1
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Borsley S, Leigh DA, Roberts BMW. Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction. Angew Chem Int Ed Engl 2024; 63:e202400495. [PMID: 38568047 DOI: 10.1002/anie.202400495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Indexed: 05/03/2024]
Abstract
Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.
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Affiliation(s)
- Stefan Borsley
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
| | - David A Leigh
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
| | - Benjamin M W Roberts
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
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2
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Wang Q, Su H. A Tale of Water Molecules in the Ribosomal Peptidyl Transferase Reaction. Biochemistry 2022; 61:2241-2247. [PMID: 36178262 DOI: 10.1021/acs.biochem.2c00098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The peptidyl transferase center (PTC) in the large subunit of the ribosome plays a critical role in protein synthesis by catalyzing the formation of peptide bonds with an astounding speed of about 15 to 20 peptide bonds per second. The ribosome coordinates the nucleophilic attack and deprotonation in the rate-limiting step at the PTC. However, the details of peptide bond formation within the ribosome, particularly the precise role of the two water molecules in the PTC, remain unclear. Here, we propose a novel stepwise "proton shuttle" mechanism which corroborates all the reported experimental measurements so far. In this mechanism, a water molecule close to A76 of peptidyl-tRNA 2'- and 3'-O stabilizes the transition state. The other one adjacent to the carbonyl oxygen of peptidyl-tRNA actively participates in the proton shuttle, playing the catalytic role of ribosome-catalyzed peptide bond formation.
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Affiliation(s)
- Qiang Wang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518048, China
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3
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Galindo-Feria AS, Notarnicola A, Lundberg IE, Horuluoglu B. Aminoacyl-tRNA Synthetases: On Anti-Synthetase Syndrome and Beyond. Front Immunol 2022; 13:866087. [PMID: 35634293 PMCID: PMC9136399 DOI: 10.3389/fimmu.2022.866087] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
Anti-synthetase syndrome (ASSD) is an autoimmune disease characterized by the presence of autoantibodies targeting one of several aminoacyl t-RNA synthetases (aaRSs) along with clinical features including interstitial lung disease, myositis, Raynaud’s phenomenon, arthritis, mechanic’s hands, and fever. The family of aaRSs consists of highly conserved cytoplasmic and mitochondrial enzymes, one for each amino acid, which are essential for the RNA translation machinery and protein synthesis. Along with their main functions, aaRSs are involved in the development of immune responses, regulation of transcription, and gene-specific silencing of translation. During the last decade, these proteins have been associated with cancer, neurological disorders, infectious responses, and autoimmune diseases including ASSD. To date, several aaRSs have been described to be possible autoantigens in different diseases. The most commonly described are histidyl (HisRS), threonyl (ThrRS), alanyl (AlaRS), glycyl (GlyRS), isoleucyl (IleRS), asparaginyl (AsnRS), phenylalanyl (PheRS), tyrosyl (TyrRS), lysyl (LysRS), glutaminyl (GlnRS), tryptophanyl (TrpRS), and seryl (SerRS) tRNA synthetases. Autoantibodies against the first eight autoantigens listed above have been associated with ASSD while the rest have been associated with other diseases. This review will address what is known about the function of the aaRSs with a focus on their autoantigenic properties. We will also describe the anti-aaRSs autoantibodies and their association to specific clinical manifestations, and discuss their potential contribution to the pathogenesis of ASSD.
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Affiliation(s)
- Angeles S. Galindo-Feria
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Antonella Notarnicola
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ingrid E. Lundberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
- *Correspondence: Begum Horuluoglu,
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4
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Feng H, Fu H, Shao X, Cai W. Insights into directional movement in molecular machines from free-energy calculations. Phys Chem Chem Phys 2020; 22:7888-7893. [PMID: 32227040 DOI: 10.1039/d0cp00003e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rotaxane composed of a symmetrical axle containing three binding stations and a cone-like macrocycle containing two secondary amines has been investigated at the atomic level. At high pH, the macrocycle binds to the intermediate di(quaternary ammonium) site, while at low pH, the protonated macrocycle selectively moves along the axle to one of the two symmetrical phenyl triazole binding sites facing its upper rim, but does not shuttle backward. The determined free-energy profile characterizing the translocation of the macrocycle indicates that the selected binding site is energetically more favorable than the one facing the lower rim of the macrocycle and the free-energy barrier against translocation to the former site is lower than to the latter one, rationalizing the directional movement. This selectivity mainly stems from the asymmetry of the macrocycle shape. The strong electrostatic repulsion between the ring and the axle is found to constitute the driving force for the shuttling of the ring and also the resistance for its reverse motion. Moreover, the effect of the solvent on the shuttling has been examined, suggesting that increasing the solvent polarity may weaken the directional preference of shuttling, due to the shielding effect of polar solvents on electrostatic interactions. Our study provides a theoretical framework for tuning the selectivity of directional movement in molecular machines.
