scholarly journals Relationship between Metabolic Fluxes and Sequence-Derived Properties of Enzymes

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Peteris Zikmanis ◽  
Inara Kampenusa
Keyword(s):  
Metabolic Pathways ◽  
Chemical Properties ◽  
Structural Features ◽  
Kinetic Properties ◽  
Net Charge ◽  
Metabolic Fluxes ◽  
Physical Chemical ◽  
Glycolysis Pathway ◽  
Derived Properties ◽  
Linear Regressions

Metabolic fluxes are key parameters of metabolic pathways being closely related to the kinetic properties of enzymes, thereby could be dependent on. This study examines possible relationships between the metabolic fluxes and the physical-chemical/structural features of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fluxes were quantified by the COPASI tool using the kinetic models of Hynne and Teusink at varied concentrations of external glucose. The enzyme sequences were taken from the UniProtKB and the average amino acid (AA) properties were computed using the set of Georgiev’s uncorrelated scales that satisfy the VARIMAX criterion and specific AA indices that show the highest correlations with those. Multiple linear regressions (88.41% < Radjusted2< 93.32%; P<0.00001) were found between the values of metabolic fluxes and the selected sets of the average AA properties. The hydrophobicity, α-helicity, and net charge were pointed out as the most influential characteristics of the sequences. The results provide an evidence that metabolic fluxes of the yeast glycolysis pathway are closely related to certain physical-chemical properties of relevant enzymes and support the view on the interdependence of catalytic, binding, and structural AA residues to ensure the efficiency of biocatalysts and, hence, physiologically adequate metabolic processes.

Relationships between metabolic fluxes and enzyme amino acid composition

2013 ◽  
Vol 8 (2) ◽  
pp. 107-120 ◽  
Author(s):  
Inara Kampenusa ◽  
Peteris Zikmanis
Keyword(s):  
Amino Acid ◽  
Metabolic Pathways ◽  
Kinetic Properties ◽  
Yeast Saccharomyces Cerevisiae ◽  
Metabolic Fluxes ◽  
Glycolysis Pathway ◽  
Stoichiometric Models ◽  
Sequence Characteristics ◽  
Linear Regressions ◽  
Key Parameter

AbstractMetabolic fluxes are a key parameter of metabolic pathways being closely related to the kinetic properties of enzymes and could be conditional on their sequence characteristics. This study examines possible relationships between the metabolic fluxes and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. Metabolic fluxes were quantified by the COPASI tool using the kinetic models of Hynne and Teusink at 25 mM, 50 mM, and 100 mM of external glucose or employing literature data for cognate kinetic or stoichiometric models. The enzyme sequences were taken from the UniProtKB, and the AAC computed by the ExPASy/ProtParam tool. Multiple linear regressions (89.07% < R2 adjusted < 91.82%; P<0.00001) were found between the values of metabolic fluxes and the selected sets of AA frequencies (5 to 7 for each model). Selected AA differed from the rest by their physicochemical and structural propensities, thus suggesting a distinctive contribution to the properties of enzymes, and hence the metabolic fluxes. The results provide evidence that metabolic fluxes of the yeast glycolysis pathway are closely related to the AAC of relevant enzymes and support the view that catalytic, binding and structural residues are interdependent to ensure the efficiency of biocatalysts.

scholarly journals Physical-Chemical Properties of L-asparaginase Mutants From Rhodospirillum Rubrum which Showed Antitelomerase Activity

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
M.V. Pokrovskaya ◽  
S.S. Aleksandrova ◽  
A.V. Veselovsky ◽  
D.D. Zdanov ◽  
V.S. Pokrovsky ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rhodospirillum Rubrum ◽  
Chemical Properties ◽  
Telomerase Activity ◽  
Kinetic Properties ◽  
Ph Optimum ◽  
Physical Chemical ◽  
Asparaginase Activity ◽  
Terminal Amino ◽  
Mutant Forms

