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Pemberton JG, Tenkova T, Felgner P, Zimmerberg J, Balla T, Heuser J. Defining the EM-signature of successful cell-transfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583927. [PMID: 38496608 PMCID: PMC10942431 DOI: 10.1101/2024.03.07.583927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent structural changes after they have entered cells, changes that not only provide new insights into the mechanism of action of these particular transfection-reagents, but also provide a convenient and robust method for identifying by EM which cells in any culture have been successfully transfected. This also provides clues to the mechanism(s) of their toxic effects, when they are applied in excess. We demonstrate that after being bulk-endocytosed by cells, the cationic spheroids of Lipofectamine remain intact throughout the entire time of culturing, but escape from their endosomes and penetrate directly into the cytoplasm of the cell. In so doing, they provoke a stereotypical recruitment and rearrangement of endoplasmic reticulum (ER), and they ultimately end up escaping into the cytoplasm and forming unique 'inclusion-bodies.' Once free in the cytoplasm, they also invariably develop dense and uniform coatings of cytoplasmic ribosomes on their surfaces, and finally, they become surrounded by 'annulate' lamellae' of the ER. In the end, these annulate-lamellar enclosures become the ultrastructural 'signatures' of these inclusion-bodies, and serve to positively and definitively identify all cells that have been effectively transfected. Importantly, these new EM-observations define several new and unique properties of these classical Lipofectamines, and allow them to be discriminated from other lipoidal or particulate transfection-reagents, which we find do not physically break out of endosomes or end up in inclusion bodies, and in fact, provoke absolutely none of these 'signature' cytoplasmic reactions.
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2
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Ohnuki J, Arimura Y, Kono T, Kino K, Kurumizaka H, Takano M. Electrostatic Ratchet for Successive Peptide Synthesis in Nonribosomal Molecular Machine RimK. J Am Chem Soc 2023. [PMID: 37452763 PMCID: PMC10375531 DOI: 10.1021/jacs.3c03926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
A nonribosomal peptide-synthesizing molecular machine, RimK, adds l-glutamic acids to the C-terminus of ribosomal protein S6 (RpsF) in vivo and synthesizes poly-α-glutamates in vitro. However, the mechanism of the successive glutamate addition, which is fueled by ATP, remains unclear. Here, we investigate the successive peptide-synthesizing mechanism of RimK via the molecular dynamics (MD) simulation of glutamate binding. We first show that RimK adopts three stable structural states with respect to the ATP-binding loop and the triphosphate chain of the bound ATP. We then show that a glutamate in solution preferentially binds to a positively charged belt-like region of RimK and the bound glutamate exhibits Brownian motion along the belt. The binding-energy landscape shows that the open-to-closed transition of the ATP-binding loop and the bent-to-straight transition of the triphosphate chain of ATP can function as an electrostatic ratchet that guides the bound glutamate to the active site. We then show the binding site of the second glutamate, which allows us to infer the ligation mechanism. Consistent with MD results, the crystal structure of RimK we obtained in the presence of RpsF presents an electron density that is presumed to correspond to the C-terminus of RpsF. We finally propose a mechanism for the successive peptide synthesis by RimK and discuss its similarity to other molecular machines.
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Affiliation(s)
- Jun Ohnuki
- Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Yasuhiro Arimura
- Institute for Quantitative Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomonori Kono
- Department of Applied Chemistry, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan
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3
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Funk RHW, Scholkmann F. The significance of bioelectricity on all levels of organization of an organism. Part 1: From the subcellular level to cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:185-201. [PMID: 36481271 DOI: 10.1016/j.pbiomolbio.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Bioelectricity plays an essential role in the structural and functional organization of biological organisms. In this first article of our three-part series, we summarize the importance of bioelectricity for the basic structural level of biological organization, i.e. from the subcellular level (charges, ion channels, molecules and cell organelles) to cells.
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Affiliation(s)
- Richard H W Funk
- Institute of Anatomy, Center for Theoretical Medicine, TU-Dresden, 01307, Dresden, Germany; Dresden International University, 01067, Dresden, Germany.
| | - Felix Scholkmann
- Biomedical Optics Research Laboratory, Department of Neonatology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland.
