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Bovdilova A, Alexandre BM, Höppner A, Luís IM, Alvarez CE, Bickel D, Gohlke H, Decker C, Nagel-Steger L, Alseekh S, Fernie AR, Drincovich MF, Abreu IA, Maurino VG. Posttranslational Modification of the NADP-Malic Enzyme Involved in C 4 Photosynthesis Modulates the Enzymatic Activity during the Day. THE PLANT CELL 2019; 31:2525-2539. [PMID: 31363039 PMCID: PMC6790091 DOI: 10.1105/tpc.19.00406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 05/07/2023]
Abstract
Evolution of the C4 photosynthetic pathway involved in some cases recruitment of housekeeping proteins through gene duplication and their further neofunctionalization. NADP-malic enzyme (ME), the most widespread C4 decarboxylase, has increased its catalytic efficiency and acquired regulatory properties that allowed it to participate in the C4 pathway. Here, we show that regulation of maize (Zea mays) C4-NADP-ME activity is much more elaborate than previously thought. Using mass spectrometry, we identified phosphorylation of the Ser419 residue of C4-NADP-ME in protein extracts of maize leaves. The phosphorylation event increases in the light, with a peak at Zeitgeber time 2. Phosphorylation of ZmC4-NADP-ME drastically decreases its activity as shown by the low residual activity of the recombinant phosphomimetic mutant. Analysis of the crystal structure of C4-NADP-ME indicated that Ser419 is involved in the binding of NADP at the active site. Molecular dynamics simulations and effective binding energy computations indicate a less favorable binding of the cofactor NADP in the phosphomimetic and the phosphorylated variants. We propose that phosphorylation of ZmC4-NADP-ME at Ser419 during the first hours in the light is a cellular mechanism that fine tunes the enzymatic activity to coordinate the carbon concentration mechanism with the CO2 fixation rate, probably to avoid CO2 leakiness from bundle sheath cells.
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Affiliation(s)
- Anastasiia Bovdilova
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University Düsseldorf, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Astrid Höppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Inês Matias Luís
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Clarisa E Alvarez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - David Bickel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems-Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Christina Decker
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center for Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - Isabel A Abreu
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Veronica G Maurino
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University Düsseldorf, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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102
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Catalogna G, Moraca F, D'Antona L, Dattilo V, Perrotti G, Lupia A, Costa G, Ortuso F, Iuliano R, Trapasso F, Amato R, Alcaro S, Perrotti N. Review about the multi-target profile of resveratrol and its implication in the SGK1 inhibition. Eur J Med Chem 2019; 183:111675. [PMID: 31539779 DOI: 10.1016/j.ejmech.2019.111675] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 01/08/2023]
Abstract
Resveratrol (trans-3,4',5-trihydroxystilbene) is a polyphenolic natural product with a well-known polypharmacological profile that places it among the multi-target-directed ligands (MTDLs). Given its protective action against a wide number of chronic diseases, in this review, we introduce a general overview about the cardioprotective and antioxidant effects, the antidiabetic, neuroprotective and anti-inflammatory effects of this polyphenol. In the second part of the manuscript, we focused our attention on the anticancer activity of Resveratrol, given the alteration of many different signaling pathways, leading to suppression of tumor cell proliferation in numerous cancer types. Among the several anticancer targets involved in the mechanism of action of Resveratrol, here we introduce experimental and molecular modeling studies performed against the SGK1 protein as a novel anticancer target of Resveratrol. SGK1 inhibitors have been demonstrated to inhibit cell growth of different cancer cells. We demonstrated that resveratrol inhibits SGK1 in vitro and in intact cells, affecting proliferation and survival of HUH7 human hepatoma cells. Our findings demonstrate that resveratrol may function as a SGK1 inhibitor, suggesting possible applications in sodium retention and cancer.
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Affiliation(s)
- Giada Catalogna
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Federica Moraca
- Dipartimento di Scienze Della Salute, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy; Department of Pharmacy, University of Napoli "Federico II", Via D. Montesano 49, I-80131 Napoli, Italy; Net4Science Srl, Università "Magna Græcia", Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy
| | - Lucia D'Antona
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Vincenzo Dattilo
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Giuseppe Perrotti
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Antonio Lupia
- Dipartimento di Scienze Della Salute, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy; Net4Science Srl, Università "Magna Græcia", Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze Della Salute, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy; Net4Science Srl, Università "Magna Græcia", Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze Della Salute, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy; Net4Science Srl, Università "Magna Græcia", Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy
| | - Rodolfo Iuliano
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Francesco Trapasso
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Rosario Amato
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze Della Salute, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy; Net4Science Srl, Università "Magna Græcia", Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy.
| | - Nicola Perrotti
- Dipartimento di Medicina Sperimentale e Clinica, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy.
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103
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Pokorná P, Krepl M, Bártová E, Šponer J. Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. J Chem Theory Comput 2019; 15:5659-5673. [DOI: 10.1021/acs.jctc.9b00434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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104
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Wang L, Gao Y, Dai F, Kong D, Wang H, Sun P, Shi Z, Sheng X, Xu B, Yin L. Geometrical and Chemical-Dependent Hydrolysis Mechanisms of Silicon Nanomembranes for Biodegradable Electronics. ACS APPLIED MATERIALS & INTERFACES 2019; 11:18013-18023. [PMID: 31010291 DOI: 10.1021/acsami.9b03546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biodegradable electronic devices that physically disappear in physiological or environmental solutions are of critical importance for widespread applications in healthcare management and environmental sustainability. The precise modulation of materials and devices dissolution with on-demand operational lifetime, however, remain a key challenge. Silicon nanomembranes (Si NMs) are one of the essential semiconductor components for high-performance biodegradable electronics at the system level. In this work, we discover unusual hydrolysis behaviors of Si NMs that are significantly dependent on the dimensions of devices as well as their surface chemistry statuses. The experiments show a pronounced increase in hydrolysis rates of p-type Si NMs with larger sizes, and mechanical stirring introduces a significant decrease in dissolution rates. The presence of phosphates and potassium ions in solutions, or lower dopant levels of Si NMs will facilitate the degradation of Si NMs and will also lead to a stronger size-dependent effect. Molecular dynamics simulations are performed to reveal ion adsorption mechanisms of Si NMs under different surface charge statuses and confirm our experimental observations. Through geometrical designs, Si NM-based electrode arrays with tunable dissolution lifetime are formed, and their electrochemical properties are analyzed in vitro. These results offer new controlling strategies to modulate the operational time frames of Si NMs through geometrical design and surface chemistry modification and provide crucial fundamental understandings for engineering high-performance biodegradable electronics.