Rru_A3730 protein is a bacterial Rhodospirillum rubrum L-asparaginase (RrA), which is known by its anticancer activity. RrA variants with point amino acid substitutions in the region of 150 amino acids residues: RrA17N, K149E, RrAE149R, V150P, F151T, RrА17N, E149R, V150P, RrAE149R, V150P, showed antiproliferative properties, and also by their ability to suppress telomerase activity. This work is devoted to comparison of physical-chemical and catalytic properties of these mutant forms of RrA. It is shown that pH optimum is in the alkaline zone (8.5 – 9.3); L-glutaminase and D-asparaginase activity is respectively not more than 0.1% and 1.6% of L-asparaginase for all studied variants of RrA. The presence of the N17-terminal amino acid sequence MASMTGGQMGRGSSRQ of the capsid protein of bacteriophage T7 in the RrA structure leads to an increase in the thermal stability of mutant RrA analogues (from 50°C to 56°C) and their resistance to denaturation in the presence of 3 – 4 M urea. It is of Metal ions exhibit multidirectional effects on L-asparaginase activity of RrA. K+, Ca2+, Zn2+, Cs+, Co2+ in significantly affect the activity of L-asparaginase, while Mn2+, Cu2+, Fe3+ ions inhibit it. There was no correlation between antitelomerase (antiproliferative) activity and kinetic properties of mutant forms of L-asparaginase RrA.

scholarly journals Infrared spectroscopy as an alternative methodology to evaluate the effect of structural features on the physical-chemical properties of inulins

2018 ◽  
Vol 109 ◽  
pp. 223-231 ◽  
Author(s):  
Nelson Romano ◽  
Cuauhtémoc Araujo-Andrade ◽  
Javier Lecot ◽  
Pablo Mobili ◽  
Andrea Gómez-Zavaglia
Keyword(s):  
Infrared Spectroscopy ◽  
Chemical Properties ◽  
Structural Features ◽  
Physical Chemical ◽  
Alternative Methodology

Physical, chemical, and mineralogical properties of Mexico City sediments: a geotechnical perspective

1998 ◽  
Vol 35 (4) ◽  
pp. 600-610 ◽  
Author(s):  
JA Díaz-Rodríguez ◽  
R Lozano-Santa Cruz ◽  
VM Dávila-Alcocer ◽  
E Vallejo ◽  
P Girón
Keyword(s):  
Mexico City ◽  
Lacustrine Sediments ◽  
Chemical Properties ◽  
Structural Features ◽  
Exchange Capacity ◽  
In Situ Tests ◽  
Physical Chemical ◽  
Mineralogical Properties ◽  
Ramon Lopez Velarde ◽  
Seismic Tests

Geotechnical, physical, chemical, and mineralogical properties of the sediments of Ramón López Velarde Park were examined. The site is located in the ancient lacustrine zone of Mexico City. In situ tests included a resistivity survey, soundings with an electric cone, and cross-hole seismic tests. In addition, a continuous core was obtained for the upper 40 m. This core was extensively studied in the laboratory to determine the variation of mineralogy, pH, organic matter, cation exchange capacity (CEC), and structural features with depth. The information is unique with respect to previous studies which focused on specimens at a single depth. Results facilitate the interpretation of the deposit evolution, leading to the current properties of this unique lacustrine sequence.Key words: Mexico City, geotechnical properties, lacustrine sediments, physical properties, mineralogy, chemical properties.

Building Attention and Edge Convolution Neural Networks for Bioactivity and Physical-Chemical Property Prediction

2019 ◽  
Author(s):  
Michael Withnall ◽  
Edvard Lindelöf ◽  
Ola Engkvist ◽  
Hongming Chen
Keyword(s):  
Message Passing ◽  
State Of The Art ◽  
A Priori ◽  
Model Performance ◽  
Learning Approaches ◽  
Physical Chemical ◽  
Chemical Descriptor ◽  
Derived Properties ◽  
Memory Schemes ◽  
Hyperparameter Selection

We introduce Attention and Edge Memory schemes to the existing Message Passing Neural Network framework for graph convolution, and benchmark our approaches against eight different physical-chemical and bioactivity datasets from the literature. We remove the need to introduce <i>a priori</i> knowledge of the task and chemical descriptor calculation by using only fundamental graph-derived properties. Our results consistently perform on-par with other state-of-the-art machine learning approaches, and set a new standard on sparse multi-task virtual screening targets. We also investigate model performance as a function of dataset preprocessing, and make some suggestions regarding hyperparameter selection.

