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Symmetry
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Symmetry, Molecular Modelling and Simulation in Biochemistry
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Symmetry, Molecular Modelling and Simulation in Biochemistry

A special issue of Symmetry (ISSN 2073-8994). This special issue belongs to the section "Chemistry: Symmetry/Asymmetry".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 6601

Special Issue Editor

Dr. Paulo Martel

E-Mail Website
Guest Editor
University of Algarve, Spain
Interests: bioinformatics; biomedicine; computational biology; biological structure

Special Issue Information

From the first principles of elementary particle physics to the formation of galactic clusters, symmetry principles are essential tools in our understanding of the physical world. Symmetry conservation and symmetry breaking play a crucial role in living systems, from the molecular scale to the macroscopic structure. In molecular modeling, symmetry arguments are crucial for describing the electronic structure of small molecules, the secondary structures of proteins and nucleic acids, and the organization of quaternary structures from monomeric units. Viral capsid structures are examples of highly complex macromolecular structures whose assembly is guided by rigorous symmetry principles. The structures of many enzymes, ion channels, and other biomolecular machines display a high level of symmetry with a definite impact on function. Macromolecular crystals, the source material for X-ray crystallography, are structures with complex symmetries arising from the interplay of the many forces between molecular units. This Special Issue of Symmetry welcomes all contributions to the analysis and application of symmetry in the study of biochemical systems, by means of molecular simulation methods.

Dr. Paulo Martel
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. Symmetry is an international peer-reviewed open access monthly 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 2400 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
  • self-assembly
  • molecular machines
  • symmetry-restrained molecular dynamics
  • crystal growth
  • quaternary structure
  • molecular modelling
  • molecular simulation

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Published Papers (2 papers)

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Research

10 pages, 821 KiB  
Article
Prediction of Partition Coefficients in SDS Micelles by DFT Calculations
by Leila Saranjam, Elisabet Fuguet, Miroslava Nedyalkova, Vasil Simeonov, Francesc Mas and Sergio Madurga
Symmetry 2021, 13(9), 1750; https://doi.org/10.3390/sym13091750 - 19 Sep 2021
Cited by 7 | Viewed by 3040
Abstract
A computational methodology using Density-Functional Theory (DFT) calculations was developed to determine the partition coefficient of a compound in a solution of Sodium Dodecyl Sulfate (SDS) micelles. Different sets of DFT calculations were used to predict the free energy of a set of [...] Read more.
A computational methodology using Density-Functional Theory (DFT) calculations was developed to determine the partition coefficient of a compound in a solution of Sodium Dodecyl Sulfate (SDS) micelles. Different sets of DFT calculations were used to predict the free energy of a set of 63 molecules in 15 different solvents with the purpose of identifying the solvents with similar physicochemical characteristics to the studied micelles. Experimental partition coefficients were obtained from Micellar Electrokinetic Chromatography (MEKC) measurements. The experimental partition coefficient of these molecules was compared with the predicted partition coefficient in heptane/water, cyclohexane/water, N-dodecane/water, pyridine/water, acetic acid/water, decan-1-ol/water, octanol/water, propan-2-ol/water, acetone/water, propan-1-ol/water, methanol/water, 1,2-ethane diol/water, dimethyl sulfoxide/water, formic acid/water, and diethyl sulphide/water systems. It is observed that the combination of pronan-1-ol/water solvent was the most appropriated to estimate the partition coefficient for SDS micelles. This approach allowed us to estimate the partition coefficient orders of magnitude faster than the classical molecular dynamics simulations. The DFT calculations were carried out with the well-known exchange correlation functional B3LYP and with the global hybrid functional M06-2X from the Minnesota functionals with 6-31++G ** basis set. The effect of solvation was considered by the continuum model based on density (SMD). The proposed workflow for the prediction rate of the participation coefficient unveiled the symmetric balance between the experimental data and the computational methods. Full article
(This article belongs to the Special Issue Symmetry, Molecular Modelling and Simulation in Biochemistry)
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17 pages, 5018 KiB  
Article
The Reactivity of Human and Equine Estrogen Quinones towards Purine Nucleosides
by Zsolt Benedek, Peter Girnt and Julianna Olah
Symmetry 2021, 13(9), 1641; https://doi.org/10.3390/sym13091641 - 6 Sep 2021
Viewed by 2549
Abstract
Conjugated estrogen medicines, which are produced from the urine of pregnant mares for the purpose of menopausal hormone replacement therapy (HRT), contain the sulfate conjugates of estrone, equilin, and equilenin in varying proportions. The latter three steroid sex hormones are highly similar in [...] Read more.
Conjugated estrogen medicines, which are produced from the urine of pregnant mares for the purpose of menopausal hormone replacement therapy (HRT), contain the sulfate conjugates of estrone, equilin, and equilenin in varying proportions. The latter three steroid sex hormones are highly similar in molecular structure as they only differ in the degree of unsaturation of the sterane ring “B”: the cyclohexene ring in estrone (which is naturally present in both humans and horses) is replaced by more symmetrical cyclohexadiene and benzene rings in the horse-specific (“equine”) hormones equilin and equilenin, respectively. Though the structure of ring “B” has only moderate influence on the estrogenic activity desired in HRT, it might still significantly affect the reactivity in potential carcinogenic pathways. In the present theoretical study, we focus on the interaction of estrogen orthoquinones, formed upon metabolic oxidation of estrogens in breast cells with purine nucleosides. This multistep process results in a purine base loss in the DNA chain (depurination) and the formation of a “depurinating adduct” from the quinone and the base. The point mutations induced in this manner are suggested to manifest in breast cancer development in the long run. We examine six reactions between deoxyadenosine and deoxyguanosine as nucleosides and estrone-3,4-quinone, equilin-3,4-quinone, and equilenin-3,4-quinone as mutagens. We performed DFT calculations to determine the reaction mechanisms and establish a structure–reactivity relationship between the degree of unsaturation of ring “B” and the expected rate of DNA depurination. As quinones might be present in the cytosol in various protonated forms, we introduce the concept of “effective barriers” to account for the different reactivity and different concentrations of quinone derivatives. According to our results, both equine estrogens have the potential to facilitate depurination as the activation barrier of one of the elementary steps (the initial Michael addition in the case of equilenin and the rearomatization step in the case of equilin) significantly decreases compared to that of estrone. We conclude that the appearance of exogenous equine estrogen quinones due to HRT might increase the risk of depurination-induced breast cancer development compared to the exposure to endogenous estrone metabolites. Still, further studies are required to identify the rate-limiting step of depurination under intracellular conditions to reveal whether the decrease in the barriers affects the overall rate of carcinogenesis. Full article
(This article belongs to the Special Issue Symmetry, Molecular Modelling and Simulation in Biochemistry)
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