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Affiliation(s)
- Heying Feng
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Haohao Fu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China. and State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Wensheng Cai
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China.
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5
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Heard A, Goldup SM. Simplicity in the Design, Operation, and Applications of Mechanically Interlocked Molecular Machines. ACS CENTRAL SCIENCE 2020; 6:117-128. [PMID: 32123730 PMCID: PMC7047278 DOI: 10.1021/acscentsci.9b01185] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 05/17/2023]
Abstract
Mechanically interlocked molecules are perhaps best known as components of molecular machines, a view further reinforced by the Nobel Prize in 2016 to Stoddart and Sauvage. Despite amazing progress since these pioneers of the field reported the first examples of molecular shuttles, genuine applications of interlocked molecular machines remain elusive, and many barriers remain to be overcome before such molecular devices make the transition from impressive prototypes on the laboratory bench to useful products. Here, we discuss simplicity as a design principle that could be applied in the development of the next generation of molecular machines with a view to moving toward real-world applications of these intriguing systems in the longer term.
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6
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Shao C, Liu Z, Yang H, Wang S, Burley SK. Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. Sci Data 2018; 5:180293. [PMID: 30532050 PMCID: PMC6289109 DOI: 10.1038/sdata.2018.293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/12/2018] [Indexed: 02/02/2023] Open
Abstract
Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.
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Affiliation(s)
- Chenghua Shao
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
| | - Zonghong Liu
- Department of Statistics and Biostatistics, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
- Department of Statistics and Biostatistics, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center and
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California
San Diego, La Jolla,
CA
92093, USA
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7
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Le DN, Hansen E, Khan HA, Kim B, Wiest O, Dong VM. Hydrogenation catalyst generates cyclic peptide stereocentres in sequence. Nat Chem 2018; 10:968-973. [PMID: 30061616 DOI: 10.1038/s41557-018-0089-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 05/22/2018] [Indexed: 11/09/2022]
Abstract
Molecular recognition plays a key role in enzyme-substrate specificity, the regulation of genes, and the treatment of diseases. Inspired by the power of molecular recognition in enzymatic processes, we sought to exploit its use in organic synthesis. Here we demonstrate how a synthetic rhodium-based catalyst can selectively bind a dehydroamino acid residue to initiate a sequential and stereoselective synthesis of cyclic peptides. Our combined experimental and theoretical study reveals the underpinnings of a cascade reduction that occurs with high stereocontrol and in one direction around a macrocyclic ring. As the catalyst can dissociate from the peptide, the C to N directionality of the hydrogenation reactions is controlled by catalyst-substrate recognition rather than a processive mechanism in which the catalyst remains bound to the macrocycle. This mechanistic insight provides a foundation for the use of cascade hydrogenations.
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Affiliation(s)
- Diane N Le
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Eric Hansen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Hasan A Khan
- Department of Chemistry, University of California, Irvine, CA, USA.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Byoungmoo Kim
- Department of Chemistry, University of California, Irvine, CA, USA.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA. .,Lab of Computational Chemistry and Drug Design, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, China.
| | - Vy M Dong
- Department of Chemistry, University of California, Irvine, CA, USA.
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8
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Zhai Y, Tye BK. Structure of the MCM2-7 Double Hexamer and Its Implications for the Mechanistic Functions of the Mcm2-7 Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:189-205. [PMID: 29357059 DOI: 10.1007/978-981-10-6955-0_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The eukaryotic minichromosome maintenance 2-7 complex is the core of the inactive MCM replication licensing complex and the catalytic core of the Cdc45-MCM-GINS replicative helicase. The years of effort to determine the structure of parts or the whole of the heterohexameric complex by X-ray crystallography and conventional cryo-EM produced limited success. Modern cryo-EM technology ushered in a new era of structural biology that allowed the determination of the structure of the inactive double hexamer at an unprecedented resolution of 3.8 Å. This review will focus on the fine details observed in the Mcm2-7 double hexameric complex and their implications for the function of the Mcm2-7 hexamer in its different roles during DNA replication.