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4
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MPEPE, a predictive approach to improve protein expression in E. coli based on deep learning. Comput Struct Biotechnol J 2022; 20:1142-1153. [PMID: 35317239 PMCID: PMC8913310 DOI: 10.1016/j.csbj.2022.02.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022] Open
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5
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Hassan A, Byju S, Whitford PC. The energetics of subunit rotation in the ribosome. Biophys Rev 2021; 13:1029-1037. [PMID: 35059025 PMCID: PMC8724491 DOI: 10.1007/s12551-021-00877-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis in the cell is controlled by an elaborate sequence of conformational rearrangements in the ribosome. The composition of a ribosome varies by species, though they typically contain ∼ 50-100 RNA and protein molecules. While advances in structural techniques have revolutionized our understanding of long-lived conformational states, a vast range of transiently visited configurations can not be directly observed. In these cases, computational/simulation methods can be used to understand the mechanical properties of the ribosome. Insights from these approaches can then help guide next-generation experimental measurements. In this short review, we discuss theoretical strategies that have been deployed to quantitatively describe the energetics of collective rearrangements in the ribosome. We focus on efforts to probe large-scale subunit rotation events, which involve the coordinated displacement of large numbers of atoms (tens of thousands). These investigations are revealing how the molecular structure of the ribosome encodes the mechanical properties that control large-scale dynamics.
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Affiliation(s)
- Asem Hassan
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
| | - Sandra Byju
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
| | - Paul C. Whitford
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
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6
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Jana S, Datta PP. In silico analysis of bacterial translation factors reveal distinct translation event specific pI values. BMC Genomics 2021; 22:220. [PMID: 33781198 PMCID: PMC8008671 DOI: 10.1186/s12864-021-07472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background Protein synthesis is a cellular process that takes place through the successive translation events within the ribosome by the event-specific protein factors, namely, initiation, elongation, release, and recycling factors. In this regard, we asked the question about how similar are those translation factors to each other from a wide variety of bacteria? Hence, we did a thorough in silico study of the translation factors from 495 bacterial sp., and 4262 amino acid sequences by theoretically measuring their pI and MW values that are two determining factors for distinguishing individual proteins in 2D gel electrophoresis in experimental procedures. Then we analyzed the output from various angles. Results Our study revealed the fact that it’s not all same, or all random, but there are distinct orders and the pI values of translation factors are translation event specific. We found that the translation initiation factors are mainly basic, whereas, elongation and release factors that interact with the inter-subunit space of the intact 70S ribosome during translation are strictly acidic across bacterial sp. These acidic elongation factors and release factors contain higher frequencies of glutamic acids. However, among all the translation factors, the translation initiation factor 2 (IF2) and ribosome recycling factor (RRF) showed variable pI values that are linked to the order of phylogeny. Conclusions From the results of our study, we conclude that among all the bacterial translation factors, elongation and release factors are more conserved in terms of their pI values in comparison to initiation and recycling factors. Acidic properties of these factors are independent of habitat, nature, and phylogeny of the bacterial species. Furthermore, irrespective of the different shapes, sizes, and functions of the elongation and release factors, possession of the strictly acidic pI values of these translation factors all over the domain Bacteria indicates that the acidic nature of these factors is a necessary criterion, perhaps to interact into the partially enclosed rRNA rich inter-subunit space of the translating 70S ribosome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07472-x.
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Affiliation(s)
- Soma Jana
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, WB, PIN 741246, India
| | - Partha P Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, WB, PIN 741246, India.
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7
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Dutagaci B, Nawrocki G, Goodluck J, Ashkarran AA, Hoogstraten CG, Lapidus LJ, Feig M. Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments. eLife 2021; 10:64004. [PMID: 33496264 PMCID: PMC7877912 DOI: 10.7554/elife.64004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Phase separation processes are increasingly being recognized as important organizing mechanisms of biological macromolecules in cellular environments. Well-established drivers of phase separation are multi-valency and intrinsic disorder. Here, we show that globular macromolecules may condense simply based on electrostatic complementarity. More specifically, phase separation of mixtures between RNA and positively charged proteins is described from a combination of multiscale computer simulations with microscopy and spectroscopy experiments. Phase diagrams were mapped out as a function of molecular concentrations in experiment and as a function of molecular size and temperature via simulations. The resulting condensates were found to retain at least some degree of internal dynamics varying as a function of the molecular composition. The results suggest a more general principle for phase separation that is based primarily on electrostatic complementarity without invoking polymer properties as in most previous studies. Simulation results furthermore suggest that such phase separation may occur widely in heterogenous cellular environment between nucleic acid and protein components.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Joyce Goodluck
- Department of Physics, Michigan State University, East Lansing, United States
| | - Ali Akbar Ashkarran
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, United States
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Lisa J Lapidus
- Department of Physics, Michigan State University, East Lansing, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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8
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Fulle S, Saini JS, Homeyer N, Gohlke H. Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit. Nucleic Acids Res 2015. [PMID: 26202966 PMCID: PMC4652758 DOI: 10.1093/nar/gkv729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The emergence of multidrug-resistant pathogens will make current antibiotics ineffective. For linezolid, a member of the novel oxazolidinone class of antibiotics, 10 nucleotide mutations in the ribosome have been described conferring resistance. Hypotheses for how these mutations affect antibiotics binding have been derived based on comparative crystallographic studies. However, a detailed description at the atomistic level of how remote mutations exert long-distance effects has remained elusive. Here, we show that the G2032A-C2499A double mutation, located > 10 Å away from the antibiotic, confers linezolid resistance by a complex set of effects that percolate to the binding site. By molecular dynamics simulations and free energy calculations, we identify U2504 and C2452 as spearheads among binding site nucleotides that exert the most immediate effect on linezolid binding. Structural reorganizations within the ribosomal subunit due to the mutations are likely associated with mutually compensating changes in the effective energy. Furthermore, we suggest two main routes of information transfer from the mutation sites to U2504 and C2452. Between these, we observe cross-talk, which suggests that synergistic effects observed for the two mutations arise in an indirect manner. These results should be relevant for the development of oxazolidinone derivatives that are active against linezolid-resistant strains.