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Affiliation(s)
| | - Yuan Gao
- Department of Mechanical and Aerospace Engineering , University of Virginia , Charlottesville , Virginia 22904 , United States
| | | | | | | | | | | | | | - Baoxing Xu
- Department of Mechanical and Aerospace Engineering , University of Virginia , Charlottesville , Virginia 22904 , United States
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105
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Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P. Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. J Chem Theory Comput 2019; 15:3288-3305. [PMID: 30896943 PMCID: PMC7491206 DOI: 10.1021/acs.jctc.8b00955] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular dynamics (MD) simulations became a leading tool for investigation of structural dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force fields, ffs), RNA ffs have persisting deficiencies, which hamper their utilization in quantitatively accurate simulations. Previous studies have shown that at least two salient problems contribute to difficulties in the description of free-energy landscapes of small RNA motifs: (i) excessive stabilization of the unfolded single-stranded RNA ensemble by intramolecular base-phosphate and sugar-phosphate interactions and (ii) destabilization of the native folded state by underestimation of stability of base pairing. Here, we introduce a general ff term (gHBfix) that can selectively fine-tune nonbonding interaction terms in RNA ffs, in particular, the H bonds. The gHBfix potential affects the pairwise interactions between all possible pairs of the specific atom types, while all other interactions remain intact; i.e., it is not a structure-based model. In order to probe the ability of the gHBfix potential to refine the ff nonbonded terms, we performed an extensive set of folding simulations of RNA tetranucleotides and tetraloops. On the basis of these data, we propose particular gHBfix parameters to modify the AMBER RNA ff. The suggested parametrization significantly improves the agreement between experimental data and the simulation conformational ensembles, although our current ff version still remains far from being flawless. While attempts to tune the RNA ffs by conventional reparametrizations of dihedral potentials or nonbonded terms can lead to major undesired side effects, as we demonstrate for some recently published ffs, gHBfix has a clear promising potential to improve the ff performance while avoiding introduction of major new imbalances.
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Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Miroslav Krepl
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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106
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Ritacco I, Spinello A, Ippoliti E, Magistrato A. Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme. J Chem Inf Model 2019; 59:2930-2940. [PMID: 31033287 DOI: 10.1021/acs.jcim.9b00157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Phosphorylation by kinases enzymes is a widespread regulatory mechanism able of rapidly altering the function of target proteins. Among these are cytochrome P450s (CYP450), a superfamily of enzymes performing the oxidation of endogenous and exogenous substrates thanks to the electron supply of a redox partner. In spite of its pivotal role, the molecular mechanism by which phosphorylation modulates CYP450s metabolism remains elusive. Here by performing microsecond-long all-atom molecular dynamics simulations, we disclose how phosphorylation regulates estrogen biosynthesis, catalyzed by the Human Aromatase (HA) enzyme. Namely, we unprecedentedly propose that HA phosphorylation at Y361 markedly stabilizes its adduct with the flavin mononucleotide domain of CYP450s reductase (CPR), the redox partner of microsomal CYP450s, and a variety of other proteins. With CPR present at physiological conditions in a limiting ratio with respect to its multiple oxidative partners, the enhanced stability of the CPR/HA adduct may favor HA in the competition with the other proteins requiring CPR's electron supply, ultimately facilitating the electron transfer and estrogen biosynthesis. As a result, our work elucidates at atomic-level the post-translational regulation of CYP450s catalysis. Given the potential for rational clinical management of diseases associated with steroid metabolism disorders, unraveling this mechanism is of utmost importance, and raises the intriguing perspective of exploiting this knowledge to devise novel therapies.
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Affiliation(s)
- Ida Ritacco
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 Trieste , Italy
| | - Angelo Spinello
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 Trieste , Italy
| | - Emiliano Ippoliti
- IAS-5/INM-9 Computational Biomedicine Institute and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Straße , 52425 Jülich , Germany
| | - Alessandra Magistrato
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA) , via Bonomea 265 , 34136 Trieste , Italy
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107
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Ebrahimi P, Kaur S, Baronti L, Petzold K, Chen AA. A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints. Methods 2019; 162-163:96-107. [PMID: 31059830 DOI: 10.1016/j.ymeth.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/26/2019] [Accepted: 05/01/2019] [Indexed: 10/26/2022] Open
Abstract
We present a 2D replica exchange protocol incorporating secondary structure information to dramatically improve 3D RNA folding using molecular dynamics simulations. We show that incorporating base-pairing restraints into all-atom, explicit solvent simulations enables the accurate recapitulation of the global tertiary fold for 4 representative RNAs ranging in length from 24 to 68 nt. This method can potentially utilize base-pairing information from a wide variety of experimental inputs to predict complex RNA tertiary folds including pseudoknots, multi-loop junctions, and non-canonical interactions.
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Affiliation(s)
- Parisa Ebrahimi
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Simi Kaur
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alan A Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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108
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Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Šponer J, Bussi G. Fitting Corrections to an RNA Force Field Using Experimental Data. J Chem Theory Comput 2019; 15:3425-3431. [DOI: 10.1021/acs.jctc.9b00206] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Cesari
- Scuola Internazionale
Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics
of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale
Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
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109
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Mao CM, Sampath J, Sprenger KG, Drobny G, Pfaendtner J. Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5911-5920. [PMID: 30955325 DOI: 10.1021/acs.langmuir.8b01392] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular recognition between peptides and metal oxide surfaces is a fundamental process in biomineralization, self-assembly, and biocompatibility. Yet, the underlying driving forces and dominant mechanisms remain unclear, bringing obstacles to understand and control this process. To elucidate the mechanism of peptide/surface recognition, specifically the role of serine phosphorylation, we employed molecular dynamics simulation and metadynamics-enhanced sampling to study five artificial peptides, DDD, DSS, DpSpS, DpSpSGKK, and DpSKGpSK, interacting with two surfaces: rutile TiO2 and quartz SiO2. On both surfaces, we observe that phosphorylation increases the binding energy. However, the interfacial peptide conformation reveals a distinct binding mechanism on each surface. We also study the impact of peptide sequence to binding free energy and interfacial conformation on both surfaces, specifically the impact on the behavior of phosphorylated serine. Finally, the results are discussed in context of prior studies investigating the role of serine phosphorylation in peptide binding to silica.
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110
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Charafeddine RA, Cortopassi WA, Lak P, Tan R, McKenney RJ, Jacobson MP, Barber DL, Wittmann T. Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH. J Biol Chem 2019; 294:8779-8790. [PMID: 30992364 DOI: 10.1074/jbc.ra118.007004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/13/2019] [Indexed: 12/20/2022] Open
Abstract
Tau, a member of the MAP2/tau family of microtubule-associated proteins, stabilizes and organizes axonal microtubules in healthy neurons. In neurodegenerative tauopathies, tau dissociates from microtubules and forms neurotoxic extracellular aggregates. MAP2/tau family proteins are characterized by three to five conserved, intrinsically disordered repeat regions that mediate electrostatic interactions with the microtubule surface. Here, we used molecular dynamics, microtubule-binding experiments, and live-cell microscopy, revealing that highly-conserved histidine residues near the C terminus of each microtubule-binding repeat are pH sensors that can modulate tau-microtubule interaction strength within the physiological intracellular pH range. We observed that at low pH (<7.5), these histidines are positively charged and interact with phenylalanine residues in a hydrophobic cleft between adjacent tubulin dimers. At higher pH (>7.5), tau deprotonation decreased binding to microtubules both in vitro and in cells. Electrostatic and hydrophobic characteristics of histidine were both required for tau-microtubule binding, as substitutions with constitutively and positively charged nonaromatic lysine or uncharged alanine greatly reduced or abolished tau-microtubule binding. Consistent with these findings, tau-microtubule binding was reduced in a cancer cell model with increased intracellular pH but was rapidly restored by decreasing the pH to normal levels. These results add detailed insights into the intracellular regulation of tau activity that may be relevant in both normal and pathological conditions.
