scholarly journals AlphaFold-Predicted Structures of KCTD Proteins Unravel Previously Undetected Relationships among the Members of the Family

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1862
Author(s):  
Luciana Esposito ◽  
Nicole Balasco ◽  
Giovanni Smaldone ◽  
Rita Berisio ◽  
Alessia Ruggiero ◽  
...  
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
Protein Family ◽  
General Sequence ◽  
Btb Domain ◽  
The Family ◽  
Three Dimensional Models ◽  
Definition Of ◽  
Sequence Similarities

One of the most striking features of KCTD proteins is their involvement in apparently unrelated yet fundamental physio-pathological processes. Unfortunately, comprehensive structure–function relationships for this protein family have been hampered by the scarcity of the structural data available. This scenario is rapidly changing due to the release of the protein three-dimensional models predicted by AlphaFold (AF). Here, we exploited the structural information contained in the AF database to gain insights into the relationships among the members of the KCTD family with the aim of facilitating the definition of the structural and molecular basis of key roles that these proteins play in many biological processes. The most important finding that emerged from this investigation is the discovery that, in addition to the BTB domain, the vast majority of these proteins also share a structurally similar domain in the C-terminal region despite the absence of general sequence similarities detectable in this region. Using this domain as reference, we generated a novel and comprehensive structure-based pseudo-phylogenetic tree that unraveled previously undetected similarities among the protein family. In particular, we generated a new clustering of the KCTD proteins that will represent a solid ground for interpreting their many functions.

A current assessment of photosystem II structure

1996 ◽  
Vol 16 (2) ◽  
pp. 159-187 ◽  
Author(s):  
William V. Nicholson ◽  
Robert C. Ford ◽  
Andreas Holzenburg
Keyword(s):  
Photosystem Ii ◽  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
X Ray Diffraction ◽  
Membrane Protein Complex ◽  
Fast Absorption ◽  
Current Assessment ◽  
Electron Microscopical ◽  
A Current

This review covers the recent progress in the elucidation of the structure of photosystem II (PSII). Because much of the structural information for this membrane protein complex has been revealed by electron microscopy (EM), the review will also consider the specific technical and interpretation problems that arise with EM where they are of particular relevance to the structural data. Most recent reviews of photosystem II structure have concentrated on molecular studies of the PSII genes and on the likely roles of the subunits that they encode or they were mainly concerned with the biophysical data and fast absorption spectroscopy largely relating to electron transfer in various purified PSII preparations. In this review, we will focus on the approaches to the three-dimensional architecture of the complex and the lipid bilayer in which it is located (the thylakoid membrane) with special emphasis placed upon electron microscopical studies of PSII-containing thylakoid membranes. There are a few reports of 3D crystals of PSII and of associated X-ray diffraction measurements and although little structural information has so far been obtained from such studies (because of the lack of 3D crystals of sufficient quality), the prospects for such studies are also assessed.

scholarly journals Protein Structure Determination in Living Cells

2019 ◽  
Vol 20 (10) ◽  
pp. 2442 ◽  
Author(s):  
Teppei Ikeya ◽  
Peter Güntert ◽  
Yutaka Ito
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Information ◽  
Nuclear Overhauser Effect ◽  
Protein Structures ◽  
Three Dimensional ◽  
Structural Data ◽  
Sample Tube ◽  
In Cells

To date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect’ structural information from peak patterns and chemical shift changes but not ‘direct’ data explicitly including interatomic distances and angles. To fully understand the functions and physical properties of proteins inside cells, it is indispensable to obtain explicit structural data or determine three-dimensional (3D) structures of proteins in cells. Whilst the short lifetime of cells in a sample tube, low sample concentrations, and massive background signals make it difficult to observe NMR signals from proteins inside cells, several methodological advances help to overcome the problems. Paramagnetic effects have an outstanding potential for in-cell structural analysis. The combination of a limited amount of experimental in-cell data with software for ab initio protein structure prediction opens an avenue to visualise 3D protein structures inside cells. Conventional nuclear Overhauser effect spectroscopy (NOESY)-based structure determination is advantageous to elucidate the conformations of side-chain atoms of proteins as well as global structures. In this article, we review current progress for the structure analysis of proteins in living systems and discuss the feasibility of its future works.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Applied Research of BIM Technology on Prestressed Steel Structures in Xuzhou Stadium

2013 ◽  
Vol 444-445 ◽  
pp. 971-975
Author(s):  
Zhan Sheng Liu ◽  
Xiao Feng Wu ◽  
Rui Long Xu
Keyword(s):  
Construction Industry ◽  
Three Dimensional ◽  
Steel Structure ◽  
Steel Structures ◽  
Space Structure ◽  
Construction Process ◽  
The Family ◽  
The Common ◽  
Three Dimensional Models ◽  
Prestressed Steel Structure

