Current Frontiers and Perspectives in Cell Biology

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Yuval Elani and Ali Salehi-Reyhani.

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Email: ku. This article is distributed under the terms of the Creative Commons Attribution 4. This article has been cited by other articles in PMC. Abstract Living cells are hugely complex chemical systems composed of a milieu of distinct chemical species including DNA, proteins, lipids, and metabolites interconnected with one another through a vast web of interactions: this complexity renders the study of cell biology in a quantitative and systematic manner a difficult task.

Impact statement Recent years have seen an increasing drive to construct cell mimics and use them as simplified experimental models to replicate and understand biological phenomena in a well-defined and controlled system. Keywords: Artificial cells, biomimetics, synthetic biology, biophysics. Introduction The construction of artificial cells that resemble biological cells in form and function is a rapidly growing area of research. Open in a separate window.

Figure 1. Figure 2. Cell membrane mimics Historically, the plasma membrane has been the most well-developed cellular component to be mimicked and used as a model. Investigating cellular structural components Artificial cell models are increasingly used in investigations relating to the mechanisms of action of various structural components and associated machineries. Figure 3. Figure 4. Macromolecular crowding It has long been known that protein folding, stability, and function, as well as enzymatic reaction kinetics and mechanisms, are influenced by molecular crowding through reduced diffusion times and increased molecular binding rates.

Cells-on-chip Construction of artificial cells for fundamental biology need not be limited to membrane-encapsulated systems. Perspectives and conclusions The synopsis above shows that cell mimics have been used for a range of studies in fundamental biological research, and towards the construction of functional artificial cells. Author contributions All authors contributed equally to the writing of this manuscript. References 1. Nature ; : — Integrating artificial with natural cells to translate chemical messages that direct E. Nature Communications ; 5 : — Engineering genetic circuit interactions within and between synthetic minimal cells.

Nature Chemistry ; 9 —9. Protein synthesis in artificial cells: using compartmentalisation for spatial organisation in vesicle bioreactors. Physical Chemistry Chemical Physics ; 17 ;—7. Vesicle-based artificial cells as chemical microreactors with spatially segregated reaction pathways. A compartmentalized out-of-equilibrium enzymatic reaction network for sustained autonomous movement. ACS Central Science ; 2 : —9. Compartmentalized reactions as a case of soft-matter biotechnology: synthesis of proteins and nucleic acids inside lipid vesicles.

Journal of Materials Chemistry ; 21 : — Polymerase chain reaction in liposomes. Giant vesicles as microreactors for enzymatic mRNA synthesis.

Journal content

ChemBioChem ; 3 : — Gene expression within cell-sized lipid vesicles. ChemBioChem ; 4 : —5. Toward an artificial cell based on gene expression in vesicles. Physical Biology ; 2 : P1—P1. Synthetic biology: applications come of age. Nature Reviews Genetics ; 11 : — A brief history of synthetic biology. Nature Reviews Microbiology ; 12 : — The quest for the minimal bacterial genome. Current Opinion in Biotechnology ; 42 : — Integrating biological redesign: where synthetic biology came from and where it needs to go.

Cell ; : — Takinoue M, Takeuchi S. Droplet microfluidics for the study of artificial cells. Analytical and Bioanalytical Chemistry ; : — Chemical Communications ; 51 : — Elani Y. Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology. Biochemical Society Transactions ; 44 : — Protein expression, aggregation, and triggered release from polymersomes as artificial cell-like structures.

Angewandte Chemie International Edition ; 51 : — Predatory behaviour in synthetic protocell communities. Nature Chemistry ; 9 : —9. Buchner E, Rapp R. Berichte der deutschen chemischen Gesellschaft ; 30 : — Multiple evidence strands suggest that there may be as few as 19 human protein-coding genes. Human Molecular Genetics ; 23 : — Perspectives for mass spectrometry and functional proteomics. Mass Spectrometry Reviews ; 20 : 1— Stano P, Luisi PL.