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Affiliation(s)
- Yuanliang Zhai
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Bik-Kwoon Tye
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.
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9
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Aminoacyl-tRNA synthetases: Structure, function, and drug discovery. Int J Biol Macromol 2018; 111:400-414. [PMID: 29305884 DOI: 10.1016/j.ijbiomac.2017.12.157] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 12/27/2017] [Accepted: 12/29/2017] [Indexed: 01/02/2023]
Abstract
Aminoacyl-tRNA synthetases (AARSs) are the enzymes that catalyze the aminoacylation reaction by covalently linking an amino acid to its cognate tRNA in the first step of protein translation. Beyond this classical function, these enzymes are also known to have a role in several metabolic and signaling pathways that are important for cell viability. Study of these enzymes is of great interest to the researchers due to its pivotal role in the growth and survival of an organism. Further, unfolding the interesting structural and functional aspects of these enzymes in the last few years has qualified them as a potential drug target against various diseases. Here we review the classification, function, and the conserved as well the appended structural architecture of these enzymes in detail, including its association with multi-synthetase complexes. We also considered their role in human diseases in terms of mutations and autoantibodies against AARSs. Finally, we have discussed the available inhibitors against AARSs. This review offers comprehensive information on AARSs under a single canopy that would be a good inventory for researchers working in this area.
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10
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Frank J. The translation elongation cycle-capturing multiple states by cryo-electron microscopy. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0180. [PMID: 28138066 DOI: 10.1098/rstb.2016.0180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
During the work cycle of elongation, the ribosome, a molecular machine of vast complexity, exists in a large number of states distinguished by constellation of its subunits, its subunit domains and binding partners. Single-particle cryogenic electron microscopy (cryo-EM), developed over the past 40 years, is uniquely suited to determine the structure of molecular machines in their native states. With the emergence, 10 years ago, of unsupervised clustering techniques in the analysis of single-particle data, it has been possible to determine multiple structures from a sample containing ribosomes equilibrating in different thermally accessible states. In addition, recent advances in detector technology have made it possible to reach near-atomic resolution for some of these states. With these capabilities, single-particle cryo-EM has been at the forefront of exploring ribosome dynamics during its functional cycle, along with single-molecule fluorescence resonance energy transfer and molecular dynamics computations, offering insights into molecular architecture uniquely honed by evolution to capitalize on thermal energy in the ambient environment.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA .,Howard Hughes Medical Institute, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA
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11
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Petersen MÅ, Rasmussen B, Andersen NN, Sauer SPA, Nielsen MB, Beeren SR, Pittelkow M. Molecular Switching in Confined Spaces: Effects of Encapsulating the DHA/VHF Photo-Switch in Cucurbiturils. Chemistry 2017; 23:17010-17016. [PMID: 28922509 DOI: 10.1002/chem.201703196] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Indexed: 11/05/2022]
Abstract
Confinement of reactive chemical species uniquely affects chemical reactivity by restricting the physical space available and by restricting access to interactions with the solvent. In Nature, for example, confined protein binding pockets govern processes following photoisomerization reactions and the isomerizations themselves. Here we describe the first example of a dihydroazulene/vinylheptafulvene (DHA/VHF) photo-switch functioning in water, and we show how its switching behavior is strongly influenced by supramolecular interactions with a series of cucurbit[n]uril (CB) host molecules. In CB7 inclusion complexes, the kinetics of the thermal VHF-to-DHA back-reaction is accelerated, while in CB8 inclusion complexes, the kinetics is slowed down as compared to the free photo-switch. The effect of the CB encapsulation of the photo-switch can be effectively canceled by introducing a guest that binds the CB more strongly. According to DFT calculations, a stabilization of the reactive s-cis VHF conformer relative to the s-trans VHF appears to be a contributing factor responsible for the accelerated back-reaction when encapsulated in CB7.