Prestressed steel structure is the common form of space structure. BIM technology is used to every field of the construction industry. In order to apply BIM technology to the design and construction of prestressed steel structures, Xuzhou stadium prestressed structure was took as an example with BIM technology. Firstly, development standards of the family are created. Secondly, three-dimensional positioning technology and then establishing three-dimensional models of BIM are designed. Finally, the construction process of Xuzhou stadium is dynamically simulated.

scholarly journals Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

2013 ◽  
Vol 368 (1632) ◽  
pp. 20130029 ◽  
Author(s):  
Harendra Guturu ◽  
Andrew C. Doxey ◽  
Aaron M. Wenger ◽  
Gill Bejerano
Keyword(s):  
Transcription Factor ◽  
Binding Site ◽  
Protein Interactions ◽  
Binding Sites ◽  
Three Dimensional ◽  
Structural Data ◽  
Regulatory Elements ◽  
Computational Method ◽  
Web Resource ◽  
Three Dimensional Models

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis -regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF–TF–DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein–protein interactions, potentially indirect interactions and ‘through-DNA’ interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex .

scholarly journals METHODS FOR MODELS PARAMETERS ESTIMATE TO SOLVE PROBLEMS ON 3D RECONSTRUCTION OF REAL OBJECTS COMPLEX MODELS

2016 ◽  
Vol 2016 (3) ◽  
pp. 233-242 ◽  
Author(s):  
Владислав Колякин ◽  
Vladislav Kolyakin ◽  
Владимир Аверченков ◽  
Vladimir Averchenkov ◽  
Максим Терехов ◽  
...  
Keyword(s):  
Computer Games ◽  
Three Dimensional ◽  
3D Models ◽  
Model Parameters ◽  
Complex Objects ◽  
Image Brightness ◽  
Real Objects ◽  
Complex Models ◽  
Three Dimensional Models ◽  
Definition Of

Virtual threedimensional (3 D) models of complex objects are used in many fields of science and engineering, such as architecture, industry, medicine, robotics. Besides, 3D models are used in geoinformation systems, computer games, virtual and supplemented reality and so on. Three dimensional models can be formed in dif-ferent ways, one of which consists in 3 D reconstruc-tion. One of the stages of the 3 D reconstruction of complex models of real objects is a definition of the mathematical models of geometric primitives emphasized on the image. One of the ways for the estimate of model parameters is a method of Hough vote and its modifications – Hough probabilistic transformation, Hough random transformation, Hough hierarchical transformation, phase space blurriness, use of a gra-dient of image brightness and so on. As an alternative way for models selection is a choice of suitable points from a set of data.

Structural Analysis of Proteins on Lipid Substrates

2000 ◽  
Vol 6 (S2) ◽  
pp. 1182-1183
Author(s):  
Elizabeth M. Wilson-Kubalek
Keyword(s):  
Structural Information ◽  
Rapid Determination ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Complexes ◽  
Structural Data ◽  
X Ray Crystallography ◽  
Helical Protein ◽  
3D Structure Determination

Electron microscopy (EM) has become an increasingly powerful method for the determination of three-dimensional (3D) structures of proteins and macromolecular complexes. EM offers advantages over X-ray crystallography and NMR for obtaining structural information about proteins in physiological conditions, as components of large assemblies, that cannot be obtained in large quantity, or that fail to yield 3D crystals. EM has been used to obtain structural data from images of isolated molecules and molecular complexes, two-dimensional (2D) protein crystals, and helical protein arrays. Helically arranged proteins allow the most rapid determination of 3D maps because they contain a complete range of equally spaced molecular views, therefore no tilting of the sample with respect to the electron beam is required. However, so far 3D structure determination of helical assemblies has been limited to proteins that naturally adopt this organization and to proteins that fortuitously crystallize as helices.

Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?

