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Malde AK, Stroet M, Caron B, Visscher KM, Mark AE. Predicting the Prevalence of Alternative Warfarin Tautomers in Solution. J Chem Theory Comput 2018; 14:4405-4415. [PMID: 29999318 DOI: 10.1021/acs.jctc.8b00453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Warfarin, a widely used oral anticoagulant, is prescribed as a racemic mixture. Each enantiomer of neutral Warfarin can exist in 20 possible tautomeric states leading to complex pharmacokinetics and uncertainty as to the relevant species under different conditions. Here, the ability of alternative computational approaches to predict the preferred tautomeric form(s) of neutral Warfarin in different solvents is examined. It is shown that varying the method used to estimate the heat of formation in vacuum (direct or via homodesmic reactions), whether entropic corrections were included, and the method used to estimate the free enthalpy of solvation (i.e., PCM, COSMO, or SMD implicit models or explicit solvent) lead to large differences in the predicted rank and relative populations of the tautomers. In this case, only a combination of the enthalpy of formation using homodesmic reactions and explicit solvent to estimate the free enthalpy of solvation yielded results compatible with the available experimental data. The work also suggests that a small but significant subset of the possible Warfarin tautomers are likely to be physiologically relevant.
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Affiliation(s)
- Alpeshkumar K Malde
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Bertrand Caron
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Koen M Visscher
- Division of Molecular Toxicology , VU University , Amsterdam , The Netherlands
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , QLD 4072 , Australia.,Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
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2
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Ariz-Extreme I, Hub JS. Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc. PLoS One 2018; 13:e0196751. [PMID: 29771936 PMCID: PMC5957342 DOI: 10.1371/journal.pone.0196751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/18/2018] [Indexed: 11/25/2022] Open
Abstract
Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative binding affinities, for instance between an ion and water, (ii) absolute binding free energies, i.e., free energies for transferring a solute from bulk solvent to a binding site, and (iii) stability assessments during equilibrium simulations may reveal the most plausible assignments. We illustrate this strategy using the crystal structure of the fluoride specific channel (Fluc), which contains five disconnected electron densities previously interpreted as four fluoride and one sodium ion. The simulations support the assignment of the sodium ion. In contrast, calculations of relative and absolute binding free energies as well as stability assessments during free MD simulations suggest that four of the densities represent water molecules instead of fluoride. The assignment of water is compatible with the loss of these densities in the non-conductive F82I/F85I mutant of Fluc. We critically discuss the role of the ion force fields for the calculations presented here. Overall, these findings indicate that MD simulations and free energy calculations are helpful tools for modeling water and ions into crystallographic density maps.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Jochen S. Hub
- Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- * E-mail:
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3
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Summers TJ, Cheng Q, DeYonker NJ. A transition state “trapped”? QM-cluster models of engineered threonyl-tRNA synthetase. Org Biomol Chem 2018; 16:4090-4100. [DOI: 10.1039/c8ob00540k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM-cluster models demonstrate how protein bioengineering alters the local energy landscape of p-biphenylalanine to stabilize a transition state analogue.
