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A method to construct the dynamic landscape of a bio-membrane with experiment and simulation.

ABSTRACT: Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use ¹³C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

SUBMITTER: Smith AA

PROVIDER: S-EPMC8748619 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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A method to construct the dynamic landscape of a bio-membrane with experiment and simulation.

Smith Albert A AA Vogel Alexander A Engberg Oskar O Hildebrand Peter W PW Huster Daniel D

Nature communications 20220110 1

Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we us ...[more]

PMID: 35013165

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Project description:In this study, surfactants were used to enhance heavy oil-solid separation, and a detailed mechanism was explored by SARA (saturates, aromatics, resins, asphaltenes) analysis, element analysis, AFM measurement, and molecular dynamic simulation. Surfactants could effectively decrease oil/solid interaction force and then oil-solid separation would be enhanced. The oil-solid interactive force was in relation to surfactants concentration, pH value, asphaltene content, and salinity. The molecular dynamics simulation results show that the dissociation of saturated hydrocarbon, aromatic hydrocarbon, resin, and asphaltene (SARA) on carbonate minerals is gradually weakened for all surfactants. In the process of molecular dynamics simulation of surfactant stripping SARA, firstly, the surfactant molecules adsorb on the surface of SARA molecules. After that, the surfactant peels SARA molecules off the surface of calcite under the influence of molecular thermal motion. In this process, surfactant molecules will not be directly adsorbed on the surface of trace minerals. The results of energy/temperature balance indicated that saturates, aromatics and resins could remain stable when the molecular dynamics simulation time reached 2000 ps with the phenomenon that saturates, aromatics could liberate from minerals totally within 2000 ps. The molecular dynamics simulation of asphaltenes will not liberate from calcite surface within 6000 ps, meanwhile, they could not reach the energy balance/energy balance within 6000 ps. The functional groups of surfactant molecules would have interactions with the SARA functional group, resulting in different dissociation effects of SARA. The results of molecular dynamics simulation are consistent with the experiment results. The separation effect of saturated hydrocarbon, aromatic hydrocarbon, resin, and asphaltene in five kinds of surfactants were different. The molecular dynamic simulation results were in accordance with the SARA analysis.

Project description:The most widely-used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms and analysis algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. All commercial tiling array platforms performed well, although each platform and analysis algorithm had distinct performance and cost characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. The spike-in DNA samples and the resulting array data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: chip-ChIP simulation For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each replicate array, we labeled 1Âµg of spike-in sample and 1Âµg of control sample. The Bioprime Plus Array CGH labeling Module (Invitrogen Catolog number 18095-014) was used. The spike-in was labeled with the red channel dye (Alexa Fluor-647) and the control was labeled with the green channel dye (Alexa Fluor-555) in two of the replicates. A dye swap was performed for the third replicate. These samples were then competitively hybridized to three replicate 244k arrays from Agilent, (AMADID 25150451). We hybridized the samples to the arrays using the Agilent Array CGH protocol, with some modifications. Briefly, labeled DNA was combined with Cot-1 DNA, blocking reagent, and hybridization buffer. The hybridizations were carried out at 60Â°C. The arrays were scanned using an Agilent dual laser scanner, and the images were processed using Agilent Feature Extraction Software.

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A method to construct the dynamic landscape of a bio-membrane with experiment and simulation.

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A method to construct the dynamic landscape of a bio-membrane with experiment and simulation.

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