Structural Features of Copper Oxidative Enzymes of Unknown 3D Structure

2001 ◽  
pp. 772-776
Keyword(s):  
3D Structure ◽  
Structural Features ◽  
Oxidative Enzymes

scholarly journals EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Parallel Implementation ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Computing Power ◽  
Error Vector ◽  
Contact Frequency ◽  
Simple Error

Abstract Background More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need. Results We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs. Conclusions EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

scholarly journals Cryo-electron Microscopy Structures of Novel Viruses from Mud Crab Scylla paramamosain with Multiple Infections

2019 ◽  
Vol 93 (7) ◽  
Author(s):  
Yuanzhu Gao ◽  
Shanshan Liu ◽  
Jiamiao Huang ◽  
Qianqian Wang ◽  
Kunpeng Li ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
3D Structure ◽  
Structural Features ◽  
Economic Losses ◽  
Scylla Paramamosain ◽  
Multiple Infections ◽  
Mud Crab ◽  
Cryo Electron Microscopy ◽  
Novel Virus ◽  
Icosahedral Capsid

ABSTRACT Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. In this study, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV) but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at a 3.5-Å resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at a 3.3-Å resolution reveals a T= 3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus. IMPORTANCE Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Here we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High-resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.

Structural features of lignin determining its biodegradation by oxidative enzymes and related systems

1998 ◽  
Vol 59 (1-3) ◽  
pp. 359-364 ◽  
Author(s):  
B. Kurek ◽  
M.J. Martinez-inigo ◽  
I. Artaud ◽  
B.R. Hames ◽  
C. Lequart ◽  
...  
Keyword(s):  
Structural Features ◽  
Oxidative Enzymes

scholarly journals EVR: Reconstruction of Bacterial Chromosome 3D Structure Using Error-Vector Resultant Algorithm

2018 ◽  
Author(s):  
Kang-Jian Hua ◽  
Bin-Guang Ma
Keyword(s):  
Closed Loop ◽  
3D Structure ◽  
Software Tool ◽  
Structural Features ◽  
Bacterial Chromosome ◽  
Modeling Tools ◽  
Error Vector ◽  
3D Structures ◽  
Contact Frequency ◽  
Simple Error

ABSTRACTMore and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structures is an important task and in great need. We have developed a new reconstruction program for bacterial chromosome 3D structures called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

Molecular Cloning and Structural Insights into pectin lyase proteins from different strains of Fusarium

2020 ◽  
Vol 17 ◽  
Author(s):  
Sangeeta Yadav ◽  
Gautam Anand ◽  
Vinay K Singh ◽  
Dinesh Yadav
Keyword(s):  
Structure Prediction ◽  
Disulfide Bonds ◽  
3D Structure ◽  
Chemical Characterization ◽  
Structural Features ◽  
Docking Studies ◽  
Biochemical Properties ◽  
Pectin Lyase ◽  
Homology Search ◽  
Multiple Sequence

: Pectin lyaseis an industrially important enzymeof pectinase group that degrade pectin polymers forming 4,5-unsaturated oligogalacturonides. Several fugal pectin lyase genes predominately from Aspergillus and Penicillium genera have been reported in the literature. Five pectin lyase genes were cloned from FusariumoxysporumMTCC1755, F.monoliforme var. subglutinansMTCC2015, FusariumavneceumMTCC10572, and FusariumsolaniMTCC3004 using PCR approach. Pectin lyase genes and proteins were subjected to homology search, multiple sequence alignment, motif search, physio-chemical characterization, phylogenetic tree construction, 3D structure prediction and molecular docking. Many conserved amino acids were found at several positions in all the pectin lyase proteins. Phylogenetic analysis of these proteins alongwith other pectinases revealed two major clusters representing members of lyases and hydrolases. In-silico characterization revealed pectin lyase proteins to be highly stable owing to the presence of disulfide bonds in their structure. Molecular weight and pI of these proteins were in the range 14.4 to 25.1 kDa and 4.47-9.39 respectively. Pectin lyase proteins from different Fusariumstrains were very much similar in their structural features and biochemical properties which might be due to their similarity on the primary sequence. Docking studies revealed that electrostatic forces, vander Waal and hydrogen bonds are the major interacting forces between the ligands and the enzyme. This might be accountable for comparatively higher and better activity of pectin lyase against galacturonic acid as compared to α-D-galactopyranuronic acid, galactofuranuronicacid and galactopyranuronate. Aspartate, tyrosine and tryptophan residues in the active site of the enzyme are responsible for ligand binding.

scholarly journals Anti-Idiotype scFv Localizes an Autoepitope in the Globular Domain of C1q

2021 ◽  
Vol 22 (15) ◽  
pp. 8288
Author(s):  
Nadezhda Todorova ◽  
Miroslav Rangelov ◽  
Vanya Bogoeva ◽  
Vishnya Stoyanova ◽  
Anna Yordanova ◽  
...  
Keyword(s):  
3D Model ◽  
Potent Inhibitor ◽  
3D Structure ◽  
Recombinant Antibodies ◽  
Structural Features ◽  
Phage Library ◽  
Apical Region ◽  
Globular Domain ◽  
Potential Inhibitors ◽  
First Time