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Affiliation(s)
| | - Qianyi Cheng
- The Department of Chemistry
- The University of Memphis
- Memphis
- USA
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4
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Kim RR, Malde AK, Nematollahi A, Scott KF, Church WB. Molecular dynamics simulations reveal structural insights into inhibitor binding modes and functionality in human Group IIA phospholipase A 2. Proteins 2017; 85:827-842. [PMID: 28056488 DOI: 10.1002/prot.25235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 11/09/2022]
Abstract
Human Group IIA phospholipase A2 (hGIIA) promotes inflammation in immune-mediated pathologies by regulating the arachidonic acid pathway through both catalysis-dependent and -independent mechanisms. The hGIIA crystal structure, both alone and inhibitor-bound, together with structures of closely related snake-venom-derived secreted phospholipase enzymes has been well described. However, differentiation of biological and nonbiological contacts and the relevance of structures determined from snake venom enzymes to human enzymes are not clear. We employed molecular dynamics (MD) and docking approaches to understand the binding of inhibitors that selectively or nonselectively block the catalysis-independent mechanism of hGIIA. Our results indicate that hGIIA behaves as a monomer in the solution environment rather than a dimer arrangement that is in the asymmetric unit of some crystal structures. The binding mode of a nonselective inhibitor, KH064, was validated by a combination of the experimental electron density and MD simulations. The binding mode of the selective pentapeptide inhibitor FLSYK to hGIIA was stipulated to be different to that of the snake venom phospholipases A2 of Daboia russelli pulchella (svPLA2 ). Our data suggest that the application of MD approaches to crystal structure data is beneficial in evaluating the robustness of conclusions drawn based on crystal structure data alone. Proteins 2017; 85:827-842. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryung Rae Kim
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Alpeshkumar K Malde
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia, 4072
| | - Alireza Nematollahi
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kieran F Scott
- School of Medicine, Western Sydney University, The Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia, 2170.,Centre for Oncology Education and Research Translation (CONCERT), The Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia, 2170
| | - W Bret Church
- Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, The University of Sydney, Sydney, NSW, 2006, Australia
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5
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Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics. J Mol Graph Model 2016; 71:192-199. [PMID: 27939931 DOI: 10.1016/j.jmgm.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/28/2022]
Abstract
The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.
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Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C, Plateau P. Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Proteins 2016; 84:240-53. [PMID: 26676967 DOI: 10.1002/prot.24972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/30/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022]
Abstract
D-Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl-tRNA synthetases (aaRSs), and this strategy might be applicable to D-amino acids. Several aaRSs can aminoacylate their tRNA with a D-amino acid; of these, tyrosyl-tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its D-Tyr binding further, relative to L-Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain L-Tyr/D-Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge-altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards D-Tyr; one of these has an inverted stereospecificity, with a large preference for D-Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled.
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Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | | | - Zoltan Palmai
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Najette Amara
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Sandra Wydau-Dematteis
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Erwan Bigan
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Karen Druart
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Clara Moch
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Pierre Plateau
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
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Vondenhoff GH, Pugach K, Gadakh B, Carlier L, Rozenski J, Froeyen M, Severinov K, Van Aerschot A. N-alkylated aminoacyl sulfamoyladenosines as potential inhibitors of aminoacylation reactions and microcin C analogues containing D-amino acids. PLoS One 2013; 8:e79234. [PMID: 24223911 PMCID: PMC3817062 DOI: 10.1371/journal.pone.0079234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/19/2013] [Indexed: 11/18/2022] Open
Abstract
Microcin C analogues were recently envisaged as important compounds for the development of novel antibiotics. Two issues that may pose problems to these potential antibiotics are possible acquisition of resistance through acetylation and in vivo instability of the peptide chain. N-methylated aminoacyl sulfamoyladenosines were synthesized to investigate their potential as aminoacyl tRNA synthetase inhibitors and to establish whether these N-alkylated analogues would escape the natural inactivation mechanism via acetylation of the alpha amine. It was shown however, that these compounds are not able to effectively inhibit their respective aminoacyl tRNA synthetase. In addition, we showed that (D)-aspartyl-sulfamoyladenosine (i.e. with a (D)-configuration for the aspartyl moiety), is a potent inhibitor of aspartyl tRNA synthetase. However, we also showed that the inhibitory effect of (D)- aspartyl-sulfamoyladenosine is relatively short-lasting. Microcin C analogues with (D)-amino acids throughout from positions two to six proved inactive. They were shown to be resistant against metabolism by the different peptidases and therefore not able to release the active moiety. This observation could not be reversed by incorporation of (L)-amino acids at position six, showing that none of the available peptidases exhibit endopeptidase activity.
