scholarly journals Benchmarking the PEPOP methods for mimicking discontinuous epitopes

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre G. de Brevern ◽  
Franck Molina ◽  
Géraldine Lavigne ◽  
Claude Granier ◽  
...  
Keyword(s):  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Comparable Method ◽  
Version 2.0 ◽  
Peptide Prediction ◽  
The Traveling Salesman Problem ◽  
Discontinuous Epitopes ◽  
Cognate Protein ◽  
Better Than

Abstract Background Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein Ag in its interaction with an Ab. In the present work, we describe these new methods and the benchmarking of their performances. Results Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 Ag-Ab complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method. Conclusion The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

scholarly journals Benchmarking the PEPOP methods for mimicking discontinuous epitopes

2018 ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre G. de Brevern ◽  
Franck Molina ◽  
Géraldine Lavigne ◽  
Claude Granier ◽  
...  
Keyword(s):  
Protein Antigens ◽  
X Ray Crystallography ◽  
New Methods ◽  
Comparable Method ◽  
Version 2.0 ◽  
Peptide Prediction ◽  
The Traveling Salesman Problem ◽  
Antigen Antibody ◽  
Discontinuous Epitopes ◽  
Better Than

AbstractComputational methods provide approaches to identify epitopes in protein antigens to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein antigen in its interaction with an antibody. In the present work, we describe these new methods and the benchmarking of their performances.Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 antigen-antibody complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method.The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

scholarly journals PEPOP: new approaches to mimic non-continous epitopes

2018 ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre de Brevern ◽  
Liza Felicori ◽  
Christophe NGuyen ◽  
Ricardo Andrez Machado de Avila ◽  
...  
Keyword(s):  
Binding Sites ◽  
Web Site ◽  
Peptide Design ◽  
Antigenic Peptides ◽  
New Methods ◽  
Bioinformatics Tools ◽  
Peptide Prediction ◽  
User Friendly ◽  
Discontinuous Epitopes ◽  
Cognate Protein

AbstractBioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits as replacing a protein difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitope predicted by bioinformatics tools are commonly used and these sequential epitopes are used as such in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools proposed so far to predict peptide sequences: Superficial and PEPOP. PEPOP can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. We have developed an improved version of PEPOP dedicated to answer to the experimentalists’ need for a tool able to handle proteins and to turn them into peptides. The PEPOP web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature.We present the user-friendly, well-structured web-site of PEPOP and its validation through the use of predicted immunogenic or antigenic peptides mimicking discontinuous epitopes in different experimental ways. PEPOP proposes 35 methods of peptide design to guide experimentalists in using peptides potentially capable of replacing the cognate protein in its interaction with an Ab.

Structural and vibrational studies of 1,1,3,3-tetracyanopropane and 2,2,4,4,6-pentacyanocyclohexenamine

1987 ◽  
Vol 65 (2) ◽  
pp. 261-270 ◽  
Author(s):  
R. A. Bell ◽  
B. E. Brown ◽  
M. Duarte ◽  
H. E. Howard-Lock ◽  
C. J. L. Lock
Keyword(s):  
Unit Cell ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Cell Dimensions ◽  
Cell Data ◽  
Unit Cell Data ◽  
Monoclinic Cell ◽  
C Nmr

1,1,3,3-Tetracyanopropane, 1, was prepared in low yields by a literature method with 2,2,4,4,6-pentacyanocyclohexenamine, 2, as a major by-product. The products were examined by X-ray crystallography. 1 has an orthorhombic space group, Pbcn (No. 60) with cell dimensions, a = 7.158(2), b = 10.510(3), c = 9.733(2) Å and has four formula units in the unit cell. 2 has a monoclinic cell, P21/c (No. 14) with cell dimensions a = 14.368(3), b = 6.626(1), c = 12.300(2) Å, β = 115.60(1)° and has 4 formula units in the unit cell. Data were collected with use of MoKα radiation and a Nicolet P3 diffractometer. The crystal structures were determined by standard methods and refined to Rw = 0.037 (1) and Rw = 0.040 (2) on the basis of 782 and 2108 unique reflections. Bond lengths and angles in the two compounds are normal. 2 has what has been considered to be the less likely tautomeric structure. Both compounds were examined by 1H, 13C nmr, vibrational spectroscopy, and mass spectroscopy. For 2 there was no evidence of the alternative tautomeric structure. New methods were developed for the preparation of both compounds and the mechanism of the original reaction rationalized.

Electron Donor-Acceptor Compounds. Synthesis and Structure of 5-(1,4-Benzoquinone-2-yl)-10,15,20-trialkylporphyrins

1998 ◽  
Vol 53 (9) ◽  
pp. 1021-1030 ◽  
Author(s):  
Steffen Runge ◽  
Mathias O. Senge
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Supramolecular Structure ◽  
Crystal Structure Analysis ◽  
Free Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Polymeric Chains ◽  
Donor Acceptor

Abstract A series of 5-(benzoquinone)-10,15,20-trialkylporphyrins was synthesized via cross condensation of the respective aldehydes, 2,5-dimethoxybenzaldehyde and pyrrole followed by demethylation with BBr3 and oxidation with PbO2. This method worked reasonably well for compounds bearing the benzoquinone substituent and butyl, isopropyl, 1 -methylpropyl and 2-ethylpropyl residues (2a-d). The free base porphyrin quinones were converted into the zinc(II) complexes (3a-d) all of which showed remarkable stability for porphyrin quinones. The zinc(II) complex 3c bearing isopropyl residues was investigated by X-ray crystallography and showed a supramolecular structure consisting of polymeric chains facilitated by coordina­tion of a benzoquinone oxygen to a neighboring zinc(II) center. Attempts to synthesize a 5-(benzoquinone)-10,15,20-tris(terr-butylporphyrin) resulted in the formation of a yellow porphomethene (4), which could not be oxidized further. A crystal structure analysis of 4, the first for a free base porphomethene, shows an extremely twisted conformation with syn-orientation of the three tert-butyl groups. The results indicate that new methods will have to be developed for the synthesis of nonplanar porphyrin quinones.

