Calculating the 3D-structure of macromolecules by hierarchical domain and function decomposition

1996 ◽  
pp. 200-207
Author(s):  
Eberhard Schmitt
Keyword(s):  
3D Structure ◽  
Function Decomposition ◽  
And Function

scholarly journals Cytolethal Distending Toxin Subunit B: A Review of Structure–Function Relationship

Toxins ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 595 ◽  
Author(s):  
Benoît J. Pons ◽  
Julien Vignard ◽  
Gladys Mirey
Keyword(s):  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
3D Structure ◽  
Cytolethal Distending Toxin ◽  
Experimental Systems ◽  
Bacterial Virulence Factor ◽  
Function Relationship ◽  
And Function ◽  
Key Residues ◽  
Cell Cycle Block

The Cytolethal Distending Toxin (CDT) is a bacterial virulence factor produced by several Gram-negative pathogenic bacteria. These bacteria, found in distinct niches, cause diverse infectious diseases and produce CDTs differing in sequence and structure. CDTs have been involved in the pathogenicity of the associated bacteria by promoting persistent infection. At the host-cell level, CDTs cause cell distension, cell cycle block and DNA damage, eventually leading to cell death. All these effects are attributable to the catalytic CdtB subunit, but its exact mode of action is only beginning to be unraveled. Sequence and 3D structure analyses revealed similarities with better characterized proteins, such as nucleases or phosphatases, and it has been hypothesized that CdtB exerts a biochemical activity close to those enzymes. Here, we review the relationships that have been established between CdtB structure and function, particularly by mutation experiments on predicted key residues in different experimental systems. We discuss the relevance of these approaches and underline the importance of further study in the molecular mechanisms of CDT toxicity, particularly in the context of different pathological conditions.

scholarly journals Effect of Weightlessness on the 3D Structure Formation and Physiologic Function of Human Cancer Cells

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Zheng-Yang Chen ◽  
Song Guo ◽  
Bin-Bin Li ◽  
Nan Jiang ◽  
Ao Li ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Human Cancer ◽  
Space Exploration ◽  
Rapid Development ◽  
3D Structure ◽  
Cell Aggregation ◽  
Migration Ability ◽  
Human Cancer Cells ◽  
Cell Cycle Inhibition ◽  
And Function

With the rapid development of modern medical technology and the deterioration of living environments, cancer, the most important disease that threatens human health, has attracted increasing concerns. Although remarkable achievements have been made in tumor research during the past several decades, a series of problems such as tumor metastasis and drug resistance still need to be solved. Recently, relevant physiological changes during space exploration have attracted much attention. Thus, space exploration might provide some inspiration for cancer research. Using on ground different methods in order to simulate microgravity, structure and function of cancer cells undergo many unique changes, such as cell aggregation to form 3D spheroids, cell-cycle inhibition, and changes in migration ability and apoptosis. Although numerous better experiments have been conducted on this subject, the results are not consistent. The reason might be that different methods for simulation have been used, including clinostats, random positioning machine (RPM) and rotating wall vessel (RWV) and so on. Therefore, we review the relevant research and try to explain novel mechanisms underlying tumor cell changes under weightlessness.

Polymorphism of follicle stimulating hormone receptor influences the 3D structure and its binding pattern to FSH in Bos taurus

2017 ◽  
Author(s):  
Hamny Hamny ◽  
Muhammad Jalaluddin ◽  
Siti Aisyah ◽  
Sri Wahyuni ◽  
Widodo . ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Follicle Stimulating Hormone ◽  
3D Structure ◽  
Amino Acid Residues ◽  
Fshr Gene ◽  
Intracellular Process ◽  
Cattle Reproduction ◽  
And Function ◽  
Alignment Analysis ◽  
Stimulating Hormone

