scholarly journals An improved 3DMax algorithm to reconstruct the three-dimensional structure of the chromosome

2020 ◽  
Author(s):  
Liwei Liu ◽  
Huili Yao
Keyword(s):  
Objective Function ◽  
Optimization Algorithm ◽  
Optimization Problem ◽  
3D Structure ◽  
Three Dimensional ◽  
Optimization Method ◽  
Dimensional Structure ◽  
Chromosome Conformation ◽  
Three Dimensional Structure ◽  
Interaction Map

AbstractIn recent years, with the development of high-throughput chromosome conformation capture (Hi-C) technology and the reduction of high-throughput sequencing cost, the data volume of whole-genome interaction has increased rapidly, and the resolution of interaction map keeps improving. Great progress has been made in the research of 3D structure modeling of chromosomes and genomes. Several methods have been proposed to construct the chromosome structure from chromosome conformation capture data. Based on the Hi-C data, this paper analyses the relevant literature of chromosome 3D structure reconstruction and it summarizes the principle of 3DMAX, which is a classical algorithm to construct the 3D structure of a chromosome. In this paper, we introduce a new gradient ascent optimization algorithm called XNadam that is a variant of Nadam optimization method. When XNadam is applied to 3DMax algorithm, the performance of 3DMax algorithm can be improved, which can be used to predict the three-dimensional structure of a chromosome.Author summaryThe exploration of the three-dimensional structure of chromosomes has gradually become a necessary means to understand the relationship between genome function and gene regulation. An important problem in the construction of three-dimensional model is how to use the interaction map. Usually, the interaction frequency can be transformed into the spatial distance according to the deterministic or non-deterministic function relationship, and the interaction frequency can be weighted as weight in the objective function of the optimization problem. When the frequency of interaction is weighted as weight in the objective function of the optimization problem, what kind of optimization method is used to optimize the objective function is the problem we consider. In order to solve this problem, we provide an improved stochastic gradient ascent optimization algorithm(XNadam). The XNadam optimization algorithm combined with maximum likelihood algorithm is applied to high resolution Hi-C data set to infer 3D chromosome structure.

scholarly journals 3D Structure of VP1 Structural Protein on Enterovirus A71 Using Swiss-Model

BIOEDUSCIENCE ◽  
2020 ◽  
Vol 4 (1) ◽  
pp. 37-47
Author(s):  
Suprianto ◽  
Made Budiarsa ◽  
Fatmah Dhafir
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Stable Structure ◽  
Target Protein ◽  
Dimensional Structure ◽  
Structural Protein ◽  
Three Dimensional Structure ◽  
Enterovirus A71 ◽  
And Function ◽  
Ramachandran Plots

Background: VP1 structural protein plays a role as a key player in the pathogenesis, has a uniqueness that is interesting enough to be studied by studying the nature and function of structural proteins VP1. This study aims to predict the three-dimensional structure of proteins VP1 on EV-A71. Methods: The target protein is obtained from UniProt server with an access code A0A097EV89using templates 4cey.1.A (PDB ID) were analyzed in silico by homology method using SWISS-MODEL server. Results: Analysis showed the target protein and the template has 95.29% identity and is composed of 297 amino acids with a value of -2.15 QMEAN. Structural protein VP1 in Ramachandran Plots have a stable structure, non-glycine residue in the outlier regions only around 0.34% (A53 ALA) Rated rotamer outliers 1.61%.    Conclusion: The three-dimensional structure model of the protein studied has a stable structure and the information obtained is useful for further research in developing vaccines for diseases caused by EV-A71.  

scholarly journals Analysis of the Thermostability Determinants of Hyperthermophilic Esterase EstE1 Based on Its Predicted Three-Dimensional Structure

2006 ◽  
Vol 72 (4) ◽  
pp. 3021-3025 ◽  
Author(s):  
Jin-Kyu Rhee ◽  
Do-Yun Kim ◽  
Dae-Gyun Ahn ◽  
Jung-Hyuk Yun ◽  
Seung-Hwan Jang ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Hydrophobic Interactions ◽  
3D Structure ◽  
Three Dimensional ◽  
Ion Pair ◽  
Archaeoglobus Fulgidus ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Structure Relationship

ABSTRACT The three-dimensional (3D) structure of the hyperthermophilic esterase EstE1 was constructed by homology modeling using Archaeoglobus fulgidus esterase as a reference, and the thermostability-structure relationship was analyzed. Our results verified the predicted 3D structure of EstE1 and identified the ion pair networks and hydrophobic interactions that are critical determinants for the thermostability of EstE1.

scholarly journals Integration of Multiple Resolution Data in 3D Chromatin Reconstruction Using ChromStruct

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 338
Author(s):  
Claudia Caudai ◽  
Monica Zoppè ◽  
Anna Tonazzini ◽  
Ivan Merelli ◽  
Emanuele Salerno
Keyword(s):  
Spatial Organization ◽  
Local Level ◽  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Rna Seq ◽  
Chromosome Conformation ◽  
Experimental Protocols ◽  
Easy Integration