Chlorinated Organics in Nearshore Waters and Tributaries of the St. Clair River

1986 ◽  
Vol 21 (3) ◽  
pp. 344-350 ◽  
Author(s):  
Barry G. Oliver ◽  
Klaus L.E. Kaiser
Keyword(s):  
United States ◽  
Suspended Sediment ◽  
Waste Disposal ◽  
Large Volume ◽  
Water Samples ◽  
Chemical Properties ◽  
Low Level ◽  
Chemical Company ◽  
Physical Chemical ◽  
The Individual

Abstract The concent rat ions of hexachloroethane (HCE), hexachlorobutadiene (HCBD), pentachlorobenzene (QCB), hexachlorobenzene (HCB) and octachlorostyrene (OCS) in large volume water samples show that the major sources of these chemicals to the St. Clair River are Dow Chemical Company effluents and, to a lesser degree, Sarnia’s Township ditch which drains one of Dow’s waste disposal sites. Tributaries entering the river on both sides of the Canada/United States border contain measurable concentrations of these chemicals indicating low level contamination throughout the area. The degree of water/suspended sediment partitioning of the chemicals (Kp) was studied. Kp values for the individual chemicals changed in a manner consistent with changes in their physical-chemical properties.

Chemical Ecology and Off-Flavour Substances

1988 ◽  
Vol 20 (8-9) ◽  
pp. 167-178
Author(s):  
O. M. Skulberg
Keyword(s):  
Environmental Factors ◽  
Chemical Ecology ◽  
Aquatic Environment ◽  
Metabolic Pathways ◽  
Chemical Properties ◽  
Relevant Research ◽  
Fundamental Research ◽  
Biotic Effects ◽  
Ecological Mechanisms ◽  
Ecological Importance

Off-flavour substances may be regarded as a resource which can be used to study special ecological mechanisms. Relevant research on off-flavours is inextricably combined with the study of perception, ethology, genetic control etc. The chemicals concerned are commonly perceived by the senses of olfaction and gustation. Thus research on the chemical ecology of off-flavour substances in the aquatic environment involves the study of a variety of disciplines. For example the biochemistry of the relevant substances and appropriate metabolic pathways must be considered. Chemical properties are important for the behaviour of the substances. The production of off-flavours by organisms is related to phenological circumstances. The biotic effects of ecologically significant substances are dependent on several environmental factors. This paper draws attention to the possible application of fundamental research in this area to selected problems of ecological importance.

Polymer-Graphene Nanoassemblies and their Applications in Cancer Theranostics

2020 ◽  
Vol 20 (11) ◽  
pp. 1340-1351 ◽  
Author(s):  
Ponnurengam M. Sivakumar ◽  
Matin Islami ◽  
Ali Zarrabi ◽  
Arezoo Khosravi ◽  
Shohreh Peimanfard
Keyword(s):  
Mechanical Stability ◽  
Chemical Properties ◽  
The Other ◽  
Hydrophilic Polymer ◽  
Two Dimensional ◽  
Normal Tissues ◽  
Physical Chemical ◽  
Anti Cancer ◽  
Good Biocompatibility ◽  
Cancer Theranostics

Background and objective: Graphene-based nanomaterials have received increasing attention due to their unique physical-chemical properties including two-dimensional planar structure, large surface area, chemical and mechanical stability, superconductivity and good biocompatibility. On the other hand, graphene-based nanomaterials have been explored as theranostics agents, the combination of therapeutics and diagnostics. In recent years, grafting hydrophilic polymer moieties have been introduced as an efficient approach to improve the properties of graphene-based nanomaterials and obtain new nanoassemblies for cancer therapy. Methods and results: This review would illustrate biodistribution, cellular uptake and toxicity of polymergraphene nanoassemblies and summarize part of successes achieved in cancer treatment using such nanoassemblies. Conclusion: The observations showed successful targeting functionality of the polymer-GO conjugations and demonstrated a reduction of the side effects of anti-cancer drugs for normal tissues.

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