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Affiliation(s)
- Rabab A Charafeddine
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143
| | - Wilian A Cortopassi
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Parnian Lak
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Ruensern Tan
- the Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Richard J McKenney
- the Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Matthew P Jacobson
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Diane L Barber
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143
| | - Torsten Wittmann
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143,
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111
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Robertson MJ, Qian Y, Robinson MC, Tirado-Rives J, Jorgensen WL. Development and Testing of the OPLS-AA/M Force Field for RNA. J Chem Theory Comput 2019; 15:2734-2742. [PMID: 30807148 PMCID: PMC6585454 DOI: 10.1021/acs.jctc.9b00054] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Significant improvements have been made to the OPLS-AA force field for modeling RNA. New torsional potentials were optimized based on density functional theory (DFT) scans at the ωB97X-D/6-311++G(d,p) level for potential energy surfaces of the backbone α and γ dihedral angles. In combination with previously reported improvements for the sugar puckering and glycosidic torsion terms, the new force field was validated through diverse molecular dynamics simulations for RNAs in aqueous solution. Results for dinucleotides and tetranucleotides revealed both accurate reproduction of 3 J couplings from NMR and the avoidance of several unphysical states observed with other force fields. Simulations of larger systems with noncanonical motifs showed significant structural improvements over the previous OPLS-AA parameters. The new force field, OPLS-AA/M, is expected to perform competitively with other recent RNA force fields and to be compatible with OPLS-AA models for proteins and small molecules.
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Affiliation(s)
- Michael J. Robertson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Yue Qian
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Matthew C. Robinson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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112
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Cassone G, Kruse H, Sponer J. Interactions between cyclic nucleotides and common cations: an ab initio molecular dynamics study. Phys Chem Chem Phys 2019; 21:8121-8132. [PMID: 30932112 DOI: 10.1039/c8cp07492e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present the first, to the best of our knowledge, ab initio molecular dynamics (AIMD) investigation on three aqueous solutions where an abasic cyclic nucleotide model is solvated in the presence of distinct cations (i.e., Na+, K+ and Mg2+). We elucidate the typical modalities of interaction between those ionic species and the nucleotide moiety by first-principles numerical simulations, starting from an inner-shell binding configuration on a time scale of 100 ps (total simulation time of ∼600 ps). Whereas the strong "structure-maker" Mg2+ is permanently bound to one of the two oxygen atoms of the phosphate group of the nucleotide model, Na+ and K+ show binding times τb of 65 ps and 10-15 ps, respectively, thus reflecting their chemical nature in aqueous solutions. Furthermore, we qualitatively relate these findings to approximate free-energy barriers of the cations' unbinding obtained by means of exploratory well-tempered metadynamics. With the aim of shedding light on the features of commonly employed force-fields (FFs), classical MD simulations (almost 200 trajectories with a total simulation time of ∼18 μs) using the biomolecular AMBER FF are also reported. By choosing several combinations of the parametrization for the water environment (i.e., TIP3P, SPC/E and OPC) and cations (i.e., Joung-Cheatham, Li-Merz 12-6 and Li-Merz 12-6-4), we found significant differences in the radial distribution functions and residence times compared to the ab initio results. The Na+ and K+ ions wrongly show quasi-identical radial distribution functions and the Li & Merz 12-6-4 Lennard-Jones parameters for Mg2+ were found to be essential in quickly reaching the binding state consistent with AIMD.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i, Královopolská 135, 61265 Brno, Czech Republic.
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113
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Tyrosine nitration of human ERK1 introduces an intra-hydrogen bond by molecular dynamics simulations. Struct Chem 2019. [DOI: 10.1007/s11224-019-01306-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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114
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Impact of lipid binding on the tertiary structure and allergenic potential of Jug r 3, the non-specific lipid transfer protein from walnut. Sci Rep 2019; 9:2007. [PMID: 30765752 PMCID: PMC6376136 DOI: 10.1038/s41598-019-38563-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/31/2018] [Indexed: 01/09/2023] Open
Abstract
Plant non-specific lipid transfer proteins type 1 (nsLTP1) are small basic proteins with a hydrophobic cavity able to host a number of different ligands: i.e. fatty acids, fatty acyl-CoA, phospholipids, glycolipids, and hydroxylated fatty acids. However, ligand binding specificity differs among nsLTPs. Within this protein family, Jug r 3 from walnut has been identified as a major allergen. So far, data on the structural characterization of Jug r 3 and its lipid binding capacity are lacking. We report the results from a fluorescence-based ligand-binding assay and ligand-based NMR experiments, to study the binding interactions between Jug r 3 and the 18-carbon monounsaturated oleic acid. Furthermore, protein-based NMR experiments were employed to detect the oleate binding site of Jug r 3. The NMR data were used to dock the oleate molecule into the structural model of Jug r 3. Finally, the impact of the interaction on the allergenic potential of Jug r 3 was investigated by IgE ELISA with 6 sera from walnut allergic patients. Our data corroborate the hypothesis of direct impact of food-derived matrix on the IgE reactivity of nsLTPs.
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115
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Dans PD, Gallego D, Balaceanu A, Darré L, Gómez H, Orozco M. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. Chem 2019. [DOI: 10.1016/j.chempr.2018.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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116
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Bochicchio A, Krepl M, Yang F, Varani G, Sponer J, Carloni P. Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. PLoS Comput Biol 2018; 14:e1006642. [PMID: 30521520 PMCID: PMC6307825 DOI: 10.1371/journal.pcbi.1006642] [Citation(s) in RCA: 9] [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: 07/11/2018] [Revised: 12/27/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox·pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations. Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement. RNA is an outstanding target for oncological intervention. Engineering the most common RNA binding motif in human proteins (called RRM) so as to bind to a specific RNA has an enormous pharmacological potential. Yet, it is highly non trivial to design RRM-bearing protein variants with RNA selectivity and affinity sufficiently high for clinical applications. Here we present an extensive molecular simulation study which shed light on the exquisite molecular recognition of the empirically-engineered complex between the RRM-bearing protein Rbfox and its RNA target pre-miR21. The simulations allow predicting a variant, the S151T, which may lead to further enhancement of selectivity and affinity for pre-miR21.
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Affiliation(s)
- Anna Bochicchio
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- * E-mail: (MK); (PC)
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czech Republic
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (MK); (PC)
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117
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Vymětal J, Jurásková V, Vondrášek J. AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation. J Chem Theory Comput 2018; 15:665-679. [PMID: 30468703 DOI: 10.1021/acs.jctc.8b00715] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often associated with important structural and functional changes. We investigated the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. We conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation. Our bias-exchange metadynamics simulations revealed that all model dipeptides sampled a great heterogeneity of ensembles affected by introduction of mono- and dianionic phosphate groups. However, the detected changes in populations of backbone conformers and side-chain rotamers did not reveal a strong discriminatory shift in preferences, as could be anticipated for the bulky, charged phosphate group. Furthermore, the AMBER and CHARMM force fields provided inconsistent populations of individual conformers as well as net structural trends upon phosphorylation. Detailed analysis of ensembles revealed competition between hydration and formation of internal hydrogen bonds involving amide hydrogens and the phosphate group. The observed difference in hydration free energy and potential for hydrogen bonding in individual force fields could be attributed to the different partial atomic charges used in each force field and, hence, the different parametrization strategies. Nevertheless, conformational propensities and net structural changes upon phosphorylation are difficult to extract from experimental measurements, and existing experimental data provide limited guidance for force field assessment and further development.
