1
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Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
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2
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Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. J Chem Inf Model 2023; 63:2133-2146. [PMID: 36989143 PMCID: PMC10091408 DOI: 10.1021/acs.jcim.2c01438] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Indexed: 03/30/2023]
Abstract
RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson-Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.
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Affiliation(s)
- Petra Kührová
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- IT4Innovations, VSB − Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Poruba, Czech Republic
| | - Jiří Šponer
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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3
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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4
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Caulfield TR, Hayes KE, Qiu Y, Coban M, Seok Oh J, Lane AL, Yoshimitsu T, Hazlehurst L, Copland JA, Tun HW. A Virtual Screening Platform Identifies Chloroethylagelastatin A as a Potential Ribosomal Inhibitor. Biomolecules 2020; 10:E1407. [PMID: 33027969 PMCID: PMC7599554 DOI: 10.3390/biom10101407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 12/03/2022] Open
Abstract
Chloroethylagelastatin A (CEAA) is an analogue of agelastatin A (AA), a natural alkaloid derived from a marine sponge. It is under development for therapeutic use against brain tumors as it has excellent central nervous system (CNS) penetration and pre-clinical therapeutic activity against brain tumors. Recently, AA was shown to inhibit protein synthesis by binding to the ribosomal A-site. In this study, we developed a novel virtual screening platform to perform a comprehensive screening of various AA analogues showing that AA analogues with proven therapeutic activity including CEAA have significant ribosomal binding capacity whereas therapeutically inactive analogues show poor ribosomal binding and revealing structural fingerprint features essential for drug-ribosome interactions. In particular, CEAA was found to have greater ribosomal binding capacity than AA. Biological tests showed that CEAA binds the ribosome and contributes to protein synthesis inhibition. Our findings suggest that CEAA may possess ribosomal inhibitor activity and that our virtual screening platform may be a useful tool in discovery and development of novel ribosomal inhibitors.
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Affiliation(s)
- Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Karen E. Hayes
- Modulation Therapeutics, Inc., Morgantown, WV 26506, USA;
| | - Yushi Qiu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Joon Seok Oh
- Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA;
| | - Amy L. Lane
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA;
| | - Takehiko Yoshimitsu
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan;
| | - Lori Hazlehurst
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, USA;
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
| | - Han W. Tun
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.Q.); (M.C.); (A.L.L.); (J.A.C.)
- Department of Hematology/Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
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5
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Coban MA, Blackburn PR, Whitelaw ML, van Haelst MM, Atwal PS, Caulfield TR. Structural Models for the Dynamic Effects of Loss-of-Function Variants in the Human SIM1 Protein Transcriptional Activation Domain. Biomolecules 2020; 10:biom10091314. [PMID: 32932609 PMCID: PMC7563489 DOI: 10.3390/biom10091314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 02/02/2023] Open
Abstract
Single-minded homologue 1 (SIM1) is a transcription factor with numerous different physiological and developmental functions. SIM1 is a member of the class I basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factor family, that includes several other conserved proteins, including the hypoxia-inducible factors, aryl hydrocarbon receptor, neuronal PAS proteins, and the CLOCK circadian regulator. Recent studies of HIF-a-ARNT and CLOCK-BMAL1 protein complexes have revealed the organization of their bHLH, PASA, and PASB domains and provided insight into how these heterodimeric protein complexes form; however, experimental structures for SIM1 have been lacking. Here, we describe the first full-length atomic structural model for human SIM1 with its binding partner ARNT in a heterodimeric complex and analyze several pathogenic variants utilizing state-of-the-art simulations and algorithms. Using local and global positional deviation metrics, deductions to the structural basis for the individual mutants are addressed in terms of the deleterious structural reorganizations that could alter protein function. We propose new experiments to probe these hypotheses and examine an interesting SIM1 dynamic behavior. The conformational dynamics demonstrates conformational changes on local and global regions that represent a mechanism for dysfunction in variants presented. In addition, we used our ab initio hybrid model for further prediction of variant hotspots that can be engineered to test for counter variant (restoration of wild-type function) or basic research probe.
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Affiliation(s)
- Mathew A. Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Patrick R. Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Murray L. Whitelaw
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide SA 5000, Australia;
| | - Mieke M. van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands;
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Paldeep S. Atwal
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
- Atwal Clinic, Jacksonville, FL 32224, USA
| | - Thomas R. Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA, MN, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Correspondence: ; Tel.: +1-904-953-6072; Fax: +1-904-953-7370
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6
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Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNA Ser3. Biomolecules 2019; 9:biom9110745. [PMID: 31752208 PMCID: PMC6920855 DOI: 10.3390/biom9110745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
In-frame decoding in the ribosome occurs through canonical or wobble Watson-Crick pairing of three mRNA codon bases (a triplet) with a triplet of anticodon bases in tRNA. Departures from the triplet-triplet interaction can result in frameshifting, meaning downstream mRNA codons are then read in a different register. There are many mechanisms to induce frameshifting, and most are insufficiently understood. One previously proposed mechanism is doublet decoding, in which only codon bases 1 and 2 are read by anticodon bases 34 and 35, which would lead to -1 frameshifting. In E. coli, tRNASer3GCU can induce -1 frameshifting at alanine (GCA) codons. The logic of the doublet decoding model is that the Ala codon's GC could pair with the tRNASer3's GC, leaving the third anticodon residue U36 making no interactions with mRNA. Under that model, a U36C mutation would still induce -1 frameshifting, but experiments refute this. We perform all-atom simulations of wild-type tRNASer3, as well as a U36C mutant. Our simulations revealed a hydrogen bond between U36 of the anticodon and G1 of the codon. The U36C mutant cannot make this interaction, as it lacks the hydrogen-bond-donating H3. The simulation thus suggests a novel, non-doublet decoding mechanism for -1 frameshifting by tRNASer3 at Ala codons.
