Modeling the Self-Assembly of Protein Complexes through a Rigid-Body Rotational Reaction–Diffusion Algorithm

The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here, we introduce a rich, intuitive and biologically realistic genotype–phenotype (GP) map that serves as a model of self-assembling biological structures, such as protein complexes, and remains computationally and analytically tractable. Our GP map arises naturally from the self-assembly of polyomino structures on a two-dimensional lattice and exhibits a number of properties: redundancy (genotypes vastly outnumber phenotypes), phenotype bias (genotypic redundancy varies greatly between phenotypes), genotype component disconnectivity (phenotypes consist of disconnected mutational networks) and shape space covering (most phenotypes can be reached in a small number of mutations). We also show that the mutational robustness of phenotypes scales very roughly logarithmically with phenotype redundancy and is positively correlated with phenotypic evolvability. Although our GP map describes the assembly of disconnected objects, it shares many properties with other popular GP maps for connected units, such as models for RNA secondary structure or the hydrophobic-polar (HP) lattice model for protein tertiary structure. The remarkable fact that these important properties similarly emerge from such different models suggests the possibility that universal features underlie a much wider class of biologically realistic GP maps.

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hu.MAP 2.0: Integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies

10.1101/2020.09.15.298216 ◽

2020 ◽

Author(s):

Kevin Drew ◽

John B. Wallingford ◽

Edward M. Marcotte

Keyword(s):

Machine Learning ◽

Mass Spectrometry ◽

Structural Biology ◽

Self Assembly ◽

Protein Complexes ◽

The Self ◽

Web Interface ◽

Valuable Resource ◽

Cellular Functions ◽

Learning Framework

AbstractA general principle of biology is the self-assembly of proteins into functional complexes. Characterizing their composition is, therefore, required for our understanding of cellular functions. Unfortunately, we lack a comprehensive set of protein complexes for human cells. To address this gap, we developed a machine learning framework to identify protein complexes in over 15,000 mass spectrometry experiments which resulted in the identification of nearly 7,000 physical assemblies. We show our resource, hu.MAP 2.0, is more accurate and comprehensive than previous resources and gives rise to many new hypotheses, including for 274 completely uncharacterized proteins. Further, we identify 259 promiscuous proteins that participate in multiple complexes pointing to possible moonlighting roles. We have made hu.MAP 2.0 easily searchable in a web interface (http://humap2.proteincomplexes.org/), which will be a valuable resource for researchers across a broad range of interests including systems biology, structural biology, and molecular explanations of disease.

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Synthesis of Extended, Self-Assembled Biological Membranes containing Membrane Proteins from Gas Phase

10.1101/661215 ◽

2019 ◽

Cited By ~ 1

Author(s):

Matthias Wilm

Keyword(s):

Membrane Proteins ◽

Membrane Protein ◽

Self Assembly ◽

Protein Function ◽

Lipid Membranes ◽

Protein Complexes ◽

Biological Membranes ◽

The Self ◽

In Vitro Systems

1.AbstractMembrane proteins carry out a wide variety of biological functions. The reproduction of specific properties that have evolved over millions of years of biological membranes in a technically controlled environment is of significant interest. Here a method is presented that allows the self-assembly of a macroscopically large, freely transportable membrane with Outer membrane porin G from Escherichia Coli. The technique does not use protein specific characteristics and therefore, could represent a method for the generation of extended layers of membranes with arbitrary membrane protein content. Such in-vitro systems are relevant in the study of membrane-protein function and structure and the self-assembly of membrane-based protein complexes. They might become important for the incorporation of the lipid-membranes in technological devices.

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The Nature of Rapidly Extracted Phycocyanin from the Blue-Green Alga Plectonema Boryanum

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100065870 ◽

1971 ◽

Vol 29 ◽

pp. 366-367

Author(s):

M. Kessel ◽

R. MacColl

Keyword(s):

