Hierarchical nanomechanics of vimentin alpha helical coiled-coil proteins

2006 ◽  
Vol 978 ◽  
Author(s):  
Theodor Ackbarow ◽  
Markus J. Buehler
Keyword(s):  
Atomistic Simulation ◽  
Coiled Coil ◽  
Building Blocks ◽  
Tensile Tests ◽  
Coiled Coils ◽  
Atomistic Modeling ◽  
Alpha Helices ◽  
Hierarchical Assembly ◽  
Leading Role ◽  
Elementary Building

AbstractCoiled-coil alpha-helical dimers are the elementary building blocks of intermediate filaments (IFs), an important component of the cell's cytoskeleton. Therefore, IFs play a leading role in the mechanical integrity of the cells. Here we use atomistic simulation to carry out tensile tests on coiled-coils as well as on single alpha-helices of the 2B segment of the vimentin dimer that has been shown to control the large-deformation behavior of cells. We compare the characteristic force-strain curves of both structures and suggest explanations for the differences on this fundamental level of hierarchical assembly. We further systematically explore the strain rate dependence of the mechanical properties of the vimentin coiled-coil protein. We develop a simple continuum model capable of reproducing the atomistic modeling results. The model enables us to extrapolate to much lower deformation rates approaching those used in experiment.

scholarly journals Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures

2020 ◽  
Vol 21 (10) ◽  
pp. 3584 ◽  
Author(s):  
Won Min Park
Keyword(s):  
Modular Design ◽  
Coiled Coil ◽  
Molecular Complexes ◽  
Building Blocks ◽  
Structural Features ◽  
Coiled Coils ◽  
Design Strategies ◽  
Protein Motifs ◽  
Self Assembling ◽  
Current Design

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.

scholarly journals A Multiplexed Bacterial Two-Hybrid for Rapid Characterization of Protein-Protein Interactions and Iterative Protein Design

2020 ◽  
Author(s):  
W. Clifford Boldridge ◽  
Ajasja Ljubetič ◽  
Hwangbeom Kim ◽  
Nathan Lubock ◽  
Dániel Szilágyi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Coiled Coil ◽  
Building Blocks ◽  
Coiled Coils ◽  
Next Generation ◽  
Protein Protein Interactions ◽  
Library Size ◽  
Large Sets ◽  
Synthetic Cell ◽  
Two Hybrid

AbstractMyriad biological functions require protein-protein interactions (PPIs), and engineered PPIs are crucial for applications ranging from drug design to synthetic cell circuits. Understanding and engineering specificity in PPIs is particularly challenging as subtle sequence changes can drastically alter specificity. Coiled-coils are small protein domains that have long served as a simple model for studying the sequence-determinants of specificity and have been used as modular building blocks to build large protein nanostructures and synthetic circuits. Despite their simple rules and long-time use, building large sets of well-behaved orthogonal pairs that can be used together is still challenging because predictions are often inaccurate, and, as the library size increases, it becomes difficult to test predictions at scale. To address these problems, we first developed a method called the Next-Generation Bacterial Two-Hybrid (NGB2H), which combines gene synthesis, a bacterial two-hybrid assay, and a high-throughput next-generation sequencing readout, allowing rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way. After validating the NGB2H system on previously characterized libraries, we designed, built, and tested large sets of orthogonal synthetic coiled-coils. In an iterative set of experiments, we assayed more than 8,000 PPIs, used the dataset to train a novel linear model-based coiled-coil scoring algorithm, and then characterized nearly 18,000 interactions to identify the largest set of orthogonal PPIs to date with twenty-two on-target interactions.

scholarly journals CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments

2017 ◽  
Author(s):  
Dmytro Guzenko ◽  
Sergei V. Strelkov
Keyword(s):  
Intermediate Filaments ◽  
Coiled Coil ◽  
General Purpose ◽  
Coiled Coils ◽  
Filament Assembly ◽  
Protein Dimer ◽  
Protein Classes ◽  
Elementary Building ◽  
Experimental Structure ◽  
Or Modelling

AbstractAccurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ∼300-residue long α-helical coiled coil which is not assessable to either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases. Here we present CCFold, a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence only. The algorithm is based on a statistical analysis of experimentally determined structures and can handle any hydrophobic repeat patterns in addition to the most common heptads. We demonstrate that CCFold outperforms general-purpose computational folding in terms of accuracy, while being faster by orders of magnitude. By combining the CCFold algorithm and Rosetta folding we generate representative dimer models for all IF protein classes. The source code is freely available at https://github.com/biocryst/IF

scholarly journals Molecular design of stapled pentapeptides as building blocks of self-assembled coiled coil–like fibers

