Simulating Protein Adsorption For Experimental Comparison

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Simulating Protein Adsorption For Experimental Comparison

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Author : Michael Deighan
language : en
Publisher:
Release Date : 2014

Simulating Protein Adsorption For Experimental Comparison written by Michael Deighan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.

Many biological processes and technological applications involve proteins coming into contact with a solid surface. Generally, we know that proteins experience some degree of conformational change at the solid/liquid interface, and can measure these changes in the lab. However, while many experimental techniques exist for characterizing surface-bound proteins, none have been able to resolve high-precision structures. Computer simulation offers a unique route to determining how proteins adsorb. Herein, we apply a popular statistical sampling technique - Parallel Tempering Metadynamics - to all-atom molecular dynamics simulations of ex- plicitly solvated proteins interacting with solid surfaces. We show that by biasing specific degrees of freedom - or collective variables - a protein can be influenced to exhaustively explore conformational space both on and off a surface. The results from these simulations can be post-processed to reveal details such as: surface- bound conformations, orientations, and finer structural details like interatomic distances and Ramachandran angles - which, in turn, can be compared to, and validated by, experimental measurements. Ultimately, this work should convey the descriptive power that can arise from a mutually beneficial partnership between surface science and computer simulation in the context of biomolecular adsorption.

Development And Use Of Molecular Simulation Tools To Study The Structure And Function Of Biomolecules At Interfaces

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Author : Kayla G. Sprenger
language : en
Publisher:
Release Date : 2017

Development And Use Of Molecular Simulation Tools To Study The Structure And Function Of Biomolecules At Interfaces written by Kayla G. Sprenger and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.

Predicting and controlling the biophysical chemistry of protein/host interactions remains a pressing challenge of high fundamental interest across many subfields in chemistry, engineering, and medicine. Our ability to (experimentally) probe interfacial interactions between a surface, polymer, or solvent and a biomolecule has increased due to high-resolution NMR and other spectroscopic techniques. However, new structural and mechanistic insights coming from experiments alone have been limited due to – in the case of the protein/liquid interface – the compounding challenges of simultaneously studying the protein/host interface and elucidating sequence specific interactions, and in the case of the protein/surface interface – the lack of a single unifying technique that can fully resolve the structure of an adsorbed protein. For the protein/liquid interface, the challenge is even worse in the case of synthetic frameworks such as ionic liquids (ILs) where the combinatorial design space of the solvent and protein sequence explodes beyond what could ever be feasibly considered in a laboratory. The field could be greatly advanced through the use of predictive, physics-based simulations; however, best practices of how to simulate protein interfacial adsorption and extract meaningful information about protein/host interactions from molecular simulations for direct experimental comparison, are still developing. Herein, we aim to address these challenges through the use of a variety of statistical enhanced sampling simulation techniques and novel analytical approaches. A number of systems are simulated, ranging from small model proteins adsorbing onto solid, idealized surfaces, to simulations of full proteins in complex solution environments. Ultimately, these simulations should lead to large improvements in the way we use computers to study multifaceted interfacial processes like protein adsorption, in addition to providing new fundamental insights into protein/host interactions.

Computational Bioengineering

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Author : Guigen Zhang
language : en
Publisher: CRC Press
Release Date : 2015-04-01

Computational Bioengineering written by Guigen Zhang and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-04-01 with Medical categories.

Arguably the first book of its kind, Computational Bioengineering explores the power of multidisciplinary computer modeling in bioengineering. Written by experts, the book examines the interplay of multiple governing principles underlying common biomedical devices and problems, bolstered by case studies. It shows you how to take advantage of the la

Authors And Friends

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Author : Annie Fields
language : en
Publisher: Boston, Houghton
Release Date : 1897

Authors And Friends written by Annie Fields and has been published by Boston, Houghton this book supported file pdf, txt, epub, kindle and other format this book has been release on 1897 with Authors, American categories.

Modeling Transport And Protein Adsorption In Microfluidic Systems

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Author : Craig Finch
language : en
Publisher:
Release Date : 2011

Modeling Transport And Protein Adsorption In Microfluidic Systems written by Craig Finch and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with Adsorption categories.