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Affiliation(s)
- Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
| | - Veronika Jurásková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
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118
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Characterization of cryptic allosteric site at IL-4Rα: New paradigm towards IL-4/IL-4R inhibition. Int J Biol Macromol 2018; 123:239-245. [PMID: 30391589 DOI: 10.1016/j.ijbiomac.2018.10.204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/26/2022]
Abstract
Interleukin-4(IL-4), an anti-inflammatory cytokine, plays significant role in pathogenesis of various diseases such as asthma, tumors, and HIV infections. These responses are mediated by expression of IL-4R (receptor) on various hematopoietic and non-hematopoietic cells surfaces. To date, the X-ray crystal structure of unbound (i.e. free) IL-4R is not reported which hampers active research on the molecular interaction mechanism between IL-4 and IL-4R. To investigate the missing gaps about stable binding mode of IL-4 and drug-ability of IL-4R active site, modelling and molecular dynamics (MD) simulation of IL-4/IL-4R complex was performed. Drug-ability of the target protein changed after modelling the loop region near C-terminal of IL-4R protein. This led to the identification of a novel druggable site other than the reported interfacial site. Our analysis showed that the modelled residues Ser111 and Ser164-Lys167 are part of newly discovered allosteric site, which underwent major fluctuation after association with its ligand protein (IL-4). The results indicated possible role of this cryptic allosteric site in IL-4/IL-4R signaling pathway that might help us to block IL-4/IL-4R association to prevent various allergic and malignant diseases.
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119
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Kiss DJ, Oláh J, Tóth G, Menyhárd DK, Ferenczy GG. Quantum chemical calculations support pseudouridine synthase reaction through a glycal intermediate and provide details of the mechanism. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2361-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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120
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Sgrignani J, Chen J, Alimonti A, Cavalli A. How phosphorylation influences E1 subunit pyruvate dehydrogenase: A computational study. Sci Rep 2018; 8:14683. [PMID: 30279533 PMCID: PMC6168537 DOI: 10.1038/s41598-018-33048-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022] Open
Abstract
Pyruvate (PYR) dehydrogenase complex (PDC) is an enzymatic system that plays a crucial role in cellular metabolism as it controls the entry of carbon into the Krebs cycle. From a structural point of view, PDC is formed by three different subunits (E1, E2 and E3) capable of catalyzing the three reaction steps necessary for the full conversion of pyruvate to acetyl-CoA. Recent investigations pointed out the crucial role of this enzyme in the replication and survival of specific cancer cell lines, renewing the interest of the scientific community. Here, we report the results of our molecular dynamics studies on the mechanism by which posttranslational modifications, in particular the phosphorylation of three serine residues (Ser-264-α, Ser-271-α, and Ser-203-α), influence the enzymatic function of the protein. Our results support the hypothesis that the phosphorylation of Ser-264-α and Ser-271-α leads to (1) a perturbation of the catalytic site structure and dynamics and, especially in the case of Ser-264-α, to (2) a reduction in the affinity of E1 for the substrate. Additionally, an analysis of the channels connecting the external environment with the catalytic site indicates that the inhibitory effect should not be due to the occlusion of the access/egress pathways to/from the active site.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - JingJing Chen
- Institute of Research in Oncology (IOR), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Andrea Alimonti
- Institute of Research in Oncology (IOR), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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121
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Havrila M, Stadlbauer P, Kührová P, Banáš P, Mergny JL, Otyepka M, Šponer J. Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. Nucleic Acids Res 2018; 46:8754-8771. [PMID: 30165550 PMCID: PMC6158699 DOI: 10.1093/nar/gky712] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/03/2018] [Accepted: 07/27/2018] [Indexed: 02/04/2023] Open
Abstract
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, Pessac, France
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
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122
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Leonarski F, Jasiński M, Trylska J. Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques. Biochimie 2018; 156:22-32. [PMID: 30244136 DOI: 10.1016/j.biochi.2018.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
Abstract
Bacterial 5' untranslated regions of mRNA, termed thermal switches or thermometers, change their structure in response to temperature change. This structural change provides for the regulation of gene expression. One of such thermal switches, called fourU, is present in the Salmonella species. Mutations of fourU were found to abrogate its regulatory properties. We investigated the thermodynamics of the fourU fragment responsible for its structural changes. All-atom molecular dynamics simulations at various temperatures and spectroscopic experiments in solution were performed for the wild-type fourU and its mutants. We found that the U11C and A8C mutations stabilize the fourU structure in comparison to the wild-type fourU, and the double-point G14A/C25U mutant has the most destabilizing effect on the fourU hairpin 2 responsible for temperature sensing. The G14A/C25U mutant is also the easiest to strand-invade by a complementary oligonucleotide as indicated by fluorescence spectroscopy experiments.
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Affiliation(s)
- Filip Leonarski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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123
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Liu T, Wang Z, Guo P, Ding N. Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 48:73-82. [DOI: 10.1007/s00249-018-1334-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/10/2018] [Accepted: 09/06/2018] [Indexed: 02/04/2023]
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124
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Li A, Gilson MK. Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. J Chem Phys 2018; 149:072311. [PMID: 30134726 DOI: 10.1063/1.5027439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Calorimetric studies of protein-ligand binding sometimes yield thermodynamic data that are difficult to understand. Today, molecular simulations can be used to seek insight into such calorimetric puzzles, and, when simulations and experiments diverge, the results can usefully motivate further improvements in computational methods. Here, we apply near-millisecond duration simulations to estimate the relative binding enthalpies of four peptidic ligands with the Grb2 SH2 domain. The ligands fall into matched pairs, where one member of each pair has an added bond that preorganizes the ligand for binding and thus may be expected to favor binding entropically, due to a smaller loss in configurational entropy. Calorimetric studies have shown that the constrained ligands do in fact bind the SH2 domain more tightly than the flexible ones, but, paradoxically, the improvement in affinity for the constrained ligands is enthalpic, rather than entropic. The present enthalpy calculations yield the opposite trend, as they suggest that the flexible ligands bind more exothermically. Additionally, the small relative binding enthalpies are found to be balances of large differences in the energies of structural components such as ligand and the binding site residues. As a consequence, the deviations from experiment in the relative binding enthalpies represent small differences between these large numbers and hence may be particularly susceptible to error, due, for example, to approximations in the force field. We also computed first-order estimates of changes in configurational entropy on binding. These too are, arguably, paradoxical, as they tend to favor binding of the flexible ligands. The paradox is explained in part by the fact that the more rigid constrained ligands reduce the entropy of binding site residues more than their flexible analogs do, at least in the simulations. This result offers a rather general counterargument to the expectation that preorganized ligands should be associated with more favorable binding entropies, other things being equal.
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Affiliation(s)
- Amanda Li
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0419, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
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125
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Šoštarić N, O'Reilly FJ, Giansanti P, Heck AJR, Gavin AC, van Noort V. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. Mol Cell Proteomics 2018; 17:2387-2401. [PMID: 30181345 DOI: 10.1074/mcp.ra118.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Indexed: 01/18/2023] Open
Abstract
Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.