2021 ◽  
Vol 7 (4) ◽  
pp. eabd0492
Author(s):  
Yixiang Jiang ◽  
Wan Zhang ◽  
Fadeng Yang ◽  
Chuan Wan ◽  
Xiang Cai ◽  
...  
Keyword(s):  
Self Assembly ◽  
Molecular Design ◽  
Chemical Space ◽  
Coiled Coil ◽  
Building Blocks ◽  
Coiled Coils ◽  
Computational Method ◽  
Side Chain ◽  
Chain Flexibility ◽  
Self Assembled

Peptide self-assembly inspired by natural superhelical coiled coils has been actively pursued but remains challenging due to limited helicity of short peptides. Side chain stapling can strengthen short helices but is unexplored in design of self-assembled helical nanofibers as it is unknown how staples could be adapted to coiled coil architecture. Here, we demonstrate the feasibility of this design for pentapeptides using a computational method capable of predicting helicity and fiber-forming tendency of stapled peptides containing noncoded amino acids. Experiments showed that the best candidates, which carried an aromatically substituted staple and phenylalanine analogs, displayed exceptional helicity and assembled into nanofibers via specific head-to-tail hydrogen bonding and packing between staple and noncoded side chains. The fibers exhibited sheet-of-helix structures resembling the recently found collapsed coiled coils whose formation was sensitive to side chain flexibility. This study expands the chemical space of coiled coil assemblies and provides guidance for their design.

scholarly journals Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ling Xin ◽  
Xiaoyang Duan ◽  
Na Liu
Keyword(s):  
Building Block ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Single Type ◽  
Hierarchical Assembly ◽  
Optical Responses ◽  
Self Association ◽  
Living Organisms ◽  
Order Structures ◽  
Chiral System

AbstractIn living organisms, proteins are organized prevalently through a self-association mechanism to form dimers and oligomers, which often confer new functions at the intermolecular interfaces. Despite the progress on DNA-assembled artificial systems, endeavors have been largely paid to achieve monomeric nanostructures that mimic motor proteins for a single type of motion. Here, we demonstrate a DNA-assembled building block with rotary and walking modules, which can introduce new motion through dimerization and oligomerization. The building block is a chiral system, comprising two interacting gold nanorods to perform rotation and walking, respectively. Through dimerization, two building blocks can form a dimer to yield coordinated sliding. Further oligomerization leads to higher-order structures, containing alternating rotation and sliding dimer interfaces to impose structural twisting. Our hierarchical assembly scheme offers a design blueprint to construct DNA-assembled advanced architectures with high degrees of freedom to tailor the optical responses and regulate multi-motion on the nanoscale.

scholarly journals Fabrication of Magnesium-Aluminum Composites under High-Pressure Torsion: Atomistic Simulation

2021 ◽  
Vol 11 (15) ◽  
pp. 6801
Author(s):  
Polina Viktorovna Polyakova ◽  
Julia Alexandrovna Pukhacheva ◽  
Stepan Aleksandrovich Shcherbinin ◽  
Julia Aidarovna Baimova ◽  
Radik Rafikovich Mulyukov
Keyword(s):  
Atomistic Simulation ◽  
High Pressure Torsion ◽  
Tensile Tests ◽  
Temperature Treatment ◽  
Embedded Atom Method ◽  
Interface Bonding ◽  
Embedded Atom ◽  
Interlayer Region ◽  
Kinetics Of ◽  
Loading Scheme

The aluminum–magnesium (Al–Mg) composite materials possess a large potential value in practical application due to their excellent properties. Molecular dynamics with the embedded atom method potentials is applied to study Al–Mg interface bonding during deformation-temperature treatment. The study of fabrication techniques to obtain composites with improved mechanical properties, and dynamics and kinetics of atom mixture are of high importance. The loading scheme used in the present work is the simplification of the scenario, experimentally observed previously to obtain Al–Cu and Al–Nb composites. It is shown that shear strain has a crucial role in the mixture process. The results indicated that the symmetrical atomic movement occurred in the Mg–Al interface during deformation. Tensile tests showed that fracture occurred in the Mg part of the final composite sample, which means that the interlayer region where the mixing of Mg, and Al atoms observed is much stronger than the pure Mg part.

