Calculating enzyme kinetic parameters from protein structures

2008 ◽  
Vol 36 (1) ◽  
pp. 51-54 ◽  
Author(s):  
Matthias Stein ◽  
Razif R. Gabdoulline ◽  
Rebecca C. Wade
Keyword(s):  
Systems Biology ◽  
Kinetic Parameters ◽  
Protein Structures ◽  
Three Dimensional ◽  
Enzyme Kinetic ◽  
Computationally Efficient ◽  
Computational Approaches ◽  
Biochemical Pathways ◽  
Catalysed Reaction ◽  
Molecular Interaction Fields

Enzyme kinetic parameters can differ between different species and isoenzymes for the same catalysed reaction. Computational approaches to calculate enzymatic kinetic parameters from the three-dimensional structures of proteins will be reviewed briefly here. Enzyme kinetic parameters may be derived by modelling and simulating the rate-determining process. An alternative, approximate, but more computationally efficient approach is the comparison of molecular interaction fields for experimentally characterized enzymes and those for which parameters should be determined. A correlation between differences in interaction fields and experimentally determined kinetic parameters can be used to determine parameters for orthologous enzymes from other species. The estimation of enzymatic kinetic parameters is an important step in setting up mathematical models of biochemical pathways in systems biology.

scholarly journals On the Reconstruction of Three-dimensional Protein Structures from Contact Maps

Algorithms ◽  
2009 ◽  
Vol 2 (1) ◽  
pp. 76-92 ◽  
Author(s):  
Pietro Di Lena ◽  
Marco Vassura ◽  
Luciano Margara ◽  
Piero Fariselli ◽  
Rita Casadio
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Contact Maps

scholarly journals Regional Distribution and Kinetics of Three Sites on the GABAA Receptor: Lack of Effect of Portacaval Shunting

1992 ◽  
Vol 12 (2) ◽  
pp. 334-346 ◽  
Author(s):  
Anke M. Mans ◽  
Kelli M. Kukulka ◽  
Keith J. McAvoy ◽  
Norman C. Rokosz
Keyword(s):  
Kinetic Parameters ◽  
Regional Distribution ◽  
Three Dimensional ◽  
Portacaval Shunt ◽  
Brain Regions ◽  
Significant Heterogeneity ◽  
Heterogeneous Distribution ◽  
Dimensional Reconstruction ◽  
Benzodiazepine Site ◽  
Gaba Neurotransmission

The regional distribution of binding sites on the GABAA receptor and their kinetic parameters were measured by quantitative autoradiography in brains from normal rats and rats with a portacaval shunt, a model of portal systemic encephalopathy in which GABA neurotransmission may be altered. The ligands used were [3H]flunitrazepam (a benzodiazepine-site agonist), [3H]-Ro 15-1788 (a benzodiazepine-site antagonist), [3H]muscimol (a GABA-site agonist), and [35S] t-butylbicyclo-phosphorothionate (35S-TBPS, a convulsant that binds to a site near the chloride channel). Some brains were analyzed by computerized image analysis and three-dimensional reconstruction. The regional distribution of binding of the benzodiazepines was very similar, but the patterns obtained with [3H]muscimol and [35S]TBPS were different in many areas, suggesting a heterogeneous distribution of several subtypes of the GABAA receptor. The kinetic parameters were determined in brain regions for [3H]flunitrazepam, [3H]Ro15-1788, and [3H]muscimol. For each ligand, the Kd showed a significant heterogeneity among brain regions (at least threefold), contrary to conclusions drawn from earlier studies. In portacaval shunted rats, binding of all four ligands was essentially unchanged from that in control rats, indicating that, if there was an abnormality in GABA neurotransmission during portal systemic shunting, it was not reflected by altered binding to the main sites on the GABAA receptor.

scholarly journals A systems biology analysis of metastatic melanoma using in-depth three-dimensional protein profiling

PROTEOMICS ◽  
2010 ◽  
Vol 10 (24) ◽  
pp. 4450-4462 ◽  
Author(s):  
Mee-Jung Han ◽  
Huan Wang ◽  
Lynn A. Beer ◽  
Hsin-Yao Tang ◽  
Meenhard Herlyn ◽  
...  
Keyword(s):  
Systems Biology ◽  
Metastatic Melanoma ◽  
Three Dimensional ◽  
Protein Profiling

Direct simulation of evolution and control of three-dimensional instabilities in attachment-line boundary layers

1995 ◽  
Vol 291 ◽  
pp. 369-392 ◽  
Author(s):  
Ronald D. Joslin
Keyword(s):  
Boundary Layer ◽  
Stokes Equations ◽  
Three Dimensional ◽  
Plate Boundary ◽  
Navier Stokes ◽  
Two Dimensional ◽  
Computationally Efficient ◽  
Simulation Results ◽  
Dimensional Simulation ◽  
Attachment Line

The spatial evolution of three-dimensional disturbances in an attachment-line boundary layer is computed by direct numerical simulation of the unsteady, incompressible Navier–Stokes equations. Disturbances are introduced into the boundary layer by harmonic sources that involve unsteady suction and blowing through the wall. Various harmonic-source generators are implemented on or near the attachment line, and the disturbance evolutions are compared. Previous two-dimensional simulation results and nonparallel theory are compared with the present results. The three-dimensional simulation results for disturbances with quasi-two-dimensional features indicate growth rates of only a few percent larger than pure two-dimensional results; however, the results are close enough to enable the use of the more computationally efficient, two-dimensional approach. However, true three-dimensional disturbances are more likely in practice and are more stable than two-dimensional disturbances. Disturbances generated off (but near) the attachment line spread both away from and toward the attachment line as they evolve. The evolution pattern is comparable to wave packets in flat-plate boundary-layer flows. Suction stabilizes the quasi-two-dimensional attachment-line instabilities, and blowing destabilizes these instabilities; these results qualitatively agree with the theory. Furthermore, suction stabilizes the disturbances that develop off the attachment line. Clearly, disturbances that are generated near the attachment line can supply energy to attachment-line instabilities, but suction can be used to stabilize these instabilities.