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7
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Padhi S, Pradhan M, Bung N, Roy A, Bulusu G. TPP riboswitch aptamer: Role of Mg 2+ ions, ligand unbinding, and allostery. J Mol Graph Model 2019; 88:282-291. [PMID: 30818079 DOI: 10.1016/j.jmgm.2019.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023]
Abstract
Riboswitches are non-coding RNAs that regulate gene expression in response to the binding of metabolites. Their abundance in bacteria makes them ideal drug targets. The prokaryotic thiamine pyrophosphate (TPP) riboswitch regulates gene expression in a wide range of bacteria by undergoing conformational changes in response to the binding of TPP. Although an experimental structure for the aptamer domain of the riboswitch is now available, details of the conformational changes that occur during the binding of the ligand, and the factors that govern these conformational changes, are still not clear. This study employs microsecond-scale molecular dynamics simulations to provide insights into the functioning of the riboswitch aptamer in atomistic detail. A mechanism for the transmission of conformational changes from the ligand-binding site to the P1 switch helix is proposed. Mg2+ ions in the binding site play a critical role in anchoring the ligand to the riboswitch. Finally, modeling the egress of TPP from the binding site reveals a two-step mechanism for TPP unbinding. Findings from this study can motivate the design of future studies aimed at modulating the activity of this drug target.
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Affiliation(s)
- Siladitya Padhi
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Meenakshi Pradhan
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Navneet Bung
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Arijit Roy
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs - Hyderabad (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad, 500081, India.
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8
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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9
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Ando M, Fiesel FC, Hudec R, Caulfield TR, Ogaki K, Górka-Skoczylas P, Koziorowski D, Friedman A, Chen L, Dawson VL, Dawson TM, Bu G, Ross OA, Wszolek ZK, Springer W. The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity. Mol Neurodegener 2017; 12:32. [PMID: 28438176 PMCID: PMC5404317 DOI: 10.1186/s13024-017-0174-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/14/2017] [Indexed: 01/24/2023] Open
Abstract
Background Mutations in PINK1 and PARKIN are the most common causes of recessive early-onset Parkinson’s disease (EOPD). Together, the mitochondrial ubiquitin (Ub) kinase PINK1 and the cytosolic E3 Ub ligase PARKIN direct a complex regulated, sequential mitochondrial quality control. Thereby, damaged mitochondria are identified and targeted to degradation in order to prevent their accumulation and eventually cell death. Homozygous or compound heterozygous loss of either gene function disrupts this protective pathway, though at different steps and by distinct mechanisms. While structure and function of PARKIN variants have been well studied, PINK1 mutations remain poorly characterized, in particular under endogenous conditions. A better understanding of the exact molecular pathogenic mechanisms underlying the pathogenicity is crucial for rational drug design in the future. Methods Here, we characterized the pathogenicity of the PINK1 p.I368N mutation on the clinical and genetic as well as on the structural and functional level in patients’ fibroblasts and in cell-based, biochemical assays. Results Under endogenous conditions, PINK1 p.I368N is expressed, imported, and N-terminally processed in healthy mitochondria similar to PINK1 wild type (WT). Upon mitochondrial damage, however, full-length PINK1 p.I368N is not sufficiently stabilized on the outer mitochondrial membrane (OMM) resulting in loss of mitochondrial quality control. We found that binding of PINK1 p.I368N to the co-chaperone complex HSP90/CDC37 is reduced and stress-induced interaction with TOM40 of the mitochondrial protein import machinery is abolished. Analysis of a structural PINK1 p.I368N model additionally suggested impairments of Ub kinase activity as the ATP-binding pocket was found deformed and the substrate Ub was slightly misaligned within the active site of the kinase. Functional assays confirmed the lack of Ub kinase activity. Conclusions Here we demonstrated that mutant PINK1 p.I368N can not be stabilized on the OMM upon mitochondrial stress and due to conformational changes in the active site does not exert kinase activity towards Ub. In patients’ fibroblasts, biochemical assays and by structural analyses, we unraveled two pathomechanisms that lead to loss of function upon mutation of p.I368N and highlight potential strategies for future drug development. Electronic supplementary material The online version of this article (doi:10.1186/s13024-017-0174-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maya Ando
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Kotaro Ogaki
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Paulina Górka-Skoczylas
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Warsaw, Poland
| | - Dariusz Koziorowski
- Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Friedman
- Department of Neurology, Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA. .,Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA.
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10
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Kayode O, Wang R, Pendlebury DF, Cohen I, Henin RD, Hockla A, Soares AS, Papo N, Caulfield TR, Radisky ES. An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis. J Biol Chem 2016; 291:26304-26319. [PMID: 27810896 DOI: 10.1074/jbc.m116.758417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/01/2016] [Indexed: 01/13/2023] Open
Abstract
The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.
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Affiliation(s)
| | | | | | - Itay Cohen
- the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | | | | | - Alexei S Soares
- the Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973
| | - Niv Papo
- the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | - Thomas R Caulfield
- Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224,
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11
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Schreck JS, Ouldridge TE, Romano F, Louis AA, Doye JPK. Characterizing the bending and flexibility induced by bulges in DNA duplexes. J Chem Phys 2016; 142:165101. [PMID: 25933790 DOI: 10.1063/1.4917199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures.
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Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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12
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Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. J Phys Chem B 2015; 119:15176-90. [DOI: 10.1021/acs.jpcb.5b08876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Havrila
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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13
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Condon D, Kennedy SD, Mort BC, Kierzek R, Yildirim I, Turner DH. Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. J Chem Theory Comput 2015; 11:2729-2742. [PMID: 26082675 PMCID: PMC4463549 DOI: 10.1021/ct501025q] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Molecular dynamics (MD) simulations for RNA tetramers r(AAAA), r(CAAU), r(GACC), and r(UUUU) are benchmarked against 1H-1H NOESY distances and 3J scalar couplings to test effects of RNA torsion parametrizations. Four different starting structures were used for r(AAAA), r(CAAU), and r(GACC), while five starting structures were used for r(UUUU). On the basis of X-ray structures, criteria are reported for quantifying stacking. The force fields, AMBER ff99, parmbsc0, parm99χ_Yil, ff10, and parmTor, all predict experimentally unobserved stacks and intercalations, e.g., base 1 stacked between bases 3 and 4, and incorrect χ, ϵ, and sugar pucker populations. The intercalated structures are particularly stable, often lasting several microseconds. Parmbsc0, parm99χ_Yil, and ff10 give similar agreement with NMR, but the best agreement is only 46%. Experimentally unobserved intercalations typically are associated with reduced solvent accessible surface area along with amino and hydroxyl hydrogen bonds to phosphate nonbridging oxygens. Results from an extensive set of MD simulations suggest that recent force field parametrizations improve predictions, but further improvements are necessary to provide reasonable agreement with NMR. In particular, intramolecular stacking and hydrogen bonding interactions may not be well balanced with the TIP3P water model. NMR data and the scoring method presented here provide rigorous benchmarks for future changes in force fields and MD methods.
