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Eskandari S, Rezayof A, Asghari SM, Hashemizadeh S. Neurobiochemical characteristics of arginine-rich peptides explain their potential therapeutic efficacy in neurodegenerative diseases. Neuropeptides 2023; 101:102356. [PMID: 37390744 DOI: 10.1016/j.npep.2023.102356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Neurodegenerative diseases, including Alzheimer̕ s disease (AD), Parkinson̕ s disease (PD), Huntington̕ s disease (HD), and Amyotrophic Lateral Sclerosis (ALS) require special attention to find new potential treatment methods. This review aims to summarize the current knowledge of the relationship between the biochemical properties of arginine-rich peptides (ARPs) and their neuroprotective effects to deal with the harmful effects of risk factors. It seems that ARPs have portrayed a promising and fantastic landscape for treating neurodegeneration-associated disorders. With multimodal mechanisms of action, ARPs play various unprecedented roles, including as the novel delivery platforms for entering the central nervous system (CNS), the potent antagonists for calcium influx, the invader molecules for targeting mitochondria, and the protein stabilizers. Interestingly, these peptides inhibit the proteolytic enzymes and block protein aggregation to induce pro-survival signaling pathways. ARPs also serve as the scavengers of toxic molecules and the reducers of oxidative stress agents. They also have anti-inflammatory, antimicrobial, and anti-cancer properties. Moreover, by providing an efficient nucleic acid delivery system, ARPs can play an essential role in developing various fields, including gene vaccines, gene therapy, gene editing, and imaging. ARP agents and ARP/cargo therapeutics can be raised as an emergent class of neurotherapeutics for neurodegeneration. Part of the aim of this review is to present recent advances in treating neurodegenerative diseases using ARPs as an emerging and powerful therapeutic tool. The applications and progress of ARPs-based nucleic acid delivery systems have also been discussed to highlight their usefulness as a broad-acting class of drugs.
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Affiliation(s)
- Sedigheh Eskandari
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ameneh Rezayof
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - S Mohsen Asghari
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
| | - Shiva Hashemizadeh
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, IPM, Tehran, Iran
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2
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Bono N, Coloma Smith B, Moreschi F, Redaelli A, Gautieri A, Candiani G. In silico prediction of the in vitro behavior of polymeric gene delivery vectors. NANOSCALE 2021; 13:8333-8342. [PMID: 33900339 DOI: 10.1039/d0nr09052b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-viral gene delivery vectors have increasingly come under the spotlight, but their performaces are still far from being satisfactory. Therefore, there is an urgent need for forecasting tools and screening methods to enable the development of ever more effective transfectants. Here, coarse-grained (CG) models of gold standard transfectant poly(ethylene imine)s (PEIs) have been profitably used to investigate and highlight the effect of experimentally-relevant parameters, namely molecular weight (2 vs. 10 kDa) and topologies (linear vs. branched), protonation state, and ammine-to-phosphate ratios (N/Ps), on the complexation and the gene silencing efficiency of siRNA molecules. The results from the in vitro screening of cationic polymers and conditions were used to validate the in silico platform that we developed, such that the hits which came out of the CG models were of high practical relevance. We show that our in silico platform enables to foresee the most suitable conditions for the complexation of relevant siRNA-polycation assemblies, thereby providing a reliable predictive tool to test bench transfectants in silico, and foster the design and development of gene delivery vectors.
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Affiliation(s)
- Nina Bono
- GenT LΛB, Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131 Milan, Italy.
