1
|
Kumar A, Åqvist J, Satpati P. Principles of tRNA Ala Selection by Alanyl-tRNA Synthetase Based on the Critical G3·U70 Base Pair. ACS OMEGA 2019; 4:15539-15548. [PMID: 31572855 PMCID: PMC6761608 DOI: 10.1021/acsomega.9b01827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Throughout evolution, the presence of a single G3·U70 mismatch in the acceptor stem of tRNAAla is the major determinant for aminoacylation with alanine by alanyl-tRNA synthetase (AlaRS). Recently reported crystal structures of the complexes AlaRS-tRNAAla/G3·U70 and AlaRS-tRNAAla/A3·U70 suggest two very different conformations, representing a reactive and a nonreactive state, respectively. On the basis of these structures, it has been proposed that the G3·U70 base pair guides the -CCA end of the tRNA acceptor stem into the active site of AlaRS, thereby enabling aminoacylation. The crystal structures open up the possibility of directly computing the energetics of tRNA specificity by AlaRS. We have carried out molecular dynamics free-energy simulations to quantitatively estimate tRNA discrimination by AlaRS, focusing on the mutations of the single critical base pair G3·U70 to uncover the energetics underlying the accuracy of tRNA selection. The calculations show that the reactive complex is highly selective in favor of the cognate tRNAAla/G3·U70 over its noncognate analogues (A3·U70/G3·C70/A3·C70). In contrast, the nonreactive complex is predicted to be unselective between tRNAAla/G3·U70 and tRNAAla/A3·U70. Utilizing our calculated relative binding free energies, we show how a simple three-step kinetic scheme for aminoacylation, involving both an initial nonspecific binding step and a subsequent transition to a selective reactive complex, accounts for the observed kinetics of the process.
Collapse
Affiliation(s)
- Amit Kumar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Johan Åqvist
- Department
of Cell and Molecular Biology, Uppsala University,
Biomedical Center, Box 596, Uppsala SE-751 24, Sweden
| | - Priyadarshi Satpati
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, Assam, India
| |
Collapse
|
2
|
Kumar A, Satpati P. Principle of K+/Na+ selectivity in the active site of group II intron at various stages of self-splicing pathway. J Mol Graph Model 2018; 84:1-9. [DOI: 10.1016/j.jmgm.2018.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/16/2018] [Accepted: 05/10/2018] [Indexed: 10/16/2022]
|
3
|
Kumar A, Satpati P. Energetics of Preferential Binding of Retinoic Acid-Inducible Gene-I to Double-Stranded Viral RNAs with 5' Tri-/Diphosphate over 5' Monophosphate. ACS OMEGA 2018; 3:3786-3795. [PMID: 30023880 PMCID: PMC6044841 DOI: 10.1021/acsomega.7b02019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Retinoic acid-inducible gene-I (RIG-I) is a cytosolic sensor protein that recognizes viral RNAs and triggers an innate immune response in cells. Panhandle-like base-paired blunt-ended 5' ppp/pp-dsRNA is a characteristic feature of viral RNAs. Structural studies of RIG-I C-terminal domain bound 5' ppp/pp-dsRNA complexes show the direct interaction between all the 5' terminal phosphates (α, β, and γ) and protein, suggesting γ phosphate might be a major recognition determinant for RIG-I binding. Biochemical studies, however, suggest that 5' pp-dsRNA is the minimal determinant for RIG-I binding and antiviral response. Despite biochemical and structural studies, the origin of viral RNA recognition by RIG-I is an unsolved problem. X-ray structures of RIG-I bound dsRNA not only provide atomic insight into the interaction network but also provide sufficiently good models for computational studies. We report structure-based molecular dynamics (MD) free energy calculations to quantitatively estimate the energetics of RIG-I binding to dsRNA containing 5' ppp, 5' pp, and 5' p. The results suggest that RIG-I weakly discriminates between 5' ppp-dsRNA and 5' pp-dsRNA (favoring former) and strongly disfavors 5' p-dsRNA with respect to the rest. Interestingly, direct interaction between γ phosphate of 5' ppp-dsRNA and RIG-I is a robust feature of the MD simulations. dsRNA binding to RIG-I is associated with Mg2+ dissociation from the 5' phosphate/s of dsRNA. The higher Mg2+ dissociation penalty from 5' ppp-dsRNA with respect to 5' pp-dsRNA offsets most of the favorable interaction between RIG-I and γ phosphate of 5' ppp-dsRNA. This leads to weak discrimination between 5' ppp-dsRNA and 5' pp-dsRNA. 5' p-dsRNA is discriminated strongly because of the loss of interaction with RIG-I.
