Computer simulations of ABC transporter componentsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease.

2006 ◽  
Vol 84 (6) ◽  
pp. 900-911 ◽  
Author(s):  
Eliud O. Oloo ◽  
Christian Kandt ◽  
Megan L. O’Mara ◽  
D. Peter Tieleman
Keyword(s):  
Abc Transporters ◽  
Simulation Techniques ◽  
Multiple Components ◽  
Functional Dynamics ◽  
Future Challenges ◽  
Health And Disease ◽  
Dynamics Simulations ◽  
Functional Mechanisms ◽  
Computer Simulation Techniques ◽  
Selection Of

Current computer simulation techniques provide robust tools for studying the detailed structure and functional dynamics of proteins, as well as their interaction with each other and with other biomolecules. In this minireview, we provide an illustration of recent progress and future challenges in computer modeling by discussing computational studies of ATP-binding cassette (ABC) transporters. ABC transporters have multiple components that work in a well coordinated fashion to enable active transport across membranes. The mechanism by which members of this superfamily execute transport remains largely unknown. Molecular dynamics simulations initiated from high-resolution crystal structures of several ABC transporters have proven to be useful in the investigation of the nature of conformational coupling events that may drive transport. In addition, fruitful efforts have been made to predict unknown structures of medically relevant ABC transporters, such as P-glycoprotein, using homology-based computational methods. The various techniques described here are also applicable to gaining an atomically detailed understanding of the functional mechanisms of proteins in general.

Critical Impact Points for Transitions and Terminals

2002 ◽  
Vol 1797 (1) ◽  
pp. 105-112
Author(s):  
Roger P. Bligh ◽  
King K. Mak
Keyword(s):  
Safety Performance ◽  
Worst Case ◽  
Roadside Safety ◽  
Simulation Techniques ◽  
Crash Testing ◽  
Families Of Curves ◽  
Impact Location ◽  
Safety Features ◽  
Computer Simulation Techniques ◽  
Selection Of

Guidelines for evaluating the safety performance of roadside safety features generally recommend that a worst case or critical impact point (CIP) be selected for crash testing. NCHRP Report 350 presents families of curves that can be used to determine the CIP for a transition section. However, these curves have been observed to overestimate the stiffness of a transition system and provide CIP values closer to the more rigid system of the transition (e.g., bridge rail end) than appropriate. New CIP selection curves for transitions are presented. A procedure is provided to aid in determining the CIP for transition sections with multiple rail elements or variations in post strength and post spacing. Various existing and theoretical transitions systems with wide-ranging combinations of beam and post strengths were used to validate the curves. The newly developed CIP relationships for transitions are recommended in lieu of the existing relationships contained in NCHRP Report 350. To facilitate the development of guidelines for the selection of a CIP for terminals, a new definition is proposed. The proposed definition for the CIP is the point along the terminal at which vehicle behavior transitions from gating to redirection. A methodology for determining the CIP using computer simulation techniques is investigated. The data clearly demonstrate that the selection of a single default impact location for all terminal configurations may not provide the CIP for many designs.

Image Analysis of Intramembrane Particles in Freeze-Fractured Biomembranes Using Computer Simulation Techniques

1975 ◽  
Vol 33 ◽  
pp. 214-215
Author(s):  
D.J. Benefiel ◽  
R.S. Weinstein
Keyword(s):  
Membrane Proteins ◽  
Freeze Fracture ◽  
Integral Membrane Proteins ◽  
Systematic Evaluation ◽  
Intramembrane Particles ◽  
Modeling Methods ◽  
Simulation Techniques ◽  
Freeze Fracture Electron Microscopy ◽  
Fracture Electron ◽  
Computer Simulation Techniques

Intramembrane particles (IMP or MAP) are components of most biomembranes. They are visualized by freeze-fracture electron microscopy, and they probably represent replicas of integral membrane proteins. The presence of MAP in biomembranes has been extensively investigated but their detailed ultrastructure has been largely ignored. In this study, we have attempted to lay groundwork for a systematic evaluation of MAP ultrastructure. Using mathematical modeling methods, we have simulated the electron optical appearances of idealized globular proteins as they might be expected to appear in replicas under defined conditions. By comparing these images with the apearances of MAPs in replicas, we have attempted to evaluate dimensional and shape distortions that may be introduced by the freeze-fracture technique and further to deduce the actual shapes of integral membrane proteins from their freezefracture images.

Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of Leishmania mexicana

2020 ◽  
Vol 16 (6) ◽  
pp. 784-795
Author(s):  
Krisnna M.A. Alves ◽  
Fábio José Bonfim Cardoso ◽  
Kathia M. Honorio ◽  
Fábio A. de Molfetta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Point Of View ◽  
New Drugs ◽  
Leishmania Mexicana ◽  
Receptor Complexes ◽  
Starting Point ◽  
Dynamics Simulations ◽  
Selection Of

Background:: Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. Objective:: The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). Methods: A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. Results:: Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. Conclusion:: he use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.