Self Assembly ◽

Analytical Ultracentrifugation ◽

Uranyl Acetate ◽

The Self ◽

Major Protein ◽

Subunit Structure ◽

Blue Green Alga ◽

Thin Sections ◽

Blue Green Algae ◽

Cacodylate Buffer

The major protein of the blue-green algae is the biliprotein, C-phycocyanin (Amax = 620 nm), which is presumed to exist in the cell in the form of distinct aggregates called phycobilisomes. The self-assembly of C-phycocyanin from monomer to hexamer has been extensively studied, but the proposed next step in the assembly of a phycobilisome, the formation of 19s subunits, is completely unknown. We have used electron microscopy and analytical ultracentrifugation in combination with a method for rapid and gentle extraction of phycocyanin to study its subunit structure and assembly.To establish the existence of phycobilisomes, cells of P. boryanum in the log phase of growth, growing at a light intensity of 200 foot candles, were fixed in 2% glutaraldehyde in 0.1M cacodylate buffer, pH 7.0, for 3 hours at 4°C. The cells were post-fixed in 1% OsO4 in the same buffer overnight. Material was stained for 1 hour in uranyl acetate (1%), dehydrated and embedded in araldite and examined in thin sections.

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Interrelationship of the cellular distribution and secretion of regular structure (RS) protein in Bacillus licheniformis nm 105

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100123969 ◽

1992 ◽

Vol 50 (1) ◽

pp. 712-713

Author(s):

Xiaorong Zhu ◽

Richard McVeigh ◽

Bijan K. Ghosh

Keyword(s):

Alkaline Phosphatase ◽

Bacillus Licheniformis ◽

Self Assembly ◽

Gel Electrophoresis ◽

Culture Supernatant ◽

Regular Structure ◽

The Self ◽

Cellular Distribution ◽

Structural Protein ◽

Laboratory Cultures

A mutant of Bacillus licheniformis 749/C, NM 105 exhibits some notable properties, e.g., arrest of alkaline phosphatase secretion and overexpression and hypersecretion of RS protein. Although RS is known to be widely distributed in many microbes, it is rarely found, with a few exceptions, in laboratory cultures of microorganisms. RS protein is a structural protein and has the unusual properties to form aggregate. This characteristic may have been responsible for the self assembly of RS into regular tetragonal structures. Another uncommon characteristic of RS is that enhanced synthesis and secretion which occurs when the cells cease to grow. Assembled RS protein with a tetragonal structure is not seen inside cells at any stage of cell growth including cells in the stationary phase of growth. Gel electrophoresis of the culture supernatant shows a very large amount of RS protein in the stationary culture of the B. licheniformis. It seems, Therefore, that the RS protein is cotranslationally secreted and self assembled on the envelope surface.

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Nanoscale Self-Assembly Using Ion and Electron Beam Techniques: A Rapid Review

MRS Advances ◽

10.1557/adv.2020.349 ◽

2020 ◽

Vol 5 (64) ◽

pp. 3507-3520

Author(s):

Chunhui Dai ◽

Kriti Agarwal ◽

Jeong-Hyun Cho

Keyword(s):

Electron Beam ◽

Self Assembly ◽

Ion Beam ◽

Three Dimensional ◽

The Self ◽

Stress Generation ◽

Rapid Review ◽

High Yield ◽

3D Nanostructures ◽

Self Assembled

AbstractNanoscale self-assembly, as a technique to transform two-dimensional (2D) planar patterns into three-dimensional (3D) nanoscale architectures, has achieved tremendous success in the past decade. However, an assembly process at nanoscale is easily affected by small unavoidable variations in sample conditions and reaction environment, resulting in a low yield. Recently, in-situ monitored self-assembly based on ion and electron irradiation has stood out as a promising candidate to overcome this limitation. The usage of ion and electron beam allows stress generation and real-time observation simultaneously, which significantly enhances the controllability of self-assembly. This enables the realization of various complex 3D nanostructures with a high yield. The additional dimension of the self-assembled 3D nanostructures opens the possibility to explore novel properties that cannot be demonstrated in 2D planar patterns. Here, we present a rapid review on the recent achievements and challenges in nanoscale self-assembly using electron and ion beam techniques, followed by a discussion of the novel optical properties achieved in the self-assembled 3D nanostructures.

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Bottom-up Evolution from Disks to High-Genus Polymersomes

10.26434/chemrxiv.6108467.v1 ◽

2018 ◽

Author(s):

Claudia Contini ◽

Russell Pearson ◽

Linge Wang ◽

Lea Messager ◽

Jens Gaitzsch ◽

...