DNA-based self-assembly of nanostructures

2017 ◽  
Author(s):  
Joshua D. Carter ◽  
Chenxiang Lin ◽  
Yan Liu ◽  
Hao Yan ◽  
Thomas H. LaBean
Keyword(s):  
Self Assembly ◽  
Materials Science ◽  
Directed Assembly ◽  
Building Blocks ◽  
Hierarchical Assembly ◽  
Synthetic Dna ◽  
Nanoscale Manufacturing ◽  
Covalently Linked ◽  
Design Construction ◽  
Proteins And Peptides

This article examines the DNA-based self-assembly of nanostructures. It first reviews the development of DNA self-assembly and DNA-directed assembly, focusing on the main strategies and building blocks available in the modern molecular construction toolbox, including the design, construction, and analysis of nanostructures composed entirely of synthetic DNA, as well as origami nanostructures formed from a mixture of synthetic and biological DNA. In particular, it considers the stepwise covalent synthesis of DNA nanomaterials, unmediated assembly of DNA nanomaterials, hierarchical assembly, nucleated assembly, and algorithmic assembly. It then discusses DNA-directed assembly of heteromaterials such as proteins and peptides, gold nanoparticles, and multicomponent nanostructures. It also describes the use of complementary DNA cohesion as 'smart glue' for bringing together covalently linked functional groups, biomolecules, and nanomaterials. Finally, it evaluates the potential future of DNA-based self-assembly for nanoscale manufacturing for applications in medicine, electronics, photonics, and materials science.

scholarly journals Stereochemical considerations for constructing α-helical protein bundles with particular application to membrane proteins

1977 ◽  
Vol 163 (1) ◽  
pp. 45-57 ◽  
Author(s):  
A K Dunker ◽  
D J Zaleske
Keyword(s):  
Membrane Proteins ◽  
Coiled Coils ◽  
Alpha Helices ◽  
Helical Protein

The stereochemical constraints originally used to construct two- and three-stranded alpha-helical coiled-coils were generalized for aggregates of alpha-helices containing from 4 to 14 alpha-helices in tubular bundles. Certain features of bacteriorhodopsin show excellent correlations with these stereochemical constraints.

scholarly journals Similarities between extreme events in the solar-terrestrial system by means of nonextensivity

2011 ◽  
Vol 18 (5) ◽  
pp. 563-572 ◽  
Author(s):  
G. Balasis ◽  
C. Papadimitriou ◽  
I. A. Daglis ◽  
A. Anastasiadis ◽  
I. Sandberg ◽  
...  
Keyword(s):  
Extreme Events ◽  
Solar Flares ◽  
Particle Physics ◽  
Building Blocks ◽  
Magnetic Storms ◽  
Earthquake Dynamics ◽  
Magnitude Distribution ◽  
Terrestrial System ◽  
Universal Principles ◽  
Elementary Building

Abstract. The dynamics of complex systems are founded on universal principles that can be used to describe disparate problems ranging from particle physics to economies of societies. A corollary is that transferring ideas and results from investigators in hitherto disparate areas will cross-fertilize and lead to important new results. In this contribution, we investigate the existence of a universal behavior, if any, in solar flares, magnetic storms, earthquakes and pre-seismic electromagnetic (EM) emissions, extending the work recently published by Balasis et al. (2011a). A common characteristic in the dynamics of the above-mentioned phenomena is that their energy release is basically fragmentary, i.e. the associated events are being composed of elementary building blocks. By analogy with earthquakes, the magnitude of the magnetic storms, solar flares and pre-seismic EM emissions can be appropriately defined. Then the key question we can ask in the frame of complexity is whether the magnitude distribution of earthquakes, magnetic storms, solar flares and pre-fracture EM emissions obeys the same law. We show that these apparently different extreme events, which occur in the solar-terrestrial system, follow the same energy distribution function. The latter was originally derived for earthquake dynamics in the framework of nonextensive Tsallis statistics.

scholarly journals Coiled-coil networking shapes cell molecular machinery

2012 ◽  
Vol 23 (19) ◽  
pp. 3911-3922 ◽  
Author(s):  
Yongqiang Wang ◽  
Xinlei Zhang ◽  
Hong Zhang ◽  
Yi Lu ◽  
Haolong Huang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Critical Role ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Protein Protein Interactions ◽  
Full Spectrum ◽  
Kinetochore Assembly ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Systematic Understanding

The highly abundant α-helical coiled-coil motif not only mediates crucial protein–protein interactions in the cell but is also an attractive scaffold in synthetic biology and material science and a potential target for disease intervention. Therefore a systematic understanding of the coiled-coil interactions (CCIs) at the organismal level would help unravel the full spectrum of the biological function of this interaction motif and facilitate its application in therapeutics. We report the first identified genome-wide CCI network in Saccharomyces cerevisiae, which consists of 3495 pair-wise interactions among 598 predicted coiled-coil regions. Computational analysis revealed that the CCI network is specifically and functionally organized and extensively involved in the organization of cell machinery. We further show that CCIs play a critical role in the assembly of the kinetochore, and disruption of the CCI network leads to defects in kinetochore assembly and cell division. The CCI network identified in this study is a valuable resource for systematic characterization of coiled coils in the shaping and regulation of a host of cellular machineries and provides a basis for the utilization of coiled coils as domain-based probes for network perturbation and pharmacological applications.

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