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Abstract:

Purpose

The purpose of this technical paper is to evaluate the emerging standard “Allotrope Data Format (ADF)” in the context of digital preservation at a major US academic library hosted at Brigham Young University. In combination with the new information management system ZONTAL Space (ZS), archiving with the ADF is compared with currently used systems CONTENTdm and ROSETTA.

Design/methodology/approach

The approach is a workflow-based comparison in terms of usability, functionality and reliability of the systems. Current workflows are replaced by optimized target processes, which limit the number of involved parties and process steps. The connectors or manual solutions between the current workflow steps are replaced with automatic functions inside of ZS. Reporting functionalities inside of ZS are used to track system and file lifecycle to ensure stability and data preservation.

Findings

The authors find that the target processes leveraging ZS drastically reduce complexity compared to current workflows. Archiving with the ADF is found to decrease integration complexity and provide a more robust data migration path for the future. The possibility to enrich data automatically with metadata and to store this information alongside the content in the same information package increases reusability of the data.

Research limitations/implications

The practical implications of this work suggest the arrival of a new information management system that can potentially revolutionize the archiving landscape within libraries. Beyond the scope of the initial proof of concept, the potential for the system can be seen to replace existing data management tools and provide access to new data analytics applications, like smart recommender systems.

Originality/value

The value of this study is a systematic introduction of ZS and the ADF, two emerging solutions from the Pharmaceutical Industry, to the broader audience of digital preservation experts within US libraries. The authors consider the exchange of best practices and solutions between industries to be of high value to the communities.

Abstract: Understanding the function of a protein requires not only knowledge of its tertiary structure but also an understanding of its conformational dynamics. Nuclear magnetic resonance (NMR) spectroscopy, polarization-resolved fluorescence spectroscopy and molecular dynamics (MD) simulations are powerful methods to provide detailed insight into protein dynamics on multiple time scales by monitoring global rotational diffusion and local flexibility (order parameters) that are sensitive to inter- and intramolecular interactions, respectively. We present an integrated approach where data from these techniques are analyzed and interpreted within a joint theoretical description of depolarization and diffusion, demonstrating their conceptual similarities. This integrated approach is then applied to the autophagy-related protein GABARAP in its cytosolic form, elucidating its dynamics on the pico- to nanosecond time scale and its rotational and translational diffusion for protein concentrations spanning 9 orders of magnitude. We compare the dynamics of GABARAP as monitored by 15N spin relaxation of the backbone amide groups, fluorescence anisotropy decays and fluorescence correlation spectroscopy of side chains labeled with BODIPY FL, and molecular movies of the protein from MD simulations. The recovered parameters agree very well between the distinct techniques if the different measurement conditions (probe localization, sample concentration) are taken into account. Moreover, we propose a method that compares the order parameters of the backbone and side chains to identify potential hinges for large-scale, functionally relevant intradomain motions, such as residues 27/28 at the interface between the two subdomains of GABARAP. In conclusion, the integrated concept of cross-fertilizing techniques presented here is fundamental to obtaining a comprehensive quantitative picture of multiscale protein dynamics and solvation. The possibility to employ these validated techniques under cellular conditions and combine them with fluorescence imaging opens up the perspective of studying the functional dynamics of GABARAP or other proteins in live cells.

Abstract: Atomic models of proteins built by homology modeling or from low-resolution experimental data may contain considerable local errors. The refinement success of molecular dynamics simulations is usually limited by both force field accuracy and by the substantial width of the conformational distribution at physiological temperatures. We propose a method to overcome both these problems by coupling homologous replicas during a molecular dynamics simulation, which narrows the conformational distribution, and smoothens and even improves the energy landscape by adding evolutionary information.