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Affiliation(s)
- Simone Fulle
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jagmohan S Saini
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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9
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Kirmizialtin S, Loerke J, Behrmann E, Spahn CMT, Sanbonmatsu KY. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods Enzymol 2015; 558:497-514. [PMID: 26068751 DOI: 10.1016/bs.mie.2015.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An explosion of new data from high-resolution cryo-electron microscopy (cryo-EM) studies has produced a large number of data sets for many species of ribosomes in various functional states over the past few years. While many methods exist to produce structural models for lower resolution cryo-EM reconstructions, high-resolution reconstructions are often modeled using crystallographic techniques and extensive manual intervention. Here, we present an automated fitting technique for high-resolution cryo-EM data sets that produces all-atom models highly consistent with the EM density. Using a molecular dynamics approach, atomic positions are optimized with a potential that includes the cross-correlation coefficient between the structural model and the cryo-EM electron density, as well as a biasing potential preserving the stereochemistry and secondary structure of the biomolecule. Specifically, we use a hybrid structure-based/ab initio molecular dynamics potential to extend molecular dynamics fitting. In addition, we find that simulated annealing integration, as opposed to straightforward molecular dynamics integration, significantly improves performance. We obtain atomistic models of the human ribosome consistent with high-resolution cryo-EM reconstructions of the human ribosome. Automated methods such as these have the potential to produce atomistic models for a large number of ribosome complexes simultaneously that can be subsequently refined manually.
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Affiliation(s)
- Serdal Kirmizialtin
- Department of Chemistry, New York University, Abu Dhabi, United Arab Emirates; New Mexico Consortium, Los Alamos, New Mexico, USA; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elmar Behrmann
- Structural Dynamics of Proteins, Center of Advanced European Studies and Research (CAESAR), Bonn, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karissa Y Sanbonmatsu
- New Mexico Consortium, Los Alamos, New Mexico, USA; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
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10
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Abstract
The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (−0.38 to −0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool.
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Affiliation(s)
- Alexandra Dana
- Department of Biomedical Engineering, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
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11
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Lott BB, Wang Y, Nakazato T. A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly. BMC BIOPHYSICS 2013; 6:13. [PMID: 24152303 PMCID: PMC4016315 DOI: 10.1186/2046-1682-6-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/17/2013] [Indexed: 01/26/2023]
Abstract
BACKGROUND Assembly of the ribosome from its protein and RNA constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. Since the early 1960's, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear.We utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembly process. We compared small subunit (30S) r-protein sequences to those of other housekeeping proteins from 560 bacterial species and searched for correlations between r-protein amino acid content and factors such as assembly binding order, environmental growth temperature, protein size, and contact with ribosomal RNA (rRNA) in the 30S complex. RESULTS We find r-proteins have a significantly high percent of positive residues, which are highly represented at rRNA contact sites. An inverse correlation between the percent of positive residues and r-protein size was identified and is mainly due to the content of Lysine residues, rather than Arginine. Nearly all r-proteins carry a net positive charge, but no statistical correlation between the net charge and the binding order was detected. Thermophilic (high-temperature) r-proteins contain increased Arginine, Isoleucine, and Tyrosine, and decreased Serine and Threonine compared to mesophilic (lower-temperature), reflecting a known distinction between thermophiles and mesophiles, possibly to account for protein thermostability. However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different. CONCLUSIONS Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction. However, the binding order of r-proteins in assembly does not appear to depend on these electrostatics interactions. Additionally, because thermophiles and mesophiles exhibit significantly different amino acid compositions in their sequences but not in the identities of contact sites, we conclude that this electrostatic component of interaction is insensitive to temperature and is not the determining factor differentiating the temperature sensitivity of ribosome assembly.
