scholarly journals Confirmation of Bioinformatics Predictions of the Structural Domains in Honeybee Silk

Polymers ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 776 ◽  
Author(s):  
Andrea Woodhead ◽  
Andrew Church ◽  
Trevor Rapson ◽  
Holly Trueman ◽  
Jeffrey Church ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Level Structure ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Advanced Materials ◽  
Structural Domain ◽  
Structural Elements ◽  
Film Properties ◽  
Structural Domains ◽  
Insight Into

Honeybee larvae produce a silk made up of proteins in predominantly a coiled coil molecular structure. These proteins can be produced in recombinant systems, making them desirable templates for the design of advanced materials. However, the atomic level structure of these proteins is proving difficult to determine: firstly, because coiled coils are difficult to crystalize; and secondly, fibrous proteins crystalize as fibres rather than as discrete protein units. In this study, we synthesised peptides from the central structural domain, as well as the N- and C-terminal domains, of the honeybee silk. We used circular dichroism spectroscopy, infrared spectroscopy, and molecular dynamics to investigate the folding behaviour of the central domain peptides. We found that they folded as predicted by bioinformatics analysis, giving the protein engineer confidence in bioinformatics predictions to guide the design of new functionality into these protein templates. These results, along with the infrared structural analysis of the N- and C-terminal domain peptides and the comparison of peptide film properties with those of the full-length AmelF3 protein, provided significant insight into the structural elements required for honeybee silk protein to form into stable materials.

scholarly journals Separation of coiled-coil structures in lamin A/C is required for elongation of the filament

2020 ◽  
Author(s):  
Jinsook Ahn ◽  
Soyeon Jeong ◽  
So-mi Kang ◽  
Inseong Jo ◽  
Bum-Joon Park ◽  
...  
Keyword(s):  
Structural Transition ◽  
Coiled Coil ◽  
Binding Mode ◽  
Coiled Coils ◽  
Lamin A ◽  
Structural Elements ◽  
Mutant Proteins ◽  
Biochemical Effects ◽  
Insight Into

AbstractIntermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the key interaction. In this study, we investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in N-terminal of coil 1a and C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in elongation of the IF proteins.

scholarly journals Separation of Coiled-Coil Structures in Lamin A/C Is Required for the Elongation of the Filament

Cells ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 55
Author(s):  
Jinsook Ahn ◽  
Soyeon Jeong ◽  
So-Mi Kang ◽  
Inseong Jo ◽  
Bum-Joon Park ◽  
...  
Keyword(s):  
Structural Transition ◽  
Coiled Coil ◽  
Binding Mode ◽  
Coiled Coils ◽  
Lamin A ◽  
Structural Elements ◽  
Mutant Proteins ◽  
Biochemical Effects ◽  
Insight Into

Intermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, the crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the critical interaction. This study investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in the N-terminal of coil 1a and the C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in the elongation of IF proteins.

DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences

2019 ◽  
Vol 35 (16) ◽  
pp. 2790-2795 ◽  
Author(s):  
Jan Ludwiczak ◽  
Aleksander Winski ◽  
Krzysztof Szczepaniak ◽  
Vikram Alva ◽  
Stanislaw Dunin-Horkawicz
Keyword(s):  
Coiled Coil ◽  
Protein Sequences ◽  
Coiled Coils ◽  
Supplementary Information ◽  
Biological Interactions ◽  
Structural Domains ◽  
Current State ◽  
Genome Wide ◽  
And Function ◽  
Higher Sensitivity

Abstract Motivation Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function. Results Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains. Availability and implementation DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil. Supplementary information Supplementary data are available at Bioinformatics online.

A similarity test for the compartementalization of crystalline rocks into structural domains

2021 ◽  
Author(s):  
Attoumane Abi ◽  
Julien Walter ◽  
Ali Saeidi ◽  
Romain Chesnaux
Keyword(s):  
Rock Mass ◽  
New Method ◽  
Structural Domain ◽  
Structural Elements ◽  
Fluid Circulation ◽  
Structural Domains ◽  
Fracture Characterization ◽  
Fracture Characteristics ◽  
Fracture Spacing ◽  
Field Investigations

<p>It is well known that fracture networks play an important role in fluid circulation in crystalline rock mass. Given that crystalline basements have a negligible primary porosity (porosity of the rock matrix) in comparison to their secondary porosity (porosity due to fractures), fracture characterization generally constitute the most important parameter for the determination of the hydraulic characteristics of the rock mass. Fracture characterization may involve fracture samples from different surveying sources such as outcrops, tunnels and boreholes. For a matter of building a conceptual model, for a study area, the geologist compartmentalizes the study area into several structural homogeneous sub-areas. Those homogeneous sub-areas are called structural domains and how fracture samples are grouped in the same structural domain is the question treated in this presentation.</p><p>From field investigations to grouping fracture samples into structural domains, geologists have used methods that are mainly based on the geologist experience and use major structural elements such as faults as domain boundaries. In the case of total absence or limited presence of major structural elements, grouping fracture samples into structural domains becomes complicated. Therefore, several statistical methods which use fracture characteristics have been developed to assist the geologist for that matter. Those methods can be classified into two approaches, which have been introduced by Miller (1983) and Mahtab and Yegulalp (1984). Miller’s approach consists of grouping fracture samples which are totally homogeneous with regard to the fracture characteristic(s) of interest, especially fracture orientation. On the other hand, Mahtab and Yegulalp’s approach consists of grouping fracture samples which share a similar fracture set. While, Miller’s approach got a lot attention, especially in the engineering fields, Mahtab and Yegulalp’s method has the advantage of allowing taking into consideration the blind zones of fracture samples as in practice a fracture sample can hardly be constituted by all the fracture sets of its belonging structural domain. However, Mahtab and Yegulalps’s method ignore fracture characteristics such as fracture spacing, aperture and persistence which are important for fluid circulation in the rock mass.</p><p>This presentation proposes a new method that improves Mahtab and Yegulalp’s method by including fracture characteristics such as aperture, persistence and fracture spacing in addition to the fracture orientation considered in the original method. The field investigations took place in the Greenville geological province of the Canadian shield, in Lanaudière region, in Quebec; where fractures were sampled from 30 outcrops and four boreholes. The new method adds a higher level of confidence with regard to the similarity of samples within a structural domain. As a result of the new method, each structural domain has a unique combination of fracture set(s) characteristics which characterize its fracture network. The structural domain compartmentalization impact on the hydrogeological behavior of water flow within the rock mass constitutes the topic of an ongoing research project.</p>

