Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae

2019 ◽  
Author(s):  
Beatriz T Magalhães ◽  
Anália Lourenço ◽  
Nuno F Azevedo
Keyword(s):  
Single Molecule ◽  
Structural Information ◽  
Computational Modelling ◽  
Main Process ◽  
Translation Process ◽  
Comprehensive Overview ◽  
Efficient Manner ◽  
Ribonucleic Acids ◽  
Scale Modelling ◽  
Computational Resources

Abstract This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.

scholarly journals Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6779
Author(s):  
Krzysztof B. Beć ◽  
Justyna Grabska ◽  
Christian W. Huck ◽  
Sylwester Mazurek ◽  
Mirosław A. Czarnecki
Keyword(s):  
Single Molecule ◽  
Near Infrared ◽  
Structural Information ◽  
Molecular System ◽  
Theoretical Calculations ◽  
Vitamin K3 ◽  
Structure Correlations ◽  
Mir Spectra ◽  
Combination Bands ◽  
The Relationship

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm−1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm−1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.

scholarly journals Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

2020 ◽  
Author(s):  
Steffen Wolf ◽  
Benedikt Sohmen ◽  
Björn Hellenkamp ◽  
Johann Thurn ◽  
Gerhard Stock ◽  
...  
Keyword(s):  
Binding Site ◽  
Single Molecule ◽  
Information Transfer ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Substrate Binding ◽  
Signal Propagation ◽  
Nonequilibrium Molecular Dynamics ◽  
Time Resolved ◽  
Substrate Binding Site

I.ABSTRACTSeveral indicators for a signal propagation from a binding site to a distant functional site have been found in the Hsp90 dimer. Here we determined a time-resolved pathway from ATP hydrolysis to changes in a distant folding substrate binding site. This was possible by combining single-molecule fluorescence-based methods with extensive atomistic nonequilibrium molecular dynamics simulations. We find that hydrolysis of one ATP effects a structural asymmetry in the full Hsp90 dimer that leads to the collapse of a central folding substrate binding site. Arg380 is the major mediator in transferring structural information from the nucleotide to the substrate binding site. This allosteric process occurs via hierarchical dynamics that involve timescales from picoto milliseconds and length scales from Ångstroms to several nanometers. We presume that similar hierarchical mechanisms are fundamental for information transfer through many other proteins.

Framing constructicography

2019 ◽  
Vol 35 (1) ◽  
pp. 41-85 ◽  
Author(s):  
Hans C. Boas ◽  
Benjamin Lyngfelt ◽  
Tiago Timponi Torrent
Keyword(s):  
Construction Grammar ◽  
Frame Semantics ◽  
Comprehensive Overview ◽  
Form And Function ◽  
And Function ◽  
Computational Resources

Abstract Constructicography can be defined as a blend between Construction Grammar and Practical Lexicography, which aims at developing constructicons: repositories of form and function pairings in a language. In this paper, we present a comprehensive overview of this emerging field by (i) tracking the origins of both Frame Semantics and Construction Grammar and the repercussions of their intertwined developments to Computational Lexicography and Constructicography; (ii) comparing the impacts of the different degrees of interconnection between constructicons and framenets and (iii) discussing the possible applications of these resources. Also, we argue that Constructicography, while obviously building on the accumulated knowledge compiled by numerous Construction Grammar approaches to language, also contributes to its mother theory, since the effort to build coherent formalized computational resources forces constructionist analysis to go beyond describing families of constructions into the enterprise of describing a coherent construction grammar of a language.

Quantitative single molecule FRET efficiencies using TIRF microscopy

2015 ◽  
Vol 184 ◽  
pp. 131-142 ◽  
Author(s):  
Lasse L. Hildebrandt ◽  
Søren Preus ◽  
Victoria Birkedal
Keyword(s):  
Single Molecule ◽  
Structural Information ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Molecular Complexes ◽  
Distance Information ◽  
Single Molecule Level ◽  
Single Molecule Fret ◽  
Wide Range ◽  
Intermolecular Distances

Förster resonance energy transfer (FRET) microscopy at the single molecule level has the potential to yield information on intra and intermolecular distances within the 2–10 nm range of molecules or molecular complexes that undergo frequent conformation changes. A pre-requirement for obtaining accurate distance information is to determine quantitative instrument independent FRET efficiency values. Here, we applied and evaluated a procedure to determine quantitative FRET efficiencies directly from individual fluorescence time traces of surface immobilized DNA molecules without the need for external calibrants. To probe the robustness of the approach over a wide range of FRET efficiencies we used a set of doubly labelled double stranded DNA samples, where the acceptor position was varied systematically. Interestingly, we found that fluorescence contributions arising from direct acceptor excitation following donor excitation are intrinsically taken into account in these conditions as other correction factors can compensate for inaccurate values of these parameters. We give here guidelines, that can be used through tools within the iSMS software (http://www.isms.au.dk), for determining quantitative FRET and assess uncertainties linked with the procedure. Our results provide insights into the experimental parameters governing quantitative FRET determination, which is essential for obtaining accurate structural information from a wide range of biomolecules.

scholarly journals Sorting of Particles Using Inertial Focusing and Laminar Vortex Technology: A Review