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Affiliation(s)
- Michael Å Petersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Brian Rasmussen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Nicolaj N Andersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Mogens Brøndsted Nielsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, Kemitorvet, bygning 207, 2800 Kgs., Lyngby, Denmark
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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12
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Stoddart JF. Mechanisch verzahnte Moleküle (MIMs) - molekulare Shuttle, Schalter und Maschinen (Nobel-Aufsatz). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703216] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- J. Fraser Stoddart
- Department of Chemistry; Northwestern University; 2145 Sheridan Road Evanston IL 60208-3113 USA
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13
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Stoddart JF. Mechanically Interlocked Molecules (MIMs)-Molecular Shuttles, Switches, and Machines (Nobel Lecture). Angew Chem Int Ed Engl 2017; 56:11094-11125. [PMID: 28815900 DOI: 10.1002/anie.201703216] [Citation(s) in RCA: 585] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Indexed: 12/20/2022]
Abstract
Chemistry welcomes a new bond: The mechanical bond has endowed molecules with component parts whose movements can be controlled and monitored. In his Nobel Lecture, J. F. Stoddart describes how being able to template the formation of mechanically interlocked molecules has led to the design and synthesis of shuttles, switches, and machines at the nanoscale.
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Affiliation(s)
- J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3113, USA
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14
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De Bo G, Gall MAY, Kitching MO, Kuschel S, Leigh DA, Tetlow DJ, Ward JW. Sequence-Specific β-Peptide Synthesis by a Rotaxane-Based Molecular Machine. J Am Chem Soc 2017; 139:10875-10879. [DOI: 10.1021/jacs.7b05850] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Guillaume De Bo
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Malcolm A. Y. Gall
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew O. Kitching
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sonja Kuschel
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Daniel J. Tetlow
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - John W. Ward
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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15
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Eichstaedt K, Jaramillo-Garcia J, Leigh DA, Marcos V, Pisano S, Singleton TA. Switching between Anion-Binding Catalysis and Aminocatalysis with a Rotaxane Dual-Function Catalyst. J Am Chem Soc 2017. [DOI: 10.1021/jacs.7b04955] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Katarzyna Eichstaedt
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | | | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Vanesa Marcos
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Simone Pisano
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Thomas A. Singleton
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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16
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Suvlu D, Samaratunga S, Thirumalai D, Rasaiah JC. Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes. J Phys Chem Lett 2017; 8:494-499. [PMID: 28060517 DOI: 10.1021/acs.jpclett.6b02620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding structure formation in polypeptide chains and synthetic polymers encapsulated in pores is important in biology and nanotechnology. We present replica exchange molecular dynamics studies of the phase diagram for α-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters, which surprisingly is comparable to the width of the ribosome tunnel. Increasing the hydrophobicity enhances helicity in the NT. Helix formation in polyalanine is driven by a small negative enthalpy and a positive entropy change at ≈300 K, in contrast to the large negative entropy change that destabilizes the helix and favors the coiled state in bulk water. There is an anticorrelation between water density inside the nanotube and structure formation. Confinement-induced helix formation depends on amino acid sequence. There is complete absence of helix in polyglutamine and polyserine confined to a open carbon nanotube.
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Affiliation(s)
- Dylan Suvlu
- Department of Chemistry, University of Maine , Orono, Maine 04469, United States
| | | | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jayendran C Rasaiah
- Department of Chemistry, University of Maine , Orono, Maine 04469, United States
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17
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Reddy GNM, Huqi A, Iuga D, Sakurai S, Marsh A, Davis JT, Masiero S, Brown SP. Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State. Chemistry 2016; 23:2315-2322. [PMID: 27897351 PMCID: PMC5396329 DOI: 10.1002/chem.201604832] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 11/24/2022]
Abstract
The formation of distinct supramolecular assemblies, including a metastable species, is revealed for a lipophilic guanosine (G) derivative in solution and in the solid state. Structurally different G‐quartet‐based assemblies are formed in chloroform depending on the nature of the cation, anion and the salt concentration, as characterized by circular dichroism and time course diffusion‐ordered NMR spectroscopy data. Intriguingly, even the presence of potassium ions that stabilize G‐quartets in chloroform was insufficient to exclusively retain such assemblies in the solid state, leading to the formation of mixed quartet and ribbon‐like assemblies as revealed by fast magic‐angle spinning (MAS) NMR spectroscopy. Distinct N−H⋅⋅⋅N and N−H⋅⋅⋅O intermolecular hydrogen bonding interactions drive quartet and ribbon‐like self‐assembly resulting in markedly different 2D 1H solid‐state NMR spectra, thus facilitating a direct identification of mixed assemblies. A dissolution NMR experiment confirmed that the quartet and ribbon interconversion is reversible–further demonstrating the changes that occur in the self‐assembly process of a lipophilic nucleoside upon a solid‐state to solution‐state transition and vice versa. A systematic study for complexation with different cations (K+, Sr2+) and anions (picrate, ethanoate and iodide) emphasizes that the existence of a stable solution or solid‐state structure may not reflect the stability of the same supramolecular entity in another phase.