Collapse
|
4
|
Simonson T, Aleksandrov A, Satpati P. Electrostatic free energies in translational GTPases: Classic allostery and the rest. Biochim Biophys Acta Gen Subj 2014; 1850:1006-1016. [PMID: 25047891 DOI: 10.1016/j.bbagen.2014.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/03/2014] [Accepted: 07/05/2014] [Indexed: 12/31/2022]
Abstract
GTPases typically switch between an inactive, OFF conformation and an active, ON conformation when a GDP ligand is replaced by GTP. Their ON/OFF populations and activity thus depend on the stabilities of four protein complexes, two apo-protein forms, and GTP/GDP in solution. A complete characterization is usually not possible experimentally and poses major challenges for simulations. We review the most important methodological challenges and we review thermodynamic data for two GTPases involved in translation of the genetic code: archaeal Initiation Factors 2 and 5B (aIF2, aIF5B). One main challenge is the multiplicity of states and conformations, including those of GTP/GDP in solution. Another is force field accuracy, especially for interactions of GTP/GDP with co-bound divalent Mg(2+) ions. The calculation of electrostatic free energies also poses specific challenges, and requires careful protocols. For aIF2, experiments and earlier simulations showed that it is a "classic" GTPase, with distinct ON/OFF conformations that prefer to bind GTP and GDP, respectively. For aIF5B, we recently proposed a non-classic mechanism, where the ON/OFF states differ only in the protonation state of Glu81 in the nucleotide binding pocket. This model is characterized here using free energy simulations. The methodological analysis should help future studies, while the aIF2, aIF5B examples illustrate the diversity of ATPase/GTPase mechanisms. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
Collapse
Affiliation(s)
- Thomas Simonson
- Laboratoire de Biochimie (CNRS unit 7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
| | - Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS unit 7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
| | - Priyadarshi Satpati
- Laboratoire de Biochimie (CNRS unit 7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France; Department of Cell and Molecular Biology, University of Uppsala, Sweden
| |
Collapse
|
5
|
Nikonov O, Stolboushkina E, Arkhipova V, Kravchenko O, Nikonov S, Garber M. Conformational transitions in the γ subunit of the archaeal translation initiation factor 2. ACTA ACUST UNITED AC 2014; 70:658-67. [PMID: 24598735 DOI: 10.1107/s1399004713032240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/26/2013] [Indexed: 12/30/2022]
Abstract
In eukaryotes and archaea, the heterotrimeric translation initiation factor 2 (e/aIF2) is pivotal for the delivery of methionylated initiator tRNA (Met-tRNA(i)) to the ribosome. It acts as a molecular switch that cycles between inactive (GDP-bound) and active (GTP-bound) states. Recent studies show that eIF2 can also exist in a long-lived eIF2γ-GDP-P(i) (inorganic phosphate) active state. Here, four high-resolution crystal structures of aIF2γ from Sulfolobus solfataricus are reported: aIF2γ-GDPCP (a nonhydrolyzable GTP analogue), aIF2γ-GDP-formate (in which a formate ion possibly mimics P(i)), aIF2γ-GDP and nucleotide-free aIF2γ. The structures describe the different states of aIF2γ and demonstrate the conformational transitions that take place in the aIF2γ `life cycle'.