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Affiliation(s)
- Nikolina Šoštarić
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Technical University of Berlin, Berlin, Germany
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium; Leiden University, Institute of Biology Leiden, Leiden, The Netherlands.
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126
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Kato HE, Kim YS, Paggi JM, Evans KE, Allen WE, Richardson C, Inoue K, Ito S, Ramakrishnan C, Fenno LE, Yamashita K, Hilger D, Lee SY, Berndt A, Shen K, Kandori H, Dror RO, Kobilka BK, Deisseroth K. Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature 2018; 561:349-354. [PMID: 30158697 PMCID: PMC6317992 DOI: 10.1038/s41586-018-0504-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/13/2018] [Indexed: 11/09/2022]
Abstract
Both designed and natural anion-conducting channelrhodopsins (dACRs and nACRs, respectively) have been widely applied in optogenetics (enabling selective inhibition of target-cell activity during animal behaviour studies), but each class exhibits performance limitations, underscoring trade-offs in channel structure-function relationships. Therefore, molecular and structural insights into dACRs and nACRs will be critical not only for understanding the fundamental mechanisms of these light-gated anion channels, but also to create next-generation optogenetic tools. Here we report crystal structures of the dACR iC++, along with spectroscopic, electrophysiological and computational analyses that provide unexpected insights into pH dependence, substrate recognition, channel gating and ion selectivity of both dACRs and nACRs. These results enabled us to create an anion-conducting channelrhodopsin integrating the key features of large photocurrent and fast kinetics alongside exclusive anion selectivity.
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Affiliation(s)
- Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Kathryn E Evans
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - William E Allen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Claire Richardson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Lief E Fenno
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | | | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Soo Yeun Lee
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Andre Berndt
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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127
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Han K, Hudson PS, Jones MR, Nishikawa N, Tofoleanu F, Brooks BR. Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. J Comput Aided Mol Des 2018; 32:1059-1073. [PMID: 30084077 DOI: 10.1007/s10822-018-0144-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
This study reports the results of binding free energy calculations for CB[8] host-guest systems in the SAMPL6 blind challenge (receipt ID 3z83m). Force-field parameters were developed specific for each of host and guest molecules to improve configurational sampling. We used quantum mechanical (QM) implicit solvent calculations and QM force matching to determine non-bonded (partial atomic charges) and bonded terms, respectively. Free energy calculations were carried out using the double-decoupling method (DDM) combined with Hamiltonian replica exchange method (HREM) and Bennett acceptance ratio (BAR) method. The root mean square error (RMSE) of the predicted values using DDM with respect to the experimental results was 4.32 kcal/mol. The coefficient of determination (R2) and Kendall rank coefficient (τ) were 0.49 and 0.52, respectively, highest of all submissions. In addition, these were compared to the results obtained by umbrella sampling (US) and weighted histogram analysis method (WHAM). Overall, DDM achieved a higher prediction accuracy than the US method. Results are discussed in terms of parameterization and free energy simulations.
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Affiliation(s)
- Kyungreem Han
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Phillip S Hudson
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Naohiro Nishikawa
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Florentina Tofoleanu
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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128
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Newkirk ML, Rubenstein KJ, Kim JY, Labrecque CL, Airas J, Taylor CA, Evans HD, McKoy Q, Parish CA, Pollock JA. Analysis of MEMO1 Binding Specificity for ErbB2 Using Fluorescence Polarization and Molecular Dynamics Simulations. Biochemistry 2018; 57:5169-5181. [DOI: 10.1021/acs.biochem.8b00582] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Madeline L. Newkirk
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Kristen J. Rubenstein
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Jessica Y. Kim
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Courtney L. Labrecque
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Justin Airas
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Cooper A. Taylor
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Hunter D. Evans
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Quincy McKoy
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Carol A. Parish
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Julie A. Pollock
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
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129
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Krepl M, Vögele J, Kruse H, Duchardt-Ferner E, Wöhnert J, Sponer J. An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch. Nucleic Acids Res 2018; 46:6528-6543. [PMID: 29893898 PMCID: PMC6061696 DOI: 10.1093/nar/gky490] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/23/2018] [Indexed: 01/04/2023] Open
Abstract
The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop-a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect. We then use NMR spectroscopy to confirm the existence of this cation-binding site and to demonstrate its effects on RNA stability. Lastly, using quantum chemical calculations, we show that the cation-binding site is altering the electronic environment of the wild-type U-turn so that it is more similar to the cytosine mutant. The study reveals an amazingly complex and delicate interplay between various energy contributions shaping up the 3D structure and evolution of nucleic acids.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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130
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Momin M, Yao XQ, Thor W, Hamelberg D. Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1. J Phys Chem B 2018; 122:6521-6527. [DOI: 10.1021/acs.jpcb.8b03819] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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131
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Fesko K, Suplatov D, Švedas V. Bioinformatic analysis of the fold type I PLP-dependent enzymes reveals determinants of reaction specificity in l-threonine aldolase from Aeromonas jandaei. FEBS Open Bio 2018; 8:1013-1028. [PMID: 29928580 PMCID: PMC5986058 DOI: 10.1002/2211-5463.12441] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/27/2018] [Indexed: 01/19/2023] Open
Abstract
Understanding the role of specific amino acid residues in the molecular mechanism of a protein's function is one of the most challenging problems in modern biology. A systematic bioinformatic analysis of protein families and superfamilies can help in the study of structure–function relationships and in the design of improved variants of enzymes/proteins, but represents a methodological challenge. The pyridoxal‐5′‐phosphate (PLP)‐dependent enzymes are catalytically diverse and include the aspartate aminotransferase superfamily which implements a common structural framework known as type fold I. In this work, the recently developed bioinformatic online methods Mustguseal and Zebra were used to collect and study a large representative set of the aspartate aminotransferase superfamily with high structural, but low sequence similarity to l‐threonine aldolase from Aeromonas jandaei (LTAaj), in order to identify conserved positions that provide general properties in the superfamily, and to reveal family‐specific positions (FSPs) responsible for functional diversity. The roles of the identified residues in the catalytic mechanism and reaction specificity of LTAaj were then studied by experimental site‐directed mutagenesis and molecular modelling. It was shown that FSPs determine reaction specificity by coordinating the PLP cofactor in the enzyme's active centre, thus influencing its activation and the tautomeric equilibrium of the intermediates, which can be used as hotspots to modulate the protein's functional properties. Mutagenesis at the selected FSPs in LTAaj led to a reduction in a native catalytic activity and increased the rate of promiscuous reactions. The results provide insight into the structural basis of catalytic promiscuity of the PLP‐dependent enzymes and demonstrate the potential of bioinformatic analysis in studying structure–function relationship in protein superfamilies.
