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Dependency of solvation effects on metal identity in surface reactions. Commun Chem 2020; 3:187. [PMID: 36703410 PMCID: PMC9814277 DOI: 10.1038/s42004-020-00428-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/09/2020] [Indexed: 01/29/2023] Open
Abstract
Solvent interactions with adsorbed moieties involved in surface reactions are often believed to be similar for different metal surfaces. However, solvents alter the electronic structures of surface atoms, which in turn affects their interaction with adsorbed moieties. To reveal the importance of metal identity on aqueous solvent effects in heterogeneous catalysis, we studied solvent effects on the activation free energies of the O-H and C-H bond cleavages of ethylene glycol over the (111) facet of six transition metals (Ni, Pd, Pt, Cu, Ag, Au) using an explicit solvation approach based on a hybrid quantum mechanical/molecular mechanical (QM/MM) description of the potential energy surface. A significant metal dependence on aqueous solvation effects was observed that suggests solvation effects must be studied in detail for every reaction system. The main reason for this dependence could be traced back to a different amount of charge-transfer between the adsorbed moieties and metals in the reactant and transition states for the different metal surfaces.
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2
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Florentz C, Giegé R. History of tRNA research in strasbourg. IUBMB Life 2019; 71:1066-1087. [PMID: 31185141 DOI: 10.1002/iub.2079] [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: 03/26/2019] [Accepted: 05/06/2019] [Indexed: 01/03/2023]
Abstract
The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl-tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two-way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health-focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066-1087, 2019.
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Affiliation(s)
- Catherine Florentz
- Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, F-67084, 15 rue René Descartes, Strasbourg, France.,Direction de la Recherche et de la Valorisation, Université de Strasbourg, F-67084, 4 rue Blaise Pascal, Strasbourg, France
| | - Richard Giegé
- Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, F-67084, 15 rue René Descartes, Strasbourg, France
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3
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Ivanov SM, Huber RG, Alibay I, Warwicker J, Bond PJ. Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway. J Chem Inf Model 2018; 59:245-261. [DOI: 10.1021/acs.jcim.8b00765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan M. Ivanov
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix 07-01, 30 Biopolis Street, Singapore 138671, Singapore
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix 07-01, 30 Biopolis Street, Singapore 138671, Singapore
| | - Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
| | - Jim Warwicker
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix 07-01, 30 Biopolis Street, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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4
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Corona A, Palmer SO, Zamacona R, Mendez B, Dean FB, Bullard JM. Discovery and Characterization of Chemical Compounds That Inhibit the Function of Aspartyl-tRNA Synthetase from Pseudomonas aeruginosa. SLAS DISCOVERY 2017; 23:294-301. [PMID: 29186665 DOI: 10.1177/2472555217744559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa, an opportunistic pathogen, is highly susceptible to developing resistance to multiple antibiotics. The gene encoding aspartyl-tRNA synthetase (AspRS) from P. aeruginosa was cloned and the resulting protein characterized. AspRS was kinetically evaluated, and the KM values for aspartic acid, ATP, and tRNA were 170, 495, and 0.5 μM, respectively. AspRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 1690 chemical compounds, resulting in the identification of two inhibitory compounds, BT02A02 and BT02C05. The minimum inhibitory concentrations (MICs) were determined against nine clinically relevant bacterial strains, including efflux pump mutant and hypersensitive strains of P. aeruginosa. The compounds displayed broad-spectrum antibacterial activity and inhibited growth of the efflux and hypersensitive strains with MICs of 16 μg/mL. Growth of wild-type strains were unaffected, indicating that efflux was likely responsible for this lack of activity. BT02A02 did not inhibit growth of human cell cultures at any concentration. However, BT02C05 did inhibit human cell cultures with a cytotoxicity concentration (CC50) of 61.6 μg/mL. The compounds did not compete with either aspartic acid or ATP for binding AspRS, indicating that the mechanism of action of the compound occurs outside the active site of aminoacylation.
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Affiliation(s)
- Araceli Corona
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | | | - Regina Zamacona
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Benjamin Mendez
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Frank B Dean
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - James M Bullard
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
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5
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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6
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Dutta S, Nandi N. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri. J Phys Chem B 2015; 119:10832-48. [PMID: 25794108 DOI: 10.1021/jp511585w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saheb Dutta
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
| | - Nilashis Nandi
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
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7
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Tamamis P, Kasotakis E, Archontis G, Mitraki A. Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides. Methods Mol Biol 2014; 1216:53-70. [PMID: 25213410 DOI: 10.1007/978-1-4939-1486-9_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. Their ability to form biocompatible nanostructures under mild conditions through non-covalent interactions offers a big biofabrication advantage. Structural motifs extracted from natural proteins are an important source of inspiration for the rational design of such peptides. Examples include designer self-assembling peptides that correspond to natural coiled-coil motifs, amyloid-forming proteins, and natural fibrous proteins. In this chapter, we focus on the exploitation of structural information from beta-structured natural fibers. We review a case study of short peptides that correspond to sequences from the adenovirus fiber shaft. We describe both theoretical methods for the study of their self-assembly potential and basic experimental protocols for the assessment of fibril-forming assembly.
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Affiliation(s)
- Phanourios Tamamis
- Department of Physics, University of Cyprus, 20537, CY1678, Nicosia, Cyprus
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8
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Maršavelski A, Lesjak S, Močibob M, Weygand-Đurašević I, Tomić S. A single amino acid substitution affects the substrate specificity of the seryl-tRNA synthetase homologue. ACTA ACUST UNITED AC 2014; 10:3207-16. [DOI: 10.1039/c4mb00416g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently described and characterizedBradyrhizobium japonicumglycine:[carrier protein] ligase 1 (Bj Gly:CP ligase 1), a homologue of methanogenic type seryl-tRNA synthetase (SerRS) is an intriguing enzyme whose physiological role is not yet known.
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Affiliation(s)
| | - Sonja Lesjak
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- Zagreb, Croatia
| | - Marko Močibob
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- Zagreb, Croatia
| | | | - Sanja Tomić
- Department of Physical Chemistry
- Rudjer Boskovic Institute
- Zagreb, Croatia
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9
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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10
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Banik SD, Nandi N. Mechanism of the activation step of the aminoacylation reaction: a significant difference between class I and class II synthetases. J Biomol Struct Dyn 2012; 30:701-15. [PMID: 22731388 DOI: 10.1080/07391102.2012.689701] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present work we report, for the first time, a novel difference in the molecular mechanism of the activation step of aminoacylation reaction between the class I and class II aminoacyl tRNA synthetases (aaRSs). The observed difference is in the mode of nucleophilic attack by the oxygen atom of the carboxylic group of the substrate amino acid (AA) to the αP atom of adenosine triphosphate (ATP). The syn oxygen atom of the carboxylic group attacks the α-phosphorous atom (αP) of ATP in all class I aaRSs (except TrpRS) investigated, while the anti oxygen atom attacks in the case of class II aaRSs. The class I aaRSs investigated are GluRS, GlnRS, TyrRS, TrpRS, LeuRS, ValRS, IleRS, CysRS, and MetRS and class II aaRSs investigated are HisRS, LysRS, ProRS, AspRS, AsnRS, AlaRS, GlyRS, PheRS, and ThrRS. The variation of the electron density at bond critical points as a function of the conformation of the attacking oxygen atom measured by the dihedral angle ψ (C(α)-C') conclusively proves this. The result shows that the strength of the interaction of syn oxygen and αP is stronger than the interaction with the anti oxygen for class I aaRSs. This indicates that the syn oxygen is the most probable candidate for the nucleophilic attack in class I aaRSs. The result is further supported by the computation of the variation of the nonbonded interaction energies between αP atom and anti oxygen as well as syn oxygen in class I and II aaRSs, respectively. The difference in mechanism is explained based on the analysis of the electrostatic potential of the AA and ATP which shows that the relative arrangement of the ATP with respect to the AA is opposite in class I and class II aaRSs, which is correlated with the organization of the active site in respective aaRSs. A comparative study of the reaction mechanisms of the activation step in a class I aaRS (Glutaminyl tRNA synthetase) and in a class II aaRS (Histidyl tRNA synthetase) is carried out by the transition state analysis. The atoms in molecule analysis of the interaction between active site residues or ions and substrates are carried out in the reactant state and the transition state. The result shows that the observed novel difference in the mechanism is correlated with the organizations of the active sites of the respective aaRSs. The result has implication in understanding the experimentally observed different modes of tRNA binding in the two classes of aaRSs.
