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Polymers
Special Issues
Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials
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Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials

A special issue of Polymers (ISSN 2073-4360). This special issue belongs to the section "Polymer Physics and Theory".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 7933

Special Issue Editors

Dr. Tarsila Gabriel Castro

E-Mail Website
Guest Editor
1. Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
2. LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
Interests: molecular modelling; molecular dynamics simulations; molecular docking; quantum chemistry; computational chemistry; biochemistry; medicinal chemistry; cosmetic and pharmaceutical formulations
Dr. Cristina E. A. Sousa

E-Mail Website
Guest Editor
BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 431, 4249-015 Porto, Portugal
Interests: molecular docking; quantum chemistry; computational chemistry; biochemistry; medicinal chemistry; biosensors; organic synthesis
Dr. Carla Silva

E-Mail Website
Guest Editor
Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
Interests: proteins for surfaces’ functionalization; enzymatic polymerization; enzymatic reactions; deep eutectic solvents for extraction, cosmetics and textile applications
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Today, molecular modelling techniques comprise valuable methods and tools assisting a wide area of knowledge and experiments, both guiding and explaining molecular processes. This Special Issue focuses on the modelling and simulation of biopolymers and biomaterials which represent a breakthrough in the field in terms of describing important biological processes or applications.

Topics of interest range from modelling the building blocks of biopolymers, amino acids and nucleotides, to more complex systems requiring multiscale simulations.

Potential topics include (but are not limited to) the following:

  • Protein folding and stability;
  • Peptidomimetics design;
  • Functional materials;
  • Quantum calculations for biopolymers;
  • Docking in DNA or in proteins/enzymes;
  • Molecular Dynamics Simulations of proteins and biomaterials;
  • MD simulations to estimate physicochemical and rheological properties;
  • Deep Eutectic mixtures as solvents for chemical reactions;
  • Modelling of Deep Eutectic mixtures. 

We hope that this Special Issue can help to promote the use of molecular modelling methods in contemporary research by offering a fresh perspective on its use in biopolymers.

Dr. Tarsila Gabriel Castro
Dr. Cristina E. A. Sousa
Dr. Carla Silva
Guest Editors

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. Polymers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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 simulations
  • structure-function relationship
  • amino acids building blocks
  • peptidomimetics
  • non-canonical amino acids
  • molecules parametrization
  • formulations
  • supramolecular structures
  • biomedical applications
  • multiscale simulations

Published Papers (5 papers)