scholarly journals Modeling of cytochrome P450 (Cyt P450, CYP) channels

2011 ◽  
Vol 25 (2) ◽  
pp. 63-87 ◽  
Author(s):  
Christopher K. Jankowski ◽  
Julien B. Chiasson ◽  
Étienne Dako ◽  
Kathy Doucet ◽  
Marc E. Surette ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Direct Method ◽  
Outer Side ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Curved Channels ◽  
Modeling Techniques ◽  
On Line ◽  
Structure Of Proteins

The precise location of a substrate in cytochrome P450 (CYP) governs the orientation of the oxidation position. Such information is generally obtained from biochemical data, but modeling approaches have also been used to explain these locations. We used X-ray data and modeling techniques to distinguish between the series of putative linear or curved channels which lead the substrate from the outer side of the protein to the inner, and then into the heme pocket; these techniques were also used to identify the largest such channels. Two new methods for precisely determining the 3-D structure of proteins using X-ray crystallography were proposed in order to identify these channels: first, the use of both straight and curved channels, and second, the sphere method. These data are compared with Poulos channels, and with Caver (or Mol on line) modeling methodologies. Our methods were developed from studies of the interaction between cytochrome P450CAM(CYP101) fromPseudomonas putida(as expressed inEscherichia coli) and the indolic base β-carboline. Apart from the identification of potential access channels leading to the heme-containing active site, a new explanation was advanced for the substrate's hydroxylation position. The sphere method seems to have potential to become a general and direct method for prediction of substrate access channels from reduced- or low-resolution crystallographic data.

scholarly journals Reciprocalspaceship: A Python Library for Crystallographic Data Analysis

2021 ◽  
Author(s):  
Jack B. Greisman ◽  
Kevin M. Dalton ◽  
Doeke R. Hekstra
Keyword(s):  
Data Analysis ◽  
Exploratory Data Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Reflection Data ◽  
Software Packages ◽  
Automated Processing ◽  
Exploratory Data ◽  
Closed Source

AbstractX-ray crystallography is an invaluable technique for studying the atomic structure of macromolecules. Much of crystallography’s success is due to the software packages developed to enable the automated processing of diffraction data. However, the analysis of unconventional diffraction experiments can still pose significant challenges—many existing programs are closed-source, sparsely documented, or are challenging to integrate with modern libraries for scientific computing and machine learning. Here we describe reciprocalspaceship, a Python library for exploring reciprocal space. It provides a tabular representation for reflection data from diffraction experiments that extends the widely-used pandas library with built-in methods for handling space group, unit cell, and symmetry-based operations. As we illustrate, this library facilitates new modes of exploratory data analysis while supporting the prototyping, development, and release of new methods.

scholarly journals Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM

2020 ◽  
Vol 76 (6) ◽  
pp. 531-541
Author(s):  
Soon Wen Hoh ◽  
Tom Burnley ◽  
Kevin Cowtan
Keyword(s):  
Model Building ◽  
Data Sets ◽  
Structural Interpretation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Model ◽  
Reference Map ◽  
Automated Model Building ◽  
Better Than

This work focuses on the use of the existing protein-model-building software Buccaneer to provide structural interpretation of electron cryo-microscopy (cryo-EM) maps. Originally developed for application to X-ray crystallography, the necessary steps to optimise the usage of Buccaneer with cryo-EM maps are shown. This approach has been applied to the data sets of 208 cryo-EM maps with resolutions of better than 4 Å. The results obtained also show an evident improvement in the sequencing step when the initial reference map and model used for crystallographic cases are replaced by a cryo-EM reference. All other necessary changes to settings in Buccaneer are implemented in the model-building pipeline from within the CCP-EM interface (as of version 1.4.0).

scholarly journals Achieving better than 3 Å resolution by single particle cryo-EM at 200 keV

2017 ◽  
Author(s):  
Mark A. Herzik ◽  
Mengyu Wu ◽  
Gabriel C. Lander
Keyword(s):  
Single Particle ◽  
Water Molecules ◽  
Macromolecular Complexes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
Electron Microscopes ◽  
Ordered Water ◽  
Better Than

AbstractTechnical and methodological advances in single-particle cryo-electron microscopy (cryo-EM) have expanded the technique into a resolution regime that was previously only attainable by X-ray crystallography. Although single-particle cryo-EM has proven to be a useful technique for determining the structures of biomedically relevant molecules at near-atomic resolution, nearly 98% of the structures resolved to better than 4 Å resolution have been determined using 300 keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain cryo-EM reconstructions of macromolecular complexes at a range of sizes to better than 3 Å resolution using a 200 keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules, features previously thought only to be resolvable using TEMs operating at 300 keV.

Beyond X-rays: an overview of emerging structural biology methods

2021 ◽  
Author(s):  
Jason E. Schaffer ◽  
Vandna Kukshal ◽  
Justin J. Miller ◽  
Vivian Kitainda ◽  
Joseph M. Jez
Keyword(s):  
Structure Determination ◽  
De Novo ◽  
Three Dimensional ◽  
Atomic Scale ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Main Technique

Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods.

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