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Gallops CE, Ziebarth JD, Wang Y. Coarse-grained Simulations of the Impact of Chain Length and Stiffness on the Formation and Aggregation of Polyelectrolyte Complexes. MACROMOL THEOR SIMUL 2020; 29:2000015. [PMID: 36117803 PMCID: PMC9480279 DOI: 10.1002/mats.202000015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 09/05/2024]
Abstract
Polyelectrolyte complexes formed from nucleic acids and synthetic polycations have been studied because of their potential in gene delivery. Coarse-grained molecular dynamics simulations are performed to examine the impact of chain length and polyanion stiffness on polyplex formation and aggregation. Polyplexes containing single polyanion chain fall into three structural regimes depending on polyanion stiffness: flexible polyanions form collapsed complexes, semiflexible polyanions form various morphologies including toroids and hairpins, and stiff polyanions form rod-like structures. Polyplex size generally decreases as polycation length increases. Aggregation (i.e., formation of complexes containing multiple polyanions) is observed in some simulations containing multiple polyanions and an excess of short polycations. Aggregation is observed to only occur for semiflexible and stiff polyanions and is promoted by shorter polycation lengths. Simulations of short, stiff polyanions condensed by long polycations are used as a model for siRNA gene delivery complexes. These simulations show multiple polyanions are spaced out along the polycation with polyanion-polyanion interactions, usually limited to overlapping chain ends. These structures differ from aggregates of longer polyanions in which the polyanions are packed together in parallel, forming bundles.
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Affiliation(s)
- Caleb E. Gallops
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152
| | - Jesse D. Ziebarth
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Abstract
The phase separation of oppositely charged polyelectrolytes in solution is of current interest. In this work, we study the driving force for polyelectrolyte complexation using molecular dynamics simulations. We calculate the potential of mean force between poly(lysine) and poly(glutamate) oligomers using three different force fields, an atomistic force field and two coarse-grained force fields. There is qualitative agreement between all force fields, i.e., the sign and magnitude of the free energy and the nature of the driving force are similar, which suggests that the molecular nature of water does not play a significant role. For fully charged peptides, we find that the driving force for association is entropic in all cases when small ions either neutralize the poly ions, or are in excess. The removal of all counterions switches the driving force, making complexation energetic. This suggests that the entropy of complexation is dominated by the counterions. When only 6 residues of a 11-mer are charged, however, the driving force is energetic in the abscence of excess salt. The simulations shed insight into the mechanism of complex coacervation and the importance of realistic models for the polyions.
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Affiliation(s)
- Aditya N Singh
- Theoretical Chemistry Institute and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53703 , United States
| | - Arun Yethiraj
- Theoretical Chemistry Institute and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53703 , United States
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de Mello LR, Hamley IW, Castelletto V, Garcia BBM, Han SW, de Oliveira CLP, da Silva ER. Nanoscopic Structure of Complexes Formed between DNA and the Cell-Penetrating Peptide Penetratin. J Phys Chem B 2019; 123:8861-8871. [DOI: 10.1021/acs.jpcb.9b05512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Ian William Hamley
- Department of Chemistry, University of Reading, Reading RGD 6AD, United Kingdom
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Reading RGD 6AD, United Kingdom
| | | | - Sang Won Han
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
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Cardoso S, de Alcântara Pessoa Filho P, Sousa F, Rodrigues Azzoni A. Arginine and di-arginine ligands for plasmid DNA purification using negative chromatography. Sep Purif Technol 2018. [DOI: 10.1016/j.seppur.2018.03.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Arginine homopeptides for plasmid DNA purification using monolithic supports. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1087-1088:149-157. [DOI: 10.1016/j.jchromb.2018.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 12/15/2022]
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Cooper BM, Putnam D. Polymers for siRNA Delivery: A Critical Assessment of Current Technology Prospects for Clinical Application. ACS Biomater Sci Eng 2016; 2:1837-1850. [PMID: 33440520 DOI: 10.1021/acsbiomaterials.6b00363] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The number of polymer-based vectors for siRNA delivery in clinical trials lags behind other delivery strategies; however, the molecular architectures and chemical compositions available to polymers make them attractive candidates for further exploration. Polymer vectors are extensively investigated in academic laboratories worldwide with fundamental progress having recently been made in the areas of high-throughput screening, synthetic methods, cellular internalization, endosomal escape and computational prediction and analysis. This review assesses recent advances within the field and highlights relevant developments from within the complementary fields of nanotechnology and protein chemistry with the intent to propose future work that addresses key gaps within the current body of knowledge, potentially advancing the development of the next generation of polymeric vectors.
