1
|
Chowdhury AR, Sapkota D, Girodat D. Conformational changes of ribosomes during translation elongation resolved by molecular dynamics simulations. Curr Opin Struct Biol 2024; 86:102804. [PMID: 38569462 DOI: 10.1016/j.sbi.2024.102804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Molecular dynamics simulations have emerged as a powerful set of tools to unravel the intricate dynamics of ribosomes during protein synthesis. Recent advancements in this field have enabled simulations to delve deep into the conformational rearrangements of ribosomes and associated factors, providing invaluable insights into the intricacies of translation. Emphasis on simulations has recently been on translation elongation, such as tRNA selection, translocation, and ribosomal head-swivel motions. These studies have offered crucial structural interpretations of how genetic information is faithfully translated into proteins. This review outlines recent discoveries concerning ribosome conformational changes occurring during translation elongation, as elucidated through molecular dynamics simulations.
Collapse
Affiliation(s)
- Anuradha Rai Chowdhury
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA. https://twitter.com/atomcellplankl
| | - Divya Sapkota
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Dylan Girodat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA.
| |
Collapse
|
2
|
Serbezeanu D, Iftime MM, Ailiesei GL, Ipate AM, Bargan A, Vlad-Bubulac T, Rîmbu CM. Evaluation of Poly(vinyl alcohol)-Xanthan Gum Hydrogels Loaded with Neomycin Sulfate as Systems for Drug Delivery. Gels 2023; 9:655. [PMID: 37623110 PMCID: PMC10454009 DOI: 10.3390/gels9080655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
In recent years, multidrug-resistant bacteria have developed the ability to resist multiple antibiotics, limiting the available options for effective treatment. Raising awareness and providing education on the appropriate use of antibiotics, as well as improving infection control measures in healthcare facilities, are crucial steps to address the healthcare crisis. Further, innovative approaches must be adopted to develop novel drug delivery systems using polymeric matrices as carriers and support to efficiently combat such multidrug-resistant bacteria and thus promote wound healing. In this context, the current work describes the use of two biocompatible and non-toxic polymers, poly(vinyl alcohol) (PVA) and xanthan gum (XG), to achieve hydrogel networks through cross-linking by oxalic acid following the freezing/thawing procedure. PVA/XG-80/20 hydrogels were loaded with different quantities of neomycin sulfate to create promising low-class topical antibacterial formulations with enhanced antimicrobial effects. The inclusion of neomycin sulfate in the hydrogels is intended to impart them with powerful antimicrobial properties, thereby facilitating the development of exceptionally efficient topical antibacterial formulations. Thus, incorporating higher quantities of neomycin sulfate in the PVA/XG-80/20-2 and PVA/XG-80/20-3 formulations yielded promising cycling characteristics. These formulations exhibited outstanding removal efficiency, exceeding 80% even after five cycles, indicating remarkable and consistent adsorption performance with repeated use. Furthermore, both PVA/XG-80/20-2 and PVA/XG-80/20-3 formulations outperformed the drug-free sample, PVA/XG-80/20, demonstrating a significant enhancement in maximum compressive stress.
Collapse
Affiliation(s)
- Diana Serbezeanu
- “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.M.I.); (G.-L.A.); (A.-M.I.); (A.B.); (T.V.-B.)
| | - Manuela Maria Iftime
- “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.M.I.); (G.-L.A.); (A.-M.I.); (A.B.); (T.V.-B.)
| | - Gabriela-Liliana Ailiesei
- “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.M.I.); (G.-L.A.); (A.-M.I.); (A.B.); (T.V.-B.)
| | - Alina-Mirela Ipate
- “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.M.I.); (G.-L.A.); (A.-M.I.); (A.B.); (T.V.-B.)
| | - Alexandra Bargan
- “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.M.I.); (G.-L.A.); (A.-M.I.); (A.B.); (T.V.-B.)
| | - Tǎchiţǎ Vlad-Bubulac
- “Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania; (M.M.I.); (G.-L.A.); (A.-M.I.); (A.B.); (T.V.-B.)
