Dataset Information

FATCAT 2.0: towards a better understanding of the structural diversity of proteins.

ABSTRACT: FATCAT 2.0 server (http://fatcat.godziklab.org/), provides access to a flexible protein structure alignment algorithm developed in our group. In such an alignment, rotations and translations between elements in the structure are allowed to minimize the overall root mean square deviation (RMSD) between the compared structures. This allows to effectively compare protein structures even if they underwent structural rearrangements in different functional forms, different crystallization conditions or as a result of mutations. The major update for the server introduces a new graphical interface, much faster database searches and several new options for visualization of the structural differences between proteins.

SUBMITTER: Li Z

PROVIDER: S-EPMC7319568 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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FATCAT 2.0: towards a better understanding of the structural diversity of proteins.

Li Zhanwen Z Jaroszewski Lukasz L Iyer Mallika M Sedova Mayya M Godzik Adam A

Nucleic acids research 20200701 W1

FATCAT 2.0 server (http://fatcat.godziklab.org/), provides access to a flexible protein structure alignment algorithm developed in our group. In such an alignment, rotations and translations between elements in the structure are allowed to minimize the overall root mean square deviation (RMSD) between the compared structures. This allows to effectively compare protein structures even if they underwent structural rearrangements in different functional forms, different crystallization conditions o ...[more]

PMID: 32469061

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Project description:IntroductionPrevious studies have shown that anticipatory postural adjustments (APAs) are altered in people with Parkinson's disease but its meaning for locomotion is less understood. This study aims to investigate the association between APAs and gait initiation, gait and freezing of gait and how a dynamic postural control challenging training may induce changes in these features.MethodsGait initiation was quantified using wearable sensors and subsequent straight walking was assessed via marker-based motion capture. Additionally, turning and FOG-related outcomes were measured with wearable sensors. Assessments were conducted one week before (Pre), one week after (Post) and 4 weeks after (Follow-up) completion of a training intervention (split-belt treadmill training or regular treadmill training), under single task and dual task (DT) conditions. Statistical analysis included a linear mixed model for training effects and correlation analysis between APAs and the other outcomes for Pre and Post-Pre delta.Results52 participants with Parkinson's disease (22 freezers) were assessed. We found that APA size in the medio-lateral direction during DT was positively associated with gait speed (p<0.001) and stride length (p<0.001) under DT conditions at Pre. The training effect was largest for first step range of motion and was similar for both training modes. For the associations between changes after the training (pooled sample) medio-lateral APA size showed a significant positive correlation with first step range of motion (p = 0.033) only in the DT condition and for the non-freezers only.ConclusionsThe findings of this work revealed new insights into how APAs were not associated with first step characteristics and freezing and only baseline APAs during DT were related with DT gait characteristics. Training-induced changes in the size of APAs were related to training benefits in the first step ROM only in non-freezers. Based on the presented results increasing APA size through interventions might not be the ideal target for overall improvement of locomotion.

Project description:Proteins perform their function by accessing a suitable conformer from the ensemble of available conformations. The conformational diversity of a chosen protein structure can be obtained by experimental methods under different conditions. A key issue is the accurate comparison of different conformations. A gold standard used for such a comparison is the root mean square deviation (RMSD) between the two structures. While extensive refinements of RMSD evaluation at the backbone level are available, a comprehensive framework including the side chain interaction is not well understood. Here we employ protein structure network (PSN) formalism, with the non-covalent interactions of side chain, explicitly treated. The PSNs thus constructed are compared through graph spectral method, which provides a comparison at the local and at the global structural level. In this work, PSNs of multiple crystal conformers of single-chain, single-domain proteins, are subject to pair-wise analysis to examine the dissimilarity in their network topologies and in order to determine the conformational diversity of their native structures. This information is utilized to classify the structural domains of proteins into different categories. It is observed that proteins typically tend to retain structure and interactions at the backbone level. However, some of them also depict variability in either their overall structure or only in their inter-residue connectivity at the sidechain level, or both. Variability of sub-networks based on solvent accessibility and secondary structure is studied. The types of specific interactions are found to contribute differently to structure variability. An ensemble analysis by computing the mathematical variance of edge-weights across multiple conformers provided information on the contribution to overall variability from each edge of the PSN. Interactions that are highly variable are identified and their impact on structure variability has been discussed with the help of a case study. The classification based on the present side-chain network-based studies provides a framework to correlate the structure-function relationships in protein structures.

Dataset Information

FATCAT 2.0: towards a better understanding of the structural diversity of proteins.

Publications

FATCAT 2.0: towards a better understanding of the structural diversity of proteins.

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