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Affiliation(s)
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis, 38152 Memphis TN, USA
- Department of Bioinformatics, The University of Memphis, 38152 Memphis TN, USA
| | - Takuya Nakazato
- Department of Bioinformatics, The University of Memphis, 38152 Memphis TN, USA
- Department of Biological Sciences, The University of Memphis, 38152 Memphis TN, USA
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12
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Knight AM, Culviner PH, Kurt-Yilmaz N, Zou T, Ozkan SB, Cavagnero S. Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics. ACS Chem Biol 2013; 8:1195-204. [PMID: 23517476 DOI: 10.1021/cb400030n] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crucial molecular events accompanying protein folding in the cell are still largely unexplored. As nascent polypeptides emerge from the ribosomal exit tunnel, they come in close proximity with the highly negatively charged ribosomal surface. How is the nascent polypeptide influenced by the ribosomal surface? We address this question via the intrinsically disordered protein PIR and a number of its variably charged mutants. Two different populations are identified: one is highly spatially biased, and the other is highly dynamic. The more negatively charged nascent polypeptides emerging from the ribosome are richer in the extremely dynamic population. Hence, nascent proteins with a net negative charge are less likely to interact with the ribosome. Surprisingly, the amplitude of the local motions of the highly dynamic population is much wider than that of disordered polypeptides under physiological conditions, implying that proximity to the ribosomal surface enhances the molecular flexibility of a subpopulation of the nascent protein, much like a denaturing agent would. This effect could be important for a proper structural channeling of the nascent protein and the prevention of cotranslational kinetic trapping. Interestingly, a significant population of the highly spatially biased nascent chain, probably interacting extensively with the ribosome, is present even for very negatively charged nascent proteins. This "sticking" effect likely serves to protect nascent proteins (e.g., from cotranslational aggregation). In all, our results highlight the influence of the ribosome in nascent protein dynamics and show that the ribosome's function in protein biogenesis extends well beyond catalysis of peptide bond formation.
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Affiliation(s)
- Anders M. Knight
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Peter H. Culviner
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Neşe Kurt-Yilmaz
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Taisong Zou
- Department of Physics, Center
for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - S. Banu Ozkan
- Department of Physics, Center
for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
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13
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Dana A, Tuller T. Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol 2012; 8:e1002755. [PMID: 23133360 PMCID: PMC3486846 DOI: 10.1371/journal.pcbi.1002755] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 09/07/2012] [Indexed: 11/25/2022] Open
Abstract
Ribosomal profiling is a promising approach with increasing popularity for studying translation. This approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides. In this study, we focused on ribosomal density profiles of mouse embryonic stem cells. Our analysis suggests, for the first time, that even in mammals such as M. musculus the elongation speed is significantly and directly affected by determinants of the coding sequence such as: 1) the adaptation of codons to the tRNA pool; 2) the local mRNA folding of the coding sequence; 3) the local charge of amino acids encoded in the codon sequence. In addition, our analyses suggest that in general, the translation velocity of ribosomes is slower at the beginning of the coding sequence and tends to increase downstream. Finally, a comparison of these data to the expected biophysical behavior of translation suggests that it suffers from some unknown biases. Specifically, the ribosomal flux measured on the experimental data increases along the coding sequence; however, according to any biophysical model of ribosomal movement lacking internal initiation sites, the flux is expected to remain constant or decrease. Thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance. Gene translation is the process by which ribosomes translate mRNA molecules to proteins, a central process in all living organisms. Thus, understanding the biophysics of gene translation and the way its efficiency is encoded in the different features of the coding sequence has ramifications to every biomedical discipline. Recently, a new large-scale experimental approach named ‘ribosomal profiling’, has been developed for monitoring the ribosomal density at a resolution of single nucleotides. In this study, we analyzed ribosomal profiling data of mouse embryonic stem cells. These data enabled us to directly show that translation velocity is affected by the adaptation of codons to the tRNA pool, local mRNA folding of coding sequence, and local charge of the amino acids encoded in the coding sequence. In addition, our analyses suggest that ribosomal speed tends to be slower at the beginning of the coding sequence. Finally, we report possible biases in the ‘ribosomal profiling’ procedure that should be considered in future studies utilizing this method.
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Affiliation(s)
| | - Tamir Tuller
- The Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
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14
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Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS). COMPUTATIONAL SCIENCE & DISCOVERY 2012; 5:015005. [PMID: 22905037 PMCID: PMC3419494 DOI: 10.1088/1749-4699/5/1/015005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a FORTRAN or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages - Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.
