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Computer Modeling in Molecular Biophysics and Nanomedical Applications

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 8143

Special Issue Editor

Prof. Dr. Igor Neelov

E-Mail Website
Guest Editor
St. Petersburg National University of Informational Technologies, Mechanics and Optics (ITMO University), Kronverksky pr.49, 197101 St. Petersburg, Russia
Interests: computer simulation of peptides; polysaccharides; artificial branched peptides; protein folding; complexes and conjugates of biological and biocompatible polymers for drug and gene delivery and tissue engineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The next year marks 50 years of molecular dynamics (MD) modeling of polymers and biopolymers, since the first paper on this topic was published in 1972. It was a preprint devoted to the classical molecular dynamics simulation of a linear polymer chain using the bead-rod model (Balabaev N.K., Grivtsov A.G., Shnol E.E. Numerical experiments on modeling the motion of molecules. Part III. Isolated polymer chain. Preprint No. 4 of the Institute of Applied Mathematics of the Academy of Sciences of the USSR, Moscow, 1972, 38 pages. A short version of this work was published later as Balabaev NK, Grivtsov AG, Shnol EE, Numerical modeling of a linear polymer chain. Academy of Sciences of the USSR, 1975, v. 220, No. 5, pp. 1096-1098). Over the next 50 years, the method of MD modeling of polymer and biopolymer systems has become the leading method for the theoretical study of the properties of these systems in silico.

With this Special Issue, we would like to celebrate the 50th anniversary of the molecular dynamics of polymer and biopolymer systems by publishing new articles devoted to both the general problems and results of modeling the structure, mobility, and self-organization of macromolecular systems (including protein folding), and the results of modeling intended for solving applied biomedical problems  (for example, the development of novel carriers for the delivery of drugs and genetic material, for the creation of new biocompatible scaffolds and biocomposites).

We would like to see in this issue not only reviews and articles on the elaboration and application of the classical molecular dynamics method, but also on the elaboration and use of its variants (Rahman–Parinello MD, non-equilibrium MD (NEMD), controlled molecular dynamics (SMD), etc.) as well as papers on other numerical methods for studying the structure, mobility, and self-organization of various polymer and biopolymer molecular systems.

Prof. Dr. Igor Neelov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular dynamics simulation
  • structure and dynamics of biopolymers
  • self-organization of biopolymers and biocompatible polymers
  • complexes, conjugates, and composite material in biomedicine
  • application of biocompatible polymers for drug and gene delivery

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Published Papers (4 papers)