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Research

12 pages, 2351 KiB  
Article
Statistical Analysis of the Role of Cavity Flexibility in Thermostability of Proteins
by So Yeon Hong, Jihyun Yoon, Young Joo An, Siseon Lee, Haeng-Geun Cha, Ashutosh Pandey, Young Je Yoo and Jeong Chan Joo
Polymers 2024, 16(2), 291; https://doi.org/10.3390/polym16020291 - 21 Jan 2024
Viewed by 983
Abstract
Conventional statistical investigations have primarily focused on the comparison of the simple one-dimensional characteristics of protein cavities, such as number, surface area, and volume. These studies have failed to discern the crucial distinctions in cavity properties between thermophilic and mesophilic proteins that contribute [...] Read more.
Conventional statistical investigations have primarily focused on the comparison of the simple one-dimensional characteristics of protein cavities, such as number, surface area, and volume. These studies have failed to discern the crucial distinctions in cavity properties between thermophilic and mesophilic proteins that contribute to protein thermostability. In this study, the significance of cavity properties, i.e., flexibility and location, in protein thermostability was investigated by comparing structural differences between homologous thermophilic and mesophilic proteins. Three dimensions of protein structure were categorized into three regions (core, boundary, and surface) and a comparative analysis of cavity properties using this structural index was conducted. The statistical analysis revealed that cavity flexibility is closely related to protein thermostability. The core cavities of thermophilic proteins were less flexible than those of mesophilic proteins (averaged B’ factor values, −0.6484 and −0.5111), which might be less deleterious to protein thermostability. Thermophilic proteins exhibited fewer cavities in the boundary and surface regions. Notably, cavities in mesophilic proteins, across all regions, exhibited greater flexibility than those in thermophilic proteins (>95% probability). The increased flexibility of cavities in the boundary and surface regions of mesophilic proteins, as opposed to thermophilic proteins, may compromise stability. Recent protein engineering investigations involving mesophilic xylanase and protease showed results consistent with the findings of this study, suggesting that the manipulation of flexible cavities in the surface region can enhance thermostability. Consequently, our findings suggest that a rational or computational approach to the design of flexible cavities in surface or boundary regions could serve as an effective strategy to enhance the thermostability of mesophilic proteins. Full article
(This article belongs to the Special Issue Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials)
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27 pages, 13986 KiB  
Article
Synthesis of Novel 2,9-Disubstituted-6-morpholino Purine Derivatives Assisted by Virtual Screening and Modelling of Class I PI3K Isoforms
by Vítor Lobo, Ashly Rocha, Tarsila G. Castro and Maria Alice Carvalho
Polymers 2023, 15(7), 1703; https://doi.org/10.3390/polym15071703 - 29 Mar 2023
Cited by 1 | Viewed by 1606
Abstract
The phosphatidylinositol-3 kinase (PI3K) pathway is one of the most frequently activated pathogenic signalling cascades in a wide variety of cancers. In the last 15 years, there has been an increase in the search for selective inhibitors of the four class I isoforms [...] Read more.
The phosphatidylinositol-3 kinase (PI3K) pathway is one of the most frequently activated pathogenic signalling cascades in a wide variety of cancers. In the last 15 years, there has been an increase in the search for selective inhibitors of the four class I isoforms of PI3K, as they demonstrate better specificity and reduced toxicity in comparison to existing inhibitors. A ligand-based and target-based rational drug design strategy was employed to build a virtual library of 105 new compounds. Through this strategy, the four isoforms were compared regarding their activity pocket availability, amino acid sequences, and prone interactions. Additionally, a known active scaffold was used as a molecular base to design new derivatives. The virtual screening of the resultant library toward the four isoforms points to the obtention of 19 selective inhibitors for the PI3Kα and PI3Kγ targets. Three selective ligands, one for α-isoform and two for γ-isoform, present a ∆ (∆Gbinding) equal or greater than 1.5 Kcal/mol and were identified as the most promising candidates. A principal component analysis was used to establish correlations between the affinity data and some of the physicochemical and structural properties of the ligands. The binding modes and interactions established by the selective ligands in the active centre of the α and γ isoforms of PI3K were also investigated. After modelling studies, a synthetic approach to generate selective ligands was developed and applied in synthesising a set of derivatives that were obtained in good to excellent yield. Full article
(This article belongs to the Special Issue Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials)
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13 pages, 18169 KiB  
Article
Mechanical and Gas Barrier Properties of Poly(Lactic Acid) Modified by Blending with Poly(Butylene 2,5-Furandicarboxylate): Based on Molecular Dynamics
by Ye Wang, Gongliang Jiang, Xiancheng Shao, Shikun Pu, Dengbang Jiang and Yaozhong Lan
Polymers 2023, 15(7), 1657; https://doi.org/10.3390/polym15071657 - 27 Mar 2023
Cited by 1 | Viewed by 1263
Abstract
Three blends of Poly(butylene 2,5-furandicarboxylate) (PBF) and Poly(lactic acid) (PLA) blends were modeled using molecular dynamics simulations, with PBF contents of 10%, 20%, and 30%, respectively. The study investigated the compatibilities of the blends, as well as the mechanical and gas barrier properties [...] Read more.