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Affiliation(s)
- G N Manjunatha Reddy
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Aida Huqi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Dinu Iuga
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Satoshi Sakurai
- JEOL (UK), Silver Court, Watchmead, Welwyn Garden City, AL7 1LT, UK
| | - Andrew Marsh
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
| | - Jeffery T Davis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Stefano Masiero
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Steven P Brown
- Department of Physics and Department of Chemistry, University of, Warwick, Coventry, CV4 7AL, UK
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18
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Abstract
The past quarter of a century has witnessed an increasing engagement on the part of physicists and chemists in the design and synthesis of molecular machines de novo. This minireview traces the development of artificial molecular machines from their prototypes in the form of shuttles and switches to their emergence as motors and pumps where supplies of energy in the form of chemical fuel, electrochemical potential and light activation become a minimum requirement for them to function away from equilibrium. The challenge facing this rapidly growing community of scientists and engineers today is one of putting wholly synthetic molecules to work, both individually and as collections. Here, we highlight some of the recent conceptual and practical advances relating to the operation of wholly synthetic rotary and linear motors.
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Affiliation(s)
- Chuyang Cheng
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA.
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19
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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20
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Świderek K, Marti S, Tuñón I, Moliner V, Bertran J. Peptide Bond Formation Mechanism Catalyzed by Ribosome. J Am Chem Soc 2015; 137:12024-34. [PMID: 26325003 PMCID: PMC4582011 DOI: 10.1021/jacs.5b05916] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708-8719), but the reaction mechanisms are noticeably different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behavior of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system.
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Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
- Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, (Poland)
| | - Sergio Marti
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, (Spain)
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
| | - Juan Bertran
- Departament de Química; Universitat Autònoma de Barcelona, 08193 Bellaterra, (Spain)
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21
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Bijelic A, Rompel A. The use of polyoxometalates in protein crystallography - An attempt to widen a well-known bottleneck. Coord Chem Rev 2015; 299:22-38. [PMID: 26339074 PMCID: PMC4504029 DOI: 10.1016/j.ccr.2015.03.018] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/23/2015] [Indexed: 02/01/2023]
Abstract
Polyoxometalates (POMs) are discrete polynuclear metal-oxo anions with a fascinating variety of structures and unique chemical and physical properties. Their application in various fields is well covered in the literature, however little information about their usage in protein crystallization is available. This review summarizes the impact of the vast class of POMs on the formation of protein crystals, a well-known (frustrating) bottleneck in macromolecular crystallography, with the associated structure elucidation and a particular emphasis focused on POM's potential as a powerful crystallization additive for future research. The Protein Data Bank (PDB) was scanned for protein structures with incorporated POMs which were assigned a PDB ligand ID resulting in 30 PDB entries. These structures have been analyzed with regard to (i) the structure of POM itself in the immediate protein environment, (ii) the kind of interaction and position of the POM within the protein structure and (iii) the beneficial effects of POM on protein crystallography apparent so far.
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Affiliation(s)
| | - Annette Rompel
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität Wien, Althanstraße 14, 1090 Wien, Austria1
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22
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Dittrich B, Matta CF. Contributions of charge-density research to medicinal chemistry. IUCRJ 2014; 1:457-69. [PMID: 25485126 PMCID: PMC4224464 DOI: 10.1107/s2052252514018867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/20/2014] [Indexed: 06/04/2023]
Abstract
This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3M, Canada
- Department of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3, Canada
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23
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Levitt M. Geburt und Zukunft der Multiskalenmodellierung von makromolekularen Systemen (Nobel-Aufsatz). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Levitt M. Birth and Future of Multiscale Modeling for Macromolecular Systems (Nobel Lecture). Angew Chem Int Ed Engl 2014; 53:10006-18. [DOI: 10.1002/anie.201403691] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 11/09/2022]
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25
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Noel JK, Whitford PC. How Simulations Reveal Dynamics, Disorder, and the Energy Landscapes of Biomolecular Function. Isr J Chem 2014. [DOI: 10.1002/ijch.201400018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Abstract
CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such as the ribosome, large ribozymes, and riboswitches. Thus, the next step in synthetic RNA design will involve new ways to implement these same types of dynamic and responsive architectures into nanostructures functioning as real nanomachines in and outside the cell. RNA nanotechnology will likely garner broader utility and influence with a greater focus on the interplay between thermodynamic and kinetic influences on RNA self-assembly and using natural RNAs as guiding principles.
