scholarly journals How much entropy is contained in NMR relaxation parameters?

2021 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans A. A. Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Time Scales ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Side Chain ◽  
Thermodynamic Quantities ◽  
T4 Lysozyme ◽  
Time Dynamics ◽  
Relaxation Parameters ◽  
Relaxation Experiments ◽  
Short Time

Solution-state NMR relaxation experiments are the cornerstone to study internalprotein dynamics at atomic resolution on time scales that are faster than the overallrotational tumbling time,τR. Since the motions described by NMR relaxation pa-rameters are connected to thermodynamic quantities like conformational entropies, thequestion arises how much of the total entropy is contained within this tumbling time.Using all-atom molecular dynamics (MD) simulations of T4 lysozyme, we found thatentropy build-up is rather fast for the backbone, such that the majority of the entropyis indeed contained in the short-time dynamics. In contrast, the contribution of slowdynamics of side chains on time scales beyondτRon the side chain conformationalentropy is significant and should be taken into account for the extraction of accuratethermodynamic properties.

scholarly journals How much entropy is contained in NMR relaxation parameters?

2021 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans A. A. Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Time Scales ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Side Chain ◽  
Thermodynamic Quantities ◽  
T4 Lysozyme ◽  
Time Dynamics ◽  
Relaxation Parameters ◽  
Relaxation Experiments ◽  
Short Time

Solution-state NMR relaxation experiments are the cornerstone to study internalprotein dynamics at atomic resolution on time scales that are faster than the overallrotational tumbling time,τR. Since the motions described by NMR relaxation pa-rameters are connected to thermodynamic quantities like conformational entropies, thequestion arises how much of the total entropy is contained within this tumbling time.Using all-atom molecular dynamics (MD) simulations of T4 lysozyme, we found thatentropy build-up is rather fast for the backbone, such that the majority of the entropyis indeed contained in the short-time dynamics. In contrast, the contribution of slowdynamics of side chains on time scales beyondτRon the side chain conformationalentropy is significant and should be taken into account for the extraction of accuratethermodynamic properties.

scholarly journals Stochastic Modelling of 13C NMR Spin Relaxation Experiments in Oligosaccharides

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2418
Author(s):  
Sergio Rampino ◽  
Mirco Zerbetto ◽  
Antonino Polimeno
Keyword(s):  
Magnetic Resonance ◽  
Degrees Of Freedom ◽  
Ad Hoc ◽  
Nmr Relaxation ◽  
Stochastic Modelling ◽  
Relaxation Processes ◽  
Relaxation Parameters ◽  
13C Nuclear Magnetic Resonance ◽  
Relaxation Experiments ◽  
Resonance Relaxation

A framework for the stochastic description of relaxation processes in flexible macromolecules including dissipative effects has been recently introduced, starting from an atomistic view, describing the joint relaxation of internal coordinates and global degrees of freedom, and depending on parameters recoverable from classic force fields (energetics) and medium modelling at the continuum level (friction tensors). The new approach provides a rational context for the interpretation of magnetic resonance relaxation experiments. In its simplest formulation, the semi-flexible Brownian (SFB) model has been until now shown to reproduce correctly correlation functions and spectral densities related to orientational properties obtained by direct molecular dynamics simulations of peptides. Here, for the first time, we applied directly the SFB approach to the practical evaluation of high-quality 13C nuclear magnetic resonance relaxation parameters, T1 and T2, and the heteronuclear NOE of several oligosaccharides, which were previously interpreted on the basis of refined ad hoc modelling. The calculated NMR relaxation parameters were in agreement with the experimental data, showing that this general approach can be applied to diverse classes of molecular systems, with the minimal usage of adjustable parameters.

scholarly journals Fitting side-chain NMR relaxation data using molecular simulations

2020 ◽  
Author(s):  
Felix Kümmerer ◽  
Simone Orioli ◽  
David Harding-Larsen ◽  
Falk Hoffmann ◽  
Yulian Gavrilov ◽  
...  
Keyword(s):  
Nmr Relaxation ◽  
Side Chain ◽  
T4 Lysozyme ◽  
Molecular Models ◽  
Static Properties ◽  
Relaxation Data ◽  
Structure And Dynamics ◽  
Relaxation Measurements ◽  
Average Block ◽  
Dynamics Simulations

AbstractProteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (Average Block Selection Using Relaxation Data with Entropy Restraints) can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme, and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties, and highlight areas needed for further improvements of the approach.

scholarly journals RING NMR dynamics: software for analysis of multiple NMR relaxation experiments