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Affiliation(s)
- Robert Konecny
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0365
- Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0374
- National Biomedical Computational Resource, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Nathan A. Baker
- National Biomedical Computational Resource, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Pacific Northwest National Laboratory, P.O. Box 999, MS K7-28, Richland, WA 99352
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0365
- Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0374
- National Biomedical Computational Resource, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Howard Hughes Medical Institute and Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0365
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15
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Voltz K, Trylska J, Calimet N, Smith JC, Langowski J. Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J 2012; 102:849-58. [PMID: 22385856 DOI: 10.1016/j.bpj.2011.11.4028] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 11/10/2011] [Accepted: 11/28/2011] [Indexed: 11/25/2022] Open
Abstract
To permit access to DNA-binding proteins involved in the control and expression of the genome, the nucleosome undergoes structural remodeling including unwrapping of nucleosomal DNA segments from the nucleosome core. Here we examine the mechanism of DNA dissociation from the nucleosome using microsecond timescale coarse-grained molecular dynamics simulations. The simulations exhibit short-lived, reversible DNA detachments from the nucleosome and long-lived DNA detachments not reversible on the timescale of the simulation. During the short-lived DNA detachments, 9 bp dissociate at one extremity of the nucleosome core and the H3 tail occupies the space freed by the detached DNA. The long-lived DNA detachments are characterized by structural rearrangements of the H3 tail including the formation of a turn-like structure at the base of the tail that sterically impedes the rewrapping of DNA on the nucleosome surface. Removal of the H3 tails causes the long-lived detachments to disappear. The physical consistency of the CG long-lived open state was verified by mapping a CG structure representative of this state back to atomic resolution and performing molecular dynamics as well as by comparing conformation-dependent free energies. Our results suggest that the H3 tail may stabilize the nucleosome in the open state during the initial stages of the nucleosome remodeling process.
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Affiliation(s)
- Karine Voltz
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
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16
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Sanbonmatsu KY. Computational studies of molecular machines: the ribosome. Curr Opin Struct Biol 2012; 22:168-74. [PMID: 22336622 DOI: 10.1016/j.sbi.2012.01.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/19/2012] [Accepted: 01/19/2012] [Indexed: 01/22/2023]
Abstract
The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, X-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information. Single molecule studies produce information on the rates of transitions between these states but do not have high-resolution spatial information. Computational studies have aided in bridging this gap by providing atomic resolution simulations of structural fluctuations and transitions between configurations.
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17
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On the origin of order in the genome organization of ssRNA viruses. Biophys J 2011; 101:774-80. [PMID: 21843467 DOI: 10.1016/j.bpj.2011.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 06/30/2011] [Accepted: 07/01/2011] [Indexed: 11/24/2022] Open
Abstract
Single-stranded RNA (ssRNA) viruses form a major class that includes important human, animal, and plant pathogens. While the principles underlying the structures of their protein capsids are generally well understood, much less is known about the organization of their encapsulated genomic RNAs. Cryo-electron microscopy and x-ray crystallography have revealed striking evidence of order in the packaged genomes of a number of ssRNA viruses. The physical determinants of such order, however, are largely unknown. We study here the relative effect of different energetic contributions, as well as the role of confinement, on the genome packaging of a representative ssRNA virus, the bacteriophage MS2, via a series of biomolecular simulations in which different energy terms are systematically switched off. We show that the bimodal radial density profile of the packaged genome is a consequence of RNA self-repulsion in confinement, suggesting that it should be similar for all ssRNA viruses with a comparable ratio of capsid size/genome length. In contrast, the detailed structure of the outer shell of the RNA density depends crucially on steric contributions from the capsid inner surface topography, implying that the various different polyhedral RNA cages observed in experiment are largely due to differences in the inner surface topography of the capsid.
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18
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Tuller T, Veksler-Lublinsky I, Gazit N, Kupiec M, Ruppin E, Ziv-Ukelson M. Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol 2011; 12:R110. [PMID: 22050731 PMCID: PMC3334596 DOI: 10.1186/gb-2011-12-11-r110] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 09/10/2011] [Accepted: 11/03/2011] [Indexed: 11/13/2022] Open
Abstract
Background Translation is a central process of life, and its regulation is crucial for cell growth. In this article, focusing on two model organisms, Escherichia coli and Saccharomyces cerevisiae, we study how three major local features of a gene's coding sequence (its adaptation to the tRNA pool, its amino acid charge, and its mRNA folding energy) affect its translation elongation. Results We find that each of these three different features has a non-negligible distinct correlation with the speed of translation elongation. In addition, each of these features might contribute independently to slowing down ribosomal speed at the beginning of genes, which was suggested in previous studies to improve ribosomal allocation and the cost of translation, and to decrease ribosomal jamming. Remarkably, a model of ribosomal translation based on these three basic features highly correlated with the genomic profile of ribosomal density. The robustness to transcription errors in terms of the values of these features is higher at the beginnings of genes, suggesting that this region is important for translation. Conclusions The reported results support the conjecture that translation elongation speed is affected by the three coding sequence determinants mentioned above, and not only by adaptation to the tRNA pool; thus, evolution shapes all these determinants along the coding sequences and across genes to improve the organism's translation efficiency.
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Affiliation(s)
- Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Israel.