Collapse
Affiliation(s)
- Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Elena Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Valentina Arkhipova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Olesya Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
| |
Collapse
|
6
|
Affiliation(s)
- Riccardo Baron
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820;
| | - J. Andrew McCammon
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0365;
| |
Collapse
|
7
|
Simonson T, Satpati P. Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysis. J Comput Chem 2012; 34:836-46. [PMID: 23280996 DOI: 10.1002/jcc.23207] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/12/2012] [Accepted: 11/28/2012] [Indexed: 11/06/2022]
Abstract
Di- and tri-phosphate nucleotides are essential cofactors for many proteins, usually in an Mg(2+) -bound form. Proteins like GTPases often detect the difference between NDP and NTP and respond by changing conformations. To study such complexes, simple, fixed charge force fields have been used, which allow long simulations and precise free energy calculations. The preference for NTP or NDP binding depends on many factors, including ligand structure and Mg(2+) coordination and the changes they undergo upon binding. Here, we use a simple force field to examine two Mg(2+) coordination modes for the unbound GDP and GTP: direct, or "Inner Sphere" (IS) coordination by one or more phosphate oxygens and indirect, "Outer Sphere" (OS) coordination involving one or more bridging waters. We compare GTP: and GDP:Mg binding with OS and IS coordination; combining the results with experimental data then indicates that GTP prefers the latter. We also examine different kinds of IS coordination and their sensitivity to a key force field parameter: the optimal Mg:oxygen van der Waals distance Rmin . Increasing Rmin improves the Mg:oxygen distances, the GTP: and GDP:Mg binding affinities, and the fraction of GTP:Mg with β + γ phosphate coordination, but does not improve or change the GTP/GDP affinity difference, which remains much larger than experiment. It has no effect on the free energy of GDP binding to a GTPase.
Collapse
Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128 Palaiseau, France.
| | | |
Collapse
|
8
|
Simonson T, Satpati P. Nucleotide recognition by the initiation factor aIF5B: free energy simulations of a neoclassical GTPase. Proteins 2012; 80:2742-57. [PMID: 22887821 DOI: 10.1002/prot.24158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/16/2012] [Accepted: 07/28/2012] [Indexed: 12/13/2022]
Abstract
The GTPase aIF5B is a universally conserved initiation factor that assists ribosome assembly. Crystal structures of its nucleotide complexes, X-ray(GTP) and X-ray(GDP), are similar in the nucleotide vicinity, but differ in the orientation of a distant domain IV. This has led to two, contradictory, mechanistic models. One postulates that X-ray(GTP) and X-ray(GDP) are, respectively, the active, "ON" and the inactive, "OFF" states; the other postulates that both structures are OFF, whereas the ON state is still uncharacterized. We study GTP/GDP binding using molecular dynamics and a continuum electrostatic free energy method. We predict that X-ray(GTP) has a ≈ 3 kcal/mol preference to bind GDP, apparently contradicting its assignment as ON. However, the preference arises mainly from a single, nearby residue from the switch 2 motif: Glu81, which becomes protonated upon GTP binding, with a free energy cost of about 4 kcal/mol. We then propose a different model, where Glu81 protonation/deprotonation defines the ON/OFF states. With this model, the X-ray(GTP):GTP complex, with its protonated Glu81, is ON, whereas X-ray(GTP):GDP is OFF. The model postulates that distant conformational changes such as domain IV rotation are "uncoupled" from GTP/GDP exchange and do not affect the relative GTP/GDP binding affinities. We analyze the model using a general thermodynamic framework for GTPases. It yields rather precise predictions for the nucleotide specificities of each state, and the state specificities of each nucleotide, which are roughly comparable to the homologues IF2 and aIF2, despite the lack of any conformational switching in the model.
Collapse
Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91128 Palaiseau, France.
| | | |
Collapse
|