The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family

2018 ◽  
Vol 122 (49) ◽  
pp. 11800-11806 ◽  
Author(s):  
Fernando Miguel Yrazu ◽  
Giovanni Pinamonti ◽  
Cecilia Clementi
Keyword(s):  
Electrostatic Interactions ◽  
Protein Family ◽  
Folding Kinetics ◽  
Helical Bundle ◽  
Kinetics Of ◽  
Bundle Protein

In situ Time-Resolved Small-Angle X-ray Scattering Reveals the Formation Kinetics of Polyelectrolyte Complex Micelles

2019 ◽  
Author(s):  
Hao Wu ◽  
Jeffrey Ting ◽  
Siqi Meng ◽  
Matthew Tirrell
Keyword(s):  
Small Angle ◽  
Self Assembly ◽  
Electrostatic Interactions ◽  
Polyelectrolyte Complex ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Kinetics Of ◽  
Ray Scattering

We have directly observed the <i>in situ</i> self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. This work has elucidated one general kinetic pathway for the process of PEC micelle formation, which provides useful physical insights for increasing our fundamental understanding of complexation and self-assembly dynamics driven by electrostatic interactions that occur on ultrafast timescales.

scholarly journals Simulation of Folding Kinetics for Aligned RNAs

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 347
Author(s):  
Jiabin Huang ◽  
Björn Voß
Keyword(s):  
Evolutionary Conservation ◽  
Folding Kinetics ◽  
New Approach ◽  
Computational Approaches ◽  
Reasonable Time ◽  
Valuable Method ◽  
Kinetics Of ◽  
Insight Into ◽  
Folding Space ◽  
Standing Problem

Studying the folding kinetics of an RNA can provide insight into its function and is thus a valuable method for RNA analyses. Computational approaches to the simulation of folding kinetics suffer from the exponentially large folding space that needs to be evaluated. Here, we present a new approach that combines structure abstraction with evolutionary conservation to restrict the analysis to common parts of folding spaces of related RNAs. The resulting algorithm can recapitulate the folding kinetics known for single RNAs and is able to analyse even long RNAs in reasonable time. Our program RNAliHiKinetics is the first algorithm for the simulation of consensus folding kinetics and addresses a long-standing problem in a new and unique way.

scholarly journals Modulation of Folding Kinetics of Repeat Proteins: Interplay between Intra- and Interdomain Interactions

2012 ◽  
Vol 103 (7) ◽  
pp. 1555-1565 ◽  
Author(s):  
Tzachi Hagai ◽  
Ariel Azia ◽  
Emmanuel Trizac ◽  
Yaakov Levy
Keyword(s):  
Folding Kinetics ◽  
Repeat Proteins ◽  
Interdomain Interactions ◽  
Kinetics Of

Stability and Folding Kinetics of Structurally Characterized Cytochromec-b562†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (35) ◽  
pp. 10504-10511 ◽  
Author(s):  
Jasmin Faraone-Mennella ◽  
F. Akif Tezcan ◽  
Harry B. Gray ◽  
Jay R. Winkler
Keyword(s):  
Folding Kinetics ◽  
Kinetics Of

Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c

2015 ◽  
Vol 585 ◽  
pp. 52-63 ◽  
Author(s):  
Rishu Jain ◽  
Rajesh Kumar ◽  
Sandeep Kumar ◽  
Ritika Chhabra ◽  
Mukesh Chand Agarwal ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Folding Kinetics ◽  
Ph Dependent ◽  
Kinetics Of ◽  
Horse Cytochrome

Sequence, Salt, Charge, and the Stability of DNA at High Pressure

1996 ◽  
Author(s):  
Robert B. Macgregor Jr ◽  
John Q. Wu
Keyword(s):  
Molar Volume ◽  
Volume Change ◽  
Salt Concentration ◽  
Electrostatic Interactions ◽  
Proposed Model ◽  
Dna Strands ◽  
Positive Volume ◽  
Ion Radius ◽  
The Stability ◽  
Kinetics Of

