Molecular characterization of the viral structural gene of the first dengue virus type 1 outbreak in Xishuangbanna, a border area of China, Burma and Laos

AbstractIn the context of recent arbovirus epidemics, dengue fever is becoming a greater concern around the world. In August 2017, Xishuangbanna, which is a border city of China, Burma and Laos, had its first major dengue outbreak. A total of 156 serum samples from febrile patients were collected; 97 DENV positive serum samples were screened out, and viral RNAs were successfully and directly extracted, including 77 cases from China and 20 cases from Myanmar. Phylogenetic analysis revealed that all of the strains were classified as DENV-1. There are eight epidemic dengue strains from Myanmar and 74 from Jinghong, Xishuangbanna, that were classified as cluster 1, which are the most similar to the strain of China Guangzhou 2011. There are three epidemic strains from Xishuangbanna Mengla that were classified as cluster 2, which have the closest relationship to the strain of China Hubei 2014. However, there are 12 epidemic strains from Myanmar that were classified as cluster 3, which have the closest relationship to the strain of Laos from 2008, which shows that there is a recycling epidemic trend of DENV in China. There were 236 mutations in the base, which caused 31 nonsynonymous mutations in the DENV structural protein C/prM/E genes when the strain of Xishuangbanna and Myanmar were compared with the DENV-1SS. There is no clear homologous recombination signal among these stains. Homology modeling possibly predicted a three-dimensional structure of the structural protein of these strains and revealed that they had the same three-dimensional structure and all had five predicted protein binding sites, but there are differences in binding site 434 (DENV-1SS: Thr434, DV-Jinghong: Ser434, DV-Myanmar: Ser434, DV-Mengla: Ser434). The results of the molecular clock phylogenetic and demographic reconstruction analysis show that DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017. In conclusion, our study lays the foundation for studying the global evolution and prevalence of DENV.Author SummaryDengue fever (DF) is a mosquito-borne illness caused by a flavivirus. Human infections with Dengue virus (DENV) could cause fever, cutaneous rash and malaise. Xishuangbanna, which is located in the southwestern Yunnan Province and is a border city with China, Burma and Laos, was reported to have outbreak of DENV in 2013 and 2015 with different types. However, there was a large outburst of dengue in May 2017. To understand the genetic characterization, potential source and evolution of the virus, 156 serum samples were analyzed. We focused on: (i) Phylogenetic analysis of the structural protein genes sequences; (ii) Mutation, recombination analysis and predicted protein binding sites of the structural protein genes; (iii) Molecular clock and demographic reconstruction of global dengue virus serotype 1(DENV-1). Our results indicated that this is the first outbreak of DENV-1 in Xishuangbanna, dengue epidemic strains on the Burma border of China show diversification, we found a virulence site changed from I to T(amino acid position: 440), which may lead to weakened virulence of the epidemic strains. We found that the evolution of DENV-1 is dominated by regional evolution. What’s more, DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017.

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Molecular characterization of the viral structural protein genes in the first outbreak of dengue virus type 2 in Hunan Province, inland China in 2018

10.21203/rs.2.20904/v2 ◽

2020 ◽

Author(s):