1. Introduction

Semi-synthetic minimal cells: origin and recent developments. Current Opinion in Biotechnology ; 24 : —8. Walde P. Building artificial cells and protocell models: experimental approaches with lipid vesicles. BioEssays ; 32 : — Martino C. Droplet-based microfluidics for artificial cell generation: a brief review.

Interface Focus ; 6 : — Matosevic S, Paegel BM. Stepwise synthesis of giant unilamellar vesicles on a microfluidic assembly line. Journal of the American Chemical Society ; : — Layer-by-layer cell membrane assembly. Nature Chemistry ; 5 ;— Microfluidic generation of encapsulated droplet interface bilayer networks multisomes and their use as cell-like reactors. Chemical Communications ; 52 ;— Multiscale computational models of complex biological systems. Annual Review of Biomedical Engineering ; 15 : — Mathematical modeling and synthetic biology. Drug Discovery Today: Disease Models ; 5 : — Modeling biology spanning different scales: an open challenge.

BioMed Research International. Epub ahead of print Model membrane systems and their applications. Current Opinion in Chemical Biology ; 11 : —7. Membrane lipid composition and cellular function. Journal of Lipid Research ; 26 : — Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating. Emerging roles for lipids in shaping membrane-protein function. Booth PJ.

Cell Biology: Mitochondria - HarvardX on edX

Sane in the membrane: designing systems to modulate membrane proteins. Current Opinion in Structural Biology ; 15 : — Effects of confinement on the self-organization of microtubules and motors. Current Biology ; 19 : — Evidence that bilayer bending rigidity affects membrane protein folding.

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Abstract Living cells are hugely complex chemical systems composed of a milieu of distinct chemical species including DNA, proteins, lipids, and metabolites interconnected with one another through a vast web of interactions: this complexity renders the study of cell biology in a quantitative and systematic manner a difficult task. Hirabayashi, S. Current Opinion in Chemical Biology ; 11 : —7. Angewandte Chemie International Edition ; 51 : — Online articles. Molecular crowding shapes gene expression in synthetic cellular nanosystems.

Biochemistry ; 36 : — Modulation of CTP:phosphocholine cytidylyltransferase by membrane curvature elastic stress. Studying the effects of asymmetry on the bending rigidity of lipid membranes formed by microfluidics. Chemical Communications ; 52 : — Measurements of the effect of membrane asymmetry on the mechanical properties of lipid bilayers. Chemical Communications ; 51 ;—9. Membrane mechanical properties of synthetic asymmetric phospholipid vesicles. Soft Matter ; 12 : —8. Fadeel B, Xue D. The ins and outs of phospholipid asymmetry in the plasma membrane: roles in health and disease.

Critical Reviews in Biochemistry and Molecular Biology ; 44 : — Simons K, Sampaio JL. Membrane organization and lipid rafts.

ISBN 13: 9789535105442

Cold Spring Harbor Perspectives in Biology ; 3 : a—a Lingwood D, Simons K. Lipid rafts as a membrane-organizing principle. Science ; : 46— Separation of liquid phases in giant vesicles of ternary mixtures of phospholipids and cholesterol. Biophysical Journal ; 85 : — Seeing spots: complex phase behavior in simple membranes. Separation of liquid domains in model membranes induced with high hydrostatic pressure.

Chemical Communications ; 51 : —8. COPI coat assembly occurs on liquid-disordered domains and the associated membrane deformations are limited by membrane tension. Proceedings of the National Academy of Sciences ; : — Journal of Molecular Biology ; : — Secondary structure and distribution of fusogenic LV-peptides in lipid membranes.

European Biophysics Journal ; 37 : — Mechanisms of integral membrane protein insertion and folding. Relative domain folding and stability of a membrane transport protein. Mechanisms of sensory transduction in the skin. Sukharev S, Anishkin A. Trends in Neurosciences ; 27 : — How curved membranes recruit amphipathic helices and protein anchoring motifs.