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Affiliation(s)
- Sindrila Dutta Banik
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, 741235, India
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11
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FORMANECK MARKS, LI GUOHUI, ZHANG XIAODONG, CUI QIANG. CALCULATING ACCURATE REDOX POTENTIALS IN ENZYMES WITH A COMBINED QM/MM FREE ENERGY PERTURBATION APPROACH. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633602000075] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An approach for computing accurate redox potentials in enzymes is developed based on the free energy perturbation technique in a QM/MM framework. With an appropriate choice of the QM level and QM/MM coupling scheme, the intermolecular interaction between the redox center and the protein environment can be adequately described; the speed of QM/MM methods also allows a sufficient configurational sampling for the convergence of free energy derivatives. Following the implementation into the simulation package CHARMM, the method was tested with an application to the first reduction potential of FAD in cholesterol oxidase (Chox). In addition to an accurate QM level and adequate conformational samplings, the effect of long-range electrostatic interactions due to the bulk solvent was also found to be essential. Using a semi-empirical density functional theory (SCC-DFTB) as the QM level, and a multi-stage charge-scaling scheme based on Poisson–Boltzmann calculations for the solvation effect, satisfactory agreements with experimental measurements were obtained. The study of Chox also indicates that large errors in the calculated redox potential might arise if changes in the conformational properties of the protein during the redox process are not taken into account, such as in energy minimization type of studies based on only the X-ray structure of the enzyme in one redox state.
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Affiliation(s)
- MARK S. FORMANECK
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison 1101 University Ave, Madison, WI 53706, USA
| | - GUOHUI LI
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison 1101 University Ave, Madison, WI 53706, USA
| | - XIAODONG ZHANG
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison 1101 University Ave, Madison, WI 53706, USA
| | - QIANG CUI
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison 1101 University Ave, Madison, WI 53706, USA
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12
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13
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Influence of the conserved active site residues of histidyl tRNA synthetase on the mechanism of aminoacylation reaction. Biophys Chem 2011; 158:61-72. [DOI: 10.1016/j.bpc.2011.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/03/2011] [Accepted: 05/03/2011] [Indexed: 11/17/2022]
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14
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Polydorides S, Amara N, Aubard C, Plateau P, Simonson T, Archontis G. Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase. Proteins 2011; 79:3448-68. [PMID: 21563215 DOI: 10.1002/prot.23042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/25/2011] [Accepted: 03/03/2011] [Indexed: 12/13/2022]
Abstract
Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a Coulomb/Accessible Surface Area (CASA) model for solvent effects. We applied this method to engineer aspartyl-adenylate (AspAMP) specificity into Asparaginyl-tRNA synthetase (AsnRS), whose substrate is asparaginyl-adenylate (AsnAMP). Here, we implement a more accurate function, with an all-atom energy for protein interactions and a residue-pairwise generalized Born model for solvent effects. As a first test, we compute aminoacid affinities for several point mutants of Aspartyl-tRNA synthetase (AspRS) and Tyrosyl-tRNA synthetase and stability changes for three helical peptides and compare with experiment. As a second test, we readdress the problem of AsnRS aminoacid engineering. We compare three design criteria, which optimize the folding free-energy, the absolute AspAMP affinity, and the relative (AspAMP-AsnAMP) affinity. The sequences and conformations are improved with respect to our previous, polar-hydrogen/CASA study: For several designed complexes, the AspAMP carboxylate forms three interactions with a conserved arginine and a designed lysine, as in the active site of the AspRS:AspAMP complex. The conformations and interactions are well maintained in molecular dynamics simulations and the sequences have an inverted specificity, favoring AspAMP over AsnAMP. The method is not fully successful, since experimental measurements with the seven most promising sequences show that they do not catalyze at a detectable level the adenylation of Asp (or Asn) with ATP. This may be due to weak AspAMP binding and/or disruption of transition-state stabilization.
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15
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Lopes A, Schmidt Am Busch M, Simonson T. Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase. J Comput Chem 2010; 31:1273-86. [PMID: 19862811 DOI: 10.1002/jcc.21414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A method for computational design of protein-ligand interactions is implemented and tested on the asparaginyl- and aspartyl-tRNA synthetase enzymes (AsnRS, AspRS). The substrate specificity of these enzymes is crucial for the accurate translation of the genetic code. The method relies on a molecular mechanics energy function and a simple, continuum electrostatic, implicit solvent model. As test calculations, we first compute AspRS-substrate binding free energy changes due to nine point mutations, for which experimental data are available; we also perform large-scale redesign of the entire active site of each enzyme (40 amino acids) and compare to experimental sequences. We then apply the method to engineer an increased binding of aspartyl-adenylate (AspAMP) into AsnRS. Mutants are obtained using several directed evolution protocols, where four or five amino acid positions in the active site are randomized. Promising mutants are subjected to molecular dynamics simulations; Poisson-Boltzmann calculations provide an estimate of the corresponding, AspAMP, binding free energy changes, relative to the native AsnRS. Several of the mutants are predicted to have an inverted binding specificity, preferring to bind AspAMP rather than the natural substrate, AsnAMP. The computed binding affinities are significantly weaker than the native, AsnRS:AsnAMP affinity, and in most cases, the active site structure is significantly changed, compared to the native complex. This almost certainly precludes catalytic activity. One of the designed sequences has a higher affinity and more native-like structure and may represent a valid candidate for Asp activity.