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Affiliation(s)
- David
E. Condon
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Scott D. Kennedy
- Department
of Biochemistry and Biophysics, University
of Rochester, Rochester, New York 14642, United States
| | - Brendan C. Mort
- University
of Rochester Center for Integrated Research Computing, Rochester, New York 14627, United States
| | - Ryszard Kierzek
- Institute
of Bioorganic Chemistry, Polish Academy
of Sciences, 60-704 Poznan, Poland
| | - Ilyas Yildirim
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Douglas H. Turner
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
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14
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Fiesel FC, Caulfield TR, Moussaud-Lamodière EL, Ogaki K, Dourado DFAR, Flores SC, Ross OA, Springer W. Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin. Hum Mutat 2015; 36:774-86. [PMID: 25939424 DOI: 10.1002/humu.22808] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/23/2015] [Indexed: 12/24/2022]
Abstract
Mutations in the PARKIN/PARK2 gene that result in loss-of-function of the encoded, neuroprotective E3 ubiquitin ligase Parkin cause recessive, familial early-onset Parkinson disease. As an increasing number of rare Parkin sequence variants with unclear pathogenicity are identified, structure-function analyses will be critical to determine their disease relevance. Depending on the specific amino acids affected, several distinct pathomechanisms can result in loss of Parkin function. These include disruption of overall Parkin folding, decreased solubility, and protein aggregation. However pathogenic effects can also result from misregulation of Parkin autoinhibition and of its enzymatic functions. In addition, interference of binding to coenzymes, substrates, and adaptor proteins can affect its catalytic activity too. Herein, we have performed a comprehensive structural and functional analysis of 21 PARK2 missense mutations distributed across the individual protein domains. Using this combined approach, we were able to pinpoint some of the pathogenic mechanisms of individual sequence variants. Similar analyses will be critical in gaining a complete understanding of the complex regulations and enzymatic functions of Parkin. These studies will not only highlight the important residues, but will also help to develop novel therapeutics aimed at activating and preserving an active, neuroprotective form of Parkin.
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Affiliation(s)
| | | | | | - Kotaro Ogaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
| | - Daniel F A R Dourado
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Samuel C Flores
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
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15
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Panecka J, Šponer J, Trylska J. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Biochimie 2015; 112:96-110. [PMID: 25748164 DOI: 10.1016/j.biochi.2015.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/23/2015] [Indexed: 01/12/2023]
Abstract
The aminoacyl-tRNA binding site (A-site) is located in helix 44 of small ribosomal subunit. The mobile adenines 1492 and 1493 (Escherichia coli numbering), forming the A-site bulge, act as a functional switch that ensures mRNA decoding accuracy. Structural data on the oligonucleotide models mimicking the ribosomal A-site with sequences corresponding to bacterial and human cytoplasmic sites confirm that this RNA motif forms also without the ribosome context. We performed all-atom molecular dynamics simulations of these crystallographic A-site models to compare their conformational properties. We found that the human A-site bulge is more internally flexible than the bacterial one and has different base pairing preferences, which result in the overall different shapes of these bulges and cation density distributions. Also, in the human A-site model we observed repetitive destacking of A1492, while A1493 was more stably paired than in the bacterial variant. Based on the dynamics of the A-sites we suggest why aminoglycoside antibiotics, which target the bacterial A-site, have lower binding affinities and anti-translational activities toward the human variant.
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Affiliation(s)
- Joanna Panecka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - 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, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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16
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Caulfield TR, Fiesel FC, Moussaud-Lamodière EL, Dourado DFAR, Flores SC, Springer W. Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PLoS Comput Biol 2014; 10:e1003935. [PMID: 25375667 PMCID: PMC4222639 DOI: 10.1371/journal.pcbi.1003935] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/25/2014] [Indexed: 11/19/2022] Open
Abstract
Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal recessive Parkinson's disease. Both gene products, the Ser/Thr kinase PINK1 and the E3 Ubiquitin ligase Parkin, functionally cooperate in a mitochondrial quality control pathway. Upon stress, PINK1 activates Parkin and enables its translocation to and ubiquitination of damaged mitochondria to facilitate their clearance from the cell. Though PINK1-dependent phosphorylation of Ser65 is an important initial step, the molecular mechanisms underlying the activation of Parkin's enzymatic functions remain unclear. Using molecular modeling, we generated a complete structural model of human Parkin at all atom resolution. At steady state, the Ub ligase is maintained inactive in a closed, auto-inhibited conformation that results from intra-molecular interactions. Evidently, Parkin has to undergo major structural rearrangements in order to unleash its catalytic activity. As a spark, we have modeled PINK1-dependent Ser65 phosphorylation in silico and provide the first molecular dynamics simulation of Parkin conformations along a sequential unfolding pathway that could release its intertwined domains and enable its catalytic activity. We combined free (unbiased) molecular dynamics simulation, Monte Carlo algorithms, and minimal-biasing methods with cell-based high content imaging and biochemical assays. Phosphorylation of Ser65 results in widening of a newly defined cleft and dissociation of the regulatory N-terminal UBL domain. This motion propagates through further opening conformations that allow binding of an Ub-loaded E2 co-enzyme. Subsequent spatial reorientation of the catalytic centers of both enzymes might facilitate the transfer of the Ub moiety to charge Parkin. Our structure-function study provides the basis to elucidate regulatory mechanisms and activity of the neuroprotective Parkin. This may open up new avenues for the development of small molecule Parkin activators through targeted drug design. Parkinson's disease (PD) is a devastating neurological condition caused by the selective and progressive degeneration of dopaminergic neurons in the brain. Loss-of-function mutations in the PINK1 or PARKIN genes are the most common causes of recessively inherited PD. Together the encoded proteins coordinate a protective cellular quality control pathway that allows elimination of impaired mitochondria in order to prevent further cellular damage and ultimately death. Although it is known that the kinase PINK1 operates upstream and activates the E3 Ubiquitin ligase Parkin, the molecular mechanisms remain elusive. Here, we combined state-of-the art computational and functional biological methods to demonstrate that Parkin is sequentially activated through PINK1-dependent phosphorylation and subsequent structural rearrangement. The induced motions result in release of Parkin's closed, auto-inhibited conformation to liberate its enzymatic functions. We provide for the first time a complete protein structure of Parkin at an all atom resolution and a comprehensive molecular dynamics simulation of its activation and opening conformations. The generated models will allow uncovering the exact mechanisms of regulation and enzymatic activity of Parkin and potentially the development of novel therapeutics through a structure-function-based drug design.