| | - Cristina Mihaela Rîmbu
- Department of Public Health, “Ion Ionescu de la Brad” Iasi University of Life Sciences, 8 Sadoveanu Alley, 707027 Iasi, Romania;
| |
Collapse
|
3
|
Adeyemi KD, Audu S, Oloke JA, Oladiji OE, Salawu KF, Ahmed RA, Sulaimon RO. Influence of Crescentia cujete and Launaea taraxacifolia leaves on growth, immune indices, gut microbiota, blood chemistry, carcass, and meat quality in broiler chickens. Trop Anim Health Prod 2021; 53:365. [PMID: 34156587 DOI: 10.1007/s11250-021-02812-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022]
Abstract
The rising concerns pertaining to the safety of synthetic supplements in livestock production have encouraged the exploration of potential alternatives. This study investigated the growth, gut microbiota, blood chemistry, immune indices, meat quality, and antioxidant status in broiler chickens supplemented with Crescentia cujete leaf (CCL), Launaea taraxacifolia leaf (LTL), and a combination of antibiotic (70% oxytetracycline + 30% neomycin) and tert-Butylhydroxyanisole. One-day-old Ross 308 chicks (n = 420) were randomly assigned to either T-1, basal diet (BD) only; T-2, BD + 0.4 g/kg antibiotic + 0.13 g/kg tert-butylhydroxyanisole; T-3, BD + 2.5 g/kg LTL; T-4, BD + 5 g/kg LTL; T-5, BD + 2.5 g/kg CCL; or T-6, BD + 5 g/kg CCL for 42 days. Each dietary group had seven replicates with ten chicks per replicate. Body weight gain and carcass weight were higher (P < 0.05) in the T-2, T-4, T-5, and T-6 birds compared with those of other birds. At 1-21 days, the T-2 and T-4 birds consumed more feed than the T-1 and T-3 birds. At 22-42 days, the T-4 birds consumed more (P < 0.05) feed than the T-1 and T-3 birds. During 1-42 days, the T-1 and T-3 birds consumed less (P < 0.05) feed than other birds. At 22-42 days and 1-42 days, the T-1 had lower feed efficiency (P < 0.05) than other birds except for the T-3 birds. The CCL and LTL birds had lower (P < 0.05) serum LDL cholesterol and higher HDL cholesterol compared with other birds. Hematology, splenic interleukin-1β, immunoglobulin M, ileal and caecal total aerobic bacteria counts, caecal Lactobacillus spp., and meat physicochemical properties were unaffected by diets. The T-1 birds had higher (P < 0.05) ileal and caecal Clostridium spp., E. coli, and Salmonella spp. compared with birds fed other diets. The CCL and LTL birds had higher ileal Lactobacillus counts. Splenic IL-10 was higher (P < 0.05) in the T-2, T-4, and T-6 birds compared with that in other birds. Dietary supplementation with CCL, LTL, and a combination of antibiotic and tert-butylhydroxyanisole repressed (P < 0.05) splenic tumor necrosis-α and immunoglobulin G. The T-1 breast meat had lower glutathione peroxidase and catalase. The T-4 meat had higher (P < 0.05) superoxide dismutase, glutathione peroxidase, catalase, and total antioxidant capacity compared with other meats. On day 3 postmortem, meats obtained from birds supplemented with CCL, LTL, and a combination of antibiotic and tert-butylhydroxyanisole had lower (P < 0.05) carbonyl and malondialdehyde contents than the meat from the non-supplemented birds. The 5 g/kg CCL and 5 g/kg LTL could be used as antimicrobial and antioxidant in broiler diets.
Collapse
Affiliation(s)
- Kazeem D Adeyemi
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria.
| | - Suleman Audu
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria
| | - Jerry A Oloke
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria
| | - Olufe E Oladiji
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria
| | - Kehinde F Salawu
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria
| | - Raheemat A Ahmed
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria
| | - Rasheed O Sulaimon
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, PMB 1515, Nigeria
| |
Collapse
|
4
|
Abu-Saleh AAAA, Sharma S, Yadav A, Poirier RA. Role of Asp190 in the Phosphorylation of the Antibiotic Kanamycin Catalyzed by the Aminoglycoside Phosphotransferase Enzyme: A Combined QM:QM and MD Study. J Phys Chem B 2020; 124:3494-3504. [DOI: 10.1021/acs.jpcb.0c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Abd Al-Aziz A. Abu-Saleh
- Chemistry Department, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| | - Sweta Sharma
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - Arpita Yadav
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - Raymond A. Poirier
- Chemistry Department, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| |
Collapse
|
5
|
Zada SL, Baruch BB, Simhaev L, Engel H, Fridman M. Chemical Modifications Reduce Auditory Cell Damage Induced by Aminoglycoside Antibiotics. J Am Chem Soc 2020; 142:3077-3087. [PMID: 31958945 DOI: 10.1021/jacs.9b12420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although aminoglycoside antibiotics are effective against Gram-negative infections, these drugs often cause irreversible hearing damage. Binding to the decoding site of the eukaryotic ribosomes appears to result in ototoxicity, but there is evidence that other effects are involved. Here, we show how chemical modifications of apramycin and geneticin, considered among the least and most toxic aminoglycosides, respectively, reduce auditory cell damage. Using molecular dynamics simulations, we studied how modified aminoglycosides influence the essential freedom of movement of the decoding site of the ribosome, the region targeted by aminoglycosides. By determining the ratio of a protein translated in mitochondria to that of a protein translated in the cytoplasm, we showed that aminoglycosides can paradoxically elevate rather than reduce protein levels. We showed that certain aminoglycosides induce rapid plasma membrane permeabilization and that this nonribosomal effect can also be reduced through chemical modifications. The results presented suggest a new paradigm for the development of safer aminoglycoside antibiotics.