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Affiliation(s)
- Kateryna Fesko
- Institute of Organic Chemistry Graz University of Technology Austria
| | - Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Russia
| | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Russia
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132
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Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. SCIENCE ADVANCES 2018; 4:eaar8521. [PMID: 29795785 PMCID: PMC5959319 DOI: 10.1126/sciadv.aar8521] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/05/2018] [Indexed: 05/08/2023]
Abstract
RNA molecules are key players in numerous cellular processes and are characterized by a complex relationship between structure, dynamics, and function. Despite their apparent simplicity, RNA oligonucleotides are very flexible molecules, and understanding their internal dynamics is particularly challenging using experimental data alone. We show how to reconstruct the conformational ensemble of four RNA tetranucleotides by combining atomistic molecular dynamics simulations with nuclear magnetic resonance spectroscopy data. The goal is achieved by reweighting simulations using a maximum entropy/Bayesian approach. In this way, we overcome problems of current simulation methods, as well as in interpreting ensemble- and time-averaged experimental data. We determine the populations of different conformational states by considering several nuclear magnetic resonance parameters and point toward properties that are not captured by state-of-the-art molecular force fields. Although our approach is applied on a set of model systems, it is fully general and may be used to study the conformational dynamics of flexible biomolecules and to detect inaccuracies in molecular dynamics force fields.
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Affiliation(s)
- Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (S.B.); (K.L.-L.)
| | - Giovanni Bussi
- International School for Advanced Studies, Trieste, Italy
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (S.B.); (K.L.-L.)
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133
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Aronica PGA, Fox SJ, Verma CS. Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization. ACS OMEGA 2018; 3:4664-4673. [PMID: 31458687 PMCID: PMC6641686 DOI: 10.1021/acsomega.8b00438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/13/2018] [Indexed: 06/10/2023]
Abstract
When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new species. As there are many variables in the charge derivation process, an investigation was devised to compare different approaches and determine their effect on simulations. This was done with the purpose to identify the methods which produced results compatible with the existing parameters. It was found in this study that all analyzed charge derivation methods reproduce with sufficient accuracy the literature values and can be used with confidence when parameterizing novel species.
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Affiliation(s)
- Pietro G. A. Aronica
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street, #07-01 Matrix, 138671, Singapore
| | - Stephen J. Fox
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street, #07-01 Matrix, 138671, Singapore
| | - Chandra S. Verma
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street, #07-01 Matrix, 138671, Singapore
- Department
of Biological Sciences, National University
of Singapore, 16 Science
Drive, 117558, Singapore
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang
Drive, 637551, Singapore
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134
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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135
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Cruz CS, Costa EP, Machado JA, Silva JN, Romeiro NC, Moraes J, Silva JR, Fonseca RN, Vaz IS, Logullo C, Campos E. A soluble inorganic pyrophosphatase from the cattle tick Rhipicephalus microplus capable of hydrolysing polyphosphates. INSECT MOLECULAR BIOLOGY 2018; 27:260-267. [PMID: 29271528 DOI: 10.1111/imb.12369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Polyphosphates have been found in all cell types examined to date and play diverse roles depending on the cell type. In eukaryotic organisms, polyphosphates have been investigated mainly in mammalian cells, and only a few studies have addressed arthropods. Pyrophosphatases have been shown to regulate polyphosphate metabolism. However, these studies were restricted to trypanosomatids. Here we focus on the tick Rhipicephalus microplus, a haematophagous ectoparasite that is highly harmful to cattle. We produced a recombinant R. microplus pyrophosphatase (rRmPPase) with the aim of investigating its kinetic parameters using polyphosphates as substrate. Molecular docking assays of RmPPase with polyphosphates were also carried out. The kinetic and Hill coefficient parameters indicated that rRmPPase has a greater affinity, higher catalytic efficiency and increased cooperativity for sodium phosphate glass type 15 (polyP15 ) than for sodium tripolyphosphate (polyP3 ). Through molecular docking, we found that polyP3 binds close to the Mg2+ atoms in the catalytic region of the protein, participating in their coordination network, whereas polyP15 interactions involve negatively charged phosphate groups and basic amino acid residues, such as Lys56, Arg58 and Lys193; polyP15 has a more favourable theoretical binding affinity than polyP3 , thus supporting the kinetic data. This study shows, for the first time in arthropods, a pyrophosphatase with polyphosphatase activity, suggesting its participation in polyphosphate metabolism.
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Affiliation(s)
- C S Cruz
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
| | - E P Costa
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J A Machado
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J N Silva
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - N C Romeiro
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - J Moraes
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - J R Silva
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - R N Fonseca
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - I S Vaz
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
- Centro de Biotecnologia e Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - C Logullo
- Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal - CBB - UENF, Horto, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
| | - E Campos
- Laboratório Integrado de Bioquímica - Hatisaburo Masuda, UFRJ, NUPEM, São José do Barreto, Macaé, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, Brazil
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136
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Bueno O, Estévez Gallego J, Martins S, Prota AE, Gago F, Gómez-SanJuan A, Camarasa MJ, Barasoain I, Steinmetz MO, Díaz JF, Pérez-Pérez MJ, Liekens S, Priego EM. High-affinity ligands of the colchicine domain in tubulin based on a structure-guided design. Sci Rep 2018; 8:4242. [PMID: 29523799 PMCID: PMC5844890 DOI: 10.1038/s41598-018-22382-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/21/2018] [Indexed: 01/05/2023] Open
Abstract
Microtubule-targeting agents that bind at the colchicine-site of tubulin are of particular interest in antitumoral therapy due to their dual mechanism of action as antimitotics and vascular disrupting agents. Cyclohexanediones derivatives have been described as a new family of colchicine-domain binders with an association constant to tubulin similar to that of colchicine. Here, the high-resolution structures of tubulin in complex with cyclohexanediones TUB015 and TUB075 were solved by X-ray crystallography. A detailed analysis of the tubulin-TUB075 interaction by means of computational affinity maps allowed the identification of two additional regions at the binding site that were addressed with the design and synthesis of a new series of cyclohexanediones with a distal 2-substituted benzofurane. These new compounds showed potent antiproliferative activity with IC50 values in the nM range, arrested cell cycle progression at the G2/M phase and induced apoptosis at sub μM concentrations. Moreover, they caused the destruction of a preformed vascular network in vitro and inhibited the migration of endothelial cells at non-toxic concentrations. Finally, these compounds displayed high affinity for tubulin as substantiated by a K b value of 2.87 × 108 M-1 which, to the best of our knowledge, represents the highest binding constant measured to date for a colchicine-domain ligand.
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Affiliation(s)
- Oskía Bueno
- Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Juan Estévez Gallego
- Centro de Investigaciones Biológicas (CIB,CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Solange Martins
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Federico Gago
- Department of Biomedical Sciences (Unidad Asociada IQM,CSIC) and Instituto de Investigación Quimica "Andrés M. del Río" (IQAR), University of Alcalá, Unidad Asociada CSIC, 28805 Alcalá de Henares, Madrid, Spain
| | - Asier Gómez-SanJuan
- Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - María-José Camarasa
- Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Isabel Barasoain
- Centro de Investigaciones Biológicas (CIB,CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
- University of Basel, Biozentrum, CH-4056, Basel, Switzerland
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas (CIB,CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | | | - Sandra Liekens
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Eva-María Priego
- Instituto de Química Médica (IQM,CSIC), Juan de la Cierva 3, 28006, Madrid, Spain.
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137
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Smith LG, Zhao J, Mathews DH, Turner DH. Physics-based all-atom modeling of RNA energetics and structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 8. [PMID: 28815951 DOI: 10.1002/wrna.1422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/03/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
Abstract
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422.
