Chapter 3 3D Structure 2. Three Dimensional Structure of Oligosaccharides Explored by NMR and Computer Calculations

1995 ◽  
pp. 67-86 ◽  
Author(s):  
S.W. Homans
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Computer Calculations

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 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 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 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.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

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