Nature Chemical Biology ; 5 : — Geometrical membrane curvature as an allosteric regulator of membrane protein structure and function. Biophysical Journal ; : —9. Biophysical approaches to protein-induced membrane deformations in trafficking. Current Opinion in Cell Biology ; 20 : — Callan-Jones A, Bassereau P. Curvature-driven membrane lipid and protein distribution. Probing polymerization forces by using actin-propelled lipid vesicles. Proceedings of the National Academy of Sciences ; : —6. Myosin motors fragment and compact membrane-bound actin filaments.

Elife ; 2 : e—e Upadhyaya A, van Oudenaarden A. Biomimetic systems for studying actin-based motility. Current Biology ; 13 : R— Assembly of MreB filaments on liposome membranes: a synthetic biology approach. ACS Synthetic Biology ; 1 : 53—9. Membrane curvature and mechanisms of dynamic cell membrane remodelling. Nature ; : —6. Anitei M, Hoflack B. Bridging membrane and cytoskeleton dynamics in the secretory and endocytic pathways. Nature Cell Biology ; 14 : 11—9. Structural basis of membrane invagination by F-BAR domains.

Let's go bananas: revisiting the endocytic BAR code. GM1 structure determines SVinduced membrane invagination and infection. Nature Cell Biology ; 12 : 11—8. Shiga toxin induces tubular membrane invaginations for its uptake into cells. Nature ; : —5. Actin dynamics drive membrane reorganization and scission in clathrin-independent endocytosis. Furrow constriction in animal cell cytokinesis. Biophysical Journal ; : — Nature Cell Biology ; 17 : —9.

Science ; : —9.

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Membrane shape at the edge of the dynamin helix sets location and duration of the fission reaction. Kretschmer S, Schwille P. Pattern formation on membranes and its role in bacterial cell division. Current Opinion in Cell Biology ; 38 : 52—9. Protein patterns and oscillations on lipid monolayers and in microdroplets. Angewandte Chemie ; : —7. Toward spatially regulated division of protocells: insights into the E.

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Indeed, ribosome biogenesis has been studied almost exclusively using genetic and biochemical approaches without the benefit of small-molecule inhibitors of this process. Here, we provide a perspective on the promise of chemical inhibitors of ribosome assembly for future research. We explore key obstacles that complicate the interpretation of studies aimed at perturbing ribosome biogenesis in vivo using genetic methods, and we argue that chemical inhibitors are especially powerful because they can be used to induce perturbations in a manner that obviates these difficulties.

Thus, in combination with leading-edge biochemical and structural methods, chemical probes offer unique advantages toward elucidating the molecular events that define the assembly of ribosomes. Full Text - Chemical modulators of ribosome biogenesis as biological probes PDF 1, KB - Chemical modulators of ribosome biogenesis as biological probes. Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell.

A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing.

Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges. The upswing in US Food and Drug Administration and European Medicines Agency drug approvals in may have marked an end to the dry spell that has troubled the pharmaceutical industry over the past decade. Regardless, the attrition rate of drugs in late clinical phases remains high, and a lack of target validation has been highlighted as an explanation.

This has led to a resurgence in appreciation of phenotypic drug screens, as these may be more likely to yield compounds with relevant modes of action. However, cell-based screening approaches do not directly reveal cellular targets, and hence target deconvolution and a detailed understanding of drug action are needed for efficient lead optimization and biomarker development. Here, recently developed functional genomics technologies that address this need are reviewed.

The approaches pioneered in model organisms, particularly in yeast, and more recently adapted to mammalian systems are discussed.

Finally, areas of particular interest and directions for future tool development are highlighted. My account Submit manuscript Register Subscribe. Top of page Editorial Frontiers in chemical biology Future perfect - p doi Frontiers in chemical biology XFELs open a new era in structural chemical biology - pp - Petra Fromme doi Frontiers in chemical biology Functional genomics to uncover drug mechanism of action - pp - Sebastian M B Nijman doi