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Affiliation(s)
- Wade W. Grabow
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Bio-Molecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
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27
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De Bo G, Kuschel S, Leigh DA, Lewandowski B, Papmeyer M, Ward JW. Efficient assembly of threaded molecular machines for sequence-specific synthesis. J Am Chem Soc 2014; 136:5811-4. [PMID: 24678971 DOI: 10.1021/ja5022415] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report on an improved strategy for the preparation of artificial molecular machines that can pick up and assemble reactive groups in sequence by traveling along a track. In the new approach a preformed rotaxane synthon is attached to the end of an otherwise fully formed strand of building blocks. This "rotaxane-capping" protocol is significantly more efficient than the "final-step-threading" method employed previously and enables the synthesis of threaded molecular machines that operate on extended oligomer, and potentially polymer, tracks. The methodology is exemplified through the preparation of a machine that adds four amino acid building blocks from a strand in sequence, featuring up to 20-membered ring native chemical ligation transition states.
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Affiliation(s)
- Guillaume De Bo
- School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL United Kingdom
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28
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Affiliation(s)
- Christian M Kaiser
- QB3 Institute, and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
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29
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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30
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Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ. Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1066-9. [PMID: 23989164 PMCID: PMC3758164 DOI: 10.1107/s174430911302099x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/27/2013] [Indexed: 12/03/2022]
Abstract
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
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Affiliation(s)
- Hasan Demirci
- Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA.
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31
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Świderek K, Tuñón I, Martí S, Moliner V, Bertrán J. Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects. J Am Chem Soc 2013; 135:8708-19. [DOI: 10.1021/ja403038t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katarzyna Świderek
- Institute of Applied Radiation
Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Sergio Martí
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Juan Bertrán
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra,
Spain
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32
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33
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SHARMA AJEETK, CHOWDHURY DEBASHISH. TEMPLATE-DIRECTED BIOPOLYMERIZATION: TAPE-COPYING TURING MACHINES. ACTA ACUST UNITED AC 2013. [DOI: 10.1142/s1793048012300083] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using another linear polymer as the corresponding template. The machine utilizes input chemical energy to move along the template which also serves as a track for the movements of the machine. In the Alan Turing year 2012, it is worth pointing out that these machines are "tape-copying Turing machines". We review the operational mechanisms of the polymerizer machines and their collective behavior from the perspective of statistical physics, emphasizing their common features in spite of the crucial differences in their biological functions. We also draw the attention of the physics community to another class of modular machines that carry out a different type of template-directed polymerization. We hope this review will inspire new kinetic models for these modular machines.
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Affiliation(s)
- AJEET K. SHARMA
- Department of Physics, Indian Institute of Technology, Kanpur 208016, India
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34
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Lewandowski B, De Bo G, Ward JW, Papmeyer M, Kuschel S, Aldegunde MJ, Gramlich PME, Heckmann D, Goldup SM, D'Souza DM, Fernandes AE, Leigh DA. Sequence-specific peptide synthesis by an artificial small-molecule machine. Science 2013; 339:189-93. [PMID: 23307739 DOI: 10.1126/science.1229753] [Citation(s) in RCA: 551] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The ribosome builds proteins by joining together amino acids in an order determined by messenger RNA. Here, we report on the design, synthesis, and operation of an artificial small-molecule machine that travels along a molecular strand, picking up amino acids that block its path, to synthesize a peptide in a sequence-specific manner. The chemical structure is based on a rotaxane, a molecular ring threaded onto a molecular axle. The ring carries a thiolate group that iteratively removes amino acids in order from the strand and transfers them to a peptide-elongation site through native chemical ligation. The synthesis is demonstrated with ~10(18) molecular machines acting in parallel; this process generates milligram quantities of a peptide with a single sequence confirmed by tandem mass spectrometry.