Mass transport limitations and surface interactions are important phenomena in microfluidic devices. The flow of water is laminar at small scales and the absence of turbulent mixing can lead to transport limitations, especially for reactions that take place at surfaces. Microscale devices have a high ratio of surface area to volume, and proteins are known to adsorb preferentially at interfaces. Protein adsorption plays a significant role in biology by mediating critical processes such as the attachment of cells to surfaces, the immune response and the coagulation of blood. Simulation tools that can quantitatively predict transport and protein adsorption will enable the rational design of microfluidic devices for biomedical applications. Two-dimensional random sequential adsorption (RSA) models are widely used to model the adsorption of proteins on surfaces. As Brownian dynamics simulations have become popular for modeling protein adsorption, the interface model has changed from two-dimensional to three-dimensional. Brownian dynamics simulations were used to model the diffusive transport of hard-sphere particles in a liquid and the adsorption of the particles onto a uniform surface. The configuration of the adsorbed particles was analyzed to quantify the chemical potential near the surface, which was used to derive a continuum model of adsorption that incorporates the results from the Brownian dynamics simulations. The equations of the continuum model were discretized and coupled to a conventional computational fluid dynamics (CFD) simulation of diffusive transport to the surface. The kinetics of adsorption predicted by the continuum model closely matched the results from the Brownian dynamics simulation. This new model allows the results from mesoscale simulations to be used as a boundary condition for micro- or macro-scale CFD simulations of transport and protein adsorption in practical devices. Continuum models were used to interpret experimental measurements of the kinetics of protein adsorption. A Whispering Gallery Mode (WGM) biosensor was constructed and used to measure the adsorption of fibronectin (FN) and glucose oxidase (GO) onto several types alkysilane self-assembled monolayers (SAMs). Computational fluid dynamics was used to model the transport of protein in the flow cell of the biosensor. Various models were fitted to the experimental data, taking into account the transport limitations predicted by the CFD simulations. The fitted parameter values and the quality of fit of the various models were analyzed to test hypotheses about the mechanisms of adsorption. Cells were cultured on silane surfaces coated with FN to assess its biological activity, and a colorimetric assay was used to determine the enzymatic activity of the adsorbed glucose oxidase. The results of the GO activity assay were compared to the activity predicted by the models. The WGM biosensor, transport simulation and kinetic model fitting enabled new insights into the adsorption of proteins on functionalized surfaces at solution concentrations that were previously unattainable. The process of CFD simulation and experimental validation was applied to the design of microfluidic bioreactors for an in vitro tissue engineered model of an alveolus. The objective was to optimize the design of the microreactors so they operate more like plug flow reactors. Microreactors experience significant deviations from plug flow due to the high ratio of surface area to volume and the no-slip boundary condition at the walls of the chamber. Iterative CFD simulations were performed to optimize microfluidic structures to minimize the width of the residence time distributions of two types of chambers. Qualitative and quantitative visualization experiments with a dye indicator demonstrated that the CFD simulations accurately predicted the residence time distributions of the chambers. The use of CFD simulations greatly reduced the time and cost required to optimize the performance of the microreactors.

An Experimental Study Of Comparison Between Ph Parametric Pumping And Ph Cycling Zone Adsorption Process On Protein Separation

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Author : Vincent P. Jajalla
language : en
Publisher:
Release Date : 1981

An Experimental Study Of Comparison Between Ph Parametric Pumping And Ph Cycling Zone Adsorption Process On Protein Separation written by Vincent P. Jajalla and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1981 with Proteins categories.

The Vroman Effect

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Author : C. H. Bamford
language : en
Publisher: VSP
Release Date : 1992-12-01

The Vroman Effect written by C. H. Bamford and has been published by VSP this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992-12-01 with Science categories.

The development of specific antibodies as probes and detectors for adsorbed proteins by Dr. Leo Vroman and co-workers in the 1960s and 1970s confirmed his earlier observations and suspicions that blood protein adsorption involved a hierarchical series of collision, adsorption, and exchange processes. These observations and concepts were confirmed by other scientists and came to be known as 'the Vroman effect'. The core concept of the Vroman effect admits many approaches and over-reaches complex and not fully resolved questions of enzymology, transport phenomena, the statistical mechanics of protein conformation, longrange forces in liquids, and surface physics. This volume contains the presentations from the symposium which was held in honour of the 75th birhday of Dr. Leo Vroman, in Gouda, The Netherlands, and deals with various aspects of the Vroman effect.

Proceedings Of The 2nd European Simulation Congress Sept 9 12 1986 The Park Hotel Antwerp Belgium

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Author : Philippe Geril
language : en
Publisher: VSP
Release Date : 1986

Proceedings Of The 2nd European Simulation Congress Sept 9 12 1986 The Park Hotel Antwerp Belgium written by Philippe Geril and has been published by VSP this book supported file pdf, txt, epub, kindle and other format this book has been release on 1986 with Digital computer simulation categories.

Bionanotechnology

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Author : V. Renugopalakrishnan
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-10-12

Bionanotechnology written by V. Renugopalakrishnan and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-10-12 with Medical categories.

Bionanotechnology is the key integrative technology of the 21st century and aims to use the knowledge, gathered from the natural construction of cellular systems, for the advancement of science and engineering. Investigating the topology and communication processes of cell parts can lead to invention of novel biological devices with exciting applications. Though microscale to nanoscale research offers an excellent space for the development of futuristic technologies, a number of challenges must be overcome. Due to paucity of a dedicated literature on the protein based nanodevices we bring you this monograph that combines collective research works of scientists probing into this fascinating universe of bionanotechnology. The monograph has been written with an aim of surveying engineering design principles of biomolecular nanodevices, prototype nanodevices based on redox proteins, bacteriorhodopsins and natural fibers, and touching upon the future developments in the field.

Adsorption

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Author : Jozsef Toth
language : en
Publisher: CRC Press
Release Date : 2002-05-10

Adsorption written by Jozsef Toth and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002-05-10 with Science categories.

This text offers an overview of the recent theoretical and practical results achieved in gas-solid, liquid-solid and gas-liquid adsorption research.