Comparative visualization of protein secondary structures

Kocincová, Lucia; Jarešová, Miroslava; Parulek, Július; Hauser, Helwig; Kozlíková, Barbora

doi:10.1186/s12859-016-1449-z

Cited by 13 publications

(8 citation statements)

References 25 publications

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“…It is worth noting that the secondary structure of the keratin changes significantly after 60 ns. It has been reported that the components ratio of the secondary structure is bound to influence the volume, shape, and biological functions of proteins [58], which are needed for the maintenance of the keratin structure integrity, and hinting that their variations are a critical parameter to evaluate the nanotoxicity of PG and GO materials on proteins. Our results, GO is more biocompatible than PG, are consistent with prior research [12,55,59,60].…”

Section: Secondary Structure Changes Of the Keratinmentioning

confidence: 99%

Nanotoxicity of two-dimensional nanomaterials on human skin and the structural evolution of keratin protein

Yin,

Yu,

Feng

et al. 2024

Nanotechnology

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Two-dimensional (2D) materials have been increasingly widely used in biomedical and cosmetical products nowadays, yet their safe usage in human body and environment necessitates a comprehensive understanding of their nanotoxicity. In this work, the effect of pristine graphene (PG) and graphene oxide (GO) on the adsorption and conformational changes of skin keratin using molecular dynamics (MD) simulations. It is found that skin keratin can be absorbed through various noncovalent driving forces, such as van der Waals (vdW) and electrostatics. In the case of GO, the oxygen-containing groups prevent tighter contact between skin keratin and the graphene basal plane through steric effects and electrostatic repulsion. On the other hand, electrostatic attraction and hydrogen bonding enhance their binding affinity to positively charged residues such as lysine and arginine. The secondary structure of skin keratin is better preserved in GO system, suggesting that GO has good biocompatibility. The charged groups on GO surface perform as the hydrogen bond acceptors, which is like to the natural receptors of keratin in this physiological environment. This work contributes to a better knowledge of the nanotoxicity of cutting-edge 2D materials on human health, thereby advancing their potential biological applications.

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Section: Secondary Structure Changes Of the Keratinmentioning

confidence: 99%

Nanotoxicity of two-dimensional nanomaterials on human skin and the structural evolution of keratin protein

Yin,

Yu,

Feng

et al. 2024

Nanotechnology

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“…Users can generate realistic millisecond-scale representations of conformational changes in proteins. Kocincová et al, 2017 introduce a visualization approach that addresses the divide between commonly used 1D and 3D representations. By incorporating details about the mutual positions of protein chains into the 1D sequential representation, users can observe spatial differences between proteins without the typical occlusion found in a 3D view.…”

Section: Scaling Up To Simulation Ensembles and Data Sharingmentioning

confidence: 99%

From complex data to clear insights: visualizing molecular dynamics trajectories

Belghit,

Spivak,

Dauchez

et al. 2024

Front. Bioinform.

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Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

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“…Comparing complex 3D structures is a difficult task and may be solved by switching to a more simple representation. Recent work by Kocincová et al [KJB*17], for instance, tackles this task by bridging between 1D amino acid sequences and their 3D‐representations. This is useful to compare time‐steps of a MD simulation of the same sequence, but fails to capture global correlations between the changes of individual elements of the sequence.…”

Section: Related Workmentioning

confidence: 99%

Analyzing Residue Surface Proximity to Interpret Molecular Dynamics

Lichtenberg

Menges

Ageev

et al. 2018

Computer Graphics Forum

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Figure 1: From an input molecule (left), we derive a surface proximity term (center, left) that represents the closeness of an atom to the molecule surface. We apply this method to a Molecular Dynamics simulation to obtain a color-coded map, representing the trajectory for each atom or residue (center). Single time-steps can be visualized in 3D (right), e.g., VdW-spheres or in a combined backbone-helix form. AbstractThe surface of a molecule holds important information about the interaction behavior with other molecules. In dynamic folding or docking processes, residues of amino acids with different properties change their position within the molecule over time. The atoms of the residues that are accessible to the solvent can directly contribute to binding interactions, while residues buried within the molecular structure contribute to the stability of the molecule. Understanding patterns and causality of structural changes is important for experts in the pharmaceutical domain, e.g., in the process of drug design. We apply an iterative computation of the Solvent Accessible Surface in order to extract virtual layers of a molecule. The extraction allows to track the movement of residues in the body of the molecule, with respect to the distance of the residue to the surface or the core during dynamics simulations. We visualize the obtained layer information for the complete time span of the molecular dynamics simulation as a 2D-map and for individual time-steps as a 3D-representation of the molecule. The data acquisition has been implemented alongside with further analysis functionality in a prototypical application, which is available to the public domain. We underline the feasibility of our approach with a study from the pharmaceutical domain, where our approach has been used for novel insights into the folding behavior of µ-conotoxins.

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Comparative visualization of protein secondary structures

Cited by 13 publications

References 25 publications

Nanotoxicity of two-dimensional nanomaterials on human skin and the structural evolution of keratin protein

Nanotoxicity of two-dimensional nanomaterials on human skin and the structural evolution of keratin protein

From complex data to clear insights: visualizing molecular dynamics trajectories

Analyzing Residue Surface Proximity to Interpret Molecular Dynamics

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