scholarly journals Making glycoproteins a little bit sweeter withPDB-REDO

2018 ◽  
Vol 74 (8) ◽  
pp. 463-472 ◽  
Author(s):  
Bart van Beusekom ◽  
Thomas Lütteke ◽  
Robbie P. Joosten
Keyword(s):  
Experimental Data ◽  
Amino Acid ◽  
Protein Data Bank ◽  
Model Building ◽  
Data Bank ◽  
Structure Model ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
High Quality ◽  
Glycoprotein Structure

Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement byPDB-REDOof 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.

scholarly journals POTENSI SENYAWA BIOAKTIF TANAMAN GENUS Phyllanthus SEBAGAI INHIBITOR REPLIKASI VIRUS HEPATITIS B

2017 ◽  
Vol 4 (2) ◽  
pp. 85
Author(s):  
. Firdayani ◽  
Susi Kusumaningrum ◽  
Yosephine Ria Miranti
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Hepatitis B ◽  
Protein Data Bank ◽  
Bioactive Compounds ◽  
Core Protein ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Virus Hepatitis ◽  
Molegro Virtual Docker

Potency of Plant Bioactive Compounds from the Genus Phyllanthus as Hepatitis B Virus Replication InhibitorIn this research, simulations of molecular docking of Phyllanthus bioactive compounds were performed into the core protein of HBV. This simulation aimed to predict the interaction between compounds with virus core protein causing disruption of capsid formation and inhibiting its replication. The docking simulation was completed by Molegro Virtual Docker 6.0. The 3D stable conformation of molecule structures were docked into HBV core protein downloaded from Protein Data Bank, then the results were analyzed to view the minimum energy and interactions that occurred. The coordinate docking was done at the same coordinate as the previously docked reference ligand position and was validated. From the results it was known that repandusinic acid formed the most stable affinity bond with amino acid residues of viral core proteins. Interaction of B chain forming hydrogen bonds with the amino acid residues of Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 and Ser 141, and C chain with Thr 128, Val 124 and Glu 117.These compounds can be used as marker for anti HBV.Keyword: Bioactive compounds, core protein, HBV , molecular docking, Phyllanthus ABSTRAKPada penelitian ini dilakukan simulasi penambatan molekul senyawa-senyawa bioaktif Phyllanthus ke dalam protein inti virus hepatitis B. Simulasi ini bertujuan untuk memprediksi interaksi terbentuk antara senyawa dengan protein yang menyebabkan terganggunya pembentukan kapsid virus dan menghambat replikasinya. Simulasi penambatan molekul dilakukan menggunakan program Molegro Virtual Docker 6.0. Sebagai reseptor target digunakan struktur 3D protein inti yang diunduh dari Protein Data Bank. Posisi penambatan dilakukan pada koordinat yang sama dengan posisi ligan referensi yang sudah tertambat sebelumnya dan tervalidasi. Dari hasil simulasi diketahui bahwa asam repandusinat membentuk komplek dengan energi afinitas ikatan yang paling kecil dengan residu asam amino protein inti virus. Interaksi terjadi dengan rantai B yang membentuk ikatan hidrogen dengan asam amino Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 dan Ser 141, dan rantai C dengan asam amino Thr 128, Val 124 dan Glu 117. Senyawa ini dapat dijadikan sebagai marka untuk anti VHB.Kata kunci: Penambatan molekul, Phyllanthus, protein inti, senyawa bioaktif, VHBReceived: 11 December 2017                 Accepted: 27 December 2017           Published: 31 December 2017 

scholarly journals Virtual Screening: Prediksi potensi 8-shogaol terhadap c-Jun N-Terminal Kinase (JNK)

2020 ◽  
Vol 4 (1) ◽  
pp. 1 ◽  
Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Sri Sulystyaningsih Natalia Daeng Tiring ◽  
Dewi Ratih Tirto Sari ◽  
Andri Maulidi
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Virtual Screening ◽  
Protein Data Bank ◽  
Van Der Waals ◽  
Data Bank ◽  
Software Visualization ◽  
Amino Acid Residues ◽  
Discovery Studio ◽  
Protein Model