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19
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Długosz M, Huber GA, McCammon JA, Trylska J. Brownian dynamics study of the association between the 70S ribosome and elongation factor G. Biopolymers 2011; 95:616-27. [PMID: 21394717 PMCID: PMC3125448 DOI: 10.1002/bip.21619] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/28/2011] [Accepted: 02/28/2011] [Indexed: 02/01/2023]
Abstract
Protein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF-G) that facilitates the translocation of transfer RNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF-G/ribosome diffusional encounter and EF-G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF-G/70S ribosome system. We estimated the EF-G association rate constants at 150 and 300 mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF-G/ribosome association paths and found that positioning of the L11 protein of the large ribosomal subunit is likely crucial for EF-G entry to its binding site.
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Affiliation(s)
- Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland.
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20
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Boschitsch AH, Fenley MO. A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids. J Chem Theory Comput 2011; 7:1524-1540. [PMID: 21984876 DOI: 10.1021/ct1006983] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent - analytical solutions are available for this case, thus allowing rigorous assessment of the solution accuracy; (ii) a pair of low dielectric charged spheres embedded in a ionic solvent to compute electrostatic interaction free energies as a function of the distance between sphere centers; (iii) surface potentials of proteins, nucleic acids and their larger-scale assemblies such as ribosomes; and (iv) electrostatic solvation free energies and their salt sensitivities - obtained with both linear and nonlinear Poisson-Boltzmann equation - for a large set of proteins. These latter results along with timings can serve as benchmarks for comparing the performance of different PBE solvers.
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21
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Kulczycka K, Długosz M, Trylska J. Molecular dynamics of ribosomal elongation factors G and Tu. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2011; 40:289-303. [PMID: 21152913 PMCID: PMC3045518 DOI: 10.1007/s00249-010-0647-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/09/2010] [Accepted: 11/16/2010] [Indexed: 11/04/2022]
Abstract
Translation on the ribosome is controlled by external factors. During polypeptide lengthening, elongation factors EF-Tu and EF-G consecutively interact with the bacterial ribosome. EF-Tu binds and delivers an aminoacyl-tRNA to the ribosomal A site and EF-G helps translocate the tRNAs between their binding sites after the peptide bond is formed. These processes occur at the expense of GTP. EF-Tu:tRNA and EF-G are of similar shape, share a common binding site, and undergo large conformational changes on interaction with the ribosome. To characterize the internal motion of these two elongation factors, we used 25 ns long all-atom molecular dynamics simulations. We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex. EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions. The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.
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Affiliation(s)
- Katarzyna Kulczycka
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Science, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Joanna Trylska
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
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22
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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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23
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Lucent D, Snow CD, Aitken CE, Pande VS. Non-bulk-like solvent behavior in the ribosome exit tunnel. PLoS Comput Biol 2010; 6:e1000963. [PMID: 20975935 PMCID: PMC2958802 DOI: 10.1371/journal.pcbi.1000963] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/17/2010] [Indexed: 11/19/2022] Open
Abstract
As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.
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Affiliation(s)
- Del Lucent
- Biophysics Program, Stanford University, Stanford, California, USA
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24
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Intrinsic molecular properties of the protein–protein bridge facilitate ratchet-like motion of the ribosome. Biochem Biophys Res Commun 2010; 399:192-7. [DOI: 10.1016/j.bbrc.2010.07.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 07/15/2010] [Indexed: 12/27/2022]
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25
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Abstract
Computational modeling studies that investigate activity of the bacterial ribosome were reviewed. Computational approaches became possible with the availability of three-dimensional atomic resolution structures of the ribosomal subunits. However, due to the enormous size of the system, theoretical efforts to study the ribosome are few and challenging. For example, to extend the simulation timescales to biologically relevant ones, often, reduced models that require tedious parameterizations need to be applied. To that end, modeling of the ribosome focused on its internal dynamics, electrostatic properties, inhibition by antibiotics, polypeptide folding in the ribosome tunnel and assembly mechanisms driving the formation of the small ribosomal subunit.
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26
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Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 2009; 75:837-45. [PMID: 19004020 DOI: 10.1002/prot.22292] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. The low frequency fluctuations indicate three distinct regions along the tunnel-the entrance, the neck, and the exit-each having distinctly different domain motions. Generally, the lining of the entrance region moves in the exit direction, with the exit region having significantly larger motions, but in a perpendicular direction, whereas the confined neck region has rotational motions. Especially the universally conserved extensions of ribosomal proteins L4 and L22 located at the narrowest and mechanistically strategic region of tunnel undergo generally anti- or non-correlated motions, which may have an important role in nascent polypeptide gating mechanism. These motions appear to be sufficiently robust so as to be unaffected by the presence of a peptide chain in the tunnel.
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Affiliation(s)
- Ozge Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey
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27
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Wittayanarakul K, Hannongbua S, Feig M. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J Comput Chem 2008; 29:673-85. [PMID: 17849388 DOI: 10.1002/jcc.20821] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities.
