NMRDyn: A Program for NMR Relaxation Studies of Protein Association

Self-association is an important biological phenomenon that is associated with many cellular processes. NMR relaxation measurements provide data about protein molecular dynamics at the atomic level and are sensitive to changes induced by self-association. Thus, measurements and analysis of NMR relaxation data can provide structurally resolved information on self-association that would not be accessible otherwise. Here, we present a computer program, NMRdyn, which analyses relaxation data to provide parameters defining protein self-association. Unlike existing relaxation analysis software, NMRdyn can explicitly model the monomer-oligomer equilibrium while fitting measured relaxation data. Additionally, the program is packaged with a user-friendly interface, which is important because relaxation data can often be large and complex. NMRdyn is available from http://research1t.imb.uq.edu.au/nmr/NMRdyn

Tractatus magistri Guillermi Aluernensis supra parabolas Salomonis [Manuscrito]

Tratado formado por XXXI capítulos numeradosTít. tomado del incipitPerg.; cuadernos de 8 h., excepto el último de 10; sin sign. ni reclamos; foliación moderna; pautado a lápiz de plomo; caja de escr.: 155 x 100 mm; espacio interlineal: 2 mm; inicial en h. 1 a tinta roja y azul con rasgueos, incipit, correciones y subrayados en rojoLas dos h. sin foliar están en bl. salvo el tít. en la primera h. y una pequeña an. ms. ilegible en la últim

Genetics as a novel tool in mining impact assessment and biomonitoring of critically endangered western chimpanzees in the Nimba Mountains, Guinea

Western chimpanzees (Pan troglodytes verus) are Critically Endangered and Guinea is a key stronghold for this subspecies. However, Guinea is also rich in minerals with some of the highest‐grade iron‐ore deposits in the world. Specifically, the Nimba Mountains, home to western chimpanzees, is one of the sites under consideration for mining activities. To assess the impact of mining activities in the area, we used non‐invasive genetic sampling to estimate chimpanzee population size, sex ratio, community composition, and range boundaries on the western flank of the massif. The level of genetic diversity and affinity between communities was estimated and recommendations for future genetic censusing provided. Between 2003 and 2018, we collected 999 fecal samples of which 663 were analyzed using a panel of 26 microsatellites. We identified a minimum of 136 chimpanzees in four communities, with evidence of migratory events, a high level of shared ancestry and genetic diversity. We assessed sampling intensities and capture rates for each community. Saturation was reached in two communities with sampling between 3.2 and 4.3 times the estimated number of chimpanzees. Our findings highlight the utility of genetic censusing for temporal monitoring of ape abundance, as well as capturing migratory events and gauging genetic diversity and population viability over time. We recommend genetic sampling, combined with camera trapping, for use in future Environmental and Social Impact Assessments, as these methods can yield robust baselines for implementing the mitigation hierarchy, future biomonitoring and conservation management

relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis. Availability and implementation: The software relax is written in Python with C modules and is released under the GPLv3+ license. Source code and precompiled binaries for all major operating systems are available from http://www.nmr-relax.com. Contact: [email protected]

relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

International audienceNuclear Magnetic Resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy to use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the GUI, is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimisation time are granted by parallelisation for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another – using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis. Availability: The software relax is written in Python with C modules and is released under the GPLv3+ licence. Source code and precompiled binaries for all major operating systems are available from http://www.nmr-relax.com

Automated NMR relaxation dispersion data analysis using NESSY

<p>Abstract</p> <p>Background</p> <p>Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR) relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary.</p> <p>Results</p> <p>The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program.</p> <p>Conclusions</p> <p>NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.</p