DNA Size (kb) Protein Size (kDa) Conversion Tool | HSLS
Target search as performed by DNA-binding proteins is a complex process, index alone does not indicate whether a causal relationship. Description: Interactive tutorials on DNA, genes, chromosomes, protein, heredity, and URL: salonjardin.info . Experiment with the forces involved and measure the relationship between the . Short answer: Using a binary code, genes (DNA) specify how proteins (among other things) are to be synthesized. Analogy: If DNA is a cooking book, genes are .
DNA ratios and other nucleic acids derived indices concomitantly with organism and ecosystems measures of responses to climate change distribution, abundance, activity, metabolic rate, survival will allow for the development of more rigorous and realistic predictions of the effects of anthropogenic climate change on marine systems.Gene To Protein: Overview - DNA, RNA and Protein Formation (4/7)
DNA ratio, ecological indicators, nucleic acid derived indices, marine ecology 1. Introduction In marine ecology the determination of the in situ physiological state of marine organisms and communities are among of the main challenges. Therefore, the developments of new direct methods are necessary to gain a better understanding of physiology, trophic interactions and changes in composition and structure in aquatic ecosystems.
Measurements of metabolic activity have been especially valuable as indicators of condition in studies of marine organisms, groups for which accurate determination of field metabolic rates is difficult [ 1 ].
Molecular methods based on nucleic acid derived indices [ 2 ] and the polymerase chain reaction has recently become an important tool in this field [ 3 ].
Many conceptually corrected biochemical measurement have been also proposed, but their implementation is often hindered by analytical complexities and problems in sampling, calibration and interpretation [ 4 ]. One of the most widely used nucleic acid derived indices in marine ecology is the RNA: DNA ratio was first proposed 38 years ago as a biochemical indicator of the physiological and nutritional state of aquatic organisms in natural environment [ 5 ] it has been continuously explored [ 6 — 10 ].
All this information can be applied in the determination of the potential survival of a captured organism in the marine environment. It is widely recognized that high mortality during the larval stages occurs and may be due directly to starvation or to poor feeding conditions, which reduce larval growth rate and increase the duration of exposure to potential predators [ 1718 ].
DNA ratio have been used to test nutrient-productivity models by demonstrating tight linkages between nearshore oceanographic processes such as upwelling and benthic rocky intertidal ecosystems [ 1 ]. The search for reliable and accurate indices of nutritional condition and growth has been the focus of a steadily growing number of studies. Though several notable studies shed light on the dynamic properties of protein—DNA complexes on both target and off-target sequences 21 — 24the molecular mechanism of dynamic sequence sampling, i.
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In particular, it is unclear to what extent the transiently bound protein can quickly identify and skip over sequences that do not resemble their targets. Also, the choice of proper strand orientation—since none is preferred a priori—requires the protein to tumble and flip in the 1D search mode, as underscored by several reports 25 — In part due to the high computational cost, few in silico studies explicitly addressed the issue of dynamic association and formation of the native protein—DNA complex, exclusively using simplified coarse-grained models with varying spatial resolution 1617 In the advent of petascale computing, however, the modelling of dynamic complex formation is becoming increasingly feasible, as has already been shown for protein-ligand interactions After TRF1 and TRF2 localize to telomeres, they thus do not remain bound to a single site but slowly move between neighboring repeats, which allows them to homodimerize and form the shelterin—a higher-order protein assembly that maintains functionality and structural integrity of telomeres.
The dynamic nature of TRF1 on telomeric tracts in the cellular environment was highlighted in another report In this work, we employ feature-length MD simulations to provide a comprehensive description of DNA binding and sequence recognition of the TRF1 homeodomain on both target and off-target DNA sequences.
Using computational mutagenesis, we describe two opposing mechanisms allowing TRF1 to achieve sequence specificity and accelerate the scanning of DNA sequence by balancing between increased affinity for the target sequence and low affinity for off-target sites. We then investigate the thermodynamics of the TRF1—DNA complex on the actual telomeric sequence by computing free energy maps that capture the sequence-dependent differences in affinity and predict the existence of additional binding sites, simultaneously reproducing experimental data with high precision.
Finally, we used data reduction and statistical inference methods to quantitatively analyze the massive amount of simulation data in order to extract intermediates of the binding process, identify residues involved in the initiation of binding, as well as quantify the kinetics of flipping and specific complex formation. Since TRF1 assumes a homeodomain fold similar to many sequence-specific transcription factors 3031we believe that these conclusions are widely applicable in the field of protein—DNA interactions.
Such an approach has been successfully used by several groups so far 33 — 36allowing to bypass common problems associated with the behavior of DNA termini and excessive elasticity of short DNA oligomers complexed with proteins.
A native structure of the specific TRF1—DNA complex was obtained by superimposing phosphorus atoms in the X-ray structure with the artificially created bp periodic model. Simulation details For all free energy simulations, a cubic 6. For spontaneous binding simulations, we employed a rectangular 6.
All simulations were performed in Gromacs 4. The Amber99sb-parmbsc0 force field was used 38and temperature was maintained at K using the stochastic velocity rescaling thermostat with a time constant of 0. Particle Mesh Ewald PME summation was used for the calculation of electrostatic interactions, and van der Waals interactions were cut off at 1. The distance between DNA phosphorus atoms and core residues of the protein 12 residues closest to the protein COM during an equilibrium simulation projected onto the XY-plane r-distance was used as the reaction coordinate.
From this trajectory, 30 frames were extracted that corresponded to geometries in 0. These geometries were then used to assess the effect of single amino acid mutations on the thermodynamics of specific and non-specific TRF1—DNA binding. The number of ions was then adjusted to ensure charge neutrality. Importantly, the use of a single steered MD trajectory results in desirable error cancellation, allowing us to capture relatively minor changes in the behavior of all systems considered with high sensitivity.
To generate initial frames for individual US windows along the DNA helix, a rotation-translation matrix was used to propagate the protein in 69 steps along a helical path about the main axis of the DNA helix, as defined by standard B-DNA geometry.
RNA:DNA Ratio and Other Nucleic Acid Derived Indices in Marine Ecology
This Z-coordinate was defined with respect to a single base pair not involved in protein binding 1. In addition, one-sided harmonic potentials were added to prevent the COM of DNA from diffusing away in the XY-plane, in order to avoid periodic boundary artifacts.
- RNA:DNA Ratio and Other Nucleic Acid Derived Indices in Marine Ecology
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- DNA Size (kb) Protein Size (kDa) Conversion Tool
For both DNA orientations, a set of ns simulations in each umbrella sampling window was ran. Spontaneous binding and spawning To study spontaneous binding of TRF1 to telomeric DNA, 50 systems have been prepared in which the protein was placed randomly in the simulation box containing a periodic DNA molecule.