceladus itself, with its geologically recent surface, appears still to be the best candidate for the ultimate source of E-ring material.

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