Folding Rate and Transition Path Time of a Single-Molecule Protein

AbstractWe investigated frictional effects on the folding rates of a human Telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat capacity from TIS model simulations, calculated using temperature replica exchange simulations, reproduces nearly quantitatively the available experimental data for the hTR HP. The corresponding results for BWYV PK serve as predictions. We calculated the folding rates (kFs) from more than 100 folding trajectories for each value of the solvent viscosity (η) at a fixed salt concentration of 200 mM. Using the theoretical estimate ( where N is number of nucleotides) for folding free energy barrier, kF data for both the RNAs are quantitatively fit using one dimensional Kramers’ theory with two parameters specifying the curvatures in the unfolded basin and the barrier top. In the high-friction regime (η ≳ 10−5 Pa·s), for both HP and PK, kFs decrease as 1/η whereas in the low friction regime kFs increase as η increases, leading to a maximum folding rate at a moderate viscosity (~ 10−6 Pa·s), which is the Kramers turnover. From the fits, we find that the speed limit to RNA folding at water viscosity is between (1 − 4)μs, which is in accord with our previous theoretical prediction as well as results from several single molecule experiments. Both the RNA constructs fold by parallel pathways. Surprisingly, we find that the flux through the pathways could be altered by changing solvent viscosity, a prediction that is more easily testable in RNA than proteins.

Download Full-text

Folding and Persistence Time of Intramolecular G-Quadruplexes Transiently Embedded in a DNA duplex

10.1101/2021.01.04.425278 ◽

2021 ◽

Author(s):

Phong Lan Thao Tran ◽

Martin Rieu ◽

Samar Hodeib ◽

Alexandra Joubert ◽

Jimmy Ouellet ◽

...

Keyword(s):

Single Molecule ◽

Critical Role ◽

Genetic Regulation ◽

Regulatory Elements ◽

Promoter Regions ◽

Folding Rate ◽

Persistence Time ◽

G4 Dna

ABSTRACTG-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA replication, transcription or repair. While many in-vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in-vivo in double-stranded DNA regions, where their formation is challenged by pairing between the two complementary strands. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on the persistence of G4 in vivo. To address this issue, we designed a single molecule assay allowing measuring G4 folding and persistence while the structure is periodically challenged by the complementary strand. We quantified both the folding rate and the persistence time of biologically relevant G4 structures and showed that the dynamics of G4 formation depends strongly on the genomic location. G4 are found much more stable in promoter regions and replication origins than in telomeric regions. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence increased. Our assay opens new perspectives for the measurement of G4 dynamics, which is critical to understand their role in genetic regulation.

Download Full-text

Testing Kinetic Identities Involving Transition-Path Properties Using Single-Molecule Folding Trajectories

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b05355 ◽

2018 ◽

Vol 122 (49) ◽

pp. 11095-11099 ◽

Cited By ~ 7

Author(s):

Krishna Neupane ◽

Noel Q. Hoffer ◽

Michael T. Woodside

Keyword(s):

Single Molecule ◽

Transition Path ◽

Path Properties

Download Full-text

Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2008307117 ◽

2020 ◽

Vol 117 (44) ◽

pp. 27116-27123 ◽

Cited By ~ 1

Author(s):

Rohit Satija ◽

Alexander M. Berezhkovskii ◽

Dmitrii E. Makarov

Keyword(s):

Free Energy ◽

Single Molecule ◽

Coefficient Of Variation ◽

Biological Membrane ◽

Energy Landscape ◽

Transition Path ◽

Activation Barriers ◽

One Dimensional ◽

Dimensional Diffusion ◽

Transition Paths

Recent single-molecule experiments have observed transition paths, i.e., brief events where molecules (particularly biomolecules) are caught in the act of surmounting activation barriers. Such measurements offer unprecedented mechanistic insights into the dynamics of biomolecular folding and binding, molecular machines, and biological membrane channels. A key challenge to these studies is to infer the complex details of the multidimensional energy landscape traversed by the transition paths from inherently low-dimensional experimental signals. A common minimalist model attempting to do so is that of one-dimensional diffusion along a reaction coordinate, yet its validity has been called into question. Here, we show that the distribution of the transition path time, which is a common experimental observable, can be used to differentiate between the dynamics described by models of one-dimensional diffusion from the dynamics in which multidimensionality is essential. Specifically, we prove that the coefficient of variation obtained from this distribution cannot possibly exceed 1 for any one-dimensional diffusive model, no matter how rugged its underlying free energy landscape is: In other words, this distribution cannot be broader than the single-exponential one. Thus, a coefficient of variation exceeding 1 is a fingerprint of multidimensional dynamics. Analysis of transition paths in atomistic simulations of proteins shows that this coefficient often exceeds 1, signifying essential multidimensionality of those systems.

Download Full-text