The three-dimensional structure of chromatin in the cellular nucleus carries important information that is connected to physiological and pathological correlates and dysfunctional cell behaviour. As direct observation is not feasible at present, on one side, several experimental techniques have been developed to provide information on the spatial organization of the DNA in the cell; on the other side, several computational methods have been developed to elaborate experimental data and infer 3D chromatin conformations. The most relevant experimental methods are Chromosome Conformation Capture and its derivatives, chromatin immunoprecipitation and sequencing techniques (CHIP-seq), RNA-seq, fluorescence in situ hybridization (FISH) and other genetic and biochemical techniques. All of them provide important and complementary information that relate to the three-dimensional organization of chromatin. However, these techniques employ very different experimental protocols and provide information that is not easily integrated, due to different contexts and different resolutions. Here, we present an open-source tool, which is an expansion of the previously reported code ChromStruct, for inferring the 3D structure of chromatin that, by exploiting a multilevel approach, allows an easy integration of information derived from different experimental protocols and referred to different resolution levels of the structure, from a few kilobases up to Megabases. Our results show that the introduction of chromatin modelling features related to CTCF CHIA-PET data, histone modification CHIP-seq, and RNA-seq data produce appreciable improvements in ChromStruct’s 3D reconstructions, compared to the use of HI-C data alone, at a local level and at a very high resolution.

scholarly journals 3D structure of NT-3 Protein (Neurotropin 3) of Pigeon (Columba livia) using Server-Swiss Model

2021 ◽  
Vol 12 (2) ◽  
pp. 85
Author(s):  
Tina Zarkiyani ◽  
I Made Budiarsa ◽  
Astija Astija ◽  
Mursito S Bialangi
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Columba Livia ◽  
Dimensional Structure ◽  
Structural Quality ◽  
Three Dimensional Structure ◽  
3 Dimensional ◽  
Access Code ◽  
Development And Differentiation

The NT-3 protein plays an important role in the development and differentiation of neurons, and is unique in the neurotropin family, that it can bind to 3 Trk receptors, namely TrkC, TrkA and TrkB. This study aimed to analyze the characteristics and three-dimensional structure of NT-3 protein in Columba livia. The target protein was obtained from Uniprot server with the access code of PKK30025.1 using template 3buk.1A (PDB-ID) analyzed in-silico through homology method using SWISS-MODEL server. The results showed that the three-dimensional structure of the target NT-3 protein with a template formed a β-sheet and loop structure, which was composed of 304 amino acids, with the highest amino acid composition was serine at 8.88 mol polar, and the lowest amino acid was tryptophan at 1.32. moles which was relatively nonpolar. The analysis results of the structural quality revealed an identity value of 98.20%, QMEAN of 0.8, QMQE of 0.25, and the analysis on the Ramachandran plot presented an outlier value of 0.92%; the most favored region value was 94.5%, with good structural quality. The results of the 3-dimensional structure of the NT-3 Columba livia protein are expected to be useful for further research to determine the active side and interactions of proteins in carrying out their functions.

scholarly journals The 3D Structure of the Galactic Bulge

2016 ◽  
Vol 33 ◽  
Author(s):  
Manuela Zoccali ◽  
Elena Valenti
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Galactic Bulge ◽  
Three Dimensional Structure ◽  
Innermost Region

AbstractWe review the observational evidences concerning the three-dimensional structure of the Galactic bulge. Although the inner few kpc of our Galaxy are normally referred to as the bulge, all the observations demonstrate that this region is dominated by a bar, i.e., the bulge is a bar. The bar has a boxy/peanut (X-shaped) structure in its outer regions, while it seems to become less and less elongated in its innermost region. A thinner and longer structure departing from the main bar has also been found, although the observational evidences that support the scenario of two separate structures has been recently challenged. Metal-poor stars ([Fe/H] ≲ −0.5 dex) trace a different structure, and also have different kinematics.

scholarly journals The 3D Structure of the Galactic Bulge from the MACHO Red Clump Stars

2001 ◽  
Vol 205 ◽  
pp. 234-235
Author(s):  
R. Fux ◽  
T. Axelrod ◽  
P. Popowski
Keyword(s):  
Milky Way ◽  
3D Structure ◽  
Three Dimensional ◽  
Mean Value ◽  
Dimensional Structure ◽  
Galactic Bulge ◽  
Three Dimensional Structure ◽  
Structure And Dynamics ◽  
Red Clump ◽  
Ongoing Project

Many evidences demonstrate that the Milky Way is a barred galaxy with the near end of the bar pointing in the first Galactic quadrant (e.g. Gerhard 1999 for a review), thus offering an exceptional chance to study the detailed three-dimensional structure and dynamics of a real bar. One of the best tracer of the Galactic bulge/bar are the red clump stars: they are very numerous, sufficiently bright to be detected throughout the bulge, and their absolute I-magnitude has an intrinsic dispersion of only 0.2 magnitude, with a mean value almost independent of colour and metallicity (Paczyński & Stanek 1998, Udalski 2000). Here we outline an ongoing project aiming to recover the 3D bulge stellar distribution as primarily traced by these stars, as in Stanek et al. (1997), but in a non-parametric way and from the VR database of the MACHO experiment within an almost fully observed ∼ 8° × 8° bulge area centred on (l, b) ≈ (4°, − 6°) (e.g. Alcock et al. 1997), soon complemented with I-band photometry.

The singular behavior of a β-type semi-synthetic two branched polypeptide: three-dimensional structure and mode of action

2016 ◽  
Vol 18 (45) ◽  
pp. 30998-31011 ◽  
Author(s):  
Giorgia Manzo ◽  
Ilaria Serra ◽  
Alessandro Pira ◽  
Manuela Pintus ◽  
Matteo Ceccarelli ◽  
...  
Keyword(s):  
Structure Function ◽  
Mode Of Action ◽  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Singular Behavior ◽  
Three Dimensional Structure ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Relationship Of

The 3D structure and the structure–function relationship of the smallest prototypical membrane active dendrimeric peptide are shown.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

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