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Affiliation(s)
- Anne Lopes
- Laboratoire de Biochimie, Department of Biology, UMR CNRS 7654, Ecole Polytechnique, 91128 Palaiseau, France
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16
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Banik SD, Nandi N. Aminoacylation reaction in the histidyl-tRNA synthetase: fidelity mechanism of the activation step. J Phys Chem B 2010; 114:2301-11. [PMID: 20104869 DOI: 10.1021/jp910730s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aminoacylation is a vital step of natural biosynthesis of peptide. Correct aminoacylation is a necessary prerequisite for the elimination of noncognate amino acids such as D-amino acids. In the present work, we studied the fidelity mechanism of histidine (His) activation (first step of aminoacylation reaction) using a combined quantum mechanical/semiempirical method based on a model of crystal structure of the oligomeric complex of histidyl-tRNA synthetase (HisRS) from Escherichia coli. The study of the variation in the energy during the mutual approach of the His and ATP to form adenylate shows that the surrounding nanospace of synthetase confines the reactants (L-His and ATP) and proximally places in a geometry suitable for the in-line nucleophilic attack. The significantly higher energy of the energy surface of the model containing D-His is due to unfavorable interaction of D-His with ATP and surrounding residues. This indicates that the network of interaction (principally electrostatic) is highly unfavorable when D-amino acid is incorporated. The reorganization of the surrounding nanospace can lower the unfavorable nature of the intermolecular energy surface of D-His and surrounding residues. However, such a rearrangement requires large-scale structural reorganization of the synthetase structure and is unfavorable. The variation in the bond angles and distances in going from the reactant state to the product state via transition state confirms the mechanism of nucleophilic attack and concomitant inversion of oxygen atoms around alpha-phosphorus (alpha-P). Calculation of the electrostatic potential indicates that in addition to the Mg(2+) the Arg residues in the active site facilitate the nucleophilic attack by reducing the negative charge distributed over the oxygen atoms attached to the alpha-P of ATP. Arg 259 residue has a role similar to that played by the two Mg(2+) cations as this residue is in close proximity of the alpha-P of ATP. Arg 113 also facilitates the reduction of the negative charge on the other side of the reaction center. The favorable electrostatic interaction of the Arg 259 with ATP and His is also concluded from the calculation of the binding energy. The Arg 259 anchors the carboxylic acid group of His and the oxygen atom of the alpha-phosphate group during the progress of reaction. Consequently, Arg 259 plays an important catalytic role in the activation step rather than merely reducing the negative charge density over the ATP.
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Affiliation(s)
- S Dutta Banik
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, 741235, India
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17
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Aleksandrov A, Thompson D, Simonson T. Alchemical free energy simulations for biological complexes: powerful but temperamental.... J Mol Recognit 2010; 23:117-27. [PMID: 19693787 DOI: 10.1002/jmr.980] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Free energy simulations compare multiple ligand:receptor complexes by "alchemically" transforming one into another, yielding binding free energy differences. Since their introduction in the 1980s, many technical and theoretical obstacles were surmounted, and the method ("MDFE," since molecular dynamics are often used) has matured into a powerful tool. We describe its current status, its effectiveness, and the challenges it faces. MDFE has provided chemical accuracy for many systems but remains expensive, with significant human overhead costs. The bottlenecks have shifted, partly due to increased computer power. To study diverse sets of ligands, force field availability and accuracy can be a major difficulty. Another difficulty is the frequent need to consider multiple states, related to sidechain protonation or buried waters, for example. Sophisticated, automated methods to sample these states are maturing, such as constant pH simulations. Meanwhile, combinations of MDFE and simpler approaches, like continuum dielectric models, can be very effective. As illustrations, we show how, with careful force field parameterization, MDFE accurately predicts binding specificities between complex tetracycline ligands and their targets. We describe substrate binding to the aspartyl-tRNA synthetase enzyme, where many distinct electrostatic states play a role, and a histidine and a Mg(2+) ion act as coupled switches that help enforce a strict preference for the aspartate substrate, relative to several analogs. Overall, MDFE has achieved a predictive status, where novel ligands can be studied and molecular recognition elucidated in depth. It should play an increasing role in the analysis of complex cellular processes and biomolecular engineering.
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Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
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18
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Cai Y, Schiffer CA. Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV. J Chem Theory Comput 2010; 6:1358-1368. [PMID: 20543885 DOI: 10.1021/ct9004678] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Darunavir (DRV) is a high affinity (4.5×10(-12) M, ΔG = -15.2 kcal/mol) HIV-1 protease inhibitor. Two drug-resistant protease variants FLAP+ (L10I, G48V, I54V, V82A) and ACT (V82T, I84V) decrease the binding affinity with DRV by 1.0 kcal/mol and 1.6 kcal/mol respectively. In this study the absolute and relative binding free energies of DRV with wild-type protease, FLAP+ and ACT were calculated with MM-PB/GBSA and thermodynamic integration methods, respectively. Free energy decomposition elucidated that the mutations conferred resistance by distorting the active site of HIV-1 protease so that the residues that lost binding free energy were not limited to the sites of mutation. Specifically the bis-tetrahydrofuranylurethane moiety of DRV maintained interactions with the FLAP+ and ACT variants, whereas the 4 - amino phenyl group lost more binding free energy with the protease in the FLAP+ and ACT complexes than in the wild-type protease which could account for the majority of the loss in binding free energy. This suggested that replacement of the 4 - amino phenyl group might generate new inhibitors less susceptible to the drug resistant mutations.
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Affiliation(s)
- Yufeng Cai
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605
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19
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Brooks B, Brooks C, MacKerell A, Nilsson L, Petrella R, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner A, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor R, Post C, Pu J, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York D, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem 2009; 30:1545-614. [PMID: 19444816 PMCID: PMC2810661 DOI: 10.1002/jcc.21287] [Citation(s) in RCA: 5949] [Impact Index Per Article: 396.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
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Affiliation(s)
- B.R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and
Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - C.L. Brooks
- Departments of Chemistry & Biophysics, University of
Michigan, Ann Arbor, MI 48109
| | - A.D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD, 21201
| | - L. Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition,
SE-141 57, Huddinge, Sweden
| | - R.J. Petrella
- Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA 02138
- Department of Medicine, Harvard Medical School, Boston, MA
02115
| | - B. Roux
- Department of Biochemistry and Molecular Biology, University of
Chicago, Gordon Center for Integrative Science, Chicago, IL 60637
| | - Y. Won
- Department of Chemistry, Hanyang University, Seoul
133–792 Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - M. Karplus
- Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, MA 02138
- Laboratoire de Chimie Biophysique, ISIS, Université de
Strasbourg, 67000 Strasbourg France
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20
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Nandi N. Chiral discrimination in the confined environment of biological nanospace: reactions and interactions involving amino acids and peptides. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350902999682] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Messmer M, Blais SP, Balg C, Chênevert R, Grenier L, Lagüe P, Sauter C, Sissler M, Giegé R, Lapointe J, Florentz C. Peculiar inhibition of human mitochondrial aspartyl-tRNA synthetase by adenylate analogs. Biochimie 2009; 91:596-603. [PMID: 19254750 DOI: 10.1016/j.biochi.2009.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/18/2009] [Indexed: 11/18/2022]
Abstract
Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs), the enzymes which esterify tRNAs with the cognate specific amino acid, form mainly a different set of proteins than those involved in the cytosolic translation machinery. Many of the mt-aaRSs are of bacterial-type in regard of sequence and modular structural organization. However, the few enzymes investigated so far do have peculiar biochemical and enzymological properties such as decreased solubility, decreased specific activity and enlarged spectra of substrate tRNAs (of same specificity but from various organisms and kingdoms), as compared to bacterial aaRSs. Here the sensitivity of human mitochondrial aspartyl-tRNA synthetase (AspRS) to small substrate analogs (non-hydrolysable adenylates) known as inhibitors of Escherichia coli and Pseudomonas aeruginosa AspRSs is evaluated and compared to the sensitivity of eukaryal cytosolic human and bovine AspRSs. L-aspartol-adenylate (aspartol-AMP) is a competitive inhibitor of aspartylation by mitochondrial as well as cytosolic mammalian AspRSs, with K(i) values in the micromolar range (4-27 microM for human mt- and mammalian cyt-AspRSs). 5'-O-[N-(L-aspartyl)sulfamoyl]adenosine (Asp-AMS) is a 500-fold stronger competitive inhibitor of the mitochondrial enzyme than aspartol-AMP (10nM) and a 35-fold lower competitor of human and bovine cyt-AspRSs (300 nM). The higher sensitivity of human mt-AspRS for both inhibitors as compared to either bacterial or mammalian cytosolic enzymes, is not correlated with clear-cut structural features in the catalytic site as deduced from docking experiments, but may result from dynamic events. In the scope of new antibacterial strategies directed against aaRSs, possible side effects of such drugs on the mitochondrial human aaRSs should thus be considered.