We addressed the issue of C1q autoantigenicity by studying the structural features of the autoepitopes recognized by the polyclonal anti-C1q antibodies present in Lupus Nephritis (LN) sera. We used six fractions of anti-C1q as antigens and selected anti-idiotypic scFv antibodies from the phage library “Griffin.1”. The monoclonal scFv A1 was the most potent inhibitor of the recognition of C1q and its fragments ghA, ghB and ghC, comprising the globular domain gC1q, by the lupus autoantibodies. It was sequenced and in silico folded by molecular dynamics into a 3D structure. The generated 3D model of A1 elucidated CDR similarity to the apical region of gC1q, thus mapping indirectly for the first time a globular autoepitope of C1q. The VH CDR2 of A1 mimicked the ghA sequence GSEAD suggested as a cross-epitope between anti-DNA and anti-C1q antibodies. Other potential inhibitors of the recognition of C1q by the LN autoantibodies among the selected recombinant antibodies were the monoclonal scFv F6, F9 and A12.

Abstract 16340: Atrial Wall Thickness Features Predefine Human Right Atrial Driver: Insights Gained From Novel Structural Analysis

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Jichao Zhao ◽  
Aleksei Mikhailov ◽  
Megan Subr ◽  
Aaqel Nalar ◽  
James Kennelly ◽  
...  
Keyword(s):  
Structural Analysis ◽  
High Resolution ◽  
Wall Thickness ◽  
Thickness Distribution ◽  
3D Structure ◽  
Structural Features ◽  
Right Atrial ◽  
Atrial Wall ◽  
Human Right ◽  
Crista Terminalis

Introduction: Atrial fibrillation (AF) is not effectively treated in clinics due to a lack of adequate tools for identifying AF drivers as targets in ablation treatment. Recent studies revealed that 30-50% of patients with persistent AF have drivers not only in the left atrium (LA) but also in the right atrium (RA). However, the precise substrate underlying RA AF drivers remains elusive. Hypothesis: High-resolution analysis of human atrial wall 3D structure can predict the occurrence of right atrial drivers. Methods: Coronary perfused explanted human atria (N=10, 46.2±14.7 y.o.;40% female) were optically mapped with high-resolution CMOS cameras. Sustained AF was induced by fast pacing and perfusion of adenosine and/or isoproterenol. Hearts were imaged at ~170μm 3 resolution by 9.4T gadolinium-enhanced MRI (Fig. A). A coupled PDE approach was utilized to estimate the atrial wall thickness (Fig. B). Fibrosis was identified above a signal intensity threshold validated by histology; and fibrosis density was constructed for each voxel by determining the percent of neighboring fibrotic voxels within a radius of 5 voxels. Results: Optical mapping identified 9 RA drivers in 6 hearts (H1-6) and 7 LA drivers in 5 hearts (H5, 6 and 8-10, Fig. C). All 9 RA AF drivers were anchored in myobundle structure in close proximity to the crista terminalis (CT). Wall thickness distribution in RA excluding the CT was similar to that in the LA (N=10, Fig. D). Structural analysis showed that RA with AF drivers (N=6) was thicker with greater wall variation and higher fibrosis density than RA without AF drivers (N=4, Fig. E). Furthermore, RA driver regions (N=9) were thicker and varied more than other RA regions (4.64±2.86 mm vs 4.56±2.57mm, p<0.05). Conclusions: For the first time, the 3D structural analysis demonstrates that structural features including atrial wall thickness and its variation near the CT can predict RA driver occurrences in human hearts and be used to improve targeted ablation.

scholarly journals PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

2019 ◽  
Vol 21 (3) ◽  
pp. 1069-1079 ◽  
Author(s):  
Fuyi Li ◽  
Cunshuo Fan ◽  
Tatiana T Marquez-Lago ◽  
André Leier ◽  
Jerico Revote ◽  
...  
Keyword(s):  
Solvent Accessibility ◽  
3D Structure ◽  
Structural Features ◽  
Biological Information ◽  
High Definition ◽  
Sequence Alignments ◽  
Post Translational Modifications ◽  
Functional Impact ◽  
Structure Database ◽  
Wide Range

Abstract Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites’ data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence–structural–functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.

scholarly journals Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Sentot Joko Raharjo ◽  
Chanif Mahdi ◽  
Nurdiana Nurdiana ◽  
Takheshi Kikuchi ◽  
Fatchiyah Fatchiyah
Keyword(s):  
Binding Energy ◽  
Molecular Dynamic ◽  
Molecular Interaction ◽  
3D Structure ◽  
Structural Features ◽  
Energy Calculation ◽  
Patchouli Alcohol ◽  
Binding Energy Calculation ◽  
Cox 2 ◽  
Cox 1

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2.

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