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Affiliation(s)
- Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
- * E-mail: (TRC); (WS)
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
| | | | - Daniel F. A. R. Dourado
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Samuel C. Flores
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
- Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida, United States of America
- * E-mail: (TRC); (WS)
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17
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Panecka J, Havrila M, Réblová K, Šponer J, Trylska J. Role of S-turn2 in the structure, dynamics, and function of mitochondrial ribosomal A-site. A bioinformatics and molecular dynamics simulation study. J Phys Chem B 2014; 118:6687-701. [PMID: 24845793 DOI: 10.1021/jp5030685] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mRNA decoding site (A-site) in the small ribosomal subunit controls fidelity of the translation process. Here, using molecular dynamics simulations and bioinformatic analyses, we investigated the structural dynamics of the human mitochondrial A-site (native and A1490G mutant) and compared it with the dynamics of the bacterial A-site. We detected and characterized a specific RNA backbone configuration, S-turn2, which occurs in the human mitochondrial but not in the bacterial A-site. Mitochondrial and bacterial A-sites show different propensities to form S-turn2 that may be caused by different base-pairing patterns of the flanking nucleotides. Also, the S-turn2 structural stability observed in the simulations supports higher accuracy and lower speed of mRNA decoding in mitochondria in comparison with bacteria. In the mitochondrial A-site, we observed collective movement of stacked nucleotides A1408·C1409·C1410, which may explain the known differences in aminoglycoside antibiotic binding affinities toward the studied A-site variants.
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Affiliation(s)
- Joanna Panecka
- Department of Biophysics, Institute of Experimental Physics and ∥Centre of New Technologies, University of Warsaw , Żwirki i Wigury 93, 02-089 Warsaw, Poland
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18
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Mundigala H, Michaux JB, Feig AL, Ennifar E, Rueda D. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway. Nucleic Acids Res 2014; 42:7281-9. [PMID: 24813449 PMCID: PMC4066764 DOI: 10.1093/nar/gku332] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The HIV-1 dimerization initiation sequence (DIS) is a conserved palindrome in the apical loop of a conserved hairpin motif in the 5′-untranslated region of its RNA genome. DIS hairpin plays an important role in genome dimerization by forming a ‘kissing complex’ between two complementary hairpins. Understanding the kinetics of this interaction is key to exploiting DIS as a possible human immunodeficiency virus (HIV) drug target. Here, we present a single-molecule Förster resonance energy transfer (smFRET) study of the dimerization reaction kinetics. Our data show the real-time formation and dissociation dynamics of individual kissing complexes, as well as the formation of the mature extended duplex complex that is ultimately required for virion packaging. Interestingly, the single-molecule trajectories reveal the presence of a previously unobserved bent intermediate required for extended duplex formation. The universally conserved A272 is essential for the formation of this intermediate, which is stabilized by Mg2+, but not by K+ cations. We propose a 3D model of a possible bent intermediate and a minimal dimerization pathway consisting of three steps with two obligatory intermediates (kissing complex and bent intermediate) and driven by Mg2+ ions.
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Affiliation(s)
- Hansini Mundigala
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA
| | | | - Andrew L Feig
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA Department of Medicine, Section of Virology, Imperial College, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College, London W12 0NN, UK
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19
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Kruse H, Havrila M, Šponer J. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. J Chem Theory Comput 2014; 10:2615-29. [DOI: 10.1021/ct500183w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Holger Kruse
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
| | - Marek Havrila
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jiřı́ Šponer
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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20
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Abstract
This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.
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Affiliation(s)
- Kristian Rother
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland,
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21
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Havrila M, Réblová K, Zirbel CL, Leontis NB, Šponer J. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop. J Phys Chem B 2013; 117:14302-19. [PMID: 24144333 PMCID: PMC3946555 DOI: 10.1021/jp408530w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Nonisosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. The MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that the inability to form stable cWW geometry is an important factor in the case of the first base pair of the flexible region of the SR motif. A comparison of structural, bioinformatics, SHAPE probing, and MD simulation data reveals that explicit solvent MD simulations neatly reflect the viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Craig L. Zirbel
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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22
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Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
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Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M. Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B 2012; 116:12721-34. [PMID: 22998634 PMCID: PMC3505677 DOI: 10.1021/jp309230v] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Riboswitches often occur in the 5'-untranslated regions of bacterial mRNA where they regulate gene expression. The preQ(1) riboswitch controls the biosynthesis of a hypermodified nucleoside queuosine in response to binding the queuosine metabolic intermediate. Structures of the ligand-bound and ligand-free states of the preQ(1) riboswitch from Thermoanaerobacter tengcongensis were determined recently by X-ray crystallography. We used multiple, microsecond-long molecular dynamics simulations (29 μs in total) to characterize the structural dynamics of preQ(1) riboswitches in both states. We observed different stabilities of the stem in the bound and free states, resulting in different accessibilities of the ribosome-binding site. These differences are related to different stacking interactions between nucleotides of the stem and the associated loop, which itself adopts different conformations in the bound and free states. We suggest that the loop not only serves to bind preQ(1) but also transmits information about ligand binding from the ligand-binding pocket to the stem, which has implications for mRNA accessibility to the ribosome. We explain functional results obscured by a high salt crystallization medium and help to refine regions of disordered electron density, which demonstrates the predictive power of our approach. Besides investigating the functional dynamics of the riboswitch, we have also utilized this unique small folded RNA system for analysis of performance of the RNA force field on the μs time scale. The latest AMBER parmbsc0χ(OL3) RNA force field is capable of providing stable trajectories of the folded molecule on the μs time scale. On the other hand, force fields that are not properly balanced lead to significant structural perturbations on the sub-μs time scale, which could easily lead to inappropriate interpretation of the simulation data.
