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Sharma AD, Grewal RK, Gorle S, Cuspoca AF, Kaushik V, Rajjak Shaikh A, Cavallo L, Chawla M. T cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach. J Biomol Struct Dyn 2024; 42:4937-4955. [PMID: 37382214 DOI: 10.1080/07391102.2023.2226721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
Gastrointestinal diarrhea is majorly caused by the rotavirus (RV) in the children who generally are under the age group of 5 years. WHO estimates that ∼95% of the children contract RV infection, by this age. The disease is highly contagious; notably in many cases, it is proven fatal with high mortality rates especially in the developing countries. In India alone, an estimated 145,000 yearly deaths occurs due to RV related gastrointestinal diarrhea. WHO pre-qualified vaccines that are available for RV are all live attenuated vaccines with modest efficacy range between 40 and 60%. Further, the risk of intussusceptions has been reported in some children on RV vaccination. Thus, in a quest to develop alternative candidate to overcome challenges associated with these oral vaccines, we chose immunoinformatics approach to design a multi-epitope vaccine (MEV) while targeting the outer capsid viral proteinsVP4 and VP7 of the neonatal strains of rotavirus. Interestingly, ten epitopes, that is, six CD8+T-cells and four CD4+T-cell epitopes were identified which were predicted to be antigenic, non-allergic, non-toxic and stable. These epitopes were then linked to adjuvants, linkers, and PADRE sequences to create a multi-epitope vaccine for RV. The in silico designed RV-MEV and human TLR5 complex displayed stable interactions during molecular dynamics simulations. Further, the immune simulation studies of RV-MEV corroborated that the vaccine candidate emerges as a promising immunogen. Future investigations while performing in vitro and in vivo analyses with designed RV-MEV construct are highly desirable to warrant the potential of this vaccine candidate in protective immunity against different strains of RVs infecting neonates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arijit Das Sharma
- School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Suresh Gorle
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Andrés Felipe Cuspoca
- Grupo de Investigación Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
- Centro de Atención e Investigación Médica - CAIMED, Chía, Colombia
| | - Vikas Kaushik
- School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Nguyen TL, Samuel Leon Magdaleno J, Rajjak Shaikh A, Choowongkomon K, Li V, Lee Y, Kim H. Designing a multi-epitope candidate vaccine by employing immunoinformatics approaches to control African swine fever spread. J Biomol Struct Dyn 2023; 41:10214-10229. [PMID: 36510707 DOI: 10.1080/07391102.2022.2153922] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
The African swine fever virus has been circulating for decades and is highly infectious, often fatal to farmed and wild pigs. There is currently no approved vaccine or treatment for the disease, making prevention even more difficult. Therefore, vaccine development is necessary and urgent to limit the consequences of ASF and ensure the food chain and sustainability of the swine industry. This research study was conducted to design a multi-epitope vaccine for controlling veterinary diseases caused by the African swine fever virus. We employed the immunoinformatics approaches to reveal 37 epitopes from different viral proteins of ASFV. These epitopes were linked to adjuvants and linkers to form a full-fledged immunogenic vaccine construct. The tertiary structure of the final vaccine was predicted using a deep-learning approach. The molecular docking and molecular dynamics predicted stable interactions between the vaccine and immune receptor TLR5 of Sus scrofa (Pig). The MD simulation studies reflect that the calculated parameters like RMSD, RMSF, number of hydrogen bonds, and finally, the buried interface surface area for the complex remained stable throughout the simulation time. This analysis suggests the stability of interface interactions between the TLR5 and the multi-epitope vaccine construct. Further, the physiochemical analysis demonstrated that our designed vaccine construct was expected to have high stability and prolonged half-life time in mammalian cells. Traditional vaccine design experiments require significant time and financial input from the development stage to the final product. Studies like this can assist in accelerating vaccine development while minimizing the cost.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jorge Samuel Leon Magdaleno
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Vladimir Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Youngho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