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16 pages, 15074 KiB  
Article
Bovine Serum Albumin Interaction with Polyanionic and Polycationic Brushes: The Case Theoretical Study
by Tatiana O. Salamatova, Ekaterina B. Zhulina and Oleg V. Borisov
Int. J. Mol. Sci. 2023, 24(4), 3395; https://doi.org/10.3390/ijms24043395 - 8 Feb 2023
Cited by 2 | Viewed by 1742
Abstract
We apply a coarse-grained self-consistent field Poisson-Boltzmann framework to study interaction between Bovine Serum Albumin (BSA) and a planar polyelectropyte brush. Both cases of negatively (polyanionic) and positively (polycationic) charged brushes are considered. Our theoretical model accounts for (1) re-ionization free energy of [...] Read more.
We apply a coarse-grained self-consistent field Poisson-Boltzmann framework to study interaction between Bovine Serum Albumin (BSA) and a planar polyelectropyte brush. Both cases of negatively (polyanionic) and positively (polycationic) charged brushes are considered. Our theoretical model accounts for (1) re-ionization free energy of the amino acid residues upon protein insertion into the brush; (2) osmotic force repelling the protein globule from the brush; (3) hydrophobic interactions between non-polar areas on the globule surface and the brush-forming chains. We demonstrate that calculated position-dependent insertion free energy exhibits different patterns, corresponding to either thermodynamically favourable BSA absorption in the brush or thermodynamically or kinetically hindered absorption (expulsion) depending on the pH and ionic strength of the solution. The theory predicts that due to the re-ionization of BSA within the brush, a polyanionic brush can efficiently absorb BSA over a wider pH range on the “wrong side” of the isoelectric point (IEP) compared to a polycationic brush. The results of our theoretical analysis correlate with available experimental data and thus validate the developed model for prediction of the interaction patterns for various globular proteins with polyelectrolyte brushes. Full article
(This article belongs to the Special Issue Computer Modeling in Molecular Biophysics and Nanomedical Applications)
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21 pages, 863 KiB  
Article
Implicit-Solvent Coarse-Grained Simulations of Linear–Dendritic Block Copolymer Micelles
by Mariano E. Brito, Sofia E. Mikhtaniuk, Igor M. Neelov, Oleg V. Borisov and Christian Holm
Int. J. Mol. Sci. 2023, 24(3), 2763; https://doi.org/10.3390/ijms24032763 - 1 Feb 2023
Cited by 3 | Viewed by 2025
Abstract
The design of nanoassemblies can be conveniently achieved by tuning the strength of the hydrophobic interactions of block copolymers in selective solvents. These block copolymer micelles form supramolecular aggregates, which have attracted great attention in the area of drug delivery and imaging in [...] Read more.
The design of nanoassemblies can be conveniently achieved by tuning the strength of the hydrophobic interactions of block copolymers in selective solvents. These block copolymer micelles form supramolecular aggregates, which have attracted great attention in the area of drug delivery and imaging in biomedicine due to their easy-to-tune properties and straightforward large-scale production. In the present work, we have investigated the micellization process of linear–dendritic block copolymers in order to elucidate the effect of branching on the micellar properties. We focus on block copolymers formed by linear hydrophobic blocks attached to either dendritic neutral or charged hydrophilic blocks. We have implemented a simple protocol for determining the equilibrium micellar size, which permits the study of linear–dendritic block copolymers in a wide range of block morphologies in an efficient and parallelizable manner. We have explored the impact of different topological and charge properties of the hydrophilic blocks on the equilibrium micellar properties and compared them to predictions from self-consistent field theory and scaling theory. We have found that, at higher degrees of branching in the corona and for short polymer chains, excluded volume interactions strongly influence the micellar aggregation as well as their effective charge. Full article
(This article belongs to the Special Issue Computer Modeling in Molecular Biophysics and Nanomedical Applications)
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20 pages, 4237 KiB  
Article
Hybrid Molecules Consisting of Lysine Dendrons with Several Hydrophobic Tails: A SCF Study of Self-Assembling
by Oleg V. Shavykin, Sofia E. Mikhtaniuk, Emil I. Fatullaev, Igor M. Neelov, Frans A. M. Leermakers, Mariano E. Brito, Christian Holm, Oleg V. Borisov and Anatoly A. Darinskii
Int. J. Mol. Sci. 2023, 24(3), 2078; https://doi.org/10.3390/ijms24032078 - 20 Jan 2023
Cited by 2 | Viewed by 1858
Abstract
In this article, we used the numerical self-consistent field method of Scheutjens–Fleer to study the micellization of hybrid molecules consisting of one polylysine dendron with charged end groups and several linear hydrophobic tails attached to its root. The main attention was paid to [...] Read more.
In this article, we used the numerical self-consistent field method of Scheutjens–Fleer to study the micellization of hybrid molecules consisting of one polylysine dendron with charged end groups and several linear hydrophobic tails attached to its root. The main attention was paid to spherical micelles and the determination of the range of parameters at which they can appear. A relationship has been established between the size and internal structure of the resulting spherical micelles and the length and number of hydrophobic tails, as well as the number of dendron generations. It is shown that the splitting of the same number of hydrophobic monomers from one long tail into several short tails leads to a decrease in the aggregation number and, accordingly, the number of terminal charges in micelles. At the same time, it was shown that the surface area per dendron does not depend on the number of hydrophobic monomers or tails in the hybrid molecule. The relationship between the structure of hybrid molecules and the electrostatic properties of the resulting micelles has also been studied. It is found that the charge distribution in the corona depends on the number of dendron generations G in the hybrid molecule. For a small number of generations (up to G=3), a standard double electric layer is observed. For a larger number of generations (G=4), the charges of dendrons in the corona are divided into two populations: in the first population, the charges are in the spherical layer near the boundary between the micelle core and shell, and in the second population, the charges are near the periphery of the spherical shell. As a result, a part of the counterions is localized in the wide region between them. These results are of potential interest for the use of spherical dendromicelles as nanocontainers for drug delivery. Full article
(This article belongs to the Special Issue Computer Modeling in Molecular Biophysics and Nanomedical Applications)
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17 pages, 2869 KiB  
Article
Effects of Substitution Ratios of Zinc-Substituted Hydroxyapatite on Adsorption and Desorption Behaviors of Bone Morphogenetic Protein-2
by Baolin Huang, Manchun Li, Hailing Mo, Chuang Chen and Kun Chen
Int. J. Mol. Sci. 2022, 23(17), 10144; https://doi.org/10.3390/ijms231710144 - 4 Sep 2022
Cited by 4 | Viewed by 1833
Abstract
Understanding interactions between bone morphogenetic proteins (BMPs) and biomaterials is of great significance in preserving the structure and bioactivity of BMPs when utilized in clinical applications. Currently, bone morphogenetic protein-2 (BMP-2) is one of the most important growth factors in bone tissue engineering; [...] Read more.
Understanding interactions between bone morphogenetic proteins (BMPs) and biomaterials is of great significance in preserving the structure and bioactivity of BMPs when utilized in clinical applications. Currently, bone morphogenetic protein-2 (BMP-2) is one of the most important growth factors in bone tissue engineering; however, atomistic interactions between BMP-2 and zinc-substituted hydroxyapatite (Zn-HAP, commonly used in artificial bone implants) have not been well clarified until now. Thus, in this work, the interaction energies, binding/debinding states, and molecular structures of BMP-2 upon a series of Zn-HAP surfaces (Zn-HAPs, 1 at%, 2.5 at%, 5 at%, and 10 at% substitution) were investigated by hybrid molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Meanwhile, cellular studies including alkaline phosphatase (ALP) activity and reverse transcription-polymerase chain reaction (RT-PCR) assay were performed to verify the theoretical modeling findings. It was found that, compared to pure HAP, Zn-HAPs exhibited a higher binding affinity of BMP-2 at the adsorption process; meanwhile, the detachment of BMP-2 upon Zn-HAPs was more difficult at the desorption process. In addition, molecular structures of BMP-2 could be well stabilized upon Zn-HAPs, especially for Zn10-HAP (with a 10 at% substitution), which showed both the higher stability of cystine-knots and less change in the secondary structures of BMP-2 than those upon HAP. Cellular studies confirmed that higher ALP activity and osteogenic marker gene expression were achieved upon BMP-2/Zn-HAPs than those upon BMP-2/HAP. These findings verified that Zn-HAPs favor the adsorption of BMP-2 and leverage the bioactivity of BMP-2. Together, this work clarified the interaction mechanisms between BMP-2 and Zn-HAPs at the atom level, which could provide new molecular-level insights into the design of BMP-2-loaded biomaterials for bone tissue engineering. Full article
(This article belongs to the Special Issue Computer Modeling in Molecular Biophysics and Nanomedical Applications)
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