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Affiliation(s)
- 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
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Petr Sklenovský
- 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
| | - Joseph E. Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Box 712, Rochester, NY 14620, USA
| | - Jiří Šponer
- 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
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- 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
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Kim T, Shapiro BA. The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures. J Biomol Struct Dyn 2012; 31:495-510. [PMID: 22881341 DOI: 10.1080/07391102.2012.706072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The subtype-B monomers of the human immunodeficiency virus type-1 (HIV-1) have experimentally been shown to dimerize at high salt concentration or in the presence of magnesium, while the dimerization of the subtype-A monomers requires magnesium binding at the G273 or G274 phosphate groups regardless of salt concentration. We used explicit solvent molecular dynamics (MD) simulations to investigate the conformational changes in subtype-A and -B monomers in different salt concentrations, and we found that our MD simulation results are consistent with those of experiments. At low salt concentration, hairpin loop structures of both subtypes were deformed and bases in the hairpin loop were turned inside. At high salt concentrations, the subtype-B monomer maintained the hairpin loop shape and most bases in the hairpin loop pointed out, while the subtype-A monomer showed a severe deformation. We also found that the flanking bases in the subtype-B stabilize the hairpin loop, while the flanking base G273 in the subtype-A caused a significant deformation. However, a bound magnesium ion at the G273 or G274 phosphate groups controlled the behavior of the G273 base and prevented the subtype-A monomer from deformation. We also applied restraints to both subtypes to examine the role of high salt concentration or magnesium binding. While restraints were applied, both subtypes at 0 M salt concentration maintained their shapes. However, when restraints were removed, they deformed significantly. Therefore, we suggest that the dimerization of both subtypes requires the proper conformation of the monomers which is induced by the appropriate salt strength and magnesium ion binding.
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Affiliation(s)
- Taejin Kim
- Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick , MD 20872, USA
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25
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Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J Phys Chem B 2012; 116:9899-916. [DOI: 10.1021/jp3014817] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ivana Beššeová
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavlína Košinová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
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26
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Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J. Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J Chem Theory Comput 2012; 8:2506-2520. [PMID: 23197943 PMCID: PMC3506181 DOI: 10.1021/ct300275s] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Refinement of empirical force fields for nucleic acids requires their extensive testing using as wide range of systems as possible. However, finding unambiguous reference data is not easy. In this paper, we analyze four systems which we suggest should be included in standard portfolio of molecules to test nucleic acids force fields, namely, parallel and antiparallel stranded DNA guanine quadruplex stems, RNA quadruplex stem, and Z-DNA. We highlight parameters that should be monitored to assess the force field performance. The work is primarily based on 8.4 μs of 100-250 ns trajectories analyzed in detail followed by 9.6 μs of additional selected back up trajectories that were monitored to verify that the results of the initial analyses are correct. Four versions of the Cornell et al. AMBER force field are tested, including an entirely new parmχ(OL4) variant with χ dihedral specifically reparametrized for DNA molecules containing syn nucleotides. We test also different water models and ion conditions. While improvement for DNA quadruplexes is visible, the force fields still do not fully represent the intricate Z-DNA backbone conformation.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- National Center for Biomolecular Research, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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Réblová K, Šponer J, Lankaš F. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res 2012; 40:6290-303. [PMID: 22451682 PMCID: PMC3401443 DOI: 10.1093/nar/gks258] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/07/2012] [Accepted: 03/07/2012] [Indexed: 01/06/2023] Open
Abstract
The L1 stalk is a key mobile element of the large ribosomal subunit which interacts with tRNA during translocation. Here, we investigate the structure and mechanical properties of the rRNA H76/H75/H79 three-way junction at the base of the L1 stalk from four different prokaryotic organisms. We propose a coarse-grained elastic model and parameterize it using large-scale atomistic molecular dynamics simulations. Global properties of the junction are well described by a model in which the H76 helix is represented by a straight, isotropically flexible elastic rod, while the junction core is represented by an isotropically flexible spherical hinge. Both the core and the helix contribute substantially to the overall H76 bending fluctuations. The presence of wobble pairs in H76 does not induce any increased flexibility or anisotropy to the helix. The half-closed conformation of the L1 stalk seems to be accessible by thermal fluctuations of the junction itself, without any long-range allosteric effects. Bending fluctuations of H76 with a bulge introduced in it suggest a rationale for the precise position of the bulge in eukaryotes. Our elastic model can be generalized to other RNA junctions found in biological systems or in nanotechnology.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Filip Lankaš
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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Bradshaw RT, Aronica PGA, Tate EW, Leatherbarrow RJ, Gould IR. Mutational Locally Enhanced Sampling (MULES) for quantitative prediction of the effects of mutations at protein–protein interfaces. Chem Sci 2012. [DOI: 10.1039/c2sc00895e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Singh A, Sethaphong L, Yingling YG. Interactions of cations with RNA loop-loop complexes. Biophys J 2011; 101:727-35. [PMID: 21806941 DOI: 10.1016/j.bpj.2011.06.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 06/16/2011] [Accepted: 06/21/2011] [Indexed: 10/17/2022] Open
Abstract
RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size.
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Affiliation(s)
- Abhishek Singh
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina, USA
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31
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Cao S, Chen SJ. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA (NEW YORK, N.Y.) 2011; 17:2130-43. [PMID: 22028361 PMCID: PMC3222126 DOI: 10.1261/rna.026658.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/12/2011] [Indexed: 05/24/2023]
Abstract
We develop a statistical mechanical model to predict the structure and folding stability of the RNA/RNA kissing-loop complex. One of the key ingredients of the theory is the conformational entropy for the RNA/RNA kissing complex. We employ the recently developed virtual bond-based RNA folding model (Vfold model) to evaluate the entropy parameters for the different types of kissing loops. A benchmark test against experiments suggests that the entropy calculation is reliable. As an application of the model, we apply the model to investigate the structure and folding thermodynamics for the kissing complex of the HIV-1 dimerization initiation signal. With the physics-based energetic parameters, we compute the free energy landscape for the HIV-1 dimer. From the energy landscape, we identify two minimal free energy structures, which correspond to the kissing-loop dimer and the extended-duplex dimer, respectively. The results support the two-step dimerization process for the HIV-1 replication cycle. Furthermore, based on the Vfold model and energy minimization, the theory can predict the native structure as well as the local minima in the free energy landscape. The root-mean-square deviations (RMSDs) for the predicted kissing-loop dimer and extended-duplex dimer are ~3.0 Å. The method developed here provides a new method to study the RNA/RNA kissing complex.