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Kumari S, Leon Magdaleno JS, Grewal RK, Narsing Rao MP, Rajjak Shaikh A, Cavallo L, Chawla M, Kumar M. High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics. J Biomol Struct Dyn 2023:1-12. [PMID: 37768075 DOI: 10.1080/07391102.2023.2262600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Kumari
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - Jorge S Leon Magdaleno
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manoj Kumar
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
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Venianakis T, Siskos MG, Papamokos G, Gerothanassis IP. Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT Calculations-Comparison with the Liquid State. Molecules 2023; 28:6144. [PMID: 37630396 PMCID: PMC10459368 DOI: 10.3390/molecules28166144] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Molecular structures, in chloroform and DMSO solution, of the free fatty acids (FFAs) caproleic acid, oleic acid, α-linolenic acid, eicosapentanoic acid (EPA) and docosahexaenoic acid (DHA) are reported with the combined use of NMR and DFT calculations. Variable temperature and concentration chemical shifts of the COOH protons, transient 1D NOE experiments and DFT calculations demonstrate the major contribution of low molecular weight aggregates of dimerized fatty acids through intermolecular hydrogen bond interactions of the carboxylic groups, with parallel and antiparallel interdigitated structures even at the low concentration of 20 mM in CDCl3. For the dimeric DHA, a structural model of an intermolecular hydrogen bond through carboxylic groups and an intermolecular hydrogen bond between the carboxylic group of one molecule and the ω-3 double bond of a second molecule is shown to play a role. In DMSO-d6 solution, NMR and DFT studies show that the carboxylic groups form strong intermolecular hydrogen bond interactions with a single discrete solvation molecule of DMSO. These solvation species form parallel and antiparallel interdigitated structures of low molecular weight, as in chloroform solution. This structural motif, therefore, is an intrinsic property of the FFAs, which is not strongly affected by the length and degree of unsaturation of the chain and the hydrogen bond ability of the solvent.
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Affiliation(s)
| | | | - George Papamokos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.V.); (M.G.S.)
| | - Ioannis P. Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.V.); (M.G.S.)
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Magdaleno JSL, Grewal RK, Medina-Franco JL, Oliva R, Shaikh AR, Cavallo L, Chawla M. Toward α-1,3/4 fucosyltransferases targeted drug discovery: In silico uncovering of promising natural inhibitors of fucosyltransferase 6. J Cell Biochem 2023; 124:1173-1185. [PMID: 37357420 DOI: 10.1002/jcb.30440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
Sialyl Lewis X (sLex ) antigen is a fucosylated cell-surface glycan that is normally involved in cell-cell interactions. The enhanced expression of sLex on cell surface glycans, which is attributed to the upregulation of fucosyltransferase 6 (FUT6), has been implicated in facilitating metastasis in human colorectal, lung, prostate, and oral cancers. The role that the upregulated FUT6 plays in the progression of tumor to malignancy, with reduced survival rates, makes it a potential target for anticancer drugs. Unfortunately, the lack of experimental structures for FUT6 has hampered the design and development of its inhibitors. In this study, we used in silico techniques to identify potential FUT6 inhibitors. We first modeled the three-dimensional structure of human FUT6 using AlphaFold. Then, we screened the natural compound libraries from the COCONUT database to sort out potential natural products (NPs) with best affinity toward the FUT6 model. As a result of these simulations, we identified three NPs for which we predicted binding affinities and interaction patterns quite similar to those we calculated for two experimentally tested FUT6 inhibitors, that is, fucose mimetic-1 and a GDP-triazole derived compound. We also performed molecular dynamics (MD) simulations for the FUT6 complexes with identified NPs, to investigate their stability. Analysis of the MD simulations showed that the identified NPs establish stable contacts with FUT6 under dynamics conditions. On these grounds, the three screened compounds appear as promising natural alternatives to experimentally tested FUT6 synthetic inhibitors, with expected comparable binding affinity. This envisages good prospects for future experimental validation toward FUT6 inhibition.