Jiaoqiong Guan ◽

Zhanlong He ◽

Meng Qin ◽

Xialin Deng ◽

Jun Chen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Protein Binding ◽

Causative Agent ◽

Binding Sites ◽

Selection Pressure ◽

Hunan Province ◽

Structural Protein ◽

Protein Binding Sites ◽

Dengue Outbreak

Abstract Background: An unexpected dengue outbreak occurred in the Hunan Province in 2018. This is the first dengue outbreak in this area of inland China, and 172 cases were reported. Methods: To verify the causative agent of this outbreak and investigate gene characterization, the structural protein C/prM/E genes of viruses isolated from local residents were sequenced followed by mutation and phylogenetic analysis. The recombination, selection pressure, potential secondary structure and three-dimensional structure analysis were also performed. Results: Phylogenetic analysis revealed that all epidemic strains were classified as the cosmopolitan DENV-2 genotype, closest to the Zhejiang strain (MH010629, 2017) and then Malaysia strain (KJ806803, 2013). Compared with the DENV-2SS, 151 base substitutions were found in 89 sequences of isolates, which resulted in 20 non-synonymous mutations, of which 17 mutations existed among all samples (two in capsid protein, six in prM/M, and nine in envelope proteins). Moreover, amino acid substitutions at 602th (E322:Q→H) and 670th (E390: N→S) may enhance virulence of the epidemic strains. One new DNA-binding site and five new protein binding sites were observed. Two polynucleotide-binding sites and seven protein binding sites were lost compared with DENV-2SS. Meanwhile, five changes were found in helix regions. Minor changes were observed in helical transmembrane and disordered regions. The 429th amino acid of E proteins was switch from histamine (positively charged) to asparagines (neutral) in all 89 isolate strains. No recombination events or positive selection pressure sites were observed. To our knowledge, this study is the first one to analyze the genetic characteristics of epidemic strain in the first dengue outbreak in Hunan Province, inland China. Conclusions: The causative agent is likely to come from Zhejiang Province, a neighbouring Province where dengue fever broke out in 2017. This study may help to understand the intrinsic geographical relatedness of DENV-2 and contributes to further research on pathogenicity and vaccine development.

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Conformation of Ribosomes from Escherichia Coli

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051062 ◽

1974 ◽

Vol 32 ◽

pp. 210-211

Author(s):

M. Boublik ◽

W. Hellmann ◽

F. Jenkins

Keyword(s):

Binding Sites ◽

Ribosomal Proteins ◽

Fluorescent Dyes ◽

Protein Biosynthesis ◽

Three Dimensional ◽

Spatial Arrangement ◽

Dimensional Structure ◽

Complete Understanding ◽

And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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Determination of the alpha-actinin-binding site on actin filaments by cryoelectron microscopy and image analysis.

The Journal of Cell Biology ◽

10.1083/jcb.126.2.433 ◽

1994 ◽

Vol 126 (2) ◽

pp. 433-443 ◽

Cited By ~ 124

Author(s):

A McGough ◽

M Way ◽

D DeRosier

Keyword(s):

Image Analysis ◽

Smooth Muscle ◽

Binding Sites ◽

Actin Filaments ◽

Three Dimensional ◽

Actin Binding ◽

Dimensional Structure ◽

Outer Face ◽

Actin Binding Domain

The three-dimensional structure of actin filaments decorated with the actin-binding domain of chick smooth muscle alpha-actinin (alpha A1-2) has been determined to 21-A resolution. The shape and location of alpha A1-2 was determined by subtracting maps of F-actin from the reconstruction of decorated filaments. alpha A1-2 resembles a bell that measures approximately 38 A at its base and extends 42 A from its base to its tip. In decorated filaments, the base of alpha A1-2 is centered about the outer face of subdomain 2 of actin and contacts subdomain 1 of two neighboring monomers along the long-pitch (two-start) helical strands. Using the atomic model of F-actin (Lorenz, M., D. Popp, and K. C. Holmes. 1993. J. Mol. Biol. 234:826-836.), we have been able to test directly the likelihood that specific actin residues, which have been previously identified by others, interact with alpha A1-2. Our results indicate that residues 86-117 and 350-375 comprise distinct binding sites for alpha-actinin on adjacent actin monomers.

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Disruption of the utrophin–actin interaction by monoclonal antibodies and prediction of an actin-binding surface of utrophin

Biochemical Journal ◽

10.1042/bj3370119 ◽

1998 ◽

Vol 337 (1) ◽

pp. 119-123 ◽

Cited By ~ 2

Author(s):

Glenn E. MORRIS ◽

Nguyen thi MAN ◽

Nguyen thi Ngoc HUYEN ◽

Alexander PEREBOEV ◽

John KENDRICK-JONES ◽

...

Keyword(s):

Binding Sites ◽

Three Dimensional ◽

Binding Domain ◽

Actin Binding ◽

Dimensional Structure ◽

Functional Regions ◽

Binding Surface ◽

Actin Binding Domain ◽

Actin Binding Site ◽

Helical Region

Monoclonal antibody (mAb) binding sites in the N-terminal actin-binding domain of utrophin have been identified using phage-displayed peptide libraries, and the mAbs have been used to probe functional regions of utrophin involved in actin binding. mAbs were characterized for their ability to interact with the utrophin actin-binding domain and to affect actin binding to utrophin in sedimentation assays. One of these antibodies was able to inhibit utrophin–F-actin binding and was shown to recognize a predicted helical region at residues 13–22 of utrophin, close to a previously predicted actin-binding site. Two other mAbs which did not affect actin binding recognized predicted loops in the second calponin homology domain of the utrophin actin-binding domain. Using the known three-dimensional structure of the homologous actin-binding domain of fimbrin, these results have enabled us to determine the likely orientation of the utrophin actin-binding domain with respect to the actin filament.