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Affiliation(s)
- Song Cao
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | - Shi-Jie Chen
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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32
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Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis. J Phys Chem B 2011; 115:13897-910. [PMID: 21999672 DOI: 10.1021/jp2065584] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA kink-turn is an important recurrent RNA motif, an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A•G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G═C receptor base pair during evolution while the inverted pair (C═G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G═C and C═G base pairs in sequences. We carried out an extended set (~5 μs) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with ~0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. The trends seen in the simulations reveal that the A-I/G═C arrangement is preferred over all three other structures. The A-I/C═G triple appears structurally entirely unstable, consistent with the covariation patterns seen during the evolution. The A-0 arrangements tend to shift toward the A-I pattern in simulations, which suggests that formation of the A-0 interaction is likely supported by the surrounding protein and RNA molecules. A-0 may also be stabilized by additional kink-turn nucleotides not belonging to the kink-turn consensus, as shown for the kink-turn from ribosomal Helix 15. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G═C and A-I/C═G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
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33
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Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput 2011; 7:2886-2902. [PMID: 21921995 PMCID: PMC3171997 DOI: 10.1021/ct200162x] [Citation(s) in RCA: 771] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Indexed: 01/19/2023]
Abstract
We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χ(OL). The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn-anti balance as well as enhance MD simulations of various RNA structures. Although χ(OL) can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χ(OL) for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χ(OL) force field is compared with several previous glycosidic torsion parametrizations.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Thomas E. Cheatham
- Departments of Medicinal Chemistry and Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, Utah 84112, United States
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
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Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J. Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J Chem Theory Comput 2011; 7:2963-80. [PMID: 26605485 DOI: 10.1021/ct200204t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Reverse kink-turn is a recurrent elbow-like RNA building block occurring in the ribosome and in the group I intron. Its sequence signature almost matches that of the conventional kink-turn. However, the reverse and conventional kink-turns have opposite directions of bending. The reverse kink-turn lacks basically any tertiary interaction between its stems. We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations with 7.4 μs of data in total) with different variants (ff94, ff99, ff99bsc0, ff99χOL, and ff99bsc0χOL) of the Cornell et al. force field. We test several ion conditions and two water models. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries. The reverse kink-turns are the most flexible RNA motifs studied so far by explicit solvent simulations which are capable at the present simulation time scale to spontaneously and reversibly sample a wide range of geometries from tightly kinked ones through flexible intermediates up to extended, unkinked structures. A possible biochemical role of the flexibility is discussed. Among the tested force fields, the latest χOL variant is essential to obtaining stable trajectories while all force field versions lacking the χ correction are prone to a swift degradation toward senseless ladder-like structures of stems, characterized by high-anti glycosidic torsions. The type of explicit water model affects the simulations considerably more than concentration and the type of ions.
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Affiliation(s)
- Petr Sklenovský
- 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
| | - Petra Florová
- 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
| | - 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
| | - Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Filip Lankaš
- Centre for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry , Flemingovo nam. 2, 166 10 Praha 6, 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
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
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Kim T, Barchi JJ, Marquez VE, Shapiro BA. Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign. J Mol Graph Model 2011; 29:624-34. [PMID: 21159533 PMCID: PMC3040123 DOI: 10.1016/j.jmgm.2010.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/05/2010] [Accepted: 11/10/2010] [Indexed: 11/28/2022]
Abstract
Relatively new types of the modified nucleotides, namely carbocyclic sugars that are constrained to north or south (C2' or C3' exo) conformations, can be used for RNA nanoparticle design to control their structures and stability by rigidifying nucleotides and altering the helical properties of RNA duplexes. Two RNA structures, an RNA dodecamer and an HIV kissing loop complex where several nucleotides were replaced with north or south constrained sugars, were studied by molecular dynamics (MD) simulations. The substituted south constrained nucleotides in the dodecamer widened the major groove and narrowed and deepened the minor groove thus inducing local conformational changes that resemble a B-form DNA helix. In the HIV kissing loop complex, north and south constrained nucleotides were substituted into flanking bases and stems. The modified HIV kissing loop complex showed a lower RMSD value than the normal kissing loop complex. The overall twist angle was also changed and its standard deviation was reduced. In addition, the modified RNA dodecamer and HIV kissing loop complex were characterized by principal component analysis (PCA) and steered molecular dynamics (SMD). PCA results showed that the constrained sugars stabilized the overall motions. The results of the SMD simulations indicated that as the backbone δ angles were increased by elongation, more force was applied to the modified RNA due to the constrained sugar analogues.
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Affiliation(s)
- Taejin Kim
- Center for Cancer Research Nanobiology Program (CCRNP), National Cancer Institute at Frederick, Frederick, MD, USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program (CCRNP), National Cancer Institute at Frederick, Frederick, MD, USA
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Spacková N, Réblová K, Sponer J. Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations. J Phys Chem B 2010; 114:10581-93. [PMID: 20701388 DOI: 10.1021/jp102572k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Kink-turns (K-turns) are recurrent elbow-like RNA motifs that participate in protein-assisted RNA folding and contribute to RNA dynamics. We carried out a set of molecular dynamics (MD) simulations using parm99 and parmbsc0 force fields to investigate structural dynamics of the box C/D RNA and its complexes with two proteins: native archaeal L7ae protein and human 15.5 kDa protein, originally bound to very similar structure of U4 snRNA. The box C/D RNA forms K-turn with A-minor 0 tertiary interaction between its canonical (C) and noncanonical (NC) stems. The local K-turn architecture is thus different from the previously studied ribosomal K-turns 38 and 42 having A-minor I interaction. The simulations reveal visible structural dynamics of this tertiary interaction involving altogether six substates which substantially contribute to the elbow-like flexibility of the K-turn. The interaction can even temporarily shift to the A-minor I type pattern; however, this is associated with distortion of the G/A base pair in the NC-stem of the K-turn. The simulations show reduction of the K-turn flexibility upon protein binding. The protein interacts with the apex of the K-turn and with the NC-stem. The protein-RNA interface includes long-residency hydration sites. We have also found long-residency hydration sites and major ion-binding sites associated with the K-turn itself. The overall topology of the K-turn remains stable in all simulations. However, in simulations of free K-turn, we observed instability of the key C16(O2')-A7(N1) H-bond, which is a signature interaction of K-turns and which was visibly more stable in simulations of K-turns possessing A-minor I interaction. It may reflect either some imbalance of the force field or it may be a correct indication of early stages of unfolding since this K-turn requires protein binding for its stabilization. Interestingly, the 16(O2')-7(N1) H- bond is usually not fully lost since it is replaced by a water bridge with a tightly bound water, which is adenine-specific similarly as the original interaction. The 16(O2')-7(N1) H-bond is stabilized by protein binding. The stabilizing effect is more visible with the human 15.5 kDa protein, which is attributed to valine to arginine substitution in the binding site. The behavior of the A-minor interaction is force-field-dependent because the parmbsc0 force field attenuates the A-minor fluctuations compared to parm99 simulations. Behavior of other regions of the box C/D RNA is not sensitive to the force field choice. Simulation with net-neutralizing Na(+) and 0.2 M excess salt conditions appear in all aspects equivalent. The simulations show loss of a hairpin tetraloop, which is not part of the K-turn. This was attributed to force field limitations.