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Affiliation(s)
- Marie Messmer
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, CNRS, IBMC 15 rue René Descartes, 67084 Strasbourg Cedex, France
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22
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Rodríguez Y, Mezei M, Osman R. The PT1-Ca2+ Gla domain binds to a membrane through two dipalmitoylphosphatidylserines. A computational study. Biochemistry 2009; 47:13267-78. [PMID: 19086158 DOI: 10.1021/bi801199v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of vitamin K-dependent proteins to cell membranes containing phosphatidylserine (PS) via gamma-carboxyglutamic acid (Gla) domains is one of the essential steps in the blood coagulation pathway. During activation of the coagulation cascade, prothrombin is converted to thrombin by prothrombinase, a complex consisting of serine protease FXa and cofactor FVa, anchored to anionic phospholipids on the surface of activated platelets in the presence of calcium ions. To investigate the binding of the Gla domain of prothrombin fragment 1 (PT1) to anionic lipids in the presence of Ca2+, we have conducted MD simulations of the protein with one and two dipalmitoylphosphatidylserines (DPPS) in a dipalmitoylphosphatidylcholine (DPPC) bilayer membrane. The results show a well-defined phosphatidylserine binding site, which agrees generally with crystallographic studies [Huang, M., et al. (2003) Nat. Struct. Biol. 10, 751-756]. However, in the presence of the lipid membrane, some of the interactions observed in the crystal structure adjust during the simulations possibly because in our system the PT1-Ca2+ complex is embedded in a DPPC lipid membrane. Our simulations confirm the existence of a second phospholipid headgroup binding site on the opposite face of the PT1-Ca2+ complex as suggested by MacDonald et al. [(1997) Biochemistry 36, 5120-5127]. The serine headgroup in the second site binds through a Gla domain-bound calcium ion Ca1, Gla30, and Lys11. On the basis of free energy simulations, we estimate the energy of binding of the PT1-Ca2+ complex to a single DPPS to be around -11.5 kcal/mol. The estimated free energy of binding of a DPPS lipid to the second binding site is around -8.8 kcal/mol and is in part caused by the nature of the second site and in part by entropic effects.
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Affiliation(s)
- Yoel Rodríguez
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
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23
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Thompson D, Miller C, McCarthy FO. Computer simulations reveal a novel nucleotide-type binding orientation for ellipticine-based anticancer c-kit kinase inhibitors. Biochemistry 2008; 47:10333-44. [PMID: 18754682 DOI: 10.1021/bi801239u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Receptor tyrosine kinase (RTK) enzymes regulate cell signaling pathways and so are an important target for cancer chemotherapy. Current inhibitors of c-kit, a key RTK stem cell factor receptor, are inactive against the most common mutated variant Asp816Val, associated with highly malignant cancers. Recent combined experimental/simulation work has highlighted the utility of the ellipticine pharmacore in inhibiting mutant c-kit, and the present simulation study applies a combination of high-level simulation tools to probe further the binding of ellipticine-based derivatives to c-kit. We find a large preference for protonation of bound ellipticine, which stabilizes the negative protein residues that coordinated ADP.Mg (2+) in the native complex. The resulting ellipticine inhibitor binding mode resembles the native nucleotide complex and serves to explain some existing experimental data on binding specificities, indicating that functionalization at the C4/C5 sites of ellipticine derivatives may be important for the design of novel nucleotide analogues that inhibit mutant c-kit.
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24
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Thompson D, Lazennec C, Plateau P, Simonson T. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. Proteins 2008; 71:1450-60. [PMID: 18076053 DOI: 10.1002/prot.21834] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Faithful genetic code translation requires that each aminoacyl-tRNA synthetase recognise its cognate amino acid ligand specifically. Aspartyl-tRNA synthetase (AspRS) distinguishes between its negatively-charged Asp substrate and two competitors, neutral Asn and di-negative succinate, using a complex network of electrostatic interactions. Here, we used molecular dynamics simulations and site-directed mutagenesis experiments to probe these interactions further. We attempt to decrease the Asp/Asn binding free energy difference via single, double and triple mutations that reduce the net positive charge in the active site of Escherichia coli AspRS. Earlier, Glutamine 199 was changed to a negatively-charged glutamate, giving a computed reduction in Asp affinity in good agreement with experiment. Here, Lysine 198 was changed to a neutral leucine; then, Lys198 and Gln199 were mutated simultaneously. Both mutants are predicted to have reduced Asp binding and improved Asn binding, but the changes are insufficient to overcome the initial, high specificity of the native enzyme, which retains a preference for Asp. Probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments, we found no detectable activity for the mutant enzymes, indicating weaker Asp binding and/or poorer transition state stabilization. The simulations show that the mutations' effect is partly offset by proton uptake by a nearby histidine. Therefore, we performed additional simulations where the nearby Histidines 448 and 449 were mutated to neutral or negative residues: (Lys198Leu, His448Gln, His449Gln), and (Lys198Leu, His448Glu, His449Gln). This led to unexpected conformational changes and loss of active site preorganization, suggesting that the AspRS active site has a limited structural tolerance for electrostatic modifications. The data give insights into the complex electrostatic network in the AspRS active site and illustrate the difficulty in engineering charged-to-neutral changes of the preferred ligand.
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Affiliation(s)
- Damien Thompson
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland.
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25
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Thompson D, Lazennec C, Plateau P, Simonson T. Ammonium Scanning in an Enzyme Active Site. J Biol Chem 2007; 282:30856-68. [PMID: 17690095 DOI: 10.1074/jbc.m704788200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
D-amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Aspartyl-tRNA synthetase (AspRS) can misacylate tRNA(Asp) with D-aspartate instead of its usual substrate, L-Asp. We investigate how the preference for L-Asp arises, using molecular dynamics simulations. Asp presents a special problem, having pseudosymmetry broken only by its ammonium group, and AspRS must protect not only against D-Asp, but against an "inverted" orientation where the two substrate carboxylates are swapped. We compare L-Asp and D-Asp, in both orientations, and succinate, where the ammonium group is removed and the ligand has an additional negative charge. All possible ammonium positions on the ligand are thus scanned, providing information on electrostatic interactions. As controls, we simulate a Q199E mutation, obtaining a reduction in binding free energy in agreement with experiment, and we simulate TyrRS, which can misacylate tRNA(Tyr) with D-Tyr. For both TyrRS and AspRS, we obtain a moderate binding free energy difference DeltaDeltaG between the L- and D-amino acids, in agreement with their known ability to misacylate their tRNAs. In contrast, we predict that AspRS is strongly protected against inverted L-Asp binding. For succinate, kinetic measurements reveal a DeltaDeltaG of over 5 kcal/mol, favoring L-Asp. The simulations show how chiral discriminations arises from the structures, with two AspRS conformations acting in different ways and proton uptake by nearby histidines playing a role. A complex network of charges protects AspRS against most binding errors, making the engineering of its specificity a difficult challenge.