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Affiliation(s)
- Jorge Samuel Leon Magdaleno
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Ravneet K Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - José L Medina-Franco
- Department of Pharmacy, DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Naples, Italy
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Venianakis T, Siskos M, Papamokos G, Gerothanassis IP. NMR and DFT studies of monounsaturated and ω-3 polyunsaturated free fatty acids in the liquid state reveal a novel atomistic structural model of DHA. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Hognon C, Bignon E, Monari A, Marazzi M, Garcia-Iriepa C. Revealing the Molecular Interactions between Human ACE2 and the Receptor Binding Domain of the SARS-CoV-2 Wild-Type, Alpha and Delta Variants. Int J Mol Sci 2023; 24:ijms24032517. [PMID: 36768842 PMCID: PMC9916449 DOI: 10.3390/ijms24032517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
After a sudden and first spread of the pandemic caused by the novel SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) wild-type strain, mutants have emerged which have been associated with increased infectivity, inducing surges in the contagions. The first of the so-called variants of concerns, was firstly isolated in the United Kingdom and later renamed Alpha variant. Afterwards, in the middle of 2021, a new variant appeared called Delta. The latter is characterized by the presence of point mutations in the Spike protein of SARS-CoV-2, especially in the Receptor Binding Domain (RBD). When in its active conformation, the RBD can interact with the human receptor Angiotensin-Converting Enzyme 2 (ACE2) to allow the entry of the virions into cells. In this contribution, by using extended all-atom molecular dynamic simulations, complemented with machine learning post-processing, we analyze the changes in the molecular interaction network induced by these different strains in comparison with the wild-type. On one hand, although relevant variations are evidenced, only limited changes in the global stability indicators and in the flexibility profiles have been observed. On the other hand, key differences were obtained by tracking hydrophilic and hydrophobic molecular interactions, concerning both positioning at the ACE2/RBD interface and formation/disruption dynamic behavior.
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Affiliation(s)
- Cécilia Hognon
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
| | - Emmanuelle Bignon
- UMR 7019 LPCT, Université de Lorraine and CNRS, F-5400 Nancy, France
| | - Antonio Monari
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
- Correspondence: (M.M.); (C.G.-I.)
| | - Cristina Garcia-Iriepa
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
- Correspondence: (M.M.); (C.G.-I.)
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Ali Z, Goyal A, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural and Energetic Features of Base-Base Stacking Contacts in RNA. J Chem Inf Model 2023; 63:655-669. [PMID: 36635230 DOI: 10.1021/acs.jcim.2c01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ambika Goyal
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
- Binary Star Research Services, LaSalle, OntarioN9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
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Dhotre K, Banerjee A, Dass D, Nema V, Mukherjee A. An In-silico Approach to Design and Validate siRNA against Monkeypox Virus. Curr Pharm Des 2023; 29:3060-3072. [PMID: 38062661 DOI: 10.2174/0113816128275065231103063935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION The monkeypox virus has emerged as an uncommon zoonotic infection. The recent outbreak of MPXV in Europe and abroad in 2022 presented a major threat to individuals at risk. At present, no specific MPXV vaccinations or medications are available. METHODS In this study, we predicted the most effective siRNA against the conserved region of the MPXV and validated the activity by performing molecular docking studies. RESULTS Ultimately, the most efficient siRNA molecule was shortlisted against the envelope protein gene (B6R) based on its toxicity, effectivity, thermodynamic stability, molecular interaction, and molecular dynamics simulations (MD) with the Human Argonaute 2 protein. CONCLUSION Thus, the strategy may offer a platform for the development of potential antiviral RNA therapeutics that target MPXV at the genomic level.
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Affiliation(s)
- Kishore Dhotre
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Anwesha Banerjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Debashree Dass
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Vijay Nema
- Molecular Biology, National AIDS Research Institute, Pune 411026, India
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
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Weigert S, Perez‐Garcia P, Gisdon FJ, Gagsteiger A, Schweinshaut K, Ullmann GM, Chow J, Streit WR, Höcker B. Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes. Protein Sci 2022; 31:e4500. [PMID: 36336469 PMCID: PMC9679969 DOI: 10.1002/pro.4500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.
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Affiliation(s)
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | | | | | | | | | - Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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Chawla M, Kalra K, Cao Z, Cavallo L, Oliva R. Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules. Nucleic Acids Res 2022; 50:11455-11469. [PMID: 36416268 PMCID: PMC9723503 DOI: 10.1093/nar/gkac1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.
