Probing the structure of human tRNA3Lys in the presence of ligands using docking, MD simulations and MSM analysis

The tRNA3Lys, which acts as a primer for human immunodeficiency virus type 1 (HIV-1) reverse transcription, undergoes structural changes required for the formation of a primer–template complex. Small molecules have been targeted against tRNA3Lys to inhibit the primer–template complex formation. The present study aims to understand the kinetics of the conformational landscape spanned by tRNA3Lys in apo form using molecular dynamics simulations and Markov state modeling. The study is taken further to investigate the effect of small molecules like 1,4T and 1,5T on structural conformations and kinetics of tRNA3Lys, and comparative analysis is presented. Markov state modeling of tRNA3Lys apo resulted in three metastable states where the conformations have shown the non-canonical structures of the anticodon loop. Based on analyses of ligand–tRNA3Lys interactions, crucial ion and water mediated H-bonds and free energy calculations, it was observed that the 1,4-triazole more strongly binds to the tRNA3Lys compared to 1,5-triazole. However, the MSM analysis suggest that the 1,5-triazole binding to tRNA3Lys has brought rigidity not only in the binding pocket (TΨC arm, D–TΨC loop) but also in the whole structure of tRNA3Lys. This may affect the easy opening of primer tRNA3Lys required for HIV-1 reverse transcription.

[1]  Chunhua Li,et al.  Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study. , 2021, The journal of physical chemistry. B.

[2]  Nathania A. Takyi,et al.  Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations , 2020, RNA.

[3]  V. Pande,et al.  Markov State Models: From an Art to a Science. , 2018, Journal of the American Chemical Society.

[4]  Hao Wu,et al.  Variational Approach for Learning Markov Processes from Time Series Data , 2017, Journal of Nonlinear Science.

[5]  S. Ranganathan,et al.  Understanding Effect of Geranylation of tRNALys on Ribosome Binding: A Computational Study , 2017 .

[6]  Frank Noé,et al.  PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. , 2015, Journal of chemical theory and computation.

[7]  F. Noé,et al.  Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models , 2015, Nature Communications.

[8]  Samuel S. Cho,et al.  MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery , 2015, International journal of molecular sciences.

[9]  D. Mathews,et al.  Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics , 2014, Journal of chemical theory and computation.

[10]  Frank Noé,et al.  Markov state models of biomolecular conformational dynamics. , 2014, Current opinion in structural biology.

[11]  Marcus Weber,et al.  Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification , 2013, Advances in Data Analysis and Classification.

[12]  Mallikarjunachari V. N. Uppuladinne,et al.  MD simulations of HIV-1 RT primer–template complex: effect of modified nucleosides and antisense PNA oligomer , 2013, Journal of biomolecular structure & dynamics.

[13]  Toni Giorgino,et al.  Identification of slow molecular order parameters for Markov model construction. , 2013, The Journal of chemical physics.

[14]  A. IJzerman,et al.  Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time , 2012, British journal of pharmacology.

[15]  Frank Noé,et al.  Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables. , 2011, Physical chemistry chemical physics : PCCP.

[16]  Frank Noé,et al.  Markov models of molecular kinetics: generation and validation. , 2011, The Journal of chemical physics.

[17]  Vijay S. Pande,et al.  Everything you wanted to know about Markov State Models but were afraid to ask. , 2010, Methods.

[18]  M. Rodnina,et al.  The crystal structure of unmodified tRNAPhe from Escherichia coli , 2010, Nucleic acids research.

[19]  V. Larue,et al.  Tether influence on the binding properties of tRNALys3 ligands designed by a fragment-based approach. , 2010, Organic & biomolecular chemistry.

[20]  C. Ehresmann,et al.  Initiation of HIV Reverse Transcription , 2010, Viruses.

[21]  C. Tisné,et al.  Design of tRNA(Lys)3 ligands: fragment evolution and linker selection guided by NMR spectroscopy. , 2009, Chemistry.

[22]  I. Kuntz,et al.  DOCK 6: combining techniques to model RNA-small molecule complexes. , 2009, RNA.

[23]  C. Murray,et al.  The rise of fragment-based drug discovery. , 2009, Nature chemistry.

[24]  D. Thirumalai,et al.  Dynamics of tRNA at different levels of hydration. , 2009, Biophysical journal.

[25]  Franck A. P. Vendeix,et al.  The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs , 2009, Nucleic acids research.

[26]  J. Moses,et al.  Click Chemistry and Medicinal Chemistry: A Case of “Cyclo‐Addiction” , 2008, ChemMedChem.

[27]  Giovanni Sorba,et al.  Click chemistry reactions in medicinal chemistry: Applications of the 1,3‐dipolar cycloaddition between azides and alkynes , 2008, Medicinal research reviews.

