Simulating Protein Adsorption for Experimental Comparison


Book Description

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.




Computational Bioengineering


Book Description

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




Modeling Transport and Protein Adsorption in Microfluidic Systems


Book Description

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.




Development of a MATLAB® Model for Estimating the Amount of Protein Adsorption on Nanoparticles Covered with Poly (ethylene Glycol)


Book Description

Targeted drug delivery to cancerous tumors is a promising strategy for the treatment of cancer that mitigates the comprehensive, deleterious effects of current chemotherapy methods. The ability to selectively deliver cancer drugs to solid tumors can be achieved with constructs like micro-bubbles, micro-particles, nanoparticles and micelles that can carry and elute a conjugated drug. Moreover, poly (ethylene glycol) (PEG) can be incorporated into these delivery vehicles to provide a "stealth" coating that prevents the immune system from recognizing and prematurely eliminating them before the drug delivery is complete. The mechanism of immune system avoidance is accomplished when the incorporated PEG chains create a steric hindrance on the surface of the carrier particle that blocks the adsorption of blood plasma proteins onto the particle surface which consequently marks the particle as an antigen that must be removed by the immune system. Mathematically modeling the amount of plasma protein that can adsorb on a carrier particle with a PEG coating offers the benefit of expediting the selection of optimal values for three key parameters of particle fabrication: 1) PEG molecular weight, 2) PEG mass fraction and 3) carrier particle diameter which are essential to the creation of a PEG-coated, carrier particle that will minimize plasma protein adsorption. The basis for this mathematical model is a characteristic formula obtained from the research paper, Gref et al. [11], which describes the surface density threshold (SDT) representing the smallest area between PEG chains on the surface of a nanoparticle that creates the maximal blockage of protein adsorption. This SDT formulation, which contains all three key parameters mentioned above, was used to represent the amount of PEG in terms of molecular weight and mass fraction which was necessary for minimizing protein adsorption on nanoparticles that were also fabricated by the Gref study. In this current study, we use MATLAB® programming to combine the SDT formula and its corresponding experimental data from the Gref study to produced two curve-fit equations (effectively two separate models) that can be used to predict the protein adsorption values that occur for either changing molecular weight of PEG or changing mass fraction of PEG. The simulated values of protein adsorption resultant from variation of the given parameter was then directly compared to the experimental values obtained from Gref et al. in order to evaluate the model accuracy in estimating protein adsorption. The evaluation indicated that the success of the models in estimating protein adsorption was restricted to the parameter it was derived from, either PEG molecular weight or PEG mass fraction. In other words, the model to estimate protein adsorption due to variation of PEG molecular weight was not valid for estimating protein adsorption due to variation of PEG mass fraction and vice versa. Therefore examining changes in a parameter of interest must be done with the appropriate model. The correlation coefficients for the correlations tests showed R2 = 0.997 for PEG molecular weight and R2 = 0.988 for PEG mass fraction. Additionally, the models were not successful in estimating the protein adsorption values that corresponded to the average diameter of the nanoparticles because there was no experimental nanoparticle diameter data from Gref et al. [11] on which to base a curve-fitted estimation model. So, the two models in this study cannot account for a changing particle diameter. The two models developed in this study still require further refinement and validation with more experimental data other than that found in the study by Gref et al. [11]. In that sense, experiments with the parameter of particle diameter can be included to broaden the modeling perspective. Attempts were made to combine the two separate models of PEG molecular weight and PEG mass fraction to find a more universal metric that could establish the optimal parameters of nanoparticle fabrication that would minimize protein adsorption. One metric was to create a ratio of the two parameters and another was to create the product (multiplication) of the two parameters, and then develop a curve fit model for each metric. The results did not show promise because the variation of each metric did not produce a matched correlation to the data. In conclusion, researchers can inexpensively use this modeling tool as a starting point for designing PEG-coated, drug-carrier nanoparticles as it pertains to variation of PEG molecular weight or PEG mass fraction. The modeling presented in this study has extended the framework for simulating plasma protein adsorption on nanoparticles that would significantly inform the fabrication of effective, immuno-evasive, drug-eluting nanoparticles for cancer treatments.




Development and Use of Molecular Simulation Tools to Study the Structure and Function of Biomolecules at Interfaces


Book Description

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.




Adsorption


Book Description

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




Authors and Friends


Book Description




Comprehensive Biomaterials II


Book Description

Comprehensive Biomaterials II, Second Edition, Seven Volume Set brings together the myriad facets of biomaterials into one expertly-written series of edited volumes. Articles address the current status of nearly all biomaterials in the field, their strengths and weaknesses, their future prospects, appropriate analytical methods and testing, device applications and performance, emerging candidate materials as competitors and disruptive technologies, research and development, regulatory management, commercial aspects, and applications, including medical applications. Detailed coverage is given to both new and emerging areas and the latest research in more traditional areas of the field. Particular attention is given to those areas in which major recent developments have taken place. This new edition, with 75% new or updated articles, will provide biomedical scientists in industry, government, academia, and research organizations with an accurate perspective on the field in a manner that is both accessible and thorough. Reviews the current status of nearly all biomaterials in the field by analyzing their strengths and weaknesses, performance, and future prospects Covers all significant emerging technologies in areas such as 3D printing of tissues, organs and scaffolds, cell encapsulation; multimodal delivery, cancer/vaccine - biomaterial applications, neural interface understanding, materials used for in situ imaging, and infection prevention and treatment Effectively describes the many modern aspects of biomaterials from basic science, to clinical applications




Foundations of Molecular Modeling and Simulation


Book Description

This book is a collection of select proceedings of the FOMMS 2015 conference. FOMMS 2015 was the sixth triennial FOMMS conference showcasing applications of theory of computational quantum chemistry, molecular science, and engineering simulation. The theme of the 2015 meeting was on Molecular Modeling and the Materials Genome. This volume comprises chapters on many distinct applications of molecular modeling techniques. The content will be useful to researchers and students alike.