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Affiliation(s)
- Mohit Chawla
- Correspondence may also be addressed to Mohit Chawla. ;
| | - Kanav Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Correspondence may also be addressed to Luigi Cavallo. Tel: +966 02 8027566; Fax: +966 02 8021347;
| | - Romina Oliva
- To whom correspondence should be addressed. Tel: +39 081 5476541; Fax: +39 081 5476514;
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Immunoinformatics-Aided Design of a Peptide Based Multiepitope Vaccine Targeting Glycoproteins and Membrane Proteins against Monkeypox Virus. Viruses 2022; 14:v14112374. [PMID: 36366472 PMCID: PMC9693848 DOI: 10.3390/v14112374] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 01/31/2023] Open
Abstract
Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The disease has a case fatality ratio of 3-6% and, recently, a multi-country outbreak of the disease has occurred. The currently available vaccines that have provided immunization against monkeypox are classified as live attenuated vaccinia virus-based vaccines, which pose challenges of safety and efficacy in chronic infections. In this study, we have used an immunoinformatics-aided design of a multi-epitope vaccine (MEV) candidate by targeting monkeypox virus (MPXV) glycoproteins and membrane proteins. From these proteins, seven epitopes (two T-helper cell epitopes, four T-cytotoxic cell epitopes and one linear B cell epitopes) were finally selected and predicted as antigenic, non-allergic, interferon-γ activating and non-toxic. These epitopes were linked to adjuvants to design a non-allergic and antigenic candidate MPXV-MEV. Further, molecular docking and molecular dynamics simulations predicted stable interactions between predicted MEV and human receptor TLR5. Finally, the immune-simulation analysis showed that the candidate MPXV-MEV could elicit a human immune response. The results obtained from these in silico experiments are promising but require further validation through additional in vivo experiments.
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Exploration of supramolecular and theoretical aspects of two new Cu(II) complexes: On the importance of lone pair···π(chelate ring) and π···π(chelate ring) interactions. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Kaushik V, Jain P, Akhtar N, Joshi A, Gupta LR, Grewal RK, Oliva R, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics-Aided Design and In Vivo Validation of a Peptide-Based Multiepitope Vaccine Targeting Canine Circovirus. ACS Pharmacol Transl Sci 2022. [DOI: 10.1021/acsptsci.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Pankaj Jain
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Nahid Akhtar
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Kaushik V, G SK, Gupta LR, Kalra U, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics Aided Design and In-Vivo Validation of a Cross-Reactive Peptide Based Multi-Epitope Vaccine Targeting Multiple Serotypes of Dengue Virus. Front Immunol 2022; 13:865180. [PMID: 35799781 PMCID: PMC9254734 DOI: 10.3389/fimmu.2022.865180] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/05/2022] [Indexed: 02/03/2023] Open
Abstract
Dengue virus (DENV) is an arboviral disease affecting more than 400 million people annually. Only a single vaccine formulation is available commercially and many others are still under clinical trials. Despite all the efforts in vaccine designing, the improvement in vaccine formulation against DENV is very much needed. In this study, we used a roboust immunoinformatics approach, targeting all the four serotypes of DENV to design a multi-epitope vaccine. A total of 13501 MHC II binding CD4+ epitope peptides were predicted from polyprotein sequences of four dengue virus serotypes. Among them, ten conserved epitope peptides that were interferon-inducing were selected and found to be conserved among all the four dengue serotypes. The vaccine was formulated using antigenic, non-toxic and conserved multi epitopes discovered in the in-silico study. Further, the molecular docking and molecular dynamics predicted stable interactions between predicted vaccine and immune receptor, TLR-5. Finally, one of the mapped epitope peptides was synthesized for the validation of antigenicity and antibody production ability where the in-vivo tests on rabbit model was conducted. Our in-vivo analysis clearly indicate that the imunogen designed in this study could stimulate the production of antibodies which further suggest that the vaccine designed possesses good immunogenicity.
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Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Sunil Krishnan G
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Utkarsh Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, India
- Department of Data Science, Innopolis University, Innopolis, Russia
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, India
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
| | - Luigi Cavallo
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
| | - Mohit Chawla
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
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Zhang W, Li Z, Sun Y, Cui P, Liang J, Xing Q, Wu J, Xu Y, Zhang W, Zhang Y, He L, Gao N. Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides. Emerg Microbes Infect 2021; 11:293-305. [PMID: 34935599 PMCID: PMC8786254 DOI: 10.1080/22221751.2021.2022439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis (Mtb). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with D. radiodurans (Dra) ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for Mtb remains elusive since the Mtb ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the Mtb ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 (E. coli numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel syn-conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C–H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.
