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Recent Advances in Biomolecular Recognition

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 July 2020) | Viewed by 17536

Special Issue Editor

Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
Interests: computational analysis of biomolecular sequence, structure, dynamics, and function
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Living cells are extremely complicated systems and comprise hundreds of thousands of different biomolecules that interact with each other to maintain fundamental cellular functions. The disruption of these interactions is frequently linked to various human diseases. The interactions, i.e., biomolecular recognitions, are very specific and are mediated by both polar and nonpolar interactions. These important interactions are also mediated strongly by water.

The goal of this Special Issue is to bring together wet- and dry-lab researchers with common interests in biomolecular recognition and to share their research efforts and to seek collaborations of common interesting questions. A Special Issue with publications from researchers utilizing and developing different experimental and computational methods would certainly help to reveal the strengths and weaknesses of their approaches and enable one to make further improvements. Potential topics may include protein–protein binding; protein–membrane interactions; protein–nucleic acid interactions; interactions with small molecules and drug design; electrostatics, polarization, and solvation in molecular recognition; and mutations in molecular recognition.

Prof. Dr. Ray Luo
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.

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Keywords

  • proteins
  • nucleic acids
  • membrane
  • ligand
  • binding

Published Papers (5 papers)

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Research

14 pages, 2192 KiB  
Article
Discrimination between G/C Binding Sites by Olivomycin A Is Determined by Kinetics of the Drug-DNA Interaction
by Artemy D. Beniaminov, Galina V. Chashchina, Mikhail A. Livshits, Olga I. Kechko, Vladimir A. Mitkevich, Olga K. Mamaeva, Anna N. Tevyashova, Alexander A. Shtil, Anna K. Shchyolkina and Dmitry N. Kaluzhny
Int. J. Mol. Sci. 2020, 21(15), 5299; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155299 - 26 Jul 2020
Cited by 7 | Viewed by 2076
Abstract
Olivomycin A (OA) exerts its cytotoxic potency due to binding to the minor groove of the G/C-rich DNA and interfering with replication and transcription. Screening of the complete set of tetranucleotide G/C sites by electrophoretic mobility gel shift assay (EMSA) revealed that the [...] Read more.
Olivomycin A (OA) exerts its cytotoxic potency due to binding to the minor groove of the G/C-rich DNA and interfering with replication and transcription. Screening of the complete set of tetranucleotide G/C sites by electrophoretic mobility gel shift assay (EMSA) revealed that the sites containing central GC or GG dinucleotides were able to bind OA, whereas the sites with the central CG dinucleotide were not. However, studies of equilibrium OA binding in solution by fluorescence, circular dichroism and isothermal titration calorimetry failed to confirm the sequence preference of OA, indicating instead a similar type of complex and comparable affinity of OA to all G/C binding sites. This discrepancy was resolved by kinetics analysis of the drug–DNA interaction: the dissociation rate significantly differed between SGCS, SGGS and SCGS sites (S stands for G or C), thereby explaining the disintegration of the complexes during EMSA. The functional relevance of the revealed differential kinetics of OA–DNA interaction was demonstrated in an in vitro transcription assay. These findings emphasize the crucial role of kinetics in the mechanism of OA action and provide an important approach to the screening of new drug candidates. Full article
(This article belongs to the Special Issue Recent Advances in Biomolecular Recognition)
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13 pages, 1352 KiB  
Article
Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm
by Aijun Deng, Huan Zhang, Wenyan Wang, Jun Zhang, Dingdong Fan, Peng Chen and Bing Wang
Int. J. Mol. Sci. 2020, 21(7), 2274; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21072274 - 25 Mar 2020
Cited by 45 | Viewed by 4178
Abstract
The study of protein-protein interaction is of great biological significance, and the prediction of protein-protein interaction sites can promote the understanding of cell biological activity and will be helpful for drug development. However, uneven distribution between interaction and non-interaction sites is common because [...] Read more.
The study of protein-protein interaction is of great biological significance, and the prediction of protein-protein interaction sites can promote the understanding of cell biological activity and will be helpful for drug development. However, uneven distribution between interaction and non-interaction sites is common because only a small number of protein interactions have been confirmed by experimental techniques, which greatly affects the predictive capability of computational methods. In this work, two imbalanced data processing strategies based on XGBoost algorithm were proposed to re-balance the original dataset from inherent relationship between positive and negative samples for the prediction of protein-protein interaction sites. Herein, a feature extraction method was applied to represent the protein interaction sites based on evolutionary conservatism of proteins, and the influence of overlapping regions of positive and negative samples was considered in prediction performance. Our method showed good prediction performance, such as prediction accuracy of 0.807 and MCC of 0.614, on an original dataset with 10,455 surface residues but only 2297 interface residues. Experimental results demonstrated the effectiveness of our XGBoost-based method. Full article