JNK adalah gen yang berperan dalam metabolisme DMT2. Dalam pengobatan T2DM digunakan JNK sebagai potensi terapi dengan menggunakan bahan alam. 8-shogaol adalah komponen kimia yang terkandung dalam jahe yang memiliki aktivitas antioksidan. Tujuan dari penelitina ini adalah menginversitagasi dan menganalisis peran 8-shogaol terhadap JNK. Protein JNK (ID: 464Y) diperoleh dari Protein Data Bank dan ligan 8-shogaol (CID:6442560 ) didapat dari pubchem. Ligan dan protein didocking menggunakan Hex 8.0.0. File dalam bentuk pdb divisualtisasi dan analisis menggunakan Discovery Studio Client 4.1 software. Interaksi ligan-protein menunjukan ikatan hidrogen pada residu asam amino LYS93 dan van der Waals pada 18 residu asam amino dengan energi ikatan-289.68cal/mol. Interkasi ini berpotensi sebagai penghambat kerja JNK dan dapat digunakan dalam terapi DMT2.Virtual screening: potential prediction of 8-shogaol againts c-Jun N-Terminal Kinase (JNK)AbstractJNK is one of gene that has a role in T2DM condition. To curve T2DM use JNK as potential healing using natural compounds. Eight-shogaol which found in ginger has function as a antioxidant.. The aim of the research is to investigate and analyze role 8-shogaol againts JNK. Protein JNK (ID: 464Y) was taken from Protein Data Bank and ligand 8-shogaol (CID:6442560 ) acquired from pubchem. Ligand and protein model were docked using Hex 8.0.0 software. Visualization and analysis molecular interactions by the Discovery Studio Client 4.1 software. Interaction ligand-protein showed one hydrogen bond in amino acid residue LYS93 and formed van der Waals in eighteen amino acid residues which energy binding -289.68cal/mol. This interaction has a potential to inhibit JNK role and lead to therapy T2DM.

scholarly journals Alignment of Alzheimer’s Disease Amyloid-β Peptide and Herpes Simplex Virus-1 pUL15 C-Terminal Nuclease Domain

2020 ◽  
Vol 4 (1) ◽  
pp. 373-377
Author(s):  
Steven Lehrer ◽  
Peter H. Rheinstein
Keyword(s):  
Herpes Simplex Virus ◽  
Immune System ◽  
Amino Acid ◽  
Herpes Simplex ◽  
Protein Data Bank ◽  
Amyloid Β ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Simplex Virus ◽  
Hsv 1

Background: The cause of Alzheimer’s disease (AD) is poorly understood. Neurotropic microbes, particularly herpesviruses, might set off chronic neuroinflammation. Amyloid-β (Aβ) has antimicrobial properties and could represent a brain defense against infection. Objective: We searched for protein sequence alignment between herpes simplex virus type I (HSV-1) HSV-2, and Aβ. Methods: Protein data bank (pdb) structures for Aβ, HSV-1, and HSV-2 were searched on the RCSB Protein Data Bank. The protein structures were superimposed and aligned on PYMOL v 2.3.4. Results: For HSV-1 and Aβ, amino acid residues ser549 – his569 of HSV-1 aligned closely with residues asp7 - asn27 of Aβ. For HSV-2 and Aβ, amino acid residues of HSV-2 aligned less closely than those of HSV-1 with residues of Aβ. Conclusion: Conjugating and binding to the same alpha helix in the HSV-1 protease, Aβ could be marking HSV-1 for attack by the immune system, providing a rapid inherited immune response to a destructive neurotropic virus that would otherwise require the more time-consuming involvement of T-cells, B-cells, and the adaptive immune system. But older people do not respond to viral infections as well as younger individuals. When HSV-1 infection advances in an old person, more and more amyloid is produced, forming an adhesive web. As the brain tries to hold the pathologic process in check, neuroinflammation increases and spreads. Progressive neurodegeneration and cognitive decline are the outcome.

scholarly journals Characteristics of Interactions at Protein Segments External to Globular Domains in the Protein Data Bank

2018 ◽  
Author(s):  
Kota Kasahara ◽  
Shintaro Minami ◽  
Yasunori Aizawa
Keyword(s):  
Amino Acid ◽  
Protein Data Bank ◽  
Protein Function ◽  
Three Dimensional ◽  
Data Bank ◽  
Side Chain ◽  
Globular Domain ◽  
Amino Acid Residues ◽  
Structural Elements