Keyword(s):

Self Assembly ◽

The Self ◽

Amphiphilic Copolymers ◽

Chain Entanglement ◽

Bottom Up ◽

New Approach ◽

High Genus ◽

Transmission Electron ◽

Minimal Radius ◽

Stop Flow

<div><div><div><p>We report the design of polymersomes using a bottom-up approach where the self-assembly of amphiphilic copolymers poly(2-(methacryloyloxy) ethyl phosphorylcholine)–poly(2-(diisopropylamino) ethyl methacrylate) (PMPC-PDPA) into membranes is tuned using pH and temperature. We study this process in detail using transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and stop-flow ab- sorbance disclosing the molecular and supramolecular anatomy of each structure observed. We report a clear evolution from disk micelles to vesicle to high-genus vesicles where each passage is controlled by pH switch or temperature. We show that the process can be rationalised adapting membrane physics theories disclosing important scaling principles that allow the estimation of the vesiculation minimal radius as well as chain entanglement and coupling. This allows us to propose a new approach to generate nanoscale vesicles with genus from 0 to 70 which have been very elusive and difficult to control so far.</p></div></div></div>

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Bottom-up Evolution from Disks to High-Genus Polymersomes

10.26434/chemrxiv.6108467 ◽

2018 ◽

Author(s):

Claudia Contini ◽

Russell Pearson ◽

Linge Wang ◽

Lea Messager ◽

Jens Gaitzsch ◽

...

Keyword(s):

Self Assembly ◽

The Self ◽

Amphiphilic Copolymers ◽

Chain Entanglement ◽

Bottom Up ◽

New Approach ◽

High Genus ◽

Transmission Electron ◽

Minimal Radius ◽

Stop Flow

<div><div><div><p>We report the design of polymersomes using a bottom-up approach where the self-assembly of amphiphilic copolymers poly(2-(methacryloyloxy) ethyl phosphorylcholine)–poly(2-(diisopropylamino) ethyl methacrylate) (PMPC-PDPA) into membranes is tuned using pH and temperature. We study this process in detail using transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and stop-flow ab- sorbance disclosing the molecular and supramolecular anatomy of each structure observed. We report a clear evolution from disk micelles to vesicle to high-genus vesicles where each passage is controlled by pH switch or temperature. We show that the process can be rationalised adapting membrane physics theories disclosing important scaling principles that allow the estimation of the vesiculation minimal radius as well as chain entanglement and coupling. This allows us to propose a new approach to generate nanoscale vesicles with genus from 0 to 70 which have been very elusive and difficult to control so far.</p></div></div></div>

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Clathrin-Inspired Coating and Stabilization of Liposomes by DNA Self-Assembly

10.26434/chemrxiv.8859017.v1 ◽

2019 ◽

Author(s):

Kevin N. Baumann ◽

Luca Piantanida ◽

Javier García-Nafría ◽

Diana Sobota ◽

Kislon Voïtchovsky ◽

...

Keyword(s):

Self Assembly ◽

Mechanical Stability ◽

Lipid Vesicles ◽

The Self ◽

Force Microscopy ◽

Atomic Force ◽

Cryo Electron Microscopy ◽

Further Development ◽

Liposome Surface ◽

Dna Coating

The self-assembly of the protein clathrin on biological membranes facilitates essential processes of endocytosis in biological systems and has provided a source of inspiration for materials design by the highly ordered structural appearance. By mimicking the architecture of clathrin self-assemblies to coat liposomes with biomaterials, new classes of hybrid carriers can be derived. Here we present a method for fabricating DNA-coated liposomes by hydrophobically anchoring and subsequently growing a DNA network on the liposome surface which structurally mimics clathrin assemblies. Dynamic light scattering (DLS), ζ-potential and cryo-electron microscopy (cryo-EM) measurements independently demonstrate successful DNA coating. Nanomechanical measurements conducted with atomic force microscopy (AFM) show that the DNA coating enhances the mechanical stability of the liposomes relative to uncoated ones. Furthermore, we provide the possibility to reverse the coating process by triggering the disassembly of the DNA coating through a toehold-mediated displacement reaction. Our results describe a straightforward, versatile, and reversible approach for coating and stabilizing lipid vesicles by an interlaced DNA network. This method has potential for further development towards the ordered arrangement of tailored functionalities on the surfaces of liposomes and for applications as hybrid nanocarrier.

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