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SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design.

ChemInform ◽

10.1002/chin.200509237 ◽

2005 ◽

Vol 36 (9) ◽

Author(s):

James R. Arnold ◽

Keith W. Burdick ◽

Scott C.-H. Pegg ◽

Samuel Toba ◽

Michelle L. Lamb ◽

...

Keyword(s):

Drug Design ◽

Protein Binding ◽

Active Site ◽

Binding Sites ◽

Three Dimensional ◽

Protein Binding Sites ◽

Site Analysis ◽

Family Based

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BiRDS - Binding Residue Detection from Protein Sequences using Deep ResNets

10.33774/chemrxiv-2021-013gn-v2 ◽

2021 ◽

Author(s):

Vineeth Chelur ◽

U. Deva Priyakumar

Keyword(s):

Binding Site ◽

Binding Sites ◽

Tertiary Structure ◽

Solvent Accessibility ◽

Three Dimensional ◽

Dimensional Structure ◽

Relative Solvent Accessibility ◽

Single Chain ◽

Sequence Alignments ◽

Multiple Sequence

Protein-drug interactions play important roles in many biological processes and therapeutics. Prediction of the active binding site of a protein helps discover and optimise these interactions leading to the design of better ligand molecules. The tertiary structure of a protein determines the binding sites available to the drug molecule. A quick and accurate prediction of the binding site from sequence alone without utilising the three-dimensional structure is challenging. Deep Learning has been used in a variety of biochemical tasks and has been hugely successful. In this paper, a Residual Neural Network (leveraging skip connections) is implemented to predict a protein's most active binding site. An Annotated Database of Druggable Binding Sites from the Protein DataBank, sc-PDB, is used for training the network. Features extracted from the Multiple Sequence Alignments (MSAs) of the protein generated using DeepMSA, such as Position-Specific Scoring Matrix (PSSM), Secondary Structure (SS3), and Relative Solvent Accessibility (RSA), are provided as input to the network. A weighted binary cross-entropy loss function is used to counter the substantial imbalance in the two classes of binding and non-binding residues. The network performs very well on single-chain proteins, providing a pocket that has good interactions with a ligand.

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

BIOEDUSCIENCE ◽

10.29405/j.bes/4137-474353 ◽

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.

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Spatiotemporal identification of druggable binding sites using deep learning

10.1101/2020.02.20.952309 ◽

2020 ◽

Cited By ~ 1

Author(s):

Igor Kozlovskii ◽

Petr Popov

Keyword(s):

Protein Binding ◽

Binding Site ◽

Binding Sites ◽

Large Scale ◽

Specific Binding ◽

Three Dimensional ◽

Growth Factor Receptor ◽

Protein Binding Sites ◽

Binding Site Identification ◽

Scale Detection

Identification of novel protein binding sites expands «druggable genome» and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site identification resemble to object detection problem in computer vision. Here we introduce a computational approach for the large-scale detection of protein binding sites, named BiteNet, that considers protein conformations as the 3D-images, binding sites as the objects on these images to detect, and conformational ensembles of proteins as the 3D-videos to analyze. BiteNet is suitable for spatiotemporal detection of hard-to-spot allosteric binding sites, as we showed for conformation-specific binding site of the epidermal growth factor receptor, oligomer-specific binding site of the ion channel, and binding sites in G protein-coupled receptors. BiteNet outperforms state-of-the-art methods both in terms of accuracy and speed, taking about 1.5 minute to analyze 1000 conformations of a protein with 2000 atoms. BiteNet is available at https://github.com/i-Molecule/bitenet.

