19 research outputs found
Relative Contributions of Intrinsic StructuralâFunctional Constraints and Translation Rate to the Evolution of Protein-Coding Genes
A long-standing assumption in evolutionary biology is that the evolution rate of protein-coding genes depends, largely, on specific constraints that affect the function of the given protein. However, recent research in evolutionary systems biology revealed unexpected, significant correlations between evolution rate and characteristics of genes or proteins that are not directly related to specific protein functions, such as expression level and proteinâprotein interactions. The strongest connections were consistently detected between protein sequence evolution rate and the expression level of the respective gene. A recent genome-wide proteomic study revealed an extremely strong correlation between the abundances of orthologous proteins in distantly related animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster. We used the extensive protein abundance data from this study along with short-term evolutionary rates (ERs) of orthologous genes in nematodes and flies to estimate the relative contributions of structuralâfunctional constraints and the translation rate to the evolution rate of protein-coding genes. Together the intrinsic constraints and translation rate account for approximately 50% of the variance of the ERs. The contribution of constraints is estimated to be 3- to 5-fold greater than the contribution of translation rate
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FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current âstate of the artâ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of âsoft recommendationsâ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage âopen scienceâ practices
Protein dynamics from single-molecule fluorescence intensity correlation functions
Fluorescence intensity correlation functions contain information about photophysical and conformational dynamics. We propose and implement a simple procedure to analyze such functions measured in the presence of resonance energy transfer. When there is a separation of time scales and the conformational dynamics is modeled as diffusion in the potential of mean force along the interdye distance, we obtain an analytic expression for the conformational correlation time. This can be used to find the diffusion coefficient describing conformational fluctuations given the photon count rate and equilibrium distribution
Analysis of Fluorescence Lifetime and Energy Transfer Efficiency in Single-Molecule Photon Trajectories of Fast-Folding Proteins
In single-molecule FoÌrster
resonance energy transfer (FRET)
spectroscopy, the dynamics of molecular processes are usually determined
by analyzing the fluorescence intensity of donor and acceptor dyes.
Since FRET efficiency is related to fluorescence lifetimes, additional
information can be extracted by analyzing fluorescence intensity and
lifetime together. For fast processes where individual states are
not well separated in a trajectory, it is not easy to obtain the lifetime
information. Here, we present analysis methods to utilize fluorescence
lifetime information from single-molecule FRET experiments, and apply
these methods to three fast-folding, two-state proteins. By constructing
2D FRET efficiency-lifetime histograms, the correlation can be visualized
between the FRET efficiency and fluorescence lifetimes in the presence
of the submicrosecond to millisecond dynamics. We extend the previously
developed method for analyzing delay times of donor photons to include
acceptor delay times. To determine the kinetics and lifetime parameters
accurately, we used a maximum likelihood method. We found that acceptor
blinking can lead to inaccurate parameters in the donor delay time
analysis. This problem can be solved by incorporating acceptor blinking
into a model. While the analysis of acceptor delay times is not affected
by acceptor blinking, it is more sensitive to the shape of the delay
time distribution resulting from a broad conformational distribution
in the unfolded state