[28]  J. Puglisi,et al.  Probing the conformation of human tRNA3 Lys in solution by NMR , 2007, FEBS letters.

[29]  C. Tisné,et al.  New insights into the formation of HIV-1 reverse transcription initiation complex. , 2007, Biochimie.

[30]  C. Tisné,et al.  NMR-guided fragment-based approach for the design of tRNA(Lys3) ligands. , 2007, Angewandte Chemie.

[31]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[32]  Maria C. Nagan,et al.  Molecular dynamics simulations of human tRNAUUULys,3: the role of modified bases in mRNA recognition , 2006, Nucleic acids research.

[33]  Florence Guillière,et al.  NMR-based identification of peptides that specifically recognize the d-arm of tRNA. , 2005, Biochimie.

[34]  D. Davis,et al.  Structural effects of hypermodified nucleosides in the Escherichia coli and human tRNALys anticodon loop: the effect of nucleosides s2U, mcm5U, mcm5s2U, mnm5s2U, t6A, and ms2t6A. , 2005, Biochemistry.

[35]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[36]  M. Congreve,et al.  Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.

[37]  Karin Musier-Forsyth,et al.  Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site. , 2004, Journal of molecular biology.

[38]  V. Pandey,et al.  PNA targeting the PBS and A-loop sequences of HIV-1 genome destabilizes packaged tRNA3(Lys) in the virions and inhibits HIV-1 replication. , 2002, Virology.

[39]  D. Myszka,et al.  An RNA complex of the HIV-1 A-loop and tRNA(Lys,3) is stabilized by nucleoside modifications. , 2002, Journal of the American Chemical Society.

[40]  K. Musier-Forsyth,et al.  Specific zinc-finger architecture required for HIV-1 nucleocapsid protein's nucleic acid chaperone function , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[41]  T. Talele,et al.  Destabilization of tRNA3(Lys) from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog. , 2001, Nucleic acids research.

[42]  B. Roques,et al.  Heteronuclear NMR studies of the interaction of tRNA3Lys with HIV-1 nucleocapsid protein , 2001 .

[43]  P. Barbara,et al.  Intra-tRNA distance measurements for nucleocapsid proteindependent tRNA unwinding during priming of HIV reverse transcription. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[44]  R. Lee,et al.  Polyamide nucleic acid targeted to the primer binding site of the HIV-1 RNA genome blocks in vitro HIV-1 reverse transcription. , 1998, Biochemistry.

[45]  J. Mak,et al.  Primer tRNAs for reverse transcription , 1997, Journal of virology.

[46]  Peter A. Kollman,et al.  Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA:RNA, and DNA:RNA hybrid duplexes , 1997 .

[47]  M. Wainberg,et al.  Human immunodeficiency virus Type 1 nucleocapsid protein (NCp7) directs specific initiation of minus-strand DNA synthesis primed by human tRNA(Lys3) in vitro: studies of viral RNA molecules mutated in regions that flank the primer binding site , 1996, Journal of virology.

[48]  Mary Lapadat-Tapolsky,et al.  Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1 , 1995, Nucleic Acids Res..

[49]  C. Ehresmann,et al.  Initiation of Reverse Transcripion of HIV-1: Secondary Structure of the HIV-1 RNA/tRNA|rlmbopopnbop|Lys|clobop|3 (Template/Primer) Complex , 1995 .

[50]  T. Darden,et al.  The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods , 1993 .

[51]  R. Plasterk,et al.  Interactions between HIV-1 nucleocapsid protein and viral DNA may have important functions in the viral life cycle. , 1993, Nucleic acids research.

[52]  B. Roques,et al.  Viral RNA annealing activities of human immunodeficiency virus type 1 nucleocapsid protein require only peptide domains outside the zinc fingers. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[53]  C. Gabus,et al.  Small finger protein of avian and murine retroviruses has nucleic acid annealing activity and positions the replication primer tRNA onto genomic RNA. , 1988, The EMBO journal.

[54]  Mark L. Pearson,et al.  Complete nucleotide sequence of the AIDS virus, HTLV-III , 1985, Nature.

[55]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[56]  B. Hingerty,et al.  Further refinement of the structure of yeast tRNAPhe. , 1978, Journal of molecular biology.

[57]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[58]  D. Baltimore.  Viral RNA-dependent DNA Polymerase: RNA-dependent DNA Polymerase in Virions of RNA Tumour Viruses , 1970, Nature.

[59]  K. Velonia,et al.  Click Chemistry: A Powerful Tool to Create Polymer‐Based Macromolecular Chimeras , 2008 .

[60]  C. Ehresmann,et al.  tRNAs as primer of reverse transcriptases. , 1995, Biochimie.