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28
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Cerutti DS, Baker NA, McCammon JA. Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models? J Chem Phys 2007; 127:155101. [PMID: 17949217 DOI: 10.1063/1.2771171] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560 ns of simulation time. A finite, positive potential of 13-24 kbTec(-1) (where T=300 K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 A from the solute surface, on average 0.008 ec/A3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0365, USA.
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29
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Radhakrishnan R, Schlick T. Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. Biochem Biophys Res Commun 2006; 350:521-9. [PMID: 17022941 PMCID: PMC1976263 DOI: 10.1016/j.bbrc.2006.09.059] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2006] [Accepted: 09/13/2006] [Indexed: 10/24/2022]
Abstract
Tracking the structural and energetic changes in the pathways of DNA replication and repair is central to the understanding of these important processes. Here we report favorable mechanisms of the polymerase-catalyzed phosphoryl transfer reactions corresponding to correct and incorrect nucleotide incorporations in the DNA by using a novel protocol involving energy minimizations, dynamics simulations, quasi-harmonic free energy calculations, and mixed quantum mechanics/molecular mechanics dynamics simulations. Though the pathway proposed may not be unique and invites variations, geometric and energetic arguments support the series of transient intermediates in the phosphoryl transfer pathways uncovered here for both the G:C and G:A systems involving a Grotthuss hopping mechanism of proton transfer between water molecules and the three conserved aspartate residues in pol beta's active-site. In the G:C system, the rate-limiting step is the initial proton hop with a free energy of activation of at least 17 kcal/mol, which corresponds closely to measured k(pol) values. Fidelity discrimination in pol beta can be explained by a significant loss of stability of the closed ternary complex of the enzyme in the G:A system and much higher activation energy of the initial step of nucleophilic attack, namely deprotonation of terminal DNA primer O3'H group. Thus, subtle differences in the enzyme active-site between matched and mismatched base pairs generate significant differences in catalytic performance.
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Affiliation(s)
- Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, 210 S. 33rd Street, Philadelphia, PA,
| | - Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012,
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30
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Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 2006; 82:106-20. [PMID: 16278831 PMCID: PMC2440512 DOI: 10.1002/bip.20409] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic virus (CMV) were investigated using numerical solutions to the Poisson-Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in the absence of divalent cations when the pH is raised from 5 to 7. CMV, although structurally homologous, does not undergo this transition. An analysis of the calculated electrostatic potential confirms that a strong electrostatic repulsion at the calcium-binding sites in the CCMV capsid is most likely the driving force for the capsid swelling process during the release of calcium. The binding interaction between the encapsulated genome material (RNA) inside of the capsid and the inner capsid shell is weakened during the swelling transition. This probably aids in the RNA release process, but it is unlikely that the RNA is released through capsid openings due to unfavorable electrostatic interaction between the RNA and capsid inner shell residues at these openings. Calculations of the calcium binding energies show that Ca(2+) can bind both to the native and swollen forms of the CCMV virion. Favorable binding to the swollen form suggests that Ca(2+) ions can induce the capsid contraction and stabilize the native form.
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Affiliation(s)
- Robert Konecny
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, 92093-0365, USA.
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31
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Abstract
Computational studies of large macromolecular assemblages have come a long way during the past 10 years. With the explosion of computer power and parallel computing, timescales of molecular dynamics simulations have been extended far beyond the hundreds of picoseconds timescale. However, limitations remain for studies of large-scale conformational changes occurring on timescales beyond nanoseconds, especially for large macromolecules. In this review, we describe recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information. Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin.
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Affiliation(s)
- Florence Tama
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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32
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Korennykh AV, Piccirilli JA, Correll CC. The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Mol Biol 2006; 13:436-43. [PMID: 16604082 PMCID: PMC1847776 DOI: 10.1038/nsmb1082] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 03/07/2006] [Indexed: 11/09/2022]
Abstract
Alpha-sarcin ribotoxins comprise a unique family of ribonucleases that cripple the ribosome by catalyzing endoribonucleolytic cleavage of ribosomal RNA at a specific location in the sarcin/ricin loop (SRL). The SRL structure alone is cleaved site-specifically by the ribotoxin, but the ribosomal context enhances the reaction rate by several orders of magnitude. We show that, for the alpha-sarcin-like ribotoxin restrictocin, this catalytic advantage arises from favorable electrostatic interactions with the ribosome. Restrictocin binds at many sites on the ribosomal surface and under certain conditions cleaves the SRL with a second-order rate constant of 1.7 x 10(10) M(-1) s(-1), a value that matches the predicted frequency of random restrictocin-ribosome encounters. The results suggest a mechanism of target location whereby restrictocin encounters ribosomes randomly and diffuses within the ribosomal electrostatic field to the SRL. These studies show a role for electrostatics in protein-ribosome recognition.