Three blends of Poly(butylene 2,5-furandicarboxylate) (PBF) and Poly(lactic acid) (PLA) blends were modeled using molecular dynamics simulations, with PBF contents of 10%, 20%, and 30%, respectively. The study investigated the compatibilities of the blends, as well as the mechanical and gas barrier properties of the composite systems. The molecular dynamics simulation results show that: (1) PLA and PBF have good compatibility in the blend system; (2) the optimal toughness modification was achieved with a 20% PBF content, resulting in a 17.3% increase in toughness compared to pure PLA; (3) the barrier properties of the blend for O2, CO2, and N2 increased when increasing the PBF content. Compared to pure PLA, the diffusion coefficients of the O2, CO2, and N2 of the blends with 30% PBF decreased by 75%, 122%, and 188%, respectively. Our simulation results are in good agreement with the actual experimental results. Full article
(This article belongs to the Special Issue Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials)
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14 pages, 4147 KiB  
Article
Controllable Production of Natural Silk Nanofibrils for Reinforcing Silk-Based Orthopedic Screws
by Shuqin Yan, Li He, Abdul Moqeet Hai, Zhanao Hu, Renchuan You, Qiang Zhang and David L. Kaplan
Polymers 2023, 15(7), 1645; https://doi.org/10.3390/polym15071645 - 25 Mar 2023
Cited by 2 | Viewed by 1556
Abstract
As a natural high-performance material with a unique hierarchical structure, silk is endowed with superior mechanical properties. However, the current approaches towards producing regenerated silk fibroin (SF) for the preparation of biomedical devices fail to fully exploit the mechanical potential of native silk [...] Read more.
As a natural high-performance material with a unique hierarchical structure, silk is endowed with superior mechanical properties. However, the current approaches towards producing regenerated silk fibroin (SF) for the preparation of biomedical devices fail to fully exploit the mechanical potential of native silk materials. In this study, using a top-down approach, we exfoliated natural silk fibers into silk nanofibrils (SNFs), through the disintegration of interfibrillar binding forces. The as-prepared SNFs were employed to reinforce the regenerated SF solution to fabricate orthopedic screws with outstanding mechanical properties (compression modulus > 1.1 GPa in a hydrated state). Remarkably, these screws exhibited tunable biodegradation and high cytocompatibility. After 28 days of degradation in protease XIV solution, the weight loss of the screw was ~20% of the original weight. The screws offered a favorable microenvironment to human bone marrow mesenchymal stem cell growth and spread as determined by live/dead staining, F-action staining, and Alamar blue staining. The synergy between native structural components (SNFs) and regenerated SF solutions to form bionanocomposites provides a promising design strategy for the fabrication of biomedical devices with improved performance. Full article
(This article belongs to the Special Issue Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials)
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18 pages, 5849 KiB  
Article
Addressing the Structural Organization of Silicone Alternatives in Formulations by Molecular Dynamics Simulations and a Novel Equilibration Protocol
by Tiago Ferreira, Ana Loureiro, Jennifer Noro, Artur Cavaco-Paulo and Tarsila G. Castro
Polymers 2023, 15(4), 796; https://doi.org/10.3390/polym15040796 - 04 Feb 2023
Viewed by 1312
Abstract
The world of cosmetics is an always-evolving field with constant updates on its formulation components. The current reality asks for an ever-increasing need for natural and sustainable replacements for synthetic compounds in all fields of modern consumer products. However, the research and development [...] Read more.
The world of cosmetics is an always-evolving field with constant updates on its formulation components. The current reality asks for an ever-increasing need for natural and sustainable replacements for synthetic compounds in all fields of modern consumer products. However, the research and development stages of finding these alternatives can be an expensive, time-consuming, and often wasteful process that turns this task into a laborious procedure. This study introduces the development of a computational methodology that will aid the research of silicone alternatives, disclosing their structural performance in a formulation. Additionally, an equilibration protocol was developed to measure the distribution and densities of these silicone alternatives to determine how they behave in relation to their counterparts, using molecular dynamics simulations. Two systems were tested, A and B, where the former is composed of one ester (Dipentaerythrityl Hexa C5 Acid Ester) and the latter by an ester combined with an alkane (Triheptanoin and C13-Isoalkane); all three molecules are commercially available and widely used. Both systems were subjected to a 3-step thermal regulation strategy. The systems went through an initial simulation at 25 °C and at 70 °C, then a temperature switch took place (25 °C « 70 °C), then a shock to 200 °C, and finally a Simulated Annealing protocol reaching 250 °C. In the end, all systems converged towards micelle-like structures. These results come to further ascertain the position of computational chemistry and Molecular Dynamics Simulations as an important part of R&D processes in modern sciences and investigation. Full article
(This article belongs to the Special Issue Modelling and Simulation of Proteins, Biopolymers and Biocompatible Materials)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Simulating chainlike structures' constrained motions - application of a sequential algorithm
Authors: Zbigniew Domanski*, Andrzej Z. Grzybowski*
Affiliation: Czestochowa University of Technology
Abstract: Molecule sequencing technologies employ a variety of pore shapes and pore arrangements to prolong translocation times. When simulating a translocation of a chained structure through such constrained geometries a generation of trajectories with a high acceptance ratio is important. In this paper, we focus on how a sequentialization of chain moves, viewed as sequences of allowable steps of consecutive segments, enables one to simulate efficiently a chain’s trajectory in a constrained motion. We survey examples of the applicability of sequential algorithms and discuss possible research goals.

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