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Affiliation(s)
- Damien Thompson
- Laboratoire de Biochimie (CNRS, UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
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26
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Zoete V, Michielin O. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: Application to the TCR-p-MHC complex. Proteins 2007; 67:1026-47. [PMID: 17377991 DOI: 10.1002/prot.21395] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recognition by the T-cell receptor (TCR) of immunogenic peptides (p) presented by Class I major histocompatibility complexes (MHC) is the key event in the immune response against virus-infected cells or tumor cells. A study of the 2C TCR/SIYR/H-2K(b) system using a computational alanine scanning and a much faster binding free energy decomposition based on the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method is presented. The results show that the TCR-p-MHC binding free energy decomposition using this approach and including entropic terms provides a detailed and reliable description of the interactions between the molecules at an atomistic level. Comparison of the decomposition results with experimentally determined activity differences for alanine mutants yields a correlation of 0.67 when the entropy is neglected and 0.72 when the entropy is taken into account. Similarly, comparison of experimental activities with variations in binding free energies determined by computational alanine scanning yields correlations of 0.72 and 0.74 when the entropy is neglected or taken into account, respectively. Some key interactions for the TCR-p-MHC binding are analyzed and some possible side chains replacements are proposed in the context of TCR protein engineering. In addition, a comparison of the two theoretical approaches for estimating the role of each side chain in the complexation is given, and a new ad hoc approach to decompose the vibrational entropy term into atomic contributions, the linear decomposition of the vibrational entropy (LDVE), is introduced. The latter allows the rapid calculation of the entropic contribution of interesting side chains to the binding. This new method is based on the idea that the most important contributions to the vibrational entropy of a molecule originate from residues that contribute most to the vibrational amplitude of the normal modes. The LDVE approach is shown to provide results very similar to those of the exact but highly computationally demanding method.
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MESH Headings
- Alanine/metabolism
- Computer Simulation
- Crystallography, X-Ray
- Entropy
- Major Histocompatibility Complex/immunology
- Models, Molecular
- Peptides/chemistry
- Peptides/metabolism
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Static Electricity
- Vibration
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Affiliation(s)
- Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode, CH-1015 Lausanne, Switzerland.
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27
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Polydoridis S, Leonidas DD, Oikonomakos NG, Archontis G. Recognition of ribonuclease A by 3'-5'-pyrophosphate-linked dinucleotide inhibitors: a molecular dynamics/continuum electrostatics analysis. Biophys J 2007; 92:1659-72. [PMID: 17142283 PMCID: PMC1796809 DOI: 10.1529/biophysj.106.093419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 11/01/2006] [Indexed: 11/18/2022] Open
Abstract
The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic effect in pathological conditions associated with these proteins. The most potent low molecular weight inhibitor of RNase reported to date is the compound 5'-phospho-2'-deoxyuridine-3-pyrophosphate (P-->5)-adenosine-3-phosphate (pdUppA-3'-p). The 3',5'-pyrophosphate group of this compound increases its affinity and introduces structural features which seem to be unique in pyrophosphate-containing ligands bound to RNase A, such as the adoption of a syn conformation by the adenosine base at RNase subsite B(2) and the placement of the 5'-beta-phosphate of the adenylate (instead of the alpha-phosphate) at subsite P(1) where the phosphodiester bond cleavage occurs. In this work, we study by multi-ns molecular dynamics simulations the structural properties of RNase A complexes with the ligand pdUppA-3'-p and the related weaker inhibitor dUppA, which lacks the 3' and 5' terminal phosphate groups of pdUppA-3'-p. The simulations show that the adenylate 5'-beta-phosphate binding position and the adenosine syn orientation constitute robust structural features in both complexes, stabilized by persistent interactions with specific active-site residues of subsites P(1) and B(2). The simulation structures are used in conjunction with a continuum-electrostatics (Poisson-Boltzmann) model, to evaluate the relative binding affinity of the two complexes. The computed relative affinity of pdUppA-3'-p varies between -7.9 kcal/mol and -2.8 kcal/mol for a range of protein/ligand dielectric constants (epsilon(p)) 2-20, in good agreement with the experimental value (-3.6 kcal/mol); the agreement becomes exact with epsilon(p) = 8. The success of the continuum-electrostatics model suggests that the differences in affinity of the two ligands originate mainly from electrostatic interactions. A residue decomposition of the electrostatic free energies shows that the terminal phosphate groups of pdUppA-3'-p make increased interactions with residues Lys(7) and Lys(66) of the more remote sites P(2) and P(0), and His(119) of site P(1).
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28
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Rodríguez Y, Mezei M, Osman R. Association free energy of dipalmitoylphosphatidylserines in a mixed dipalmitoylphosphatidylcholine membrane. Biophys J 2007; 92:3071-80. [PMID: 17277191 PMCID: PMC1852338 DOI: 10.1529/biophysj.106.089078] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blood coagulation is strongly dependent on the binding of vitamin K-dependent proteins to cell membranes containing phosphatidylserine (PS) via gamma-carboxyglutamic acid (Gla) domains. The process depends on calcium, which can induce nonideal behavior in membranes through domain formation. Such domain separation mediated by Ca(2+) ions or proteins can have an important contribution to the thermodynamics of the interaction between charged peripheral proteins and oppositely charged membranes. To characterize the properties of lipid-lipid interactions, molecular dynamics, and free energy simulations in a mixed bilayer membrane containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine were carried out. The free energy of association between dipalmitoylphosphatidylserines in the environment of dipalmitoylphosphatidylcholines has been calculated by using a novel approach to the dual topology technique of the PS-PC hybrid. Two different methods, free energy perturbation and thermodynamic integration, were used to calculate the free energy difference. In thermodynamic integration runs three schemes were applied to evaluate the integral at the limits of lambda --> 0 or lambda --> 1. Our studies show that the association of two PSs in the environment of PCs is repulsive in the absence of Ca(2+) and becomes favorable in their presence. We also show that the mixed component membrane should exhibit nonideal behavior that will lead to PS clustering.
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Affiliation(s)
- Yoel Rodríguez
- Department of Molecular Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York, USA
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29
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Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/1-4020-5372-x_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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30
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31
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Wan S, Stote RH, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. J Chem Phys 2006; 121:9539-48. [PMID: 15538876 DOI: 10.1063/1.1789935] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the advent of more powerful computers, the question of calculating thermodynamic quantities, such as the energy and the entropy, in solute-solvent systems is revisited. The calculation of these thermodynamic quantitites was limited in the past by their slow convergence relative to the free energy. Using molecular dynamics simulations, the energy, entropy, and free energy of solvation of NMA and CH(3)NH(2), as well as their relative values, have been determined. Three different methods (the thermodynamic perturbation method, the thermodynamic integration method, and a finite-difference method) are compared. The finite difference method gives the best results and accurate values for the entropy and energy were obtained using a reasonable amount to computer time. The results suggest that a meaningful thermodynamic description of biomolecular processes can be realized with present methods and the available computer time.