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Affiliation(s)
- Bailey M Cooper
- Meinig School of Biomedical Engineering and ‡Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - David Putnam
- Meinig School of Biomedical Engineering and Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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Yao C, Liu J, Wu X, Tai Z, Gao Y, Zhu Q, Li J, Zhang L, Hu C, Gu F, Gao J, Gao S. Reducible self-assembling cationic polypeptide-based micelles mediate co-delivery of doxorubicin and microRNA-34a for androgen-independent prostate cancer therapy. J Control Release 2016; 232:203-14. [DOI: 10.1016/j.jconrel.2016.04.034] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/30/2016] [Accepted: 04/23/2016] [Indexed: 01/04/2023]
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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Uusitalo JJ, Ingólfsson HI, Akhshi P, Tieleman DP, Marrink SJ. Martini Coarse-Grained Force Field: Extension to DNA. J Chem Theory Comput 2015; 11:3932-45. [PMID: 26574472 DOI: 10.1021/acs.jctc.5b00286] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base-base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.
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Affiliation(s)
- Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Parisa Akhshi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Tai Z, Wang X, Tian J, Gao Y, Zhang L, Yao C, Wu X, Zhang W, Zhu Q, Gao S. Biodegradable Stearylated Peptide with Internal Disulfide Bonds for Efficient Delivery of siRNA In Vitro and In Vivo. Biomacromolecules 2015; 16:1119-30. [PMID: 25686200 DOI: 10.1021/bm501777a] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zongguang Tai
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Xiaoyu Wang
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Jing Tian
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Yuan Gao
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Lijuan Zhang
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Chong Yao
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Xin Wu
- Department
of Pharmaceutics, Shanghai First People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Wei Zhang
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Quangang Zhu
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
- Department
of Pharmacy, Yueyang Hospital of Integrated Traditional Chinese and
Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Shen Gao
- Department
of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
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Lee H, Jeon TJ. The binding and insertion of imidazolium-based ionic surfactants into lipid bilayers: the effects of the surfactant size and salt concentration. Phys Chem Chem Phys 2015; 17:5725-33. [DOI: 10.1039/c4cp05537c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Imidazolium-based ionic surfactants with hydrocarbon tails of different sizes were simulated with lipid bilayers at different salt concentrations.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering
- Dankook University
- Yongin
- South Korea
| | - Tae-Joon Jeon
- Department of Biological Engineering
- Inha University
- Incheon
- South Korea
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15
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New Techniques to Assess In Vitro Release of siRNA from Nanoscale Polyplexes. Pharm Res 2014; 32:1957-74. [DOI: 10.1007/s11095-014-1589-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/24/2014] [Indexed: 12/29/2022]
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16
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Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J. Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochim Biophys Acta Gen Subj 2014; 1850:1072-1090. [PMID: 25450173 DOI: 10.1016/j.bbagen.2014.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Many prokaryotic genomes comprise Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) offering defense against foreign nucleic acids. These immune systems are conditioned by the production of small CRISPR-derived RNAs matured from long RNA precursors. This often requires a Csy4 endoribonuclease cleaving the RNA 3'-end. METHODS We report extended explicit solvent molecular dynamic (MD) simulations of Csy4/RNA complex in precursor and product states, based on X-ray structures of product and inactivated precursor (55 simulations; ~3.7μs in total). RESULTS The simulations identify double-protonated His29 and deprotonated terminal phosphate as the likely dominant protonation states consistent with the product structure. We revealed potential substates consistent with Ser148 and His29 acting as the general base and acid, respectively. The Ser148 could be straightforwardly deprotonated through solvent and could without further structural rearrangements deprotonate the nucleophile, contrasting similar studies investigating the general base role of nucleobases in ribozymes. We could not locate geometries consistent with His29 acting as general base. However, we caution that the X-ray structures do not always capture the catalytically active geometries and then the reactive structures may be unreachable by the simulation technique. CONCLUSIONS We identified potential catalytic arrangement of the Csy4/RNA complex but we also report limitations of the simulation technique. Even for the dominant protonation state we could not achieve full agreement between the simulations and the structural data. GENERAL SIGNIFICANCE Potential catalytic arrangement of the Csy4/RNA complex is found. Further, we provide unique insights into limitations of simulations of protein/RNA complexes, namely, the influence of the starting experimental structures and force field limitations. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Carolina Estarellas
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
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