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Affiliation(s)
- Nad'a Spacková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J Chem Theory Comput 2010; 6:3836-3849. [DOI: 10.1021/ct100481h] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - Daniel Hollas
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - Marie Zgarbová
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - Petr Jurečka
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - Modesto Orozco
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - Thomas E. Cheatham
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - Jiří Šponer
- 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
| | - 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, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, Joint Research Program in Computational Biology, Institut de Recerca Biomédica and Barcelona Superocomputing Center, Baldiri i Reixac 10, Barcelona 08028, Spain, Jordi Girona 31, Barcelona 08028, Spain
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Mlýnský V, Banáš P, Hollas D, Réblová K, Walter NG, Šponer J, Otyepka M. Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B 2010; 114:6642-52. [PMID: 20420375 PMCID: PMC2872159 DOI: 10.1021/jp1001258] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The hairpin ribozyme is a prominent member of the group of small catalytic RNAs (RNA enzymes or ribozymes) because it does not require metal ions to achieve catalysis. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants in cleavage and ligation catalyzed by the hairpin ribozyme, yet their exact role in catalysis remains disputed. To gain insight into dynamics in the active site of a minimal self-cleaving hairpin ribozyme, we have performed extensive classical, explicit-solvent molecular dynamics (MD) simulations on time scales of 50-150 ns. Starting from the available X-ray crystal structures, we investigated the structural impact of the protonation states of G8 and A38, and the inactivating A-1(2'-methoxy) substitution employed in crystallography. Our simulations reveal that a canonical G8 agrees well with the crystal structures while a deprotonated G8 profoundly distorts the active site. Thus MD simulations do not support a straightforward participation of the deprotonated G8 in catalysis. By comparison, the G8 enol tautomer is structurally well tolerated, causing only local rearrangements in the active site. Furthermore, a protonated A38H(+) is more consistent with the crystallography data than a canonical A38. The simulations thus support the notion that A38H(+) is the dominant form in the crystals, grown at pH 6. In most simulations, the canonical A38 departs from the scissile phosphate and substantially perturbs the structures of the active site and S-turn. Yet, we occasionally also observe formation of a stable A-1(2'-OH)...A38(N1) hydrogen bond, which documents the ability of the ribozyme to form this hydrogen bond, consistent with a potential role of A38 as general base catalyst. The presence of this hydrogen bond is, however, incompatible with the expected in-line attack angle necessary for self-cleavage, requiring a rapid transition of the deprotonated 2'-oxyanion to a position more favorable for in-line attack after proton transfer from A-1(2'-OH) to A38(N1). The simulations revealed a potential force field artifact, occasional but irreversible formation of "ladder-like", underwound A-RNA structure in one of the external helices. Although it does not affect the catalytic center of the hairpin ribozyme, further studies are under way to better assess possible influence of such force field behavior on long RNA simulations.
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Affiliation(s)
- Vojtěch Mlýnský
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Daniel Hollas
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109-1055, USA
| | - Jiří Šponer
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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Freedman H, Huynh LP, Le L, Cheatham TE, Tuszynski JA, Truong TN. Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer. J Phys Chem B 2010; 114:2227-37. [PMID: 20099932 DOI: 10.1021/jp9059664] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To provide more accurate computational estimates of binding free energies in solution from molecular dynamics (MD) simulations, a separate solvation contribution for the binding ligand is determined from a linear response treatment. We use explicit water coordinates for this term and combine with MM-PBSA (molecular mechanics, Poisson-Boltzmann, and surface area contributions) in a new approach (MM-PB/LRA-SA). To assess this method, application to the binding between theophylline and its derivatives to an RNA aptamer was performed and compared with experimental binding affinities. Explicitly solvated MD trajectories were generated with the same parameter set used in the previous work by Gouda et al., who compared the relative binding of these molecules by both the MM-PBSA and thermodynamic integration methods. Substituting the linear response term for the ligand in the MM-PB/LRA-SA approach led to an improvement upon MM-PBSA when compared with experimental and thermodynamic integration results at approximately twice the computational cost. The balance between accuracy and computational expense achieved using this method suggests potential advantages in applying it in the virtual drug-screening process.
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Affiliation(s)
- Holly Freedman
- Department of Experimental Oncology, Room 3336, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada
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40
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Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Šponer J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5′-UAA/5′-GAN Internal Loops Studied by Molecular Dynamics Methods. J Chem Theory Comput 2010; 6:910-29. [DOI: 10.1021/ct900440t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Zora Střelcová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Petr Kulhánek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Ivana Beššeová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - David H. Mathews
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Keith Van Nostrand
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Ilyas Yildirim
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Douglas H. Turner
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
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Ditzler MA, Otyepka M, Šponer J, Walter NG. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res 2010; 43:40-7. [PMID: 19754142 PMCID: PMC2808146 DOI: 10.1021/ar900093g] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structure and dynamics are both critical to RNA’s vital functions in biology. Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. In this Account, we highlight areas wherein molecular dynamics (MD) and quantum mechanical (QM) techniques are applied to RNA, particularly in relation to complementary experimental studies.