2015 ◽  
Vol 11 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Michal Brylinski
Keyword(s):  
Protein Structure ◽  
Protein Data Bank ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Structural Information ◽  
Three Dimensional ◽  
Data Bank ◽  
Prediction Problem ◽  
Three Dimensional Models ◽  
Protein Structure Prediction Problem

AbstractThe Protein Data Bank (PDB) undergoes an exponential expansion in terms of the number of macromolecular structures deposited every year. A pivotal question is how this rapid growth of structural information improves the quality of three-dimensional models constructed by contemporary bioinformatics approaches. To address this problem, we performed a retrospective analysis of the structural coverage of a representative set of proteins using remote homology detected by COMPASS and HHpred. We show that the number of proteins whose structures can be confidently predicted increased during a 9-year period between 2005 and 2014 on account of the PDB growth alone. Nevertheless, this encouraging trend slowed down noticeably around the year 2008 and has yielded insignificant improvements ever since. At the current pace, it is unlikely that the protein structure prediction problem will be solved in the near future using existing template-based modeling techniques. Therefore, further advances in experimental structure determination, qualitatively better approaches in fold recognition, and more accurate template-free structure prediction methods are desperately needed.

scholarly journals Relevant aspects to the recognition of extensional environments in the field

2021 ◽  
Vol 48 (2) ◽  
pp. 95-106
Author(s):  
Ana Milena Suárez Arias ◽  
Julián Andrés López Isaza ◽  
Anny Juieth Forero Ortega ◽  
Mario Andrés Cuéllar Cárdenas ◽  
Carlos Augusto Quiroz Prada ◽  
...  
Keyword(s):  
Hanging Wall ◽  
Image Interpretation ◽  
Three Dimensional ◽  
Normal Fault ◽  
Structural Data ◽  
Structural Aspect ◽  
Half Graben ◽  
Regional Tectonic ◽  
History Of ◽  
Definition Of

The understanding of each geological-structural aspect in the field is fundamental to be able to reconstruct the geological history of a region and to give a geological meaning to the data acquired in the outcrop. The description of a brittle extensional environment, which is dominated by normal fault systems, is based on: (I)  image interpretation, which aims to find evidence suggestive of an extensional geological environment, such  as the presence of scarp lines and fault scarps, horst, graben and/or half-graben, among others, that allow the identification of the footwall and hanging wall blocks; ii) definition of the sites of interest for testing; and  iii) analysis of the outcrops, following a systematic procedure that consists of the observation and identification of the deformation markers, their three-dimensional schematic representation, and their  subsequent interpretation, including the stereographic representation in the outcrop. This procedure implies the unification of the parameters of structural data acquisition in the field, mentioning the minimum fields  necessary for the registration of the data in tables. Additionally, the integration of geological and structural observations of the outcrop allows to understand the nature of the geological units, the deformation related to the extensional environment and the regional tectonic context of the study area.

scholarly journals Cysteine Mutagenesis and Computer Modeling of the S6 Region of an Intermediate Conductance IKCa Channel

2002 ◽  
Vol 120 (1) ◽  
pp. 99-116 ◽  
Author(s):  
Manuel Simoes ◽  
Line Garneau ◽  
Hélène Klein ◽  
Umberto Banderali ◽  
Fadi Hobeila ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Structural Features ◽  
K Channel ◽  
Crystallographic Structure ◽  
Channel Pore ◽  
State Dependent ◽  
Cysteine Scanning Mutagenesis ◽  
Three Dimensional Models ◽  
State Configuration

Cysteine-scanning mutagenesis (SCAM) and computer-based modeling were used to investigate key structural features of the S6 transmembrane segment of the calcium-activated K+ channel of intermediate conductance IKCa. Our SCAM results show that the interaction of [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET) with cysteines engineered at positions 275, 278, and 282 leads to current inhibition. This effect was state dependent as MTSET appeared less effective at inhibiting IKCa in the closed (zero Ca2+ conditions) than open state configuration. Our results also indicate that the last four residues in S6, from A283 to A286, are entirely exposed to water in open IKCa channels, whereas MTSET can still reach the 283C and 286C residues with IKCa maintained in a closed state configuration. Notably, the internal application of MTSET or sodium (2-sulfonatoethyl) methanethiosulfonate (MTSES) caused a strong Ca2+-dependent stimulation of the A283C, V285C, and A286C currents. However, in contrast to the wild-type IKCa, the MTSET-stimulated A283C and A286C currents appeared to be TEA insensitive, indicating that the MTSET binding at positions 283 and 286 impaired the access of TEA to the channel pore. Three-dimensional structural data were next generated through homology modeling using the KcsA structure as template. In accordance with the SCAM results, the three-dimensional models predict that the V275, T278, and V282 residues should be lining the channel pore. However, the pore dimensions derived for the A283–A286 region cannot account for the MTSET effect on the closed A283C and A286 mutants. Our results suggest that the S6 domain extending from V275 to V282 possesses features corresponding to the inner cavity region of KcsA, and that the COOH terminus end of S6, from A283 to A286, is more flexible than predicted on the basis of the closed KcsA crystallographic structure alone. According to this model, closure by the gate should occur at a point located between the T278 and V282 residues.

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