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Affiliation(s)
- Shunzhou Wan
- Laboratoire de Chimie Biophysique ISIS (UMR 7006-CNRS), Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg, France
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32
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Thompson D, Larsson JA. Modeling Competitive Guest Binding to β-Cyclodextrin Molecular Printboards. J Phys Chem B 2006; 110:16640-5. [PMID: 16913800 DOI: 10.1021/jp062553n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anchoring of functionalized guest molecules to self-assembled monolayers (SAMs) is key to the development of molecular printboards for nanopatterning. One very promising system involves guest binding to immobilized beta-cyclodextrin (beta-CD) hosts, with guest:host recognition facilitated by a hydrophobic interaction between uncharged anchor groups on the guest molecule and beta-CD hosts self-assembled at gold surfaces. We use molecular dynamics free energy (MDFE) simulations to describe the specificity of guest:beta-CD association. We find good agreement with experimental thermodynamic measurements for binding enthalpy differences between three commonly used phenyl guests: benzene, toluene, and t-butylbenzene. van der Waals interaction with the inside of the host cavity accounts for almost all of the net stabilization of the larger phenyl guests in beta-CD. Partial and full methylation of the secondary rim of beta-CD decreases host rigidity and significantly impairs binding of both phenyl and larger adamantane guest molecules. The beta-CD cavity is also very intolerant of guest charging, penalizing the oxidized state of ferrocene by at least 7 kcal/mol. beta-CD hence expresses moderate specificity toward uncharged organic guest molecules by van der Waals recognition, with a much higher specificity calculated for electrostatic recognition of organometallic guests.
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Affiliation(s)
- D Thompson
- Tyndall National Institute, Lee Maltings, Cork, Ireland.
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33
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Thompson D, Simonson T. Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions. J Biol Chem 2006; 281:23792-803. [PMID: 16774919 DOI: 10.1074/jbc.m602870200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular recognition between the aminoacyl-tRNA synthetase enzymes and their cognate amino acid ligands is essential for the faithful translation of the genetic code. In aspartyl-tRNA synthetase (AspRS), the co-substrate ATP binds preferentially with three associated Mg2+ cations in an unusual, bent geometry. The Mg2+ cations play a structural role and are thought to also participate catalytically in the enzyme reaction. Co-binding of the ATP x Mg3(2+) complex was shown recently to increase the Asp/Asn binding free energy difference, indicating that amino acid discrimination is substrate-assisted. Here, we used molecular dynamics free energy simulations and continuum electrostatic calculations to resolve two related questions. First, we showed that if one of the Mg2+ cations is removed, the Asp/Asn binding specificity is strongly reduced. Second, we computed the relative stabilities of the three-cation complex and the 2-cation complexes. We found that the 3-cation complex is overwhelmingly favored at ordinary magnesium concentrations, so that the protein is protected against the 2-cation state. In the homologous LysRS, the 3-cation complex was also strongly favored, but the third cation did not affect Lys binding. In tRNA-bound AspRS, the single remaining Mg2+ cation strongly favored the Asp-adenylate substrate relative to Asn-adenylate. Thus, in addition to their structural and catalytic roles, the Mg2+ cations contribute to specificity in AspRS through long range electrostatic interactions with the Asp side chain in both the pre- and post-adenylation states.
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Affiliation(s)
- Damien Thompson
- Laboratoire de Biochimie, CNRS, UMR7654, Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
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34
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Hughes SJ, Tanner JA, Miller AD, Gould IR. Molecular dynamics simulations of LysRS: an asymmetric state. Proteins 2006; 62:649-62. [PMID: 16317719 DOI: 10.1002/prot.20609] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report molecular dynamics simulations of the Escherichia coli Lysyl-tRNA synthetase LysU isoform carried out as a benchmark for mutant simulations in in silico protein engineering efforts. Unlike previous studies of aminoacyl-tRNA synthetases, LysU is modelled in its full dimeric form with explicit solvent. While developing a suitable simulation protocol, we observed an asymmetry that persists despite improvements to the model. This prediction has directly led to experiments that establish a functional asymmetry in nucleotide binding by LysU. The development of a simulation protocol and validation of the model are presented here. The observed asymmetry is described and the role of protein flexibility in developing the asymmetry is discussed.
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Affiliation(s)
- Samantha J Hughes
- Imperial College Genetic Therapies Centre, Department of Chemistry, Imperial College London
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35
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Thompson D, Plateau P, Simonson T. Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase. Chembiochem 2006; 7:337-44. [PMID: 16408313 DOI: 10.1002/cbic.200500364] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Specific recognition of their cognate amino acid substrates by the aminoacyl-tRNA synthetase enzymes is essential for the correct translation of the genetic code. For aspartyl-tRNA synthetase (AspRS), electrostatic interactions are expected to play an important role, since its three substrates (aspartate, ATP, tRNA) are all electrically charged. We used molecular-dynamics free-energy simulations and experiments to compare the binding of the substrate Asp and its electrically neutral analogue Asn to AspRS. The preference for Asp is found to be very strong, with good agreement between simulations and experiment. The simulations reveal long-range interactions that electrostatically couple the amino acid ligand, ATP, and its associated Mg2+ cations, a histidine side chain (His448) next to the amino acid ligand and a flexible loop that closes over the active site in response to amino acid binding. Closing this loop brings a negatively charged glutamate into the active site; this causes His448 to recruit a labile proton, which interacts favorably with Asp and accounts for most of the Asp/Asn discrimination. Cobinding of the second substrate, ATP, increases specificity for Asp further and makes the system robust towards removal of His448, which is mutated to a neutral amino acid in many organisms. Thus, AspRS specificity is assisted by a labile proton and a cosubstrate, and ATP acts as a mobile discriminator for specific Asp binding to AspRS. In asparaginyl-tRNA synthetase, a close homologue of AspRS, a few binding-pocket differences modify the charge balance so that asparagine binding predominates.
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Affiliation(s)
- Damien Thompson
- Laboratoire de Biochimie (CNRS, UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
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36
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Yang W, Bitetti-Putzer R, Karplus M. Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. J Chem Phys 2006; 120:2618-28. [PMID: 15268405 DOI: 10.1063/1.1638996] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A method is proposed for improving the accuracy and efficiency of free energy simulations. The essential idea is that the convergence of the relevant measure (e.g., the free energy derivative in thermodynamic integration) is monitored in the reverse direction starting from the last frame of the trajectory, instead of the usual approach, which begins with the first frame and goes in the forward direction. This simple change in the use of the simulation data makes it straightforward to eliminate the contamination of the averages by contributions from the equilibrating region. A statistical criterion is introduced for distinguishing the equilibrated (production) region from the equilibrating region. The proposed method, called reverse cumulative averaging, is illustrated by its application to the well-studied case of the alchemical free energy simulation of ethane to methanol.