Collapse
Affiliation(s)
- Sivan Louzoun Zada
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , Israel , 6997801
| | - Bar Ben Baruch
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , Israel , 6997801
| | - Luba Simhaev
- Blavatnik Center for Drug Discovery , Tel Aviv University , Tel Aviv , 6997801 , Israel
| | - Hamutal Engel
- Blavatnik Center for Drug Discovery , Tel Aviv University , Tel Aviv , 6997801 , Israel
| | - Micha Fridman
- School of Chemistry, Raymond and Beverley Sackler Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , Israel , 6997801
| |
Collapse
|
6
|
Sanbonmatsu KY. Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR. Curr Opin Struct Biol 2019; 55:104-113. [PMID: 31125796 DOI: 10.1016/j.sbi.2019.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022]
Abstract
Recent advances in biotechnology such as Hi-C, CRISPR/Cas9 and ribosome display have placed nucleoprotein complexes at center stage. Understanding the structural dynamics of these complexes aids in optimizing protocols and interpreting data for these new technologies. The integration of simulation and experiment has helped advance mechanistic understanding of these systems. Coarse-grained simulations, reduced-description models, and explicit solvent molecular dynamics simulations yield useful complementary perspectives on nucleoprotein complex structural dynamics. When combined with Hi-C, cryo-EM, and single molecule measurements, these simulations integrate disparate forms of experimental data into a coherent mechanism.
Collapse
|
7
|
Abstract
Aminoglycoside antibiotics are protein synthesis inhibitors applied to treat infections caused mainly by aerobic Gram-negative bacteria. Due to their adverse side effects they are last resort antibiotics typically used to combat pathogens resistant to other drugs. Aminoglycosides target ribosomes. We describe the interactions of aminoglycoside antibiotics containing a 2-deoxystreptamine (2-DOS) ring with 16S rRNA. We review the computational studies, with a focus on molecular dynamics (MD) simulations performed on RNA models mimicking the 2-DOS aminoglycoside binding site in the small ribosomal subunit. We also briefly discuss thermodynamics of interactions of these aminoglycosides with their 16S RNA target.
Collapse
|
8
|
Electrostatic interactions in aminoglycoside-RNA complexes. Biophys J 2015; 108:655-65. [PMID: 25650932 DOI: 10.1016/j.bpj.2014.12.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/20/2014] [Accepted: 12/10/2014] [Indexed: 11/21/2022] Open
Abstract
Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity.
Collapse
|
9
|
Dudek M, Romanowska J, Wituła T, Trylska J. Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies. Biochimie 2014; 102:188-202. [PMID: 24769038 DOI: 10.1016/j.biochi.2014.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding.
Collapse
Affiliation(s)
- Marta Dudek
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland.
| |
Collapse
|
10
|
Trylska J, Thoduka SG, Dąbrowska Z. Using sequence-specific oligonucleotides to inhibit bacterial rRNA. ACS Chem Biol 2013; 8:1101-9. [PMID: 23631412 DOI: 10.1021/cb400163t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The majority of antibiotics used in the clinic target bacterial protein synthesis. However, the widespread emergence of bacterial resistance to existing drugs creates a need to discover or develop new therapeutic agents. Ribosomal RNA (rRNA) has been a target for numerous antibiotics that bind to functional rRNA regions such as the peptidyl transferase center, polypeptide exit tunnel, and tRNA binding sites. Even though the atomic resolution structures of many ribosome-antibiotic complexes have been solved, improving the ribosome-acting drugs is difficult because the large rRNA has a complicated 3D architecture and is surrounded by numerous proteins. Computational approaches, such as structure-based design, often fail when applied to rRNA binders because electrostatics dominate the interactions and the effect of ions and bridging waters is difficult to account for in the scoring functions. Improving the classical anti-ribosomal agents has not proven particularly successful and has not kept pace with acquired resistance. So one needs to look for other ways to combat the ribosomes, finding either new rRNA targets or totally different compounds. There have been some efforts to design translation inhibitors that act on the basis of the sequence-specific hybridization properties of nucleic acid bases. Indeed oligonucleotides hybridizing with functional regions of rRNA have been shown to inhibit translation. Also, some peptides have been shown to be reasonable inhibitors. In this review we describe these nonconventional approaches to screening for ribosome inhibition and function of particular rRNA regions. We discuss inhibitors against rRNA that may be designed according to nucleotide sequence and higher order structure.