scholarly journals Structure of the human FERRY Rab5 effector complex

2021 ◽  
Author(s):  
Dennis Quentin ◽  
Jan Schuhmacher ◽  
Bjoern Udo Klink ◽  
Janelle Lauer ◽  
Tanvir Shaikh ◽  
...  
Keyword(s):  
Regulation Of Gene Expression ◽  
Coiled Coil ◽  
Early Endosome ◽  
Coiled Coils ◽  
Mrna Transport ◽  
Long Distance ◽  
Temporal Regulation ◽  
Complex Core ◽  
Spatio Temporal ◽  
Insight Into

Long-range mRNA transport is crucial for the spatio-temporal regulation of gene expression, and its malfunction is linked to neurological disorders. The pentameric FERRY Rab5 effector complex is the molecular link between mRNA and the early endosome in mRNA intracellular distribution. Here, we determine the cryo-EM structure of the human FERRY complex, composed of Fy-1 to Fy-5. The structure reveals a clamp-like architecture, in which two arm-like appendages, each consisting of Fy-2 and a Fy-5 dimer, protrude from the central Fy-4 dimer. We demonstrate that the coiled-coil domains of Fy-2 are flexible and project into opposite directions from the FERRY complex core. While the C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils together with Fy-5 bind mRNA. Thus, Fy-2 serves as binding hub that connects not only all five complex subunits, but also mediates the binding to mRNA and to the early endosome via Rab5. The FERRY structure provides novel mechanistic insight into long-distance mRNA transport.

scholarly journals Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome

2021 ◽  
Vol 22 (15) ◽  
pp. 8012
Author(s):  
Rongxin Zhang ◽  
Yajun Liu ◽  
Xingxing Zhang ◽  
Ke Xiao ◽  
Yue Hou ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Biological Functions ◽  
Bioinformatics Pipeline ◽  
The Real ◽  
Human Transcriptome ◽  
Gene Sets ◽  
Nucleic Acid Structures ◽  
Regulatory Functions ◽  
Whole Transcriptome ◽  
Insight Into

G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways and the COVID-19-related gene sets. Bioinformatics analysis reveals the potential regulatory functions of G-quadruplexes on miRNA targeting at the scale of the whole transcriptome. In addition, the G-quadruplexes are depleted in the putative, not the real, PAS-strong poly(A) sites, which may weaken the possibility of such sites being the real cleaved sites. In brief, our study provides insight into the potential function of RNA G-quadruplexes in post-transcription.

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.

scholarly journals Structure Formation in Anisotropic Disks

2006 ◽  
Vol 2 (S235) ◽  
pp. 143-143
Author(s):  
Eduard Vorobyov ◽  
Christian Theis
Keyword(s):  
Stability Analysis ◽  
Linear Stability ◽  
Linear Stability Analysis ◽  
Disk Galaxies ◽  
Structural Elements ◽  
Small Perturbations ◽  
Gravitational Instabilities ◽  
Hydrodynamical Simulations ◽  
Axisymmetric Structures ◽  
Insight Into

The majority of normal disk galaxies are characterized by non-axisymmetric structures like spirals or bars. These structural elements have been widely discussed in the literature as a result of gravitational instabilities which are connected to growing density waves or global instabilities of disks. A first insight into the properties of galactic discs was provided by linear stability analysis. However, a disadvantage of linear stability analysis remained its restriction to small perturbations, both in amplitude and wavelength. Thus, numerical simulations, especially hydrodynamical and stellar-hydrodynamical simulations became a primary tool for the analysis of galactic evolution.

scholarly journals ARCIMBOLDOon coiled coils

2018 ◽  
Vol 74 (3) ◽  
pp. 194-204 ◽  
Author(s):  
Iracema Caballero ◽  
Massimo Sammito ◽  
Claudia Millán ◽  
Andrey Lebedev ◽  
Nicolas Soler ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Translational Symmetry ◽  
Command Line ◽  
Phase Problem ◽  
Final Solution ◽  
Resolution Limit ◽  
Helical Structures ◽  
Small Model ◽  
Test Pool

ARCIMBOLDOsolves the phase problem by combining the location of small model fragments usingPhaserwith density modification and autotracing usingSHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers.ARCIMBOLDO_LITEhas been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures usingARCIMBOLDO. Features fromPhaserv.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification andSHELXEautotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode withinARCIMBOLDOfor the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) orARCIMBOLDO_LITEtask interface inCCP4i.

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