ABSTRACTThe principle of three-dimensional protein structure formation is a long-standing conundrum in structural biology. A globular domain of a soluble protein is formed by a network of atomic contacts among amino acid residues, but regions external to globular domains, like loop and linker, often do not have intramolecular contacts with globular domains. Although these regions can play key roles for protein function as interfaces for intermolecular interactions, their nature remains unclear. Here, we termed protein segments external to globular domains as floating segments and sought for them in tens of thousands of entries in the Protein Data Bank. As a result, we found that 0.72 % of residues are in floating segments. Regarding secondary structural elements, coil structures are enriched in floating segments, especially for long segments. Interactions with polypeptides and polynucleotides, but not small compounds, are enriched in floating segments. The amino acid preferences of floating segments are similar to those of surface residues, with exceptions; the small side chain amino acids, Gly and Ala, are preferred, and some charged side chains, Arg and His, are disfavored for floating segments compared to surface residues. Our comprehensive characterization of floating segments may provide insights into understanding protein sequence-structure-function relationships.

scholarly journals IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

2013 ◽  
Vol 41 (W1) ◽  
pp. W432-W440 ◽  
Author(s):  
Nurul Nadzirin ◽  
Peter Willett ◽  
Peter J. Artymiuk ◽  
Mohd Firdaus-Raih
Keyword(s):  
Amino Acid ◽  
Protein Data Bank ◽  
Data Bank ◽  
Side Chain ◽  
Amino Acid Side Chain

scholarly journals Possible role for a human adenovirus in the pathogenesis of celiac disease.

1984 ◽  
Vol 160 (5) ◽  
pp. 1544-1557 ◽  
Author(s):  
M F Kagnoff ◽  
R K Austin ◽  
J J Hubert ◽  
J E Bernardin ◽  
D D Kasarda
Keyword(s):  
Celiac Disease ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Monozygotic Twins ◽  
Human Adenovirus ◽  
Adenovirus Type ◽  
Data Bank ◽  
Antigenic Determinants ◽  
Amino Acid Residues ◽  
Primary Amino

Celiac disease in humans is activated by the dietary ingestion of wheat, rye, triticale, barley, and possibly oats. Gliadins in wheat and similar proteins in the other grains are known to activate disease in susceptible individuals. There is a striking association between celiac disease and HLA-B8, -DR3 and/or -DR7, and -DC3. Nonetheless, less than 0.2% of individuals with those serologic HLA specificities develop celiac disease and disease is not always concordant among monozygotic twins. We propose that additional environmental factors may be important in the pathogenesis of celiac disease. To investigate that possibility, we examined a data bank of protein sequences for other proteins that might share amino acid sequence homologies with A-gliadin, an alpha-gliadin component known to activate celiac disease and whose complete primary amino acid sequence is known. These studies demonstrate that A-gliadin shares a region of amino acid sequence homology with the 54-kD E1b protein of human adenovirus type 12 (Ad12), an adenovirus usually isolated from the intestinal tract. The region spans 12 amino acid residues, includes 8 residue identities and an identical pentapeptide, and is hydrophilic in both proteins. Antibody reactive with the 54-kD Ad12 E1b protein cross-reacts with A-gliadin, a 119 amino acid cyanogen bromide peptide of A-gliadin that spans the region of homology and a synthetic heptapeptide of A-gliadin from within the region of homology. We suggest that an encounter of the immune system with antigenic determinants produced during intestinal viral infection may be important in the pathogenesis of celiac disease.

scholarly journals Evidence that glutathione S-transferases B1B1 and B2B2 are the products of separate genes and that their expression in human liver is subject to inter-individual variation. Molecular relationships between the B1 and B2 subunits and other Alpha class glutathione S-transferases

1989 ◽  
Vol 264 (2) ◽  
pp. 437-445 ◽  
Author(s):  
J D Hayes ◽  
L A Kerr ◽  
A D Cronshaw
Keyword(s):  
Amino Acid ◽  
Human Liver ◽  
Sequence Data ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Amino Acid Sequence Analysis ◽  
Cdna Sequences ◽  
Glutathione S Transferases ◽  
Molecular Relationships ◽  
The Relationship