Boiler Implosion Control in Fossil Fuel Power Plants

1985 ◽  
Vol 107 (4) ◽  
pp. 267-269 ◽  
Author(s):  
S. Z. Wu ◽  
D. N. Wormley ◽  
D. Rowell ◽  
P. Griffith
Keyword(s):  
Power Plants ◽  
Fossil Fuel ◽  
Companion Paper ◽  
Simulation Techniques ◽  
Power Plant Boiler ◽  
Induced Draft Fan ◽  
Fossil Fuel Power Plants ◽  
Computer Simulation Techniques ◽  
Plant Boiler ◽  
Furnace Pressure

An evaluation of systems for control of fossil fuel power plant boiler and stack implosions has been performed using computer simulation techniques described in a companion paper. The simulations have shown that forced and induced draft fan control systems and induced draft fan bypass systems reduce the furnace pressure excursions significantly following a main fuel trip. The limitations of these systems are associated with actuator range and response time and stack pressure excursions during control actions. Preliminary study suggests that an alternative control solution may be achieved by discharging steam into the furnace after a fuel trip.

Three-dimensional predator–prey interactions: a computer simulation of bird flocks and aircraft

1986 ◽  
Vol 64 (11) ◽  
pp. 2624-2633 ◽  
Author(s):  
Peter F. Major ◽  
Lawrence M. Dill ◽  
David M. Eaves
Keyword(s):  
Computer Simulation ◽  
Prey Species ◽  
Three Dimensional ◽  
Aircraft Engine ◽  
Aquatic Environments ◽  
Aircraft Engines ◽  
Predator Prey ◽  
Simulation Techniques ◽  
Computer Simulation Techniques ◽  
Individual Prey

Three-dimensional interactions between grouped aerial predators (frontal discs of aircraft engines), either linearly arrayed or clustered, and flocks of small birds were studied using interactive computer simulation techniques. Each predator modelled was orders of magnitude larger than an individual prey, but the prey flock was larger than each predator. Expected numbers of individual prey captured from flocks were determined for various predator speeds and trajectories, flock–predator initial distances and angles, and flock sizes, shapes, densities, trajectories, and speeds. Generally, larger predators and clustered predators caught more prey. The simulation techniques employed in this study may also prove useful in studies of predator–prey interactions between schools or swarms of small aquatic prey species and their much larger vertebrate predators, such as mysticete cetaceans.The study also provides a method to study problems associated with turbine aircraft engine damage caused by the ingestion of small flocking birds, as well as net sampling of organisms in open aquatic environments.

DIFFUSION MECHANISMS AT fcc METAL SURFACES — EMBEDDED ATOM METHOD CALCULATIONS

1995 ◽  
Vol 09 (01) ◽  
pp. 1-44 ◽  
Author(s):  
CHUN-LI LIU
Keyword(s):  
Metal Surfaces ◽  
Diffusion Processes ◽  
Embedded Atom Method ◽  
Embedded Atom ◽  
Simulation Techniques ◽  
Theoretical Investigations ◽  
Diffusion Mechanisms ◽  
Fcc Metal ◽  
Dynamic Diffusion ◽  
Computer Simulation Techniques

Recent development in theoretical investigations using computer simulation techniques and the embedded atom method (EAM) on diffusion processes critical to nucleation and growth of thin films at fcc metal surfaces is reviewed. Through these investigations, interactions between adatoms and substrate, adatoms and steps, and clusters and substrate and the effect of these interactions on dynamic diffusion processes are further understood. The results from these theoretical investigations are generally consistent with available experimental data and have provided explanations for some experimental observations. Some predictions made a few years ago from these studies have been confirmed by the latest experiments.

scholarly journals A Comprehensive Review of Cholinesterase Modeling and Simulation

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 580
Author(s):  
Danna De Boer ◽  
Nguyet Nguyen ◽  
Jia Mao ◽  
Jessica Moore ◽  
Eric J. Sorin
Keyword(s):  
Modeling And Simulation ◽  
Binding Site ◽  
Catalytic Efficiency ◽  
Site Location ◽  
Simulation Techniques ◽  
Therapeutic Value ◽  
Docking Calculations ◽  
Computer Based ◽  
Dynamics Simulations ◽  
And Function

The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.

Methionine as a double-edged sword in health and disease: Current perspective and future challenges

2021 ◽  
pp. 101500
Author(s):  
Umashanker Navik ◽  
Vaibhav G. Sheth ◽  
Amit Khurana ◽  
Snehal Sainath Jawalekar ◽  
Prince Allawadhi ◽  
...  
Keyword(s):  
Current Perspective ◽  
Future Challenges ◽  
Health And Disease

scholarly journals From the theory to practice: Five years of urban regeneration workshops

2018 ◽  
Vol 8 (3) ◽  
pp. 179
Author(s):  
Raimundo Bambó-Naya ◽  
Pablo De la Cal-Nicolás ◽  
Carmen Díez-Medina ◽  
Sergio García-Pérez ◽  
Javier Monclús-Fraga
Keyword(s):  
Urban Regeneration ◽  
Joint Work ◽  
Teaching Innovation ◽  
Academic Field ◽  
Future Challenges ◽  
Academic Courses ◽  
The Subject ◽  
The University ◽  
Previous Phase ◽  
Selection Of

The aim of this communication is to present the experience of four academic courses in the subject of Integrated Urban and Landscape Design, taught in the framework of the Master in Architecture of the School of Engineering and Architecture of the University of Zaragoza. It addresses urban regeneration interventions in vulnerable areas of the consolidated city with approaches to teaching innovation in the academic field and in the topic of user participation.The workshop methodology is explained in detail, paying more attention to the process followed than to the specific results of the workshop. The different stages of the process are presented: previous phase and selection of the study area, phase of analysis and diagnosis, phase of proposals, where a joint work is carried out with vision of action in the whole of the neighbourhood, and phase of presentation of the results to the Neighbours. Finally, some future challenges of this workshop are outlined.

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