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Affiliation(s)
- Wei Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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37
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Nikolic-Hughes I, O'brien PJ, Herschlag D. Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions. J Am Chem Soc 2005; 127:9314-5. [PMID: 15984827 DOI: 10.1021/ja051603j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli alkaline phosphatase (AP) is a prototypical bimetalloenzyme, facilitating catalysis of phosphate monoester hydrolysis with two Zn2+ metal ions that are only 4 A apart. In the reaction's transition state, one of the nonbridging oxygen atoms of the transferred group appears to interact directly with the Zn2+ ion metallocluster. To determine the importance and the energetic properties of this interaction, we systematically varied the charge on this oxygen atom, exploiting the ability of AP to catalyze reactions of different classes of substrates. We observed that the AP catalytic proficiency correlates very well (R2 = 0.98) with the charge on this oxygen atom, over 8 orders of magnitude of catalytic proficiency. The slope of this linear correlation (31 +/- 2 kcal/mol per unit charge) is extraordinarily steep, indicating that AP greatly discriminates between differentially charged substrates. We suggest that this discrimination arises via an electrostatic interaction with the bimetallocluster. The dependence of the AP catalytic proficiency on the nonbridging oxygen charge is much larger than charge perturbation effects observed previously for other proteins. We propose that AP uses folding energy to position the two Zn2+ metal ions in close proximity, thereby creating an active site with a high electrostatic potential that is extraordinarily sensitive to the charge that "solvates" the metallocluster. The sensitivity of enzyme energetics to systematic variation in electrostatic properties provides a powerful measure of the active site environment. Future work comparing the sensitivity of related enzymes that have been optimized to catalyze different reactions will help reveal how natural selection has tuned related active sites to favor different reactions.
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Affiliation(s)
- Ivana Nikolic-Hughes
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
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38
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Wan S, Coveney PV, Flower DR. Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing. THE JOURNAL OF IMMUNOLOGY 2005; 175:1715-23. [PMID: 16034112 DOI: 10.4049/jimmunol.175.3.1715] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Free energy calculations of the wild-type and the variant human T cell lymphotropic virus type 1 Tax peptide presented by the MHC to the TCR have been performed using large scale massively parallel molecular dynamics simulations. The computed free energy difference (-1.86 +/- 0.44 kcal/mol) using alchemical mutation-based thermodynamic integration agrees well with experimental data (-2.9 +/- 0.2 kcal/mol). Our simulations exploit state-of-the-art hardware and codes whose algorithms have been optimized for supercomputing platforms. This enables us to simulate larger, more realistic biological systems for longer durations without the imposition of artificial constraints.
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MESH Headings
- Binding Sites/immunology
- Computational Biology/methods
- Computational Biology/standards
- Computational Biology/statistics & numerical data
- Computer Simulation
- Crystallography, X-Ray/methods
- Crystallography, X-Ray/standards
- Crystallography, X-Ray/statistics & numerical data
- HLA-A Antigens/chemistry
- HLA-A Antigens/metabolism
- HLA-A2 Antigen
- Models, Immunological
- Nanotechnology/methods
- Nanotechnology/standards
- Nanotechnology/statistics & numerical data
- Peptide Fragments/chemistry
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding/immunology
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Reference Standards
- Software
- Thermodynamics
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, United Kingdom
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39
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Fowler PW, Jha S, Coveney PV. Grid-based steered thermodynamic integration accelerates the calculation of binding free energies. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:1999-2015. [PMID: 16099763 DOI: 10.1098/rsta.2005.1625] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differences using thermodynamic integration can be significantly reduced: potentially from weeks or months to days of wall-clock time. To be able to perform such accelerated calculations requires the ability to both run concurrently and control in realtime several parallel simulations on a computational Grid. We describe how the RealityGrid computational steering system, in conjunction with a scalable classical MD code, can be used to dramatically reduce the time to achieve a result. This is necessary to improve the adoption of this technique and further allows more detailed investigations into the accuracy and precision of thermodynamic integration. Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.
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Affiliation(s)
- Philip W Fowler
- Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, UK
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40
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Green DF, Tidor B. Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates. J Mol Biol 2004; 342:435-52. [PMID: 15327945 DOI: 10.1016/j.jmb.2004.06.087] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 05/24/2004] [Accepted: 06/30/2004] [Indexed: 10/26/2022]
Abstract
Natural evolution has resulted in protein molecules displaying a wide range of binding properties that include extremes of affinity and specificity. A detailed understanding of the principles underlying protein structure-function relationships, particularly with respect to binding properties, would greatly enhance molecular engineering and ligand design studies. Here, we have analyzed the interactions of an aminoacyl-tRNA synthetase for which strong evolutionary pressure has enforced high specificity for substrate binding and catalysis. Electrostatic interactions have been identified as one efficient mechanism for enhancing binding specificity; as such, the effects of charged and polar groups were the focus of this study. The binding of glutaminyl-tRNA synthetase from Escherichia coli to several ligands, including the natural substrates, was analyzed. The electrostatic complementarity of the enzyme to its ligands was assessed using measures derived from affinity optimization theory. The results were independent of the details of the calculational parameters, including the value used for the protein dielectric constant. Glutamine and ATP, two of the natural ligands, were found to be extremely complementary to their binding sites, particularly in regions seen to make electrostatic interactions in the structure. These data suggest that the optimization of electrostatic interactions has played an important role in guiding the evolution of this enzyme. The results also show that the enzyme is able to effectively select for high affinity and specificity for the same chemical moieties both in the context of smaller substrates, and in that of a larger reactive intermediate. The regions of greatest non-complementarity between the enzyme and ligands are the portions of the ligand that make few polar contacts with the binding site, as well as the sites of chemical reaction, where overly strong electrostatic binding interactions with the substrate could hinder catalysis. The results also suggest that the negative charge on the phosphorus center of glutaminyl-adenylate plays an important role in the tight binding of this intermediate, and thus that adenylate analogs that preserve the negative charge in this region may bind substantially tighter than analogs where this group is replaced with a neutral group, such as the sulfamoyl family, which can make similar hydrogen bonds but is uncharged.
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Affiliation(s)
- David F Green
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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41
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Stultz CM, Edelman ER. A structural model that explains the effects of hyperglycemia on collagenolysis. Biophys J 2004; 85:2198-204. [PMID: 14507685 PMCID: PMC1303446 DOI: 10.1016/s0006-3495(03)74645-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Prior investigations into the effects hyperglycemia on collagen degradation have yielded conflicting results. We present a new formalism for understanding the biochemistry of collagenolysis and the effects of hyperglycemia on collagen degradation. The analysis is based on an understanding of environments that affect the conformational stability of collagen. We suggest that collagen can exist in two distinct conformational states-a native state and a vulnerable state. Vulnerable collagen corresponds to a non-native conformation where partially unfolded regions near collagenase cleavage sites enable collagenases to efficiently degrade collagen. Theoretical calculations on collagen-like model peptides suggest that relatively short periods of hyperglycemia can alter the equilibrium distribution of states to favor vulnerable states of collagen. These data provide new insights into the mechanism of collagenolysis and resolve apparently discrepant experimental data on the effects of hyperglycemia on collagen degradation.
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Affiliation(s)
- Collin M Stultz
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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42
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Simonson T, Carlsson J, Case DA. Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models. J Am Chem Soc 2004; 126:4167-80. [PMID: 15053606 DOI: 10.1021/ja039788m] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionizable residues play important roles in protein structure and activity, and proton binding is a valuable reporter of electrostatic interactions in these systems. We use molecular dynamics free energy simulations (MDFE) to compute proton pKa shifts, relative to a model compound in solution, for three aspartate side chains in two proteins. Simulations with explicit solvent and with an implicit, dielectric continuum solvent are reported. The implicit solvent simulations use the generalized Born (GB) model, which provides an approximate, analytical solution to Poisson's equation. With explicit solvent, the direction of the pKa shifts is correct in all three cases with one force field (AMBER) and in two out of three cases with another (CHARMM). For two aspartates, the dielectric response to ionization is found to be linear, even though the separate protein and solvent responses can be nonlinear. For thioredoxin Asp26, nonlinearity arises from the presence of two substates that correspond to the two possible orientations of the protonated carboxylate. For this side chain, which is partly buried and has a large pKa upshift, very long simulations are needed to correctly sample several slow degrees of freedom that reorganize in response to the ionization. Thus, nearby Lys57 rotates to form a salt bridge and becomes buried, while three waters intercalate along the opposite edge of Asp26. Such strong and anisotropic reorganization is very difficult to predict with Poisson-Boltzmann methods that only consider electrostatic interactions and employ a single protein structure. In contrast, MDFE with a GB dielectric continuum solvent, used for the first time for pKa calculations, can describe protein reorganization accurately and gives encouraging agreement with experiment and with the explicit solvent simulations.