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Affiliation(s)
- Gaston H. Vondenhoff
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Ksenia Pugach
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Bharat Gadakh
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Laurence Carlier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Mathy Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Konstantin Severinov
- Department of Molecular Biology and Biochemistry Waksman Institute, Rutgers, the State University, Piscataway, New Jersey, United States of America
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Arthur Van Aerschot
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
- * E-mail:
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8
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Bushnell EAC, Huang W, Llano J, Gauld JW. Molecular Dynamics Investigation into Substrate Binding and Identity of the Catalytic Base in the Mechanism of Threonyl-tRNA Synthetase. J Phys Chem B 2012; 116:5205-12. [DOI: 10.1021/jp302556e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Eric A. C. Bushnell
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor,
Ontario N9B 3P4, Canada
| | - WenJuan Huang
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor,
Ontario N9B 3P4, Canada
| | - Jorge Llano
- Department of Physical Sciences, Grant MacEwan University, Edmonton, Alberta T5J 4S2,
Canada
| | - James W. Gauld
- Department of Chemistry and
Biochemistry, University of Windsor, Windsor,
Ontario N9B 3P4, Canada
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9
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Structural modelling and dynamics of proteins for insights into drug interactions. Adv Drug Deliv Rev 2012; 64:323-43. [PMID: 22155026 DOI: 10.1016/j.addr.2011.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/17/2011] [Accepted: 11/24/2011] [Indexed: 12/27/2022]
Abstract
Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural rearrangements during ligand entry, ligand binding and protein-protein interactions. Hence, the knowledge of protein structure and, importantly, the dynamic behaviour of the structure are critical for understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour can be performed by combinations of structure modelling and molecular dynamics simulations. The simulations also need to be sensitive to the constraints of the environment in which the protein resides. Standard computational methods now exist in this field to support the experimental effort of solving protein structures. This review presents a comprehensive overview of the basis of the calculations and the well-established computational methods used to generate and understand protein structure and function and the study of their dynamic behaviour with the reference to lung-related targets.
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Nair PC, Malde AK, Mark AE. Using Theory to Reconcile Experiment: The Structural and Thermodynamic Basis of Ligand Recognition by Phenylethanolamine N-Methyltransferase (PNMT). J Chem Theory Comput 2011; 7:1458-68. [DOI: 10.1021/ct1007229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pramod C. Nair
- School of Chemistry and Molecular Biosciences (SCMB) and ‡Institute for Molecular Bioscience (IMB), The University of Queensland (UQ), St. Lucia Campus, Brisbane, QLD 4072 Australia
| | - Alpeshkumar K. Malde
- School of Chemistry and Molecular Biosciences (SCMB) and ‡Institute for Molecular Bioscience (IMB), The University of Queensland (UQ), St. Lucia Campus, Brisbane, QLD 4072 Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences (SCMB) and ‡Institute for Molecular Bioscience (IMB), The University of Queensland (UQ), St. Lucia Campus, Brisbane, QLD 4072 Australia
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11
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Malde AK, Mark AE. Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. J Comput Aided Mol Des 2010; 25:1-12. [PMID: 21053051 DOI: 10.1007/s10822-010-9397-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 10/25/2010] [Indexed: 10/18/2022]
Abstract
Despite its central role in structure based drug design the determination of the binding mode (position, orientation and conformation in addition to protonation and tautomeric states) of small heteromolecular ligands in protein:ligand complexes based on medium resolution X-ray diffraction data is highly challenging. In this perspective we demonstrate how a combination of molecular dynamics simulations and free energy (FE) calculations can be used to correct and identify thermodynamically stable binding modes of ligands in X-ray crystal complexes. The consequences of inappropriate ligand structure, force field and the absence of electrostatics during X-ray refinement are highlighted. The implications of such uncertainties and errors for the validation of virtual screening and fragment-based drug design based on high throughput X-ray crystallography are discussed with possible solutions and guidelines.
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Affiliation(s)
- Alpeshkumar K Malde
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia
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12
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Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010; 24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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13
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Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature 2010; 462:808-12. [PMID: 20010690 PMCID: PMC2799227 DOI: 10.1038/nature08612] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 10/26/2009] [Indexed: 12/02/2022]
Abstract
Mistranslation from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences1-3. Throughout evolution, two editing-checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly1,2. One checkpoint is the AlaRS editing center, while the other is from widely distributed AlaXps—free-standing, genome-encoded editing proteins that clear Ser-tRNAAla. The paradox of misincorporating both a smaller (glycine) and a larger amino acid (serine) suggests a deep conflict for nature-designed AlaRS. To understand the chemical basis for this conflict, kinetic and mutational analysis, together with nine crystal structures, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the α–amino group of the bound amino acid using an acidic residue. This design, of more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently not able to find better architecture for recognition of alanine, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.
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