scholarly journals Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET

2015 ◽  
Vol 142 (3) ◽  
pp. 034110 ◽  
Author(s):  
Irina V. Gopich
Keyword(s):  
Maximum Likelihood ◽  
Single Molecule ◽  
State Model ◽  
Maximum Likelihood Estimates ◽  
Single Molecule Fret ◽  
Two State Model

scholarly journals Single-molecule FRET supports the two-state model of Argonaute action

RNA Biology ◽  
2013 ◽  
Vol 11 (1) ◽  
pp. 45-56 ◽  
Author(s):  
Adrian Zander ◽  
Phil Holzmeister ◽  
Daniel Klose ◽  
Philip Tinnefeld ◽  
Dina Grohmann
Keyword(s):  
Single Molecule ◽  
State Model ◽  
Single Molecule Fret ◽  
Two State Model

THE EFFECT OF MECHANICAL TENSION ON DNA POLYMERASE ACTIVITY STUDIED WITH A TWO-STATE MODEL

2007 ◽  
Vol 21 (17) ◽  
pp. 1097-1105 ◽  
Author(s):  
YAOGEN SHU ◽  
HUALIN SHI
Keyword(s):  
Dna Polymerase ◽  
Single Molecule ◽  
Polymerase Activity ◽  
State Model ◽  
Replication Rate ◽  
Base Stacking ◽  
Mechanical Tension ◽  
Two State Model ◽  
Good Agreement ◽  
Peak Value

Single-molecule experiments revealed that the replication rate of T7 DNA polymerase has a peak value at tension of about 5.5 pN. However, the mechanism leading to this peak has only been partially investigated. Here, we present a two-state model to investigate the effect of mechanical tension on DNA polymerase activity. The model consists of polymerase and exonuclease. The polymerase's kinetic pathway has been simplified into Michaelis–Menten form with two steps. One is the conformational change from "open" to "close". The other is the base-stacking. The results are in good agreement with experimental observations. We also predict that the tension on template is beneficial to the fidelity of DNA replication.

Polarographic studies on renaturation of urea-denatured human serum albumin

1989 ◽  
Vol 54 (2) ◽  
pp. 536-543 ◽  
Author(s):  
Josef Chmelík ◽  
Pavel Anzenbacher ◽  
Vítěz Kalous
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Irreversible Process ◽  
State Model ◽  
Native Protein ◽  
Main Components ◽  
Two State Model ◽  
Kinetics Of

The renaturation of the two main components of human serum albumin, i.e. of mercaptalbumin and nonmercaptalbumin, was studied polarographically. It has been demonstrated that renaturation of both proteins after 1-min denaturation in 8M urea is reversible. By contrast, renaturation after 200 min denaturation in 8M urea is an irreversible process; the characteristics of renatured mercaptalbumin differ more from the properties of the native protein than the characteristics of nonmercaptalbumin. The studies of the kinetics of renaturation of both proteins have shown that the renaturation can be represented by a two-state model. This means that the existence of stable intermediary products during the renaturation process was not determined polarographically.

scholarly journals Directional Selection and the Site-Frequency Spectrum

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1779-1788 ◽  
Author(s):  
Carlos D Bustamante ◽  
John Wakeley ◽  
Stanley Sawyer ◽  
Daniel L Hartl
Keyword(s):  
Maximum Likelihood ◽  
High Power ◽  
Negative Selection ◽  
Likelihood Estimation ◽  
Directional Selection ◽  
Likelihood Ratio Tests ◽  
Maximum Likelihood Estimates ◽  
Likelihood Methods ◽  
Ancestral States ◽  
Asymptotic Variances

Abstract In this article we explore statistical properties of the maximum-likelihood estimates (MLEs) of the selection and mutation parameters in a Poisson random field population genetics model of directional selection at DNA sites. We derive the asymptotic variances and covariance of the MLEs and explore the power of the likelihood ratio tests (LRT) of neutrality for varying levels of mutation and selection as well as the robustness of the LRT to deviations from the assumption of free recombination among sites. We also discuss the coverage of confidence intervals on the basis of two standard-likelihood methods. We find that the LRT has high power to detect deviations from neutrality and that the maximum-likelihood estimation performs very well when the ancestral states of all mutations in the sample are known. When the ancestral states are not known, the test has high power to detect deviations from neutrality for negative selection but not for positive selection. We also find that the LRT is not robust to deviations from the assumption of independence among sites.

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