scholarly journals Direct coevolutionary couplings reflect biophysical residue interactions in proteins

2016 ◽  
Author(s):  
Alice Coucke ◽  
Guido Uguzzoni ◽  
Francesco Oteri ◽  
Simona Cocco ◽  
Remi Monasson ◽  
...  
Keyword(s):  
Structural Information ◽  
Synthetic Data ◽  
Chemical Properties ◽  
Quantitative Information ◽  
Protein Families ◽  
Homologous Proteins ◽  
Homologous Protein ◽  
Residue Contact ◽  
Physico Chemical ◽  
Statistical Coupling

AbstractCoevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21×21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families

2018 ◽  
Vol 16 (02) ◽  
pp. 1840005 ◽  
Author(s):  
Dmitry Suplatov ◽  
Yana Sharapova ◽  
Daria Timonina ◽  
Kirill Kopylov ◽  
Vytas Švedas
Keyword(s):  
Rational Design ◽  
Visual Analysis ◽  
Structural Information ◽  
Protein Structures ◽  
Web Server ◽  
Physical Contact ◽  
Protein Families ◽  
Sequence Alignments ◽  
Homologous Proteins ◽  
Correlated Mutations

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand’s binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

scholarly journals DynaStI: A Dynamic Retention Time Database for Steroidomics

Metabolites ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 85 ◽  
Author(s):  
Santiago Codesido ◽  
Giuseppe Marco Randazzo ◽  
Fabio Lehmann ◽  
Víctor González-Ruiz ◽  
Arnaud García ◽  
...  
Keyword(s):  
Liquid Chromatography ◽  
Metabolic Pathways ◽  
Structural Information ◽  
Chemical Properties ◽  
Reversed Phase ◽  
Liquid Chromatography Mass Spectrometry ◽  
Phase Gradient ◽  
Physico Chemical ◽  
Solvent Strength ◽  
Reversed Phase Lc

Steroidomics studies face the challenge of separating analytical compounds with very similar structures (i.e., isomers). Liquid chromatography (LC) is commonly used to this end, but the shared core structure of this family of compounds compromises effective separations among the numerous chemical analytes with comparable physico-chemical properties. Careful tuning of the mobile phase gradient and an appropriate choice of the stationary phase can be used to overcome this problem, in turn modifying the retention times in different ways for each compound. In the usual workflow, this approach is suboptimal for the annotation of features based on retention times since it requires characterizing a library of known compounds for every fine-tuned configuration. We introduce a software solution, DynaStI, that is capable of annotating liquid chromatography-mass spectrometry (LC–MS) features by dynamically generating the retention times from a database containing intrinsic properties of a library of metabolites. DynaStI uses the well-established linear solvent strength (LSS) model for reversed-phase LC. Given a list of LC–MS features and some characteristics of the LC setup, this software computes the corresponding retention times for the internal database and then annotates the features using the exact masses with predicted retention times at the working conditions. DynaStI (https://dynasti.vital-it.ch) is able to automatically calibrate its predictions to compensate for deviations in the input parameters. The database also includes identification and structural information for each annotation, such as IUPAC name, CAS number, SMILES string, metabolic pathways, and links to external metabolomic or lipidomic databases.

Decoration of specific sites on freeze-fractured membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 140-141
Author(s):  
H. Gross ◽  
H. Moor
Keyword(s):  
Pure Water ◽  
Freeze Fracture ◽  
Chemical Properties ◽  
Surface Forces ◽  
Sulfate Pentahydrate ◽  
Copper Sulfate Pentahydrate ◽  
Physico Chemical ◽  
Water Of Hydration ◽  
Small Container ◽  
Binding Forces

Fracturing under ultrahigh vacuum (UHV, p ≤ 10-9 Torr) produces membrane fracture faces devoid of contamination. Such clean surfaces are a prerequisite foe studies of interactions between condensing molecules is possible and surface forces are unequally distributed, the condensate will accumulate at places with high binding forces; crystallites will arise which may be useful a probes for surface sites with specific physico-chemical properties. Specific “decoration” with crystallites can be achieved nby exposing membrane fracture faces to water vopour. A device was developed which enables the production of pure water vapour and the controlled variation of its partial pressure in an UHV freeze-fracture apparatus (Fig.1a). Under vaccum (≤ 10-3 Torr), small container filled with copper-sulfate-pentahydrate is heated with a heating coil, with the temperature controlled by means of a thermocouple. The water of hydration thereby released enters a storage vessel.