Follicle stimulating hormone (FSH) bond with the extracellular domain of the FSH receptor (FSHR) stimulates a cascade of the intracellular process that leads to folliculogenesis. This study aimed to elucidate the effects of FSHR polymorphism of its structure and function on Bos taurus through computational technology. The FSHR sequences were retrieved from Genebank. The polymorphism was identified using alignment analysis and the 3D structure of the FSHR was done by Swiss models. Results showed that FSHR of Bos taurus has three polymorphisms that located at amino acid residues 18th to 259th. The polymorphisms may alter its ability to bind with FSH. Molecular docking analysis indicated that all variant of FSHR potentially changes the pattern and affinity binding into FSH that may have an impact on reproduction status of Bos taurus. The study is a warrant for further investigation to explore biomarker of cattle reproduction status based on FSHR gene.

scholarly journals Deciphering the 3D Structure and Function of Phosphofructokinase from Fission Yeast

2014 ◽  
Vol 20 (S3) ◽  
pp. 1246-1247
Author(s):  
Shaun Benjamin ◽  
Michael Radermacher ◽  
Teresa Ruiz
Keyword(s):  
Fission Yeast ◽  
3D Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization

2004 ◽  
Vol 1 (1) ◽  
pp. 80-89
Author(s):  
Guido Dieterich ◽  
Dirk W. Heinz ◽  
Joachim Reichelt
Keyword(s):  
Genetic Disorders ◽  
Protein Structures ◽  
3D Structure ◽  
Data Bank ◽  
Mendelian Inheritance ◽  
Biological Information ◽  
Structure Comparison ◽  
3D Structures ◽  
Functional Sites ◽  
And Function

Abstract The 3D structures of biomacromolecules stored in the Protein Data Bank [1] were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT [2] entries as well InterPro [3] domains and function sites with the corresponding 3D-structures. OMIM [4] (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure comparison of protein structures stored in DALI [5] was condensed into single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be identified upon visualization.

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 Computational Analysis of Missense Variants in the Human Transmembrane Protease Serine 2 (TMPRSS2) and SARS-CoV-2

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Asmae Saih ◽  
Meryem Bouqdayr ◽  
Hanâ Baba ◽  
Salsabil Hamdi ◽  
Samya Moussamih ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Viral Entry ◽  
Posttranslational Modifications ◽  
Computational Analysis ◽  
3D Structure ◽  
Target Cells ◽  
Prostate Cancer Progression ◽  
Missense Variants ◽  
Stability Structure ◽  
And Function

The human transmembrane protease serine 2 (TMPRSS2) protein plays an important role in prostate cancer progression. It also facilitates viral entry into target cells by proteolytically cleaving and activating the S protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the current study, we used different available tools like SIFT, PolyPhen2.0, PROVEAN, SNAP2, PMut, MutPred2, I-Mutant Suite, MUpro, iStable, ConSurf, ModPred, SwissModel, PROCHECK, Verify3D, and TM-align to identify the most deleterious variants and to explore possible effects on the TMPRSS2 stability, structure, and function. The six missense variants tested were evaluated to have deleterious effects on the protein by SIFT, PolyPhen2.0, PROVEAN, SNAP2, and PMut. Additionally, V160M, G181R, R240C, P335L, G432A, and D435Y variants showed a decrease in stability by at least 2 servers; G181R, G432A, and D435Y are highly conserved and identified posttranslational modifications sites (PTMs) for proteolytic cleavage and ADP-ribosylation using ConSurf and ModPred servers. The 3D structure of TMPRSS2 native and mutants was generated using 7 meq as a template from the SwissModeller group, refined by ModRefiner, and validated using the Ramachandran plot. Hence, this paper can be advantageous to understand the association between these missense variants rs12329760, rs781089181, rs762108701, rs1185182900, rs570454392, and rs867186402 and susceptibility to SARS-CoV-2.

scholarly journals Using AlphaFold to predict the impact of single mutations on protein stability and function

2021 ◽  
Author(s):  
Marina A Pak ◽  
Karina A Markhieva ◽  
Mariia S Novikova ◽  
Dmitry S Petrov ◽  
Ilya S Vorobyev ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Stability ◽  
Structure Prediction ◽  
Large Scale ◽  
3D Structure ◽  
Three Dimensional ◽  
Single Mutation ◽  
Before And After ◽  
And Function ◽  
The Impact

AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is "solved". However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the AlphaFold predictions on the impact of a single mutation on structure with a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold cannot be immediately applied to other problems or applications in protein folding.

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