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Molecular characterization of the viral structural protein genes in the first outbreak of dengue virus type 2 in Hunan Province, inland China in 2018

10.21203/rs.2.20904/v3 ◽

2021 ◽

Author(s):

Jiaoqiong Guan ◽

Zhanlong He ◽

Meng Qin ◽

Xialin Deng ◽

Jun Chen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Protein Binding ◽

Causative Agent ◽

Binding Sites ◽

Selection Pressure ◽

Hunan Province ◽

Genetic Characteristics ◽

Protein Binding Sites ◽

Dengue Outbreak

Abstract Background: An unexpected dengue outbreak occurred in Hunan Province in 2018. This was the first dengue outbreak in this area of inland China, and 172 cases were reported.Methods: To verify the causative agent of this outbreak and characterise the viral genes, the genes encoding the structural proteins C/prM/E of viruses isolated from local residents were sequenced followed by mutation and phylogenetic analysis. Recombination, selection pressure, potential secondary structure and three-dimensional structure analyses were also performed. Results: Phylogenetic analysis revealed that all epidemic strains were of the cosmopolitan DENV-2 genotype and were most closely related to the Zhejiang strain (MH010629, 2017) and then the Malaysia strain (KJ806803, 2013). Compared with the sequence of DENV-2SS, 151 base substitutions were found in the sequences of 89 isolates; these substitutions resulted in 20 non-synonymous mutations, of which 17 mutations existed in all samples (two in the capsid protein, six in the prM/M proteins, and nine in the envelope proteins). Moreover, amino acid substitutions at the 602nd (E322:Q→H) and 670th (E390: N→S) amino acids may have enhanced the virulence of the epidemic strains. One new DNA binding site and five new protein binding sites were observed. Two polynucleotide binding sites and seven protein binding sites were lost in the epidemic strains compared with DENV-2SS. Meanwhile, five changes were found in helical regions. Minor changes were observed in helical transmembrane and disordered regions. The 429th amino acid of the E protein switched from a histamine (positively charged) to an asparagine (neutral) in all 89 isolated strains. No recombination events or positive selection pressure sites were observed. To our knowledge, this study is the first to analyse the genetic characteristics of epidemic strains in the first dengue outbreak in Hunan Province in inland China.Conclusions: The causative agent is likely to come from Zhejiang Province, a neighbouring province where dengue fever broke out in 2017. This study may help clarify the intrinsic geographical relatedness of DENV-2 and contribute to further research on pathogenicity and vaccine development.

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Molecular characterization of the viral structural gene of the first dengue virus type 2 outbreak in Hunan Province, inland China

10.21203/rs.2.20904/v1 ◽

2020 ◽

Author(s):

Jiaoqiong Guan ◽

Zhanlong He ◽

Meng Qin ◽

Xialin Deng ◽

Jun Chen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Protein Binding ◽

Causative Agent ◽

Binding Sites ◽

Selection Pressure ◽

Tertiary Structure ◽

Hunan Province ◽

Protein Binding Sites ◽

Dengue Outbreak

Abstract Background: An unexpected dengue outbreak occurred in the Hunan Province in 2018. This is the first dengue outbreak in this area of inland China resulting 172 infected. Methods: To verify the causative agent of this outbreak and investigate gene characterization, the structural protein C/prM/E genes of viruses isolated from local residents were sequenced followed by mutation, phylogenetic analysis. The recombination, selection pressure, potential secondary structure and three-dimensional structure analysis were also performed. Results: Phylogenetic analysis revealed that all epidemic strains were classified as the cosmopolitan DENV-2 genotype, closest to the Zhejiang strain (MH010629, 2017) and then Malaysia strain (KJ806803, 2013). Compared with the DENV-2SS, 151 base substitutions were found in 89 sequences of isolates, resulting in 20 nonsynonymous mutations, of which 17 mutations existed among all samples (two in capsid protein, six in prM/M, and nine in envelope proteins). Moreover, amino acid substitutions at 602 th (E322:Q→H) and 670 th (E390: N→S) may result in heightened virulence of the epidemic strains. One new DNA-binding site and five new protein binding sites were observed. Two polynucleotide-binding sites and seven protein binding sites were lost compared with DENV-2SS. Meanwhile, five changes were found in helix regions. The helical transmembrane and disordered regions have minor changes. Protein tertiary structure prediction revealed the 429 th amino acid of E proteins was switch from histamine (positively charged) to asparagines (neutral) in 89 isolate strains. No recombination events or positive selection pressure sites were detected. To our knowledge, this study is the first gene analysis of epidemic strain in the first dengue outbreak in Hunan Province, inland China. Conclusions: The causative agent is likely to come from Zhejiang Province, a neighbouring Province where dengue fever broke out in 2017. This study may help understand the intrinsic geographical relatedness of DENV-2 and contributes further to research on pathogenicity and vaccine development.

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