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Affiliation(s)
- Alexei V Korennykh
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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33
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Law MJ, Linde ME, Chambers EJ, Oubridge C, Katsamba PS, Nilsson L, Haworth IS, Laird-Offringa IA. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res 2006; 34:275-85. [PMID: 16407334 PMCID: PMC1326249 DOI: 10.1093/nar/gkj436] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes.
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Affiliation(s)
- Michael J. Law
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Michael E. Linde
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Eric J. Chambers
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Chris Oubridge
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 2QH, UK
| | - Phinikoula S. Katsamba
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Lennart Nilsson
- Karolinska Institutet, Department of Biosciences at NovumSE-141 57 Huddinge, Sweden
| | - Ian S. Haworth
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
| | - Ite A. Laird-Offringa
- Department of Biochemistry and Molecular Biology, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- Department of Surgery, Keck School of Medicine, University of Southern CaliforniaLos Angeles, CA 90089-9176, USA
- To whom correspondence should be addressed. Tel: +1 323 865 0655; Fax: +1 323 865 0158;
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Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL. The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. J Chem Theory Comput 2006; 2:696-704. [PMID: 17710199 PMCID: PMC1948848 DOI: 10.1021/ct600060d] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode analysis for multiple scales on a high-resolution protein data set using various cutoff radii to define the residues considered to be interacting, or the extent of cooperativity of their motions. These scales include the residue-, atomic-, proton-, and explicit solvent-levels. Interestingly, atomic, proton, and explicit solvent level calculations all provide similar results at the same cutoff value, with the computed mean-square fluctuations showing only a slightly higher correlation (0.61) with the experimental temperature factors from crystallography than the results of the residue-level coarse-graining. The qualitative behavior of each level of coarse graining is similar at different cutoff values. The correlations between these fluctuations and the number of internal contacts improve with increased cutoff values. Our results demonstrate that atomic level elastic network models provide an improved representation for the collective motions of proteins compared to the coarse-grained models.
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Affiliation(s)
- Taner Z. Sen
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Yaping Feng
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011
| | - John V. Garcia
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
| | - Andrzej Kloczkowski
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
| | - Robert L. Jernigan
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
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Feig M, Chocholoušová J, Tanizaki S. Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail. Theor Chem Acc 2005. [DOI: 10.1007/s00214-005-0062-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Sanbonmatsu KY, Joseph S, Tung CS. Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A 2005; 102:15854-9. [PMID: 16249344 PMCID: PMC1266076 DOI: 10.1073/pnas.0503456102] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Decoding is the key step during protein synthesis that enables information transfer from RNA to protein, a process critical for the survival of all organisms. We have used large-scale (2.64 x 10(6) atoms) all-atom simulations of the entire ribosome to understand a critical step of decoding. Although the decoding problem has been studied for more than four decades, the rate-limiting step of cognate tRNA selection has only recently been identified. This step, known as accommodation, involves the movement inside the ribosome of the aminoacyl-tRNA from the partially bound "A/T" state to the fully bound "A/A" state. Here, we show that a corridor of 20 universally conserved ribosomal RNA bases interacts with the tRNA during the accommodation movement. Surprisingly, the tRNA is impeded by the A-loop (23S helix 92), instead of enjoying a smooth transition to the A/A state. In particular, universally conserved 23S ribosomal RNA bases U2492, C2556, and C2573 act as a 3D gate, causing the acceptor stem to pause before allowing entrance into the peptidyl transferase center. Our simulations demonstrate that the flexibility of the acceptor stem of the tRNA, in addition to flexibility of the anticodon arm, is essential for tRNA selection. This study serves as a template for simulating conformational changes in large (>10(6) atoms) biological and artificial molecular machines.
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Affiliation(s)
- Kevin Y Sanbonmatsu
- Department of Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Abstract
We studied slower global coupled motions of the ribosome with half a microsecond of coarse-grained molecular dynamics. A low-resolution anharmonic network model that allows for the evolution of tertiary structure and long-scale sampling was developed and parameterized. Most importantly, we find that functionally important movements of L7/L12 and L1 lateral stalks are anticorrelated. Other principal directions of motions include widening of the tRNA cleft and the rotation of the small subunit which occurs as one block and is in phase with the movement of L1 stalk. The effect of the dynamical correlation pattern on the elongation process is discussed. Small fluctuations of the 3' tRNA termini and anticodon nucleotides show tight alignment of substrates for the reaction. Our model provides an efficient and reliable way to study the dynamics of large biomolecular systems composed of both proteins and nucleic acids.
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Affiliation(s)
- Joanna Trylska
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California, USA.
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Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers 2004; 75:325-37. [PMID: 15386271 PMCID: PMC2426774 DOI: 10.1002/bip.20120] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations.
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Affiliation(s)
- Deqiang Zhang
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0365, USA.
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