Visualizing Biological Membrane Organization and Dynamics

Baaden, Marc

doi:10.1016/j.jmb.2019.02.018

Cited by 19 publications

(17 citation statements)

References 303 publications

(399 reference statements)

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“…For this purpose it is particularly important to form structural models in our minds. Advanced visualization is a particularly powerful approach already extensively used to understand biological membrane objects [55]. We will get back to the strengths of novel technological approaches such as using virtual reality gear or high-resolution and large-scale display walls a little later in this discussion [56][57][58][59][60].…”

Section: A Roadmap For Improving Our Current Understandingmentioning

confidence: 99%

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Martinez

Hardiagon

Santuz

et al. 2020

Advances in Bionanomaterials II

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In biology, metabolite transport across cell membranes occurs through natural channels and pores. Artificial ion-channel architectures represent potential mimics of natural ionic conduction. Many such systems were produced leading to a remarkable set of alternative artificial ion-channels. Far less advances were achieved in the area of synthetic biomimetic water channels, even though they could improve our understanding of the natural function of protein channels and may provide new strategies to generate highly selective, advanced water purification systems. Most realizations have used the selectivity components of natural protein channels embedded in artificial systems. Such biomolecules provide building blocks to constitute highly selective membrane-spanning water transport architectures. The simplification of such compounds, while preserving the high conduction activity of natural macromolecules, lead to fully synthetic artificial biomimetic channels. These simplified systems offer a particular chance to understand mechanistic and structural behaviors, providing rationales to engineer better artificial water-channels. Here we focus on computer simulations as a tool to complement experiment in understanding the properties of such systems with the aim to rationalize important concepts, design and optimize better compounds. Molecular dynamics simulations combined with advanced visual scrutiny thereof are central to such an approach. Novel technologies such as virtual reality headsets and stereoscopic large-scale display walls offer immersive collaborative insight into the complex mechanisms underlying artificial water channel function.

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Section: A Roadmap For Improving Our Current Understandingmentioning

confidence: 99%

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Martinez

Hardiagon

Santuz

et al. 2020

Advances in Bionanomaterials II

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“…In fact, the measurement using sophisticated microscopy techniques suggests that the distances spanned by different isoforms of CD45 from the membrane are proportional to their ectodomain size [4], meaning, these molecules stand erect on the cell surface. Although, current techniques such as super-resolution microscopy [5]and single-molecule tracking [6,7]and allied techniques have revolutionized the way we look at the biological systems [8], in particular, the molecular organization and their dynamics on the cell surface, unfortunately, even the improved resolution does not provide a comprehensive mechanism controlling their association and function [9]. Even a fundamental question, how cell-surface proteins position themselves 'upright' on the membrane prior to their interaction with a cognate partner on the opposing cell is a mystery.…”

Section: Introductionmentioning

confidence: 99%

How does an ectodomain of membrane-associated proteins stand upright and exert robust signal?

Lankipalli

Ramagopal

2020

Preprint

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Even after decades of research, a comprehensive mechanism that elucidates the underpinnings of signalling through the cell membrane is still elusive. Here, we address a simple question “how do the ectodomain of a membrane-associated protein consisting of multiple domains and connected by flexible linkers stand ‘upright’ on the membrane?”. Our analysis based on large amount of available functional and structural data, looking for a pattern of association of these molecules in the crystal structures and with the concept that ‘random things seldom repeat’ lead to a surprisingly interesting and consistent observation that the weak cis interaction mediated ordered array of constitutively expressed signalling molecules not only support their ‘upright’ orientation but also bury their ligand-binding surface to avoid spurious signaling in the non-signalling resting state. With CD4, pMHCII, CD2 and TNFR1 as examples, we show that the observed association of molecules also correlate well with their functional role. Further, our model reconciles the long-standing controversies related to these molecules and appear to be generic enough to be applied to other signalling molecules

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“…A very good recent overview in terms of other membrane modelling and visualization approaches is provided by [7].…”

Section: Introductionmentioning

confidence: 99%

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development

Sommer

2019

Journal of Integrative Bioinformatics

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For more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.

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Visualizing Biological Membrane Organization and Dynamics

Cited by 19 publications

References 303 publications

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

How does an ectodomain of membrane-associated proteins stand upright and exert robust signal?

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development

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