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Affiliation(s)
- Thomas Simonson
- Laboratoire de Biochimie (UMR7654 du CNRS), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
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43
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Gohlke H, Kiel C, Case DA. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 2003; 330:891-913. [PMID: 12850155 DOI: 10.1016/s0022-2836(03)00610-7] [Citation(s) in RCA: 976] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Absolute binding free energy calculations and free energy decompositions are presented for the protein-protein complexes H-Ras/C-Raf1 and H-Ras/RalGDS. Ras is a central switch in the regulation of cell proliferation and differentiation. In our study, we investigate the capability of the molecular mechanics (MM)-generalized Born surface area (GBSA) approach to estimate absolute binding free energies for the protein-protein complexes. Averaging gas-phase energies, solvation free energies, and entropic contributions over snapshots extracted from trajectories of the unbound proteins and the complexes, calculated binding free energies (Ras-Raf: -15.0(+/-6.3)kcal mol(-1); Ras-RalGDS: -19.5(+/-5.9)kcal mol(-1)) are in fair agreement with experimentally determined values (-9.6 kcal mol(-1); -8.4 kcal mol(-1)), if appropriate ionic strength is taken into account. Structural determinants of the binding affinity of Ras-Raf and Ras-RalGDS are identified by means of free energy decomposition. For the first time, computationally inexpensive generalized Born (GB) calculations are applied in this context to partition solvation free energies along with gas-phase energies between residues of both binding partners. For selected residues, in addition, entropic contributions are estimated by classical statistical mechanics. Comparison of the decomposition results with experimentally determined binding free energy differences for alanine mutants of interface residues yielded correlations with r(2)=0.55 and 0.46 for Ras-Raf and Ras-RalGDS, respectively. Extension of the decomposition reveals residues as far apart as 25A from the binding epitope that can contribute significantly to binding free energy. These "hotspots" are found to show large atomic fluctuations in the unbound proteins, indicating that they reside in structurally less stable regions. Furthermore, hotspot residues experience a significantly larger-than-average decrease in local fluctuations upon complex formation. Finally, by calculating a pair-wise decomposition of interactions, interaction pathways originating in the binding epitope of Raf are found that protrude through the protein structure towards the loop L1. This explains the finding of a conformational change in this region upon complex formation with Ras, and it may trigger a larger structural change in Raf, which is considered to be necessary for activation of the effector by Ras.
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Affiliation(s)
- Holger Gohlke
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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44
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Li G, Zhang X, Cui Q. Free Energy Perturbation Calculations with Combined QM/MM Potentials Complications, Simplifications, and Applications to Redox Potential Calculations. J Phys Chem B 2003. [DOI: 10.1021/jp034286g] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Guohui Li
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, Wisconsin 53706
| | - Xiaodong Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, Wisconsin 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, Wisconsin 53706
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45
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Hughes SJ, Tanner JA, Hindley AD, Miller AD, Gould IR. Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment. BMC STRUCTURAL BIOLOGY 2003; 3:5. [PMID: 12787471 PMCID: PMC165585 DOI: 10.1186/1472-6807-3-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2003] [Accepted: 06/04/2003] [Indexed: 11/26/2022]
Abstract
BACKGROUND Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. RESULTS Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. CONCLUSIONS The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-tRNA synthetases, and may play an important functional role. We suggest a manner in which catalytic efficiency could be improved by LysU operating in an alternating sites mechanism.
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Affiliation(s)
- Samantha J Hughes
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London, SW7 2AZ, UK
| | - Julian A Tanner
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London, SW7 2AZ, UK
- Present Address: Department of Biochemistry, University of Hong Kong, Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Alison D Hindley
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London, SW7 2AZ, UK
| | - Andrew D Miller
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London, SW7 2AZ, UK
| | - Ian R Gould
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London, SW7 2AZ, UK
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46
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Affiliation(s)
- Chung F Wong
- Howard Hughes Medical Institute and Department of Pharmacology, University of California-San Diego, La Jolla, California 92093-0365, USA
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47
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Michielin O, Karplus M. Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. J Mol Biol 2002; 324:547-69. [PMID: 12445788 DOI: 10.1016/s0022-2836(02)00880-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recognition by the T-cell receptor (TCR) of immunogenic peptides presented by class I major histocompatibility complexes (MHCs) is the determining event in the specific cellular immune response against virus-infected cells or tumor cells. It is of great interest, therefore, to elucidate the molecular principles upon which the selectivity of a TCR is based. These principles can in turn be used to design therapeutic approaches, such as peptide-based immunotherapies of cancer. In this study, free energy simulation methods are used to analyze the binding free energy difference of a particular TCR (A6) for a wild-type peptide (Tax) and a mutant peptide (Tax P6A), both presented in HLA A2. The computed free energy difference is 2.9 kcal/mol, in good agreement with the experimental value. This makes possible the use of the simulation results for obtaining an understanding of the origin of the free energy difference which was not available from the experimental results. A free energy component analysis makes possible the decomposition of the free energy difference between the binding of the wild-type and mutant peptide into its components. Of particular interest is the fact that better solvation of the mutant peptide when bound to the MHC molecule is an important contribution to the greater affinity of the TCR for the latter. The results make possible identification of the residues of the TCR which are important for the selectivity. This provides an understanding of the molecular principles that govern the recognition. The possibility of using free energy simulations in designing peptide derivatives for cancer immunotherapy is briefly discussed.
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Affiliation(s)
- Olivier Michielin
- Ludwig Institute for Cancer Research, Lausanne Branch, Chemin des Boveresses, 155 1066, Epalinges, Switzerland
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48
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Banavali NK, Im W, Roux B. Electrostatic free energy calculations using the generalized solvent boundary potential method. J Chem Phys 2002. [DOI: 10.1063/1.1507108] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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49
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Simonson T, Archontis G, Karplus M. Free energy simulations come of age: protein-ligand recognition. Acc Chem Res 2002; 35:430-7. [PMID: 12069628 DOI: 10.1021/ar010030m] [Citation(s) in RCA: 290] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide an understanding of the interactions involved that goes beyond, and is an important complement to, experimental studies. Poisson-Boltzmann electrostatic models provide a faster and simpler free energy method in cases where electrostatic interactions are important. We illustrate both molecular dynamics and Poisson-Boltzmann methods with a detailed study of amino acid recognition by aspartyl-tRNA synthetase, whose specificity is important for maintaining the integrity of the genetic code.
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Affiliation(s)
- Thomas Simonson
- Laboratoire de Biologie et G'enomique Structurales (CNRS), IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Strasbourg, France
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50
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Cui Q, Elstner M, Karplus M. A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH). J Phys Chem B 2002. [DOI: 10.1021/jp013012v] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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