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Affiliation(s)
- Bartosz Lewandowski
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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35
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36
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Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
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37
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Fukushima K, Iwahashi H, Nishikimi M. ONIOM Study of a Proton Shuttle-Catalyzed Stepwise Mechanism for Peptide Bond Formation in the Ribosome. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Morimitsu Nishikimi
- Department of Food Science and Nutrition, Faculty of Human Life and Environmental Sciences, Nagoya Women’s University
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38
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Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Struktur und Funktion nicht-kanonischer Nukleobasen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201193] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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39
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Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Structure and function of noncanonical nucleobases. Angew Chem Int Ed Engl 2012; 51:7110-31. [PMID: 22744788 DOI: 10.1002/anie.201201193] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/07/2012] [Indexed: 12/19/2022]
Abstract
DNA and RNA contain, next to the four canonical nucleobases, a number of modified nucleosides that extend their chemical information content. RNA is particularly rich in modifications, which is obviously an adaptation to their highly complex and variable functions. In fact, the modified nucleosides and their chemical structures establish a second layer of information which is of central importance to the function of the RNA molecules. Also the chemical diversity of DNA is greater than originally thought. Next to the four canonical bases, the DNA of higher organisms contains a total of four epigenetic bases: m(5) dC, hm(5) dC, f(5) dC und ca(5) dC. While all cells of an organism contain the same genetic material, their vastly different function and properties inside complex higher organisms require the controlled silencing and activation of cell-type specific genes. The regulation of the underlying silencing and activation process requires an additional layer of epigenetic information, which is clearly linked to increased chemical diversity. This diversity is provided by the modified non-canonical nucleosides in both DNA and RNA.
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Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany.
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40
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Biro JC. The concept of RNA-assisted protein folding: the role of tRNA. Theor Biol Med Model 2012; 9:10. [PMID: 22462735 PMCID: PMC3359187 DOI: 10.1186/1742-4682-9-10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 04/02/2012] [Indexed: 02/07/2023] Open
Abstract
We suggest that tRNA actively participates in the transfer of 3D information from mRNA to peptides--in addition to its well-known, "classical" role of translating the 3-letter RNA codes into the one letter protein code. The tRNA molecule displays a series of thermodynamically favored configurations during translation, a movement which places the codon and coded amino acids in proximity to each other and make physical contact between some amino acids and their codons possible. This specific codon-amino acid interaction of some selected amino acids is necessary for the transfer of spatial information from mRNA to coded proteins, and is known as RNA-assisted protein folding.
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Affiliation(s)
- Jan C Biro
- Karolinska Institute, Stockholm, Sweden.
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41
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum-Mechanical Study on the Mechanism of Peptide Bond Formation in the Ribosome. J Am Chem Soc 2012; 134:5817-31. [DOI: 10.1021/ja209558d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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42
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Li H, Ulge UY, Hovde BT, Doyle LA, Monnat RJ. Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications. Nucleic Acids Res 2011; 40:2587-98. [PMID: 22121229 PMCID: PMC3315327 DOI: 10.1093/nar/gkr1072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Homing endonucleases (HEs) promote the evolutionary persistence of selfish DNA elements by catalyzing element lateral transfer into new host organisms. The high site specificity of this lateral transfer reaction, termed homing, reflects both the length (14-40 bp) and the limited tolerance of target or homing sites for base pair changes. In order to better understand molecular determinants of homing, we systematically determined the binding and cleavage properties of all single base pair variant target sites of the canonical LAGLIDADG homing endonucleases I-CreI and I-MsoI. These Chlorophyta algal HEs have very similar three-dimensional folds and recognize nearly identical 22 bp target sites, but use substantially different sets of DNA-protein contacts to mediate site-specific recognition and cleavage. The site specificity differences between I-CreI and I-MsoI suggest different evolutionary strategies for HE persistence. These differences also provide practical guidance in target site finding, and in the generation of HE variants with high site specificity and cleavage activity, to enable genome engineering applications.
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Affiliation(s)
- Hui Li
- Department of Pathology, University of Washington, Box 357705, Seattle, WA 98195, USA
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Kast P. Making Proteins with Unnatural Amino Acids: The First Engineered Aminoacyl-tRNA Synthetase Revisited. Chembiochem 2011; 12:2395-8. [DOI: 10.1002/cbic.201100533] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Indexed: 11/07/2022]
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Erdmann VA, Barciszewski J. 2011: 50th Anniversary of the Discovery of the Genetic Code. Angew Chem Int Ed Engl 2011; 50:9546-52. [DOI: 10.1002/anie.201103895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Indexed: 11/10/2022]
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Steger J, Micura R. Functionalized polystyrene supports for solid-phase synthesis of glycyl-, alanyl-, and isoleucyl-RNA conjugates as hydrolysis-resistant mimics of peptidyl-tRNAs. Bioorg Med Chem 2011; 19:5167-74. [PMID: 21807524 PMCID: PMC3162138 DOI: 10.1016/j.bmc.2011.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/08/2011] [Accepted: 07/10/2011] [Indexed: 12/20/2022]
Abstract
RNA-peptide conjugates that mimic amino acid-charged tRNAs and peptidyl-tRNAs are of high importance for structural and functional investigations of ribosomal complexes. Here, we present the synthesis of glycyl-, alanyl-, and isoleucyladenosine modified solid supports that are eligible for the synthesis of stable 3′-aminoacyl- and 3′-peptidyl-tRNA termini with an amide instead of the natural ester linkage. The present work significantly expands the range of accessible peptidyl-tRNA mimics for ribosomal studies.