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Affiliation(s)
- Wen Zhang
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - ZhiFei Li
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.,China National Center for Biotechnology Development. 10039, Beijing, China
| | - Yufan Sun
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Peng Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jianhua Liang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Qinghe Xing
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jing Wu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ying Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China.,State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Lin He
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Bio-X Institute, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
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Abstract
Biochar is a porous material obtained by biomass thermal degradation in oxygen-starved conditions. It is nowadays applied in many fields. For instance, it is used to synthesize new materials for environmental remediation, catalysis, animal feeding, adsorbent for smells, etc. In the last decades, biochar has been applied also to soils due to its beneficial effects on soil structure, pH, soil organic carbon content, and stability, and, therefore, soil fertility. In addition, this carbonaceous material shows high chemical stability. Once applied to soil it maintains its nature for centuries. Consequently, it can be considered a sink to store atmospheric carbon dioxide in soils, thereby mitigating the effects of global climatic changes. The literature contains plenty of papers dealing with biochar’s environmental effects. However, a discrepancy exists between studies dealing with biochar applications and those dealing with the physical-chemistry behind biochar behavior. On the one hand, the impression is that most of the papers where biochar is tested in soils are based on trial-and-error procedures. Sometimes these give positive results, sometimes not. Consequently, it appears that the scientific world is divided into two factions: either supporters or detractors. On the other hand, studies dealing with biochar’s physical-chemistry do not appear helpful in settling the factions’ problem. This review paper aims at collecting all the information on physical-chemistry of biochar and to use it to explain biochar’s role in different fields of application.
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Chawla M, Gorle S, Shaikh AR, Oliva R, Cavallo L. Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study. Comput Struct Biotechnol J 2021; 19:1312-1324. [PMID: 33738080 PMCID: PMC7940798 DOI: 10.1016/j.csbj.2021.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abdul Rajjak Shaikh
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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H-Bonds, π-Stacking and (Water)O-H/π Interactions in (µ4-EDTA)Bis(Imidazole) Dicopper(II) Dihydrate. CRYSTALS 2021. [DOI: 10.3390/cryst11010048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We synthesized and studied the polymeric compound {[Cu2(µ4-EDTA)(Him)2] 2H2O}n (1). The single-crystal structure is reported along with an in depth characterization of its thermal stability (TGA), spectral properties (FT-IR, Vis-UV and RSE), and magnetic behavior. The crystal consists of infinite 2D-networks built by centrosymmetric dinuclear motifs, constructed by means of a bridging anti,syn-carboxylate group from each asymmetric unit. Each layer guides Him ligands toward their external faces. They are connected by intermolecular (Him)N-H···O(carboxylate) bonds and antiparallel π–π stacking between symmetry related pairs of Him ligands, and then pillared in a 3D-network with parallel channels, where disordered water molecules are guested. About half of the labile water is lost from these channels over a wide temperature range (r.t. to 210 °C) before the other one, most strongly retained by the cooperating action of (water)O1-H(1A)···O(carboxylate) and (water) O1-H(1B)···π(Him) interactions. The latter is lost when organic ligands start to burn. ESR spectra and magnetic measurements indicated that symmetry related Cu(II) centers connected by the bridging carboxylate groups behave magnetically not equivalently, enabling an exchange interaction larger than their individual Zeeman energies.
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Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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Salsbury AM, Lemkul JA. Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics. Curr Opin Struct Biol 2020; 67:9-17. [PMID: 32950937 DOI: 10.1016/j.sbi.2020.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 01/24/2023]
Abstract
Nucleic acids play critical roles in carrying genetic information, participating in catalysis, and preserving chromosomal structure. Despite over a century of study, efforts to understand the dynamics and structure-function relationships of DNA and RNA at the atomic level are still ongoing. Molecular dynamics (MD) simulations augment experiments by providing atomistic resolution and quantitative relationships between structure and conformational energy. Steady advancements in computer hardware, software, and atomistic force fields (FFs) over 40 years have facilitated new discoveries. Here, we review nucleic acid FF development with emphasis on recent refinements that have improved descriptions of important nucleic acid properties. We then discuss several key examples of successes and challenges in modeling nucleic acid structure and dynamics using the latest FFs.
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Affiliation(s)
- Alexa M Salsbury
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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