scholarly journals Wet-spinning of magneto-responsive helical chitosan microfibers

2020 ◽  
Vol 11 ◽  
pp. 991-999
Author(s):  
Dorothea Brüggemann ◽  
Johanna Michel ◽  
Naiana Suter ◽  
Matheus Grande de Aguiar ◽  
Michael Maas
Keyword(s):  
Tissue Engineering ◽  
Magnetic Properties ◽  
Magnetic Nanoparticles ◽  
Mechanical Energy ◽  
Accessible Surface Area ◽  
Wet Spinning ◽  
Helical Structures ◽  
Structural Reinforcement ◽  
Electron Microscopy Analysis ◽  
Accessible Surface

Helical structures can be found in nature at various length scales ranging from the molecular level to the macroscale. Due to their ability to store mechanical energy and to optimize the accessible surface area, helical shapes contribute particularly to motion-driven processes and structural reinforcement. Due to these special features, helical fibers have become highly attractive for biotechnological and tissue engineering applications. However, there are only a few methods available for the production of biocompatible helical microfibers. Given that, we present here a simple technique for the fabrication of helical chitosan microfibers with embedded magnetic nanoparticles. Composite fibers were prepared by wet-spinning and coagulation in an ethanol bath. Thereby, no toxic components were introduced into the wet-spun chitosan fibers. After drying, the helical fibers had a diameter of approximately 130 µm. Scanning electron microscopy analysis of wet-spun helices revealed that the magnetic nanoparticles agglomerated into clusters inside the fiber matrix. The helical constructs exhibited a diameter of approximately 500 µm with one to two windings per millimeter. Due to their ferromagnetic properties they are easily attracted to a permanent magnet. The results from the tensile testing show that the helical chitosan microfibers exhibited an average Young’s modulus of 14 MPa. By taking advantage of the magnetic properties of the feedstock solution, the production of the helical fibers could be automated. The fabrication of the helical fibers was achieved by utilizing the magnetic properties of the feedstock solution and winding the emerging fiber around a rotating magnetic collector needle upon coagulation. In summary, our helical chitosan microfibers are very attractive for future use in magnetic tissue engineering or for the development of biocompatible actuator systems.

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

scholarly journals An automated protocol for modelling peptide substrates to proteases

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rodrigo Ochoa ◽  
Mikhail Magnitov ◽  
Roman A. Laskowski ◽  
Pilar Cossio ◽  
Janet M. Thornton
Keyword(s):  
Substrate Recognition ◽  
Accessible Surface Area ◽  
Conformational Sampling ◽  
Structural Determinants ◽  
Peptide Substrates ◽  
The Family ◽  
Protease Substrate ◽  
Peptide Complexes ◽  
Accessible Surface ◽  
Automated Protocol

Abstract Background Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition. Results As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. Conclusion Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.

scholarly journals Effect of coverage on the magnetic properties of -COOH, -SH, and -NH2 ligand-protected cobalt nanoparticles

Nanoscale ◽  
2021 ◽  
Author(s):  
Barbara Farkas ◽  
Nora Henriette De Leeuw
Keyword(s):  
Magnetic Properties ◽  
Magnetic Nanoparticles ◽  
Cobalt Nanoparticles ◽  
Magnetic Behaviour

Implementation of magnetic nanoparticles in biomedicine requires their passivation, which often comes at a cost of diminished magnetic properties. For the design of nano-agents with targeted magnetic behaviour, it is...

scholarly journals PAMAM dendrimer: a pH-controlled nanosponge

2017 ◽  
Vol 95 (9) ◽  
pp. 991-998 ◽  
Author(s):  
Prabal K. Maiti
Keyword(s):  
Accessible Surface Area ◽  
Pamam Dendrimer ◽  
Low Ph ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Water Molecules ◽  
Accessible Volume ◽  
Accessible Surface ◽  
Solvent Accessible Surface ◽  
Ph Controlled

Using fully atomistic molecular dynamics simulation that are several hundred nanoseconds long, we demonstrate the pH-controlled sponge action of PAMAM dendrimer. We show how at varying pH levels, the PAMAM dendrimer acts as a wet sponge; at neutral or low pH levels, the dendrimer expands noticeably and the interior of the dendrimer opens up to host several hundreds to thousands of water molecules depending on the generation number. Increasing the pH (i.e., going from low pH to high pH) leads to the collapse of the dendrimer size, thereby expelling the inner water, which mimics the ‘sponge’ action. As the dendrimer size swells up at a neutral pH or low pH due to the electrostatic repulsion between the primary and tertiary amines that are protonated at this pH, there is dramatic increase in the available solvent accessible surface area (SASA), as well as solvent accessible volume (SAV).

scholarly journals The Potential of Intrinsically Magnetic Mesenchymal Stem Cells for Tissue Engineering

2018 ◽  
Vol 19 (10) ◽  
pp. 3159 ◽  
Author(s):  
Fransiscus Kerans ◽  
Lisa Lungaro ◽  
Asim Azfer ◽  
Donald Salter
Keyword(s):  
Tissue Engineering ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Magnetic Nanoparticles ◽  
Mammalian Cells ◽  
Cell Tracking ◽  
Magnetic Domain ◽  
Superparamagnetic Iron Oxide ◽  
In Vitro Assays

The magnetization of mesenchymal stem cells (MSC) has the potential to aid tissue engineering approaches by allowing tracking, targeting, and local retention of cells at the site of tissue damage. Commonly used methods for magnetizing cells include optimizing uptake and retention of superparamagnetic iron oxide nanoparticles (SPIONs). These appear to have minimal detrimental effects on the use of MSC function as assessed by in vitro assays. The cellular content of magnetic nanoparticles (MNPs) will, however, decrease with cell proliferation and the longer-term effects on MSC function are not entirely clear. An alternative approach to magnetizing MSCs involves genetic modification by transfection with one or more genes derived from Magnetospirillum magneticum AMB-1, a magnetotactic bacterium that synthesizes single-magnetic domain crystals which are incorporated into magnetosomes. MSCs with either or mms6 and mmsF genes are followed by bio-assimilated synthesis of intracytoplasmic magnetic nanoparticles which can be imaged by magnetic resonance (MR) and which have no deleterious effects on MSC proliferation, migration, or differentiation. The stable transfection of magnetosome-associated genes in MSCs promotes assimilation of magnetic nanoparticle synthesis into mammalian cells with the potential to allow MR-based cell tracking and, through external or internal magnetic targeting approaches, enhanced site-specific retention of cells for tissue engineering.

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/

Sign in / Sign up

Export Citation Format

Share Document