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Affiliation(s)
- Louis G Smith
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Jianbo Zhao
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA
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138
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Hayatshahi HS, Henriksen NM, Cheatham TE. Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:1456-1470. [PMID: 29323894 DOI: 10.1021/acs.jctc.7b00581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dinucleoside monophosphates (DNMPs) have been described using various experimental approaches as flexible molecules which generate ensembles populating at least a small set of different conformations in solution. However, due to limitations of each approach in its ability to delineate the ensemble of conformations, an accurate and quantitative description of certain conformational features has not been performed for all DNMPs. Here, we apply a temperature replica-exchange molecular dynamics approach to fully and quickly converge conformational distributions of all RNA DNMPs immersed in the TIP3P water model using the AMBER ff14 force field. For a selection of DNMPs, the conformational ensembles were also generated when immersed in the OPC water model using alternative AMBER and CHARMM force fields. The OPC water model and other force field choices did not introduce new conformational classes but shifted the populations among existing conformations. Except for pyrimidine-pyrimidine dinucleosides, all other DNMPs populated four major conformations (which are defined in the main text and labeled A-form, Ladder, Inverted, and Sheared), in addition to an Extended form. Pyrimidine-pyrimidines did not generate the Sheared conformation. Distinguishing features and stabilizing factors of each conformation were identified and assessed based on the known experimental interpretations. The configuration of the glycosidic bond and the nonbonding interactions of hydrogen bond acceptors with the 2'-hydroxyl group were found to play determining roles in stabilizing particular conformations which could serve as a guide for potential force field modifications to improve the accuracy. Additionally, we computed stacking free energies based on the DNMP conformational distributions and found significant discrepancies with a previous study. Our investigation determined that the AMBER force field was incorrectly implemented in the previous study. In the future, this simulation approach can be used to quickly analyze the effects of new force field modifications in shifting the conformational populations of DNMPs, and can can be further applied to foresee such effects in larger RNA motifs including tetranucleotides and tetraloops.
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Affiliation(s)
- Hamed S Hayatshahi
- Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California at San Diego , 9500 Gilman Drive , MC 0736, La Jolla , California 92093 , United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States
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139
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Kashefolgheta S, Vila Verde A. Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions. Phys Chem Chem Phys 2018; 19:20593-20607. [PMID: 28731091 DOI: 10.1039/c7cp02557b] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.
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Affiliation(s)
- Sadra Kashefolgheta
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany.
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140
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Abstract
The complex and often highly dynamic 3D structures of RNA molecules are central to their diverse cellular functions. Molecular dynamics (MD) simulations have played a major role in characterizing the structure and dynamics of proteins, but the physical models (“force fields”) used for simulating nucleic acids are substantially less accurate overall than those used in protein simulations, creating a major challenge for MD studies of RNA. Here, we report an RNA force field capable of describing the structural and thermodynamic properties of RNA molecules with accuracy comparable to state-of-the-art protein force fields. This force field should facilitate the use of MD simulation as a tool for the study of biologically significant RNA molecules and protein–RNA complexes. Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models (“force fields”) available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, we introduce an extensive revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures. We evaluate these revised parameters through long-timescale MD simulations of a set of RNA molecules that covers a wide range of structural complexity, including single-stranded RNAs, RNA duplexes, RNA hairpins, and riboswitches. The structural and thermodynamic properties measured in these simulations exhibited dramatically improved agreement with experimentally determined values. Based on the comparisons we performed, this RNA force field appears to achieve a level of accuracy comparable to that of state-of-the-art protein force fields, thus significantly advancing the utility of MD simulation as a tool for elucidating the structural dynamics and function of RNA molecules and RNA-containing biological assemblies.
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141
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Sprenger KG, Prakash A, Drobny G, Pfaendtner J. Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1199-1207. [PMID: 28981294 DOI: 10.1021/acs.langmuir.7b02868] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.
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Affiliation(s)
- K G Sprenger
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Arushi Prakash
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
| | - Gary Drobny
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98105, United States
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142
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Vidal-Vidal Á, Silva López C, Faza ON. Lennard-Jones Potentials for the Interaction of CO2 with Five-Membered Aromatic Heterocycles. J Phys Chem A 2017; 121:9518-9530. [DOI: 10.1021/acs.jpca.7b09382] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ángel Vidal-Vidal
- Departamento
de Química Orgánica, Campus Lagoas-Marcosende, 36310 Vigo Spain
| | - Carlos Silva López
- Departamento
de Química Orgánica, Campus Lagoas-Marcosende, 36310 Vigo Spain
| | - Olalla Nieto Faza
- Departamento
de Quı́mica Orgánica, Facultade de Ciencias, Universidade de Vigo, Campus As Lagoas, 32004 Ourense, Spain
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143
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Johnson MB, Halman JR, Satterwhite E, Zakharov AV, Bui MN, Benkato K, Goldsworthy V, Kim T, Hong E, Dobrovolskaia MA, Khisamutdinov EF, Marriott I, Afonin KA. Programmable Nucleic Acid Based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201701255. [PMID: 28922553 PMCID: PMC6258062 DOI: 10.1002/smll.201701255] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/14/2017] [Indexed: 05/13/2023]
Abstract
In the past few years, the study of therapeutic RNA nanotechnology has expanded tremendously to encompass a large group of interdisciplinary sciences. It is now evident that rationally designed programmable RNA nanostructures offer unique advantages in addressing contemporary therapeutic challenges such as distinguishing target cell types and ameliorating disease. However, to maximize the therapeutic benefit of these nanostructures, it is essential to understand the immunostimulatory aptitude of such tools and identify potential complications. This paper presents a set of 16 nanoparticle platforms that are highly configurable. These novel nucleic acid based polygonal platforms are programmed for controllable self-assembly from RNA and/or DNA strands via canonical Watson-Crick interactions. It is demonstrated that the immunostimulatory properties of these particular designs can be tuned to elicit the desired immune response or lack thereof. To advance the current understanding of the nanoparticle properties that contribute to the observed immunomodulatory activity and establish corresponding designing principles, quantitative structure-activity relationship modeling is conducted. The results demonstrate that molecular weight, together with melting temperature and half-life, strongly predicts the observed immunomodulatory activity. This framework provides the fundamental guidelines necessary for the development of a new library of nanoparticles with predictable immunomodulatory activity.
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Affiliation(s)
- M. Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Emily Satterwhite
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - My N. Bui
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Taejin Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Enping Hong
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | | | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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144
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Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B. J Comput Aided Mol Des 2017; 31:915-928. [DOI: 10.1007/s10822-017-0066-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 01/24/2023]
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145
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Henriksen NM, Gilson MK. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. J Chem Theory Comput 2017; 13:4253-4269. [PMID: 28696692 PMCID: PMC5606194 DOI: 10.1021/acs.jctc.7b00359] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Computational
prediction of noncovalent binding free energies with
methods based on molecular mechanical force fields has become increasingly
routine in drug discovery projects, where they promise to speed the
discovery of small molecule ligands to bind targeted proteins with
high affinity. Because the reliability of free energy methods still
has significant room for improvement, new force fields, or modifications
of existing ones, are regularly introduced with the aim of improving
the accuracy of molecular simulations. However, comparatively little
work has been done to systematically assess how well force fields
perform, particularly in relation to the calculation of binding affinities.