Micromachines ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 594 ◽  
Author(s):  
Annalisa Volpe ◽  
Caterina Gaudiuso ◽  
Antonio Ancona
Keyword(s):  
Particle Sizes ◽  
Label Free ◽  
Comprehensive Overview ◽  
Efficient Manner ◽  
Medical Treatments ◽  
Inertial Focusing ◽  
Physical Mechanisms ◽  
Micro Fluidics ◽  
Wide Range ◽  
Sample Separation

The capability of isolating and sorting specific types of cells is crucial in life science, particularly for the early diagnosis of lethal diseases and monitoring of medical treatments. Among all the micro-fluidics techniques for cell sorting, inertial focusing combined with the laminar vortex technology is a powerful method to isolate cells from flowing samples in an efficient manner. This label-free method does not require any external force to be applied, and allows high throughput and continuous sample separation, thus offering a high filtration efficiency over a wide range of particle sizes. Although rather recent, this technology and its applications are rapidly growing, thanks to the development of new chip designs, the employment of new materials and microfabrication technologies. In this review, a comprehensive overview is provided on the most relevant works which employ inertial focusing and laminar vortex technology to sort particles. After briefly summarizing the other cells sorting techniques, highlighting their limitations, the physical mechanisms involved in particle trapping and sorting are described. Then, the materials and microfabrication methods used to implement this technology on miniaturized devices are illustrated. The most relevant evolution steps in the chips design are discussed, and their performances critically analyzed to suggest future developments of this technology.

Quantitative structural information from single-molecule FRET

2015 ◽  
Vol 184 ◽  
pp. 117-129 ◽  
Author(s):  
M. Beckers ◽  
F. Drechsler ◽  
T. Eilert ◽  
J. Nagy ◽  
J. Michaelis
Keyword(s):  
Single Molecule ◽  
Structural Information ◽  
Monte Carlo Sampling ◽  
Dye Molecules ◽  
Distance Information ◽  
Single Molecule Fret ◽  
Single Molecule Studies ◽  
Archaeal Transcription ◽  
Short Time ◽  
Fluorescence Energy

Single-molecule studies can be used to study biological processes directly and in real-time. In particular, the fluorescence energy transfer between reporter dye molecules attached to specific sites on macromolecular complexes can be used to infer distance information. When several measurements are combined, the information can be used to determine the position and conformation of certain domains with respect to the complex. However, data analysis schemes that include all experimental uncertainties are highly complex, and the outcome depends on assumptions about the state of the dye molecules. Here, we present a new analysis algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering termed Fast-NPS that can analyse large smFRET networks in a relatively short time and yields the position of the dye molecules together with their respective uncertainties. Moreover, we show what effects different assumptions about the dye molecules have on the outcome. We discuss the possibilities and pitfalls in structure determination based on smFRET using experimental data for an archaeal transcription pre-initiation complex, whose architecture has recently been unravelled by smFRET measurements.

scholarly journals High-Definition Electronic Genome Maps from Single Molecule Data

2017 ◽  
Author(s):  
John S. Oliver ◽  
Anthony Catalano ◽  
Jennifer R. Davis ◽  
Boris S. Grinberg ◽  
Timothy E. Hutchins ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Information ◽  
Signal To Noise Ratio ◽  
Physical Distance ◽  
Viscous Drag ◽  
High Signal ◽  
High Definition ◽  
Base Pairs ◽  
Solid State Detector ◽  
Genome Maps

With the advent of routine short-read genome sequencing has come a growing recognition of the importance of long-range, structural information in applications ranging from sequence assembly to the detection of structural variation. Here we describe the Nabsys solid-state detector capable of detecting tags on single molecules of DNA 100s of kilobases in length as they translocate through the detector at a velocity greater than 1 megabase pair per second. Sequence-specific tags are detected with a high signal-to-noise ratio. The physical distance between tags is determined after accounting for viscous drag-induced intramolecular velocity fluctuations. The accurate measurement of the physical distance between tags on each molecule and the ability of the detector to resolve distances between tags of less than 300 base-pairs enables the construction of high-density genome maps.

Introduction

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
Structural Biology ◽  
Single Molecule ◽  
Small Angle ◽  
Structural Information ◽  
Complementary Technique ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Future ◽  
The Relationship ◽  
Basic Level

This chapter provides an introduction to small angle solution scattering with particular reference to the complementary technique of X-ray crystallography and the relationship between the two. It describes at its most basic level the theoretical underpinnings of solution scattering starting from a single molecule and how this information is sampled in crystals versus in solution. A brief introduction is given to some of the primary types of structural information that can be obtained from experiments. The chapter concludes discussing some of the most common applications of the technique in structural biology, and where the future is likely headed.

Single-Molecule Studies of Nucleic Acids and Their Proteins

2018 ◽  
Author(s):  
David Bensimon ◽  
Vincent Croquette ◽  
Jean-François Allemand ◽  
Xavier Michalet ◽  
Terence Strick
Keyword(s):  
Single Molecule ◽  
Protein Interactions ◽  
Radiative Decay ◽  
Dynamic Properties ◽  
Rna Polymerases ◽  
Chiral Discrimination ◽  
Triplet States ◽  
Comprehensive Overview ◽  
Dna And Rna ◽  
Single Molecule Studies

This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.

Sign in / Sign up

Export Citation Format

Share Document