Collapse
Affiliation(s)
- Joanna Trylska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Sapna G. Thoduka
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Zofia Dąbrowska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| |
Collapse
|
11
|
Frazier AD, Champney WS. Impairment of ribosomal subunit synthesis in aminoglycoside-treated ribonuclease mutants of Escherichia coli. Arch Microbiol 2012; 194:1033-41. [PMID: 22930249 DOI: 10.1007/s00203-012-0839-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 06/29/2012] [Accepted: 08/13/2012] [Indexed: 10/28/2022]
Abstract
The bacterial ribosome is an important target for many antimicrobial agents. Aminoglycoside antibiotics bind to both 30S and 50S ribosomal subunits, inhibiting translation and subunit formation. During ribosomal subunit biogenesis, ribonucleases (RNases) play an important role in rRNA processing. E. coli cells deficient for specific processing RNases are predicted to have an increased sensitivity to neomycin and paromomycin. Four RNase mutant strains showed an increased growth sensitivity to both aminoglycoside antibiotics. E. coli strains deficient for the rRNA processing enzymes RNase III, RNase E, RNase G or RNase PH showed significantly reduced subunit amounts after antibiotic treatment. A substantial increase in a 16S RNA precursor molecule was observed as well. Ribosomal RNA turnover was stimulated, and an enhancement of 16S and 23S rRNA fragmentation was detected in E. coli cells deficient for these enzymes. This work indicates that bacterial RNases may be novel antimicrobial targets.
Collapse
Affiliation(s)
- Ashley D Frazier
- Department of Biochemistry and Molecular Biology, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | | |
Collapse
|
12
|
Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
Collapse
Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
| |
Collapse
|
13
|
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.
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland.
| | | | | | | |
Collapse
|
15
|
Romanowska J, McCammon JA, Trylska J. Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site. PLoS Comput Biol 2011; 7:e1002099. [PMID: 21814503 PMCID: PMC3140962 DOI: 10.1371/journal.pcbi.1002099] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/08/2011] [Indexed: 01/15/2023] Open
Abstract
Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406C∶U1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations.
Collapse
MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Drug Resistance, Bacterial/drug effects
- Drug Resistance, Bacterial/genetics
- Hydrogen Bonding
- Molecular Dynamics Simulation
- Mutation
- Paromomycin/pharmacology
- Protein Binding
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
Collapse
Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw Poland.
| | | | | |
Collapse
|
16
|
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.
Collapse
|
17
|
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.
Collapse
|
18
|
Houghton JL, Green KD, Chen W, Garneau-Tsodikova S. The future of aminoglycosides: the end or renaissance? Chembiochem 2010; 11:880-902. [PMID: 20397253 DOI: 10.1002/cbic.200900779] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 11/05/2022]
Abstract
Although aminoglycosides have been used as antibacterials for decades, their use has been hindered by their inherent toxicity and the resistance that has emerged to these compounds. It seems that such issues have relegated a formerly front-line class of antimicrobials to the proverbial back shelf. However, recent advances have demonstrated that novel aminoglycosides have a potential to overcome resistance as well as to be used to treat HIV-1 and even human genetic disorders, with abrogated toxicity. It is not the end for aminoglycosides, but rather, the challenges faced by researchers have led to ingenuity and a change in how we view this class of compounds, a renaissance.
Collapse
Affiliation(s)
- Jacob L Houghton
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | | | | | | |
Collapse
|
19
|
Stansfeld PJ, Hopkinson R, Ashcroft FM, Sansom MSP. PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations. Biochemistry 2009; 48:10926-33. [PMID: 19839652 PMCID: PMC2895862 DOI: 10.1021/bi9013193] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Phosphatidylinositol bisphosphate (PIP(2)) is an activator of mammalian inwardly rectifying potassium (Kir) channels. Multiscale simulations, via a sequential combination of coarse-grained and atomistic molecular dynamics, enabled exploration of the interactions of PIP(2) molecules within the inner leaflet of a lipid bilayer membrane with possible binding sites on Kir channels. Three Kir channel structures were investigated: X-ray structures of KirBac1.1 and of a Kir3.1-KirBac1.3 chimera and a homology model of Kir6.2. Coarse-grained simulations of the Kir channels in PIP(2)-containing lipid bilayers identified the PIP(2)-binding site on each channel. These models of the PIP(2)-channel complexes were refined by conversion to an atomistic representation followed by molecular dynamics simulation in a lipid bilayer. All three channels were revealed to contain a conserved binding site at the N-terminal end of the slide (M0) helix, at the interface between adjacent subunits of the channel. This binding site agrees with mutagenesis data and is in the proximity of the site occupied by a detergent molecule in the Kir chimera channel crystal. Polar contacts in the coarse-grained simulations corresponded to long-lived electrostatic and H-bonding interactions between the channel and PIP(2) in the atomistic simulations, enabling identification of key side chains.
Collapse
Affiliation(s)
- Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | | | | |
Collapse
|