Hardware advances have made these calculations feasible, but comprehensive
force field assessments for protein–ligand sized systems still
remain costly. Here, we turn to cyclodextrin host–guest systems,
which feature many hallmarks of protein–ligand binding interactions
but are generally much more tractable due to their small size. We
present absolute binding free energy and enthalpy calculations, using
the attach-pull-release (APR) approach, on a set of 43 cyclodextrin-guest
pairs for which experimental ITC data are available. The test set
comprises both α- and β-cyclodextrin hosts binding a series
of small organic guests, each with one of three functional groups:
ammonium, alcohol, or carboxylate. Four water models are considered
(TIP3P, TIP4Pew, SPC/E, and OPC), along with two partial charge assignment
procedures (RESP and AM1-BCC) and two cyclodextrin host force fields.
The results suggest a complex set of considerations when choosing
a force field for biomolecular simulations. For example, some force
field combinations clearly outperform others at the binding enthalpy
calculations but not for the binding free energy. Additionally, a
force field combination which we expected to be the worst performer
gave the most accurate binding free energies – but the least
accurate binding enthalpies. The results have implications for the
development of improved force fields, and we propose this test set,
and potential future elaborations of it, as a powerful validation
suite to evaluate new force fields and help guide future force field
development.
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Affiliation(s)
- Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, California 92093-0736, United States
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146
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Rhinehardt KL, Vance SA, Mohan RV, Sandros M, Srinivas G. Molecular modeling and SPRi investigations of interleukin 6 (IL6) protein and DNA aptamers. J Biomol Struct Dyn 2017; 36:1934-1947. [PMID: 28592206 DOI: 10.1080/07391102.2017.1338619] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interleukin 6 (IL6), an inflammatory response protein has major implications in immune-related inflammatory diseases. Identification of aptamers for the IL6 protein aids in diagnostic, therapeutic, and theranostic applications. Three different DNA aptamers and their interactions with IL6 protein were extensively investigated in a phosphate buffed saline (PBS) solution. Molecular-level modeling through molecular dynamics provided insights of structural, conformational changes and specific binding domains of these protein-aptamer complexes. Multiple simulations reveal consistent binding region for all protein-aptamer complexes. Conformational changes coupled with quantitative analysis of center of mass (COM) distance, radius of gyration (Rg), and number of intermolecular hydrogen bonds in each IL6 protein-aptamer complex was used to determine their binding performance strength and obtain molecular configurations with strong binding. A similarity comparison of the molecular configurations with strong binding from molecular-level modeling concurred with Surface Plasmon Resonance imaging (SPRi) for these three aptamer complexes, thus corroborating molecular modeling analysis findings. Insights from the natural progression of IL6 protein-aptamer binding modeled in this work has identified key features such as the orientation and location of the aptamer in the binding event. These key features are not readily feasible from wet lab experiments and impact the efficacy of the aptamers in diagnostic and theranostic applications.
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Affiliation(s)
- Kristen L Rhinehardt
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Stephen A Vance
- b Department of Nanoscience , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Ram V Mohan
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Marinella Sandros
- b Department of Nanoscience , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Goundla Srinivas
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
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147
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Momin M, Xin Y, Hamelberg D. Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective. J Phys Chem B 2017; 121:6131-6138. [PMID: 28570811 DOI: 10.1021/acs.jpcb.7b03470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis-trans isomerization of a peptidyl-prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic. Here, we explore the conformational dynamics and free energy landscape of the SH2 domain of interleukin-2-inducible T-cell or tyrosine kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch and its binding pocket of the phosphotyrosine motif. We use multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs. We show that cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly coupled to the dynamics of the binding pocket of the phosphotyrosine motif, in agreement with previous NMR experiments. Unlike the cis state that is localized and less dynamic in a single free energy basin, the trans state samples two distinct conformations of the binding pocket-one that recognizes the phosphotyrosine motif and the other that is somewhat similar to that of the cis state. The results provide an atomic-level description of a less well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant subcellular processes and the identification of these elusive molecular switches in other proteins.
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Affiliation(s)
- Mohamed Momin
- Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Yao Xin
- Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and ‡Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States
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148
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Li MJ, Wu GZ, Kaas Q, Jiang T, Yu RL. Development of efficient docking strategies and structure-activity relationship study of the c-Met type II inhibitors. J Mol Graph Model 2017; 75:241-249. [PMID: 28601708 DOI: 10.1016/j.jmgm.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 02/02/2023]
Abstract
c-Met is a transmembrane receptor tyrosine kinase and an important therapeutic target for anticancer drugs. In the present study, we systematically investigated the influence of a range of parameters on the correlation between experimental and calculated binding free energies of type II c-Met inhibitors. We especially focused on evaluating the impact of different force fields, binding energy calculation methods, docking protocols, conformation sampling strategies, and conformations of the binding site captured in several crystallographic structures. Our results suggest that the force fields, the protein flexibility, and the selected conformation of the binding site substantially influence the correlation coefficient, while the sampling strategies and ensemble docking only mildly affect the prediction accuracy. Structure-activity relationship study suggests that the structural determinants to the high binding affinity of the type II inhibitors originate from its overall linear shape, hydrophobicity, and two conserved hydrogen bonds. Results from this study will form the basis for establishing an efficient computational docking approach for c-Met type II inhibitors design.
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Affiliation(s)
- Ming-Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Guan-Zhao Wu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072 Australia
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Ri-Lei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
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149
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Aytenfisu A, Spasic A, Grossfield A, Stern HA, Mathews DH. Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics. J Chem Theory Comput 2017; 13:900-915. [PMID: 28048939 PMCID: PMC5312698 DOI: 10.1021/acs.jctc.6b00870] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Indexed: 12/27/2022]
Abstract
The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG-CC-PVTZ basis set). Umbrella sampling was used to determine conformational free energies along the dihedral angles, and these better agree with the population of conformations observed in the protein data bank for the new parameters than for the conventional parameters. Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramers CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters. For the tetramers, the new parameters largely avoid the incorrect intercalated structures that dominate the conformational samples from the conventional parameters. For the internal loop, the major conformation solved by NMR is stable with the new parameters, but not with the conventional parameters. The new force field performs similarly to the conventional parameters for the UUCG and GCAA hairpin loops and the [U(UA)6A]2 duplex.
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Affiliation(s)
- Asaminew
H. Aytenfisu
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
- Center
for RNA Biology, University of Rochester
Medical Center, Rochester, New York 14642, United States
| | - Aleksandar Spasic
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
- Center
for RNA Biology, University of Rochester
Medical Center, Rochester, New York 14642, United States
| | - Alan Grossfield
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
| | - Harry A. Stern
- Center
for Integrated Research Computing, University
of Rochester, Rochester, New York 14642, United
States
| | - David H. Mathews
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
- Center
for RNA Biology, University of Rochester
Medical Center, Rochester, New York 14642, United States
- Department
of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
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Margreitter C, Reif MM, Oostenbrink C. Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. J Comput Chem 2017; 38:714-720. [DOI: 10.1002/jcc.24733] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Margreitter
- Department of Material Sciences and Process Engineering; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences; Vienna Austria
| | - Maria M. Reif
- Physics Department T38; Technical University of Munich; Munich Germany
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences; Vienna Austria
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