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Affiliation(s)
- Jessica Steger
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, University of Innsbruck, Innsbruck, Austria
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Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Proc Natl Acad Sci U S A 2011; 108:9827-32. [PMID: 21617092 DOI: 10.1073/pnas.1105714108] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crucial process of aminoacyl-tRNA delivery to the ribosome is energized by the GTPase reaction of the elongation factor Tu (EF-Tu). Advances in the elucidation of the structure of the EF-Tu/ribosome complex provide the rare opportunity of gaining a detailed understanding of the activation process of this system. Here, we use quantitative simulation approaches and reproduce the energetics of the GTPase reaction of EF-Tu with and without the ribosome and with several key mutants. Our study provides a novel insight into the activation process. It is found that the critical H84 residue is not likely to behave as a general base but rather contributes to an allosteric effect, which includes a major transition state stabilization by the electrostatic effect of the P loop and other regions of the protein. Our findings have general relevance to GTPase activation, including the processes that control signal transduction.
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Jang TH, Park JH, Jeon JH, Lee DS, Choi K, Kim IG, Kim YW, Park HH. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of human ribosomal protein L7a (RPL7a). Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:510-2. [PMID: 21505254 PMCID: PMC3080163 DOI: 10.1107/s1744309111006415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 02/20/2011] [Indexed: 11/10/2022]
Abstract
Ribosomal proteins are a major component of ribosomes, which catalyze protein synthesis. One ribosomal protein, L7a (RPL7a), which is a component of the 60S large ribosomal subunit, has additional functions involved in cell growth and differentiation that occur via interaction with human thyroid hormone receptor (THR) and retinoic acid receptor (RAR) and in turn inhibit the activities of the two nuclear hormone receptors. In this study, the N-terminal domain of human RPL7a was overexpressed in Escherichia coli using an engineered C-terminal His tag. The N-terminal domain of human RPL7a was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 3.5 Å from a crystal belonging to the tetragonal space group P4(1)22 or P4(3)22 with unit-cell parameters a = 92.28, b = 92.28, c = 236.59 Å.
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Affiliation(s)
- Tae-ho Jang
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jin Hee Park
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Ju-Hong Jeon
- Department of Physiology and Institute of Dermatological Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Sup Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kihang Choi
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - In-Gyu Kim
- Department of Biochemistry and Molecular Biology/Aging and Apoptosis Research Center (AARC), Seoul National University College of Medicine, Seoul Republic of Korea
| | - Young Whan Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and Lung Institute of Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Ho Park
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
- School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
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Sharma AK, Chowdhury D. Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding. Phys Biol 2011; 8:026005. [PMID: 21263169 DOI: 10.1088/1478-3975/8/2/026005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechanochemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Wherever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.
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Affiliation(s)
- Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Kanpur 208016, India
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Trylska J. Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:453101. [PMID: 21339588 DOI: 10.1088/0953-8984/22/45/453101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biopolymers are of dynamic nature and undergo functional motions spanning a large spectrum of timescales. To study the internal dynamics of nano-sized molecular complexes that exceed hundred thousands of atoms with atomic detail is computationally inefficient. Therefore, to achieve both the spatial and temporal scales of biological interest coarse-grained models of macromolecules are often used. By uniting groups of atoms into single interacting centers one decreases the resolution of the system and gets rid of the irrelevant degrees of freedom. This simplification, even though it requires parameterization, makes the studies of biomolecular dynamics computationally tractable and allows us to reach beyond the microsecond time frame. Here, I review the coarse-grained models of macromolecules composed of proteins and nucleic acids. I give examples of one-bead models that were developed to investigate the internal dynamics and focus on their applications to the ribosome--the nanoscale protein synthesis machine.
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Affiliation(s)
- Joanna Trylska
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, Warsaw 02-106, Poland.
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