Molecular Understanding of Conformational Dynamics of a Fibronectin Module on Rutile (110) Surface

Wu, Congcong; Chen, Mingjun; Cheng, Xing

doi:10.1021/la103010c

Cited by 30 publications

(30 citation statements)

References 45 publications

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“…The grounded flat copper collection plate was kept at a distance of 25 cm from the charged needle tip. A syringe pump (Braintree Scientific Co., Braintree, MA) was used to feed polymer solution into the needle at a feed rate of 0.05 mL min 21 .…”

Section: Scaffold Electrospinningmentioning

confidence: 99%

“…Before performing the MD simulation, each system is optimized using Smart algorithm which is a cascade of the steepest descent, adopted basis Newton-Raphson, and quasi-Newton method. Ewald is the summation method used for electrostatic interactions with accuracy of 0.001 kcal mol 21 , and for Van der Waals an atom-based summation is used with truncation of atoms, further than the cutoff distance of 12.5 Å. All the polymer surface atoms are fixed while the protein can move freely.…”

Section: Simulationsmentioning

confidence: 99%

See 1 more Smart Citation

Fibronectin adsorption on functionalized electrospun polycaprolactone scaffolds: Experimental and molecular dynamics studies

Regis

Youssefian

Jassal

et al. 2013

J Biomedical Materials Res

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Designing scaffolds to modulate protein adsorption is a key to building advanced scaffolds for tissue regeneration. Protein adsorption to tissue engineering scaffolds is critical in early cell attachment, survival, and eventual proliferation. The goal of this study is to examine the effect of functionalization on fibronectin adsorption to electrospun polycaprolactone (PCL) scaffolds through experimentation using fluorescently labeled fibronectin and to couple this experimental data with analysis of interaction energies obtained through molecular dynamics (MD) simulations to develop a better understanding of the adsorption process. This study is the first to analyze and compare experimental and MD simulation results of fibronectin adsorption on functionalized electrospun PCL scaffolds. Electrospun nanofiber PCL scaffolds were treated with either 1 N NaOH (hydrolyzed) or 46% hexamethylenediamine (HMD) (aminated) solution to be compared with untreated (control) scaffolds. We found that aminated PCL scaffolds experimentally adsorbed more fibronectin than control scaffolds, whereas hydrolyzed scaffolds showed decreased adsorption. MD simulations carried out with NVT ensemble at a temperature of 310 K indicated a higher work of adhesion for both functionalized scaffolds over control. Also, the simulations revealed different conformations of fibronectin on each scaffold type after adsorption, with the arginine-glycine-aspartic acid sequence appearing most accessible on the aminated scaffolds. This suggests that functionalization affects not only the quantity of protein that will adsorb on a scaffold but how it attaches as well, which could affect subsequent cell attachment.

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Section: Scaffold Electrospinningmentioning

confidence: 99%

Section: Simulationsmentioning

confidence: 99%

Fibronectin adsorption on functionalized electrospun polycaprolactone scaffolds: Experimental and molecular dynamics studies

Regis

Youssefian

Jassal

et al. 2013

J Biomedical Materials Res

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show abstract

“…21−23 The effect of surface defects on protein adsorption behavior could be particularly important because the surface topology may affect the biological activity of adsorbed proteins. 24,25 Protein−surface interactions are a fundamental issue in various fields and devices. The orientation of an adsorbed protein on a medical device, for example, greatly determines the activity of the protein.…”

Section: Introductionmentioning

confidence: 99%

Replica-Exchange Molecular Dynamics Simulation of Basic Fibroblast Growth Factor Adsorption on Hydroxyapatite

Liao

Jian

2014

J. Phys. Chem. B

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The adsorption of basic fibroblast growth factor (bFGF) on the hydroxyapatite (001) surface was investigated by a combination of replica-exchange molecular dynamics (REMD) and conventional molecular dynamics (CMD) methods. In CMD, the protein cannot readily cross the surface water layer, whereas in REMD, the protein can cross the adsorption barrier from the surface water layer and go through weak, medium, then strong adsorption states with three energetically preferred configurations: heparin-binding-up (HP-up), heparin-binding-middle (HP-middle), and heparin-binding-down (HP-down). The HP-middle orientation, with the strongest adsorption energy (-1149 ± 40 kJ·mol(-1)), has the largest adsorption population (52.1-52.6%) and exhibits the largest conformational charge (RMSD of 0.26 ± 0.01 nm) among the three orientations. The HP-down and HP-up orientations, with smaller adsorption energies of -1022 ± 55 and -894 ± 70 kJ·mol(-1), respectively, have smaller adsorption populations of 27.4-27.7% and 19.7-20.5% and present smaller RMSD values of 0.21 ± 0.01 and 0.19 ± 0.01 nm, respectively. The convergent distribution indicates that nearly half of the population (in the HP-middle orientation) will support both FGF/FGFR and DGR-integrin signaling and another half (in the HP-up and HP-down orientations) will support DGR-integrin signaling. The major population (~80%) has the protein dipole directed outward. In the strong adsorption state, there are usually 2 to 3 basic residues that form the anchoring interactions of 210-332 kJ·mol(-1) per residue or that are accompanied by an acidic residue with an adsorption energy of ~207 kJ·mol(-1). Together, the major bound residues form a triangle or a quadrilateral on the surface and stabilize the adsorption geometrically, which indicates topologic matching between the protein and HAP surfaces.

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“…Other analyses included the general structure of the protein itself, which was characterized by parameters such as the root-mean-square deviation of the adsorbed protein compared to its native structure, the protein's radius of gyration, and the orientation of the protein's dipole moment with respect to the surface plane. Others have investigated the influence of adsorption on the structure and orientation of the arginine-glycine-aspartic acid (RGD) loop of fibronectin on various types of surfaces as an approach to assess the availability of this bioactive site for cell-receptor binding [74,75]. …”

Section: Methodsmentioning

confidence: 99%

Perspectives on the simulation of protein–surface interactions using empirical force field methods

Latour

2014

Colloids and Surfaces B: Biointerfaces

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Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation.

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Molecular Understanding of Conformational Dynamics of a Fibronectin Module on Rutile (110) Surface

Cited by 30 publications

References 45 publications

Fibronectin adsorption on functionalized electrospun polycaprolactone scaffolds: Experimental and molecular dynamics studies

Fibronectin adsorption on functionalized electrospun polycaprolactone scaffolds: Experimental and molecular dynamics studies

Replica-Exchange Molecular Dynamics Simulation of Basic Fibroblast Growth Factor Adsorption on Hydroxyapatite

Perspectives on the simulation of protein–surface interactions using empirical force field methods

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