The effect of pressure on the helix-coil transition temperature (Tm) is reported for the double-stranded polymers poly(dA)poly(dT), poly[d(A-T)], poly[d(l-C], and poly[d(G-C] and triple-stranded poly(dA)2poly(dT). The Tm increases as a function of pressure, implying a positive volume change for the transition and leading to the conclusion that the molar volume of the coil form is larger than the molar volume of the helix. From the change in Tm as a function of pressure, molar volume changes of the transition (ΔVt) are calculated using the Clapeyron equation and calorimetrically determined enthalpies. For the doublestranded polymers, ΔVt, increases in the order poly[d(l-C] < polyt[d(A-T)] < poly(dA)-poly(dT) < polylcl(G-C)]. The value of ΔVt, for the triple-stranded to single-stranded transition of poly(dA) 2poly(dT) is larger than that of poly[d(G-C)I. The magnitude of ΔVt increases with salt concentration in all cases studied; however, the change of ΔVt with salt concentration depends on the sequence of the DNA and the number of strands involved in the transition. In the model proposed to explain the results, the overall molar volume change of the transition is a function of a negative volume change arising from changes in the electrostatic interactions of the DNA strands, and a positive volume change due to unstacking the bases. The model predicted the direction of the change in the ΔVt for several experiments. The magnitude of AVJ increases with counter ion radius, thus for polyld(A-T)], ΔVt, increases in the series Na+ , K+, Cs+, The ΔVt also increases if the charge on the phosphodiester groups is removed. The kinetics of the formation of double-stranded (dA)19(dT)19 in 50 mM NaCI are slowed approximately 14-fold at 200 MPa relative to atmospheric pressure. The implied volume of activation of +37 ml mol−l in the direction of this change is also in agreement with the proposed model. The stability of double- and triple-stranded DNA helices in water around neutral pH depends on the base composition and sequence, as well as on the ionic strength of the solution. Each of these dependencies also defines how DNA interacts with water.

scholarly journals Study of the Adhesion Mechanism of Acidithiobacillus ferrooxidans to Pyrite in Fresh and Saline Water

Minerals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 306 ◽  
Author(s):  
Francisca San Martín ◽  
Claudio Aguilar
Keyword(s):  
Fresh Water ◽  
Electrostatic Interactions ◽  
Saline Water ◽  
Streaming Potential ◽  
Bacterial Attachment ◽  
Van Der Waals Interactions ◽  
Streaming Potentials ◽  
Ph Values ◽  
Na Ions ◽  
Kinetics Of

In the present work, the streaming potential of A. ferrooxidans and pyrite was measured in two environments: fresh and saline water (water with 35 g/L of NaCl) at different pH values. Also, attachment kinetics of A. ferrooxidans to pyrite was studied in fresh and saline water at pH 4. The results show that A. ferrooxidans and pyrite had lower streaming potentials (comparing absolute values) in saline water than in fresh water, indicating the compression in the electrical double layer caused by Cl− and Na+ ions. It was also determined that the bacteria had a higher level of attachment to pyrite in fresh water than in saline water. The high ionic strength of saline water reduced the attractive force between A. ferrooxidans and pyrite, which in turn reduced bacterial attachment. Electrostatic interactions were determined to be mainly repulsive, since the bacteria and mineral had the same charge at pH 4. Despite this, the bacteria adhered to pyrite, indicating that hydrophobic attraction forces and Lifshitz–van der Waals interactions were stronger than electrostatic interactions, which caused the adhesion of A. ferrooxidans to pyrite.

scholarly journals Ultrafast folding kinetics of WW domains reveal how the amino acid sequence determines the speed limit to protein folding

2019 ◽  
Vol 116 (17) ◽  
pp. 8137-8142 ◽  
Author(s):  
Malwina Szczepaniak ◽  
Manuel Iglesias-Bexiga ◽  
Michele Cerminara ◽  
Mourad Sadqi ◽  
Celia Sanchez de Medina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Essential Element ◽  
Nanosecond Laser ◽  
Speed Limit ◽  
Free Energy Barrier ◽  
Folding Kinetics ◽  
Folding Rate ◽  
Ww Domains ◽  
Kinetics Of

Protein (un)folding rates depend on the free-energy barrier separating the native and unfolded states and a prefactor term, which sets the timescale for crossing such barrier or folding speed limit. Because extricating these two factors is usually unfeasible, it has been common to assume a constant prefactor and assign all rate variability to the barrier. However, theory and simulations postulate a protein-specific prefactor that contains key mechanistic information. Here, we exploit the special properties of fast-folding proteins to experimentally resolve the folding rate prefactor and investigate how much it varies among structural homologs. We measure the ultrafast (un)folding kinetics of five natural WW domains using nanosecond laser-induced temperature jumps. All five WW domains fold in microseconds, but with a 10-fold difference between fastest and slowest. Interestingly, they all produce biphasic kinetics in which the slower phase corresponds to reequilibration over the small barrier (<3RT) and the faster phase to the downhill relaxation of the minor population residing at the barrier top [transition state ensemble (TSE)]. The fast rate recapitulates the 10-fold range, demonstrating that the folding speed limit of even the simplest all-β fold strongly depends on the amino acid sequence. Given this fold’s simplicity, the most plausible source for such prefactor differences is the presence of nonnative interactions that stabilize the TSE but need to break up before folding resumes. Our results confirm long-standing theoretical predictions and bring into focus the rate prefactor as an essential element for understanding the mechanisms of folding.

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