(This article belongs to the Special Issue Recent Advances in Biomolecular Recognition)
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19 pages, 3809 KiB  
Article
Insights into Interactions of Flavanones with Target Human Respiratory Syncytial Virus M2-1 Protein from STD-NMR, Fluorescence Spectroscopy, and Computational Simulations
by Hêmily M. R. Piva, Jéssica M. Sá, Artemiza S. Miranda, Ljubica Tasic, Marcelo A. Fossey, Fátima P. Souza and Ícaro P. Caruso
Int. J. Mol. Sci. 2020, 21(6), 2241; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21062241 - 24 Mar 2020
Cited by 12 | Viewed by 3159
Abstract
The human Respiratory Syncytial Virus (hRSV) is the most frequent agent of respiratory infections in infants and children with no currently approved vaccine. The M2-1 protein is an important transcriptional antitermination factor and a potential target for viral replication inhibitor development. Hesperetin [...] Read more.
The human Respiratory Syncytial Virus (hRSV) is the most frequent agent of respiratory infections in infants and children with no currently approved vaccine. The M2-1 protein is an important transcriptional antitermination factor and a potential target for viral replication inhibitor development. Hesperetin (HST) and hesperidin (HSD) are flavonoids from the flavanone group, naturally found in citrus and have, as one of their properties, antiviral activity. The present study reports on the interactions between hRSV M2-1 and these flavanones using experimental techniques in association with computational tools. STD-NMR results showed that HST and HSD bind to M2-1 by positioning their aromatic rings into the target protein binding site. Fluorescence quenching measurements revealed that HST had an interaction affinity greater than HSD towards M2-1. The thermodynamic analysis suggested that hydrogen bonds and van der Waals interactions are important for the molecular stabilization of the complexes. Computational simulations corroborated with the experimental results and indicated that the possible interaction region for the flavonoids is the AMP-binding site in M2-1. Therefore, these results point that HST and HSD bind stably to a critical region in M2-1, which is vital for its biological function, and thus might play a possible role antiviral against hRSV. Full article
(This article belongs to the Special Issue Recent Advances in Biomolecular Recognition)
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18 pages, 3271 KiB  
Article
Experimental Approaches and Computational Modeling of Rat Serum Albumin and Its Interaction with Piperine
by Gabriel Zazeri, Ana Paula Ribeiro Povinelli, Marcelo de Freitas Lima and Marinônio Lopes Cornélio
Int. J. Mol. Sci. 2019, 20(12), 2856; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20122856 - 12 Jun 2019
Cited by 12 | Viewed by 3861
Abstract
The bioactive piperine (1-piperoyl piperidine) compound found in some pepper species (Piper nigrum linn and Piper sarmentosum Roxb) has been shown to have therapeutic properties and to be useful for well-being. The tests used to validate these properties were performed in [...] Read more.
The bioactive piperine (1-piperoyl piperidine) compound found in some pepper species (Piper nigrum linn and Piper sarmentosum Roxb) has been shown to have therapeutic properties and to be useful for well-being. The tests used to validate these properties were performed in vitro or with small rats. However, in all these assays, the molecular approach was absent. Although the first therapeutic trials relied on the use of rats, no proposal was mentioned either experimentally or computationally at the molecular level regarding the interaction between piperine and rat serum albumin (RSA). In the present study, several spectroscopic techniques were employed to characterize rat serum albumin and, aided by computational techniques, the protein modeling was proposed. From the spectroscopic results, it was possible to estimate the binding constant (3.9 × 104 M−1 at 288 K) using the Stern–Volmer model and the number of ligands (three) associated with the protein applying interaction density function model. The Gibbs free energy, an important thermodynamic parameter, was determined (−25 kJ/mol), indicating that the interaction was spontaneous. This important set of experimental results served to parameterize the computational simulations. The results of molecular docking and molecular dynamics matched appropriately made it possible to have detailed microenvironments of RSA accessed by piperine. Full article
(This article belongs to the Special Issue Recent Advances in Biomolecular Recognition)
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14 pages, 2580 KiB  
Article
The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses
by Yuejiao Xian, Chitra B. Karki, Sebastian Miki Silva, Lin Li and Chuan Xiao
Int. J. Mol. Sci. 2019, 20(8), 1876; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20081876 - 16 Apr 2019
Cited by 24 | Viewed by 3657
Abstract
In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so [...] Read more.
In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures. Full article
(This article belongs to the Special Issue Recent Advances in Biomolecular Recognition)
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