Physico-Chemical Properties of Recombinant Desulphatohirudin

1990 ◽  
Vol 63 (03) ◽  
pp. 499-504 ◽  
Author(s):  
A Electricwala ◽  
L Irons ◽  
R Wait ◽  
R J G Carr ◽  
R J Ling ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Gel Filtration ◽  
Chemical Properties ◽  
Alpha Helix ◽  
Apparent Molecular Weight ◽  
Correlation Spectroscopy ◽  
Nmr Studies ◽  
Recombinant Hirudin ◽  
Physico Chemical ◽  
Recombinant Molecule

SummaryPhysico-chemical properties of recombinant desulphatohirudin expressed in yeast (CIBA GEIGY code No. CGP 39393) were reinvestigated. As previously reported for natural hirudin, the recombinant molecule exhibited abnormal behaviour by gel filtration with an apparent molecular weight greater than that based on the primary structure. However, molecular weight estimation by SDS gel electrophoresis, FAB-mass spectrometry and Photon Correlation Spectroscopy were in agreement with the theoretical molecular weight, with little suggestion of dimer or aggregate formation. Circular dichroism studies of the recombinant molecule show similar spectra at different pH values but are markedly different from that reported by Konno et al. (13) for a natural hirudin-variant. Our CD studies indicate the presence of about 60% beta sheet and the absence of alpha helix in the secondary structure of recombinant hirudin, in agreement with the conformation determined by NMR studies (17)

Physico-chemical properties of the rare-earth metals, scandium, and yttrium

1963 ◽  
Vol 79 (2) ◽  
pp. 263-293 ◽  
Author(s):  
E.M. Savitskii ◽  
V.F. Terekhova ◽  
O.P. Naumkin
Keyword(s):  
Rare Earth ◽  
Rare Earth Metals ◽  
Chemical Properties ◽  
Physico Chemical ◽  
The Rare Earth

Physico chemical properties and gas adsorption separation characteristics of Itaya zeolite and its modified products.

1990 ◽  
Vol 39 (442) ◽  
pp. 996-1000 ◽  
Author(s):  
Ayao TAKASAKA ◽  
Hideyuki NEMOTO ◽  
Hirohiko KONO ◽  
Yoshihiro MATSUDA
Keyword(s):  
Gas Adsorption ◽  
Chemical Properties ◽  
Physico Chemical

Development of Ketchup from Sudanese Red karkade (Hibiscus sabdariffa L.) byproduct

Food Biology ◽  
1970 ◽  
pp. 19-23
Author(s):  
Nawal Abdel-Gayoum Abdel-Rahman
Keyword(s):  
Sensory Quality ◽  
Chemical Properties ◽  
Storage Period ◽  
Gum Arabic ◽  
Raw Material ◽  
Soluble Solids ◽  
Hibiscus Sabdariffa ◽  
Overall Acceptability ◽  
Physico Chemical ◽  
Tomato Ketchup

The aim of this study is to use of karkede (Hibiscus sabdariffa L.) byproduct as raw material to make ketchup instead of tomato. Ketchup is making of various pulps, but the best type made from tomatoes. Roselle having adequate amounts of macro and micro elements, and it is rich in source of anthocyanine. The ketchup made from pulped of waste of soaked karkede, and homogenized with starch, salt, sugar, ginger (Zingiber officinale), kusbara (Coriandrum sativum) and gum Arabic. Then processed and filled in glass bottles and stored at two different temperatures, ambient and refrigeration. The total solids, total soluble solids, pH, ash, total titratable acidity and vitamin C of ketchup were determined. As well as, total sugars, reducing sugars, colour density, and sodium chloride percentage were evaluated. The sensory quality of developed product was determined immediately and after processing, which included colour, taste, odour, consistency and overall acceptability. The suitability during storage included microbial growth, physico-chemical properties and sensory quality. The karkede ketchup was found free of contaminants throughout storage period at both storage temperatures. Physico-chemical properties were found to be significantly differences at p?0.05 level during storage. There were no differences between karkade ketchup and market tomato ketchup concerning odour, taste, odour, consistency and overall acceptability. These results are encouraging for use of roselle cycle as a raw material to make acceptable karkade ketchup.

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