2020 ◽  
Author(s):  
Martha A. Beckwith ◽  
Teddy Erazo-Colon ◽  
Bruce A. Johnson
Keyword(s):  
Nmr Relaxation ◽  
Relaxation Dispersion ◽  
Molecular Characteristics ◽  
Model Parameters ◽  
Relaxation Data ◽  
Software Application ◽  
Relaxation Parameters ◽  
Initial Release ◽  
Relaxation Experiments ◽  
User Friendly

Abstract Molecular motions are fundamental to the existence of life, and NMR spectroscopy remains one of the most useful and powerful methods to measure their rates and molecular characteristics. Multiple experimental methods are available for measuring the NMR relaxation properties and these can require different methods for extracting model parameters. We present here a new software application, RING NMR Dynamics, that is designed to support analysis of multiple relaxation types. The initial release of RING NMR Dynamics supports the analysis of exponential decay experiments such as T1 and T2, as well as CEST and R2 and R1ρ relaxation dispersion. The software runs on multiple operating systems in both a command line mode and a user-friendly GUI that allows visualizing and simulating relaxation data. Interaction with another program, NMRFx Analyst, allows drilling down from the derived relaxation parameters to the raw spectral data.

The Spread of Pollutants from Harbour Sludge Depots

1984 ◽  
Vol 16 (3-4) ◽  
pp. 623-633
Author(s):  
M Loxham ◽  
F Weststrate
Keyword(s):  
Time Scales ◽  
Molecular Diffusion ◽  
Near Field ◽  
Parameter Analysis ◽  
Migration Patterns ◽  
Long Time ◽  
Dilution Effects ◽  
Short Time ◽  
Harbour Sludge

It is generally agreed that both the landfill option, or the civil techniques option for the final disposal of contaminated harbour sludge involves the isolation of the sludge from the environment. For short time scales, engineered barriers such as a bentonite screen, plastic sheets, pumping strategies etc. can be used. However for long time scales the effectiveness of such measures cannot be counted upon. It is thus necessary to be able to predict the long term environmenttal spread of contaminants from a mature landfill. A model is presented that considers diffusion and adsorption in the landfill site and convection and adsorption in the underlaying aquifer. From a parameter analysis starting form practical values it is shown that the adsorption behaviour and the molecular diffusion coefficient of the sludge, are the key parameters involved in the near field. The dilution effects of the far field migration patterns are also illustrated.

scholarly journals Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yafei Wang ◽  
Erik Brodin ◽  
Kenichiro Nishii ◽  
Hermann B. Frieboes ◽  
Shannon M. Mumenthaler ◽  
...  
Keyword(s):  
Time Scales ◽  
Constitutive Relations ◽  
Elastic Tissue ◽  
Metastatic Progression ◽  
Patient Death ◽  
Metastatic Growth ◽  
Tumor Parenchyma ◽  
Short Time ◽  
Model Approach

AbstractColorectal cancer and other cancers often metastasize to the liver in later stages of the disease, contributing significantly to patient death. While the biomechanical properties of the liver parenchyma (normal liver tissue) are known to affect tumor cell behavior in primary and metastatic tumors, the role of these properties in driving or inhibiting metastatic inception remains poorly understood, as are the longer-term multicellular dynamics. This study adopts a multi-model approach to study the dynamics of tumor-parenchyma biomechanical interactions during metastatic seeding and growth. We employ a detailed poroviscoelastic model of a liver lobule to study how micrometastases disrupt flow and pressure on short time scales. Results from short-time simulations in detailed single hepatic lobules motivate constitutive relations and biological hypotheses for a minimal agent-based model of metastatic growth in centimeter-scale tissue over months-long time scales. After a parameter space investigation, we find that the balance of basic tumor-parenchyma biomechanical interactions on shorter time scales (adhesion, repulsion, and elastic tissue deformation over minutes) and longer time scales (plastic tissue relaxation over hours) can explain a broad range of behaviors of micrometastases, without the need for complex molecular-scale signaling. These interactions may arrest the growth of micrometastases in a dormant state and prevent newly arriving cancer cells from establishing successful metastatic foci. Moreover, the simulations indicate ways in which dormant tumors could “reawaken” after changes in parenchymal tissue mechanical properties, as may arise during aging or following acute liver illness or injury. We conclude that the proposed modeling approach yields insight into the role of tumor-parenchyma biomechanics in promoting liver metastatic growth, and advances the longer term goal of identifying conditions to clinically arrest and reverse the course of late-stage cancer.

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