We have expanded on atomic-resolution crystal structures of RNAs in functionally relevant states by applying explicit solvent MD simulations to explore their dynamics and conformational changes on the submicrosecond time scale. MD relies on simplified atomistic, pairwise additive interaction potentials (force fields). Because of limited sampling, due to the finite accessible simulation time scale and the approximated force field, high-quality starting structures are required. Despite their imperfection, we find that currently available force fields empower MD to provide meaningful and predictive information on RNA dynamics around a crystallographically defined energy minimum. The performance of force fields can be estimated by precise QM calculations on small model systems. Such calculations agree reasonably well with the Cornell et al. AMBER force field, particularly for stacking and hydrogen-bonding interactions. A final verification of any force field is accomplished by simulations of complex nucleic acid structures. The performance of the Cornell et al. AMBER force field generally corresponds well with and augments experimental data, but one notable exception could be the capping loops of double-helical stems. In addition, the performance of pairwise additive force fields is obviously unsatisfactory for inclusion of divalent cations, because their interactions lead to major polarization and charge-transfer effects neglected by the force field. Neglect of polarization also limits, albeit to a lesser extent, the description accuracy of other contributions, such as interactions with monovalent ions, conformational flexibility of the anionic sugar−phosphate backbone, hydrogen bonding, and solute polarization by solvent. Still, despite limitations, MD simulations are a valid tool for analyzing the structural dynamics of existing experimental structures. Careful analysis of MD simulations can identify problematic aspects of an experimental RNA structure, unveil structural characteristics masked by experimental constraints, reveal functionally significant stochastic fluctuations, evaluate the structural role of base ionization, and predict structurally and potentially functionally important details of the solvent behavior, including the presence of tightly bound water molecules. Moreover, combining classical MD simulations with QM calculations in hybrid QM/MM approaches helps in the assessment of the plausibility of chemical mechanisms of catalytic RNAs (ribozymes). In contrast, the reliable prediction of structure from sequence information is beyond the applicability of MD tools. The ultimate utility of computational studies in understanding RNA function thus requires that the results are neither blindly accepted nor flatly rejected, but rather considered in the context of all available experimental data, with great care given to assessing limitations through the available starting structures, force field approximations, and sampling limitations. The examples given in this Account showcase how the judicious use of basic MD simulations has already served as a powerful tool to help evaluate the role of structural dynamics in biological function of RNA.
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Affiliation(s)
- Mark A. Ditzler
- Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. Svobody 26, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiřì Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
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Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Nostrand KV, Yildirim I, Turner DH, Šponer J. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. J Chem Theory Comput 2010; 2010:910-929. [PMID: 21132104 PMCID: PMC2994019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na(+) vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational transition towards the solution 2D structure. Free energy calculations confirm that the X-ray arrangement is less stable than the solution structure. LES, TMD and NEB provide a rather consistent pathway for interconversion between the X-ray and NMR structures. In simulations, the incomplete cWS A/U base pair of the NMR structure is water mediated and alternates with the canonical A-U base pair, which is not indicated by the NMR data. Completion of full cWS A/U base pair is prevented by the overall internal loop arrangement. In summary, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Zora Střelcová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Kulhánek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Ivana Beššeová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642
| | - Keith Van Nostrand
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642
| | - Ilyas Yildirim
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
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Réblová K, Rázga F, Li W, Gao H, Frank J, Sponer J. Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res 2009; 38:1325-40. [PMID: 19952067 PMCID: PMC2831300 DOI: 10.1093/nar/gkp1057] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Helix 38 (H38) of the large ribosomal subunit, with a length of 110 A, reaches the small subunit through intersubunit bridge B1a. Previous cryo-EM studies revealed that the tip of H38 moves by more than 10 A from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible H38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. We investigate a region including the elbow-shaped kink-turn (Kt-38) in the Haloarcula marismortui archaeal ribosome, and equivalently positioned elbows in three eubacterial species, located at the H38 base. We performed explicit solvent molecular dynamics simulations on the H38 elbows in all four species. They are formed by at first sight unrelated sequences resulting in diverse base interactions but built with the same overall topology, as shown by X-ray crystallography. The elbows display similar fluctuations and intrinsic flexibilities in simulations indicating that the eubacterial H38 elbows are structural and dynamical analogs of archaeal Kt-38. We suggest that this structural element plays a pivotal role in the large motions of H38 and may act as fulcrum for the abovementioned tip motion. The directional flexibility inferred from simulations correlates well with the cryo-EM results.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolská 135, 61265 Brno, Czech Republic
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Banáš P, Jurečka P, Walter NG, Šponer J, Otyepka M. Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods 2009; 49:202-16. [PMID: 19398008 PMCID: PMC2753711 DOI: 10.1016/j.ymeth.2009.04.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2009] [Revised: 04/07/2009] [Accepted: 04/07/2009] [Indexed: 11/28/2022] Open
Abstract
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.
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Affiliation(s)
- Pavel Banáš
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. Svobody 26, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. Svobody 26, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109-1055, USA
| | - Jiří Šponer
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. Svobody 26, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. Svobody 26, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. J Chem Theory Comput 2009; 5:2514-30. [DOI: 10.1021/ct900200k] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Nad’a Špačková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Joanna Sarzyñska
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Modesto Orozco
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Thomas E. Cheatham
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Tadeusz Kulinski
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jiří Šponer
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
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Noy A, Soteras I, Luque FJ, Orozco M. The impact of monovalent ion force field model in nucleic acids simulations. Phys Chem Chem Phys 2009; 11:10596-607. [PMID: 20145804 DOI: 10.1039/b912067j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Different classical models for monovalent ions (typically used to neutralize proteins or nucleic acids) are available in the literature and are widely used in molecular dynamics simulations without a great knowledge of their quality, consistency with the macromolecular force field and impact on the global simulation results. In this paper the ability of several of the most popular ion models to reproduce both quantum mechanics and experimental results is examined. Artefacts due to the use of incorrect ion models in molecular dynamics simulations of concentrated solutions of NaCl and KCl in water and of a short DNA duplex in 500 mM aqueous solutions of NaCl and KCl have been analyzed. Our results allow us to discuss the robustness and reliability of different ion models and to highlight the source of potential errors arising from non-optimal models. However, it is also found that the structural and dynamic characteristics of DNA (as an example of a heavily charged macromolecule) in near-physiological conditions are quite independent of the ion model used, providing support to most already-published simulations of macromolecules.
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Affiliation(s)
- Agnes Noy
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK S3 7RH
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Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P. Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J Chem Theory Comput 2009; 5:1166-79. [DOI: 10.1021/ct800547k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Marie Zgarbová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Petr Jurečka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Kevin E. Riley
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Pavel Hobza
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
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Beššeová I, Otyepka M, Réblová K, Šponer J. Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys 2009; 11:10701-11. [DOI: 10.1039/b911169g] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Sarzyńska J, Réblová K, Šponer J, Kuliński T. Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics. Biopolymers 2008; 89:732-46. [DOI: 10.1002/bip.21001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sponer J, Riley KE, Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 2008; 10:2595-610. [PMID: 18464974 DOI: 10.1039/b719370j] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.
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Affiliation(s)
- Jirí Sponer
- Institute of Organic Chemistry and Biochemistry, vvi, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic
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