The Alpha class glutathione S-transferases (GSTs) in human liver are composed of polypeptides of Mr 25,900. These enzymes are dimeric, and two immunochemically distinct subunits, B1 and B2, have been described that combine to form GSTs B1B1, B1B2 and B2B2 [Stockman, Beckett & Hayes (1985) Biochem. J. 227, 457-465]. Gradient affinity elution from GSH-Sepharose has been used to resolve the three Alpha class GSTs, and this method has been applied to demonstrate marked inter-individual differences in the hepatic content of GSTs B1B1, B1B2 and B2B2. The B1 and B2 subunits can be resolved by reverse-phase h.p.l.c., and their elution positions suggest that they are equivalent to the alpha chi and alpha y h.p.l.c. peaks described by Ketterer and his colleagues [Ostlund Farrants, Meyer, Coles, Southan, Aitken, Johnson & Ketterer (1987) Biochem. J. 245, 423-428]. The B1 and B2 subunits have now been cleaved with CNBr and the fragments subjected to automated amino acid sequence analysis. The sequence data show that B1 and B2 subunits do not arise from post-translational modification, as had been previously believed for the hepatic Alpha class GSTs, but are instead the products of separate genes; B1 and B2 subunits were found to contain different amino acid residues at positions 88, 110, 111, 112, 116, 124 and 127. The relationship between the B1 and B2 subunits and the cloned GTH1 and GTH2 cDNA sequences [Rhoads, Zarlengo & Tu (1987) Biochem. Biophys. Res. Commun. 145, 474-481] is discussed.

scholarly journals The Potential Role of 6-gingerol and 6-shogaol as ACE Inhibitors in Silico Study

2020 ◽  
Vol 8 (2) ◽  
pp. 210
Author(s):  
Yohanes Bare ◽  
Maria Helvina ◽  
Gabriella Chandrakirana Krisnamurti ◽  
Mansur S
Keyword(s):  
Amino Acid ◽  
Angiotensin Converting Enzyme ◽  
Binding Site ◽  
Potential Role ◽  
Enzyme Inhibitor ◽  
Renin Angiotensin System ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Converting Enzyme

Hypertension has become the third highest cause of death in Indonesia. The condition is correlated with angiotensin-converting enzyme (ACE), and possibly managed with the use of drugs. In addition, some natural compounds, including 6-shogaol and 6-gingerol from ginger, are used to decrease blood pressure. However, the mechanism and binding site of these compounds to ACE protein is currently unclear. This study, therefore, aims to investigate the potential role of these compounds as an angiotensin-converting enzyme inhibitor. The ACE protein was downloaded from Protein Data Bank (PDB) database with the ID: 3bkk, while the 6-shogaol (CID: 5281794) and 6-gingerol (CID: 44559528) ligands were obtained from the PubChem database. Meanwhile, molecular docking was established using HEX 8.0.0 software. The analysis examined the amino acid residues and the bonds formed from these interactions. According to the results, fourteen amino acid residues were formed by the interaction between 6-shogaol and ACE, while the interaction between 6-gingerol and ACE formed eight amino acids. Also, thirteen amino acid residues in the novelty binding site of ACE were discovered to be blocked by the ligands from ginger. Therefore, the compounds have potential roles as inhibitors, and this possibly helps to prevent regulation of the renin-angiotensin system. These interactions also formed hydrogen bonds, as well as electrostatic, unfavorable, and hydrophobic sites, making the binding stronger than others. 

scholarly journals Crystallographic raw data, education and refereeing

2016 ◽  
Vol 62 (3) ◽  
pp. 257-261
Author(s):  
John R. Helliwell
Keyword(s):  
Experimental Data ◽  
Protein Data Bank ◽  
Structural Biology ◽  
Diffraction Data ◽  
Review Process ◽  
Data Bank ◽  
The Impact ◽  
And Training ◽  
Scientific Achievements ◽  
Future Plans

This article provides an overview of the preservation of raw diffraction data, then addresses the impact on future plans in the education and training of our community with respect to raw diffraction data and its potential reuse, and, thirdly presents the issue of referee access to the underpinning diffraction data and coordinates, as well as the Protein Data Bank Validation Report, in the review process of structural biology articles submitted for publication. Overall I pay tribute to the scientific achievements of Alex Wlodawer, who is also an ardent advocate of the importance of experimental data

Sign in / Sign up

Export Citation Format

Share Document