Analytical method for the estimation of enzyme kinetic parameters

1969 ◽  
Vol 191 (1) ◽  
pp. 155-157 ◽  
Author(s):  
A.P. Brestkin ◽  
E.V. Rozengart ◽  
V.A. Samokish ◽  
I.N. Soboleva
Keyword(s):  
Kinetic Parameters ◽  
Analytical Method ◽  
Enzyme Kinetic

A Fast View Synthesis Implementation Method for Light Field Applications

2021 ◽  
Vol 17 (4) ◽  
pp. 1-20
Author(s):  
Wei Gao ◽  
Linjie Zhou ◽  
Lvfang Tao
Keyword(s):  
Neural Networks ◽  
Light Field ◽  
Three Dimensional ◽  
Super Resolution ◽  
View Synthesis ◽  
Compact Representation ◽  
Light Weight ◽  
Computationally Efficient ◽  
Full Resolution ◽  
Time Systems

View synthesis (VS) for light field images is a very time-consuming task due to the great quantity of involved pixels and intensive computations, which may prevent it from the practical three-dimensional real-time systems. In this article, we propose an acceleration approach for deep learning-based light field view synthesis, which can significantly reduce calculations by using compact-resolution (CR) representation and super-resolution (SR) techniques, as well as light-weight neural networks. The proposed architecture has three cascaded neural networks, including a CR network to generate the compact representation for original input views, a VS network to synthesize new views from down-scaled compact views, and a SR network to reconstruct high-quality views with full resolution. All these networks are jointly trained with the integrated losses of CR, VS, and SR networks. Moreover, due to the redundancy of deep neural networks, we use the efficient light-weight strategy to prune filters for simplification and inference acceleration. Experimental results demonstrate that the proposed method can greatly reduce the processing time and become much more computationally efficient with competitive image quality.

Prediction of Slamming Loads on Catamaran Wetdeck Using CFD

2015 ◽  
Author(s):  
Ahmed Swidan ◽  
Giles Thomas ◽  
Dev Ranmuthugala ◽  
Irene Penesis ◽  
Walid Amin ◽  
...  
Keyword(s):  
Model Simulation ◽  
Three Dimensional ◽  
Grid Method ◽  
Computationally Efficient ◽  
Overset Grid ◽  
Force Magnitude ◽  
Overset Grid Method ◽  
Drop Tests ◽  
Transient Velocity ◽  
Transient Velocity Profile

Wetdeck slamming is one of the principal hydrodynamic loads acting on catamarans. CFD techniques are shown to successfully characterise wetdeck slamming loads, as validated through a series of controlled-speed drop tests on a three-dimensional catamaran hullform model. Simulation of water entry at constant speed by applying a fixed grid method was found to be more computationally efficient than applying an overset grid. However, the overset grid method for implementing the exact transient velocity profile resulted in better prediction of slam force magnitude. In addition the splitting force concurrent with wetdeck slam event was quantified to be 21% of the vertical slamming force.

PUTRACER: A NOVEL METHOD FOR IDENTIFICATION OF CONTINUOUS-DOMAINS IN MULTI-DOMAIN PROTEINS

2013 ◽  
Vol 11 (01) ◽  
pp. 1340012 ◽  
Author(s):  
SEYED SHAHRIAR ARAB ◽  
MOHAMMADBAGHER PARSA GHARAMALEKI ◽  
ZAIDDODINE PASHANDI ◽  
REZVAN MOBASSERI
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Accessible Surface Area ◽  
Computer Assisted ◽  
Correct Assignment ◽  
Critical Boundary ◽  
Novel Method ◽  
Accessible Surface ◽  
A Chain

Computer assisted assignment of protein domains is considered as an important issue in structural bioinformatics. The exponential increase in the number of known three dimensional protein structures and the significant role of proteins in biology, medicine and pharmacology illustrate the necessity of a reliable method to automatically detect structural domains as protein units. For this aim, we have developed a program based on the accessible surface area (ASA) and the hydrogen bonds energy in protein backbone (HBE). PUTracer (Protein Unit Tracer) is built on the features of a fast top-down approach to cut a chain into its domains (contiguous domains) with minimal change in ASA as well as HBE. Performance of the program was assessed by a comprehensive benchmark dataset of 124 protein chains, which is based on agreement among experts (e.g. CATH, SCOP) and was expanded to include structures with different types of domain combinations. Equal number of domains and at least 90% agreement in critical boundary accuracy were considered as correct assignment conditions. PUTracer assigned domains correctly in 81.45% of protein chains. Although low critical boundary accuracy in 18.55% of protein chains leads to the incorrect assignments, adjusting the scales causes to improve the performance up to 89.5%. We discuss here the success or failure of adjusting the scales with provided evidences. Availability: PUTracer is available at http://bioinf.modares.ac.ir/software/PUTracer/

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