publication . Article . 2016

Molecular docking and molecular dynamics simulation studies on Thermus thermophilus leucyl-tRNA synthetase complexed with different amino acids and pre-transfer editing substrates

A. V. Rayevsky; M. A. Tukalo;
Open Access English
  • Published: 29 Feb 2016 Journal: Biopolymers and Cell, volume 32, issue 1, pages 61-69 (issn: 0233-7657, eissn: 1993-6842, Copyright policy)
  • Publisher: National Academy of Sciences of Ukraine, Institute of Molecular Biology and Genetics
Abstract
Aim. To investigate the structural bases for the amino acid selectivity of the Thermus thermophilus leucyl-tRNA synthetase (LeuRSTT) aminoacylation site and to disclose the binding pattern of pre-transfer editing substrates. Methods. Eight amino acids proposed as semi-cognate substrates for aminoacylation and eight aminoacyl-adenylates (formed from AMP and eight amino acids) were prepared in zwitterions form. The protein structure with a co-crystallized substrate in the aminoacylation site [PDBID: 1OBH] was taken from RCSB. Docking settings and evaluation of substrate efficiency were followed by twofold docking function analysis for each conformation with Gold C...
Persistent Identifiers
Subjects
free text keywords: leucyl-tRNAsynthetase, editing, amino acids, aminoacyl-adenylate, molecular docking, MD simulations, Biology (General), QH301-705.5, Genetics, QH426-470, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Biochemistry, Docking (molecular), Biology, Leucyl-tRNA synthetase, Thermus thermophilus, biology.organism_classification, Amino acid, chemistry.chemical_classification, chemistry, Molecular dynamics
24 references, page 1 of 2

1. Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617-50. [OpenAIRE]

2. Cusack S, Berthet-Colominas C, Härtlein M, Nassar N, Leberman R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A. Nature. 1990;347(6290):249-55.

3. Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990;347(6289):203-6.

4. Yadavalli SS, Ibba M. Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol. 2012;86:1-43. [OpenAIRE]

5. Fersht AR. Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase. Biochemistry. 1977;16(5):1025-30. [OpenAIRE]

6. Cusack S, Yaremchuk A, Tukalo M. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyladenylate analogue. EMBO J. 2000;19(10):2351-61. [OpenAIRE]

7. Martinis SA, Fox GE. Non-standard amino acid recognition by Escherichia coli leucyl-tRNA synthetase. Nucleic Acids Symp Ser. 1997;36:125-8.

8. Zhu B, Yao P, Tan M, Eriani G, Wang ED. tRNA-independent pretransfer editing by class I leucyl-tRNA synthetase. J Biol Chem. 2009;284(6):3418-24.

9. Cvetesic N, Palencia A, Halasz I, Cusack S, Gruic-Sovulj I. The physiological target for LeuRS translational quality control is norvaline. EMBO J. 2014;33(15):1639-53.

10. Lincecum TL Jr, Tukalo M, Yaremchuk A, Mursinna RS, Williams AM, Sproat BS, Van Den Eynde W, Link A, Van Calenbergh S, Grøtli M, Martinis SA, Cusack S. Structural and mechanistic basis of pre- and posttransfer editing by leucyltRNA synthetase. Mol Cell. 2003;11(4):951-63.

11. Dulic M, Cvetesic N, Perona JJ, Gruic-Sovulj I. Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J Biol Chem. 2010;285(31):23799-809.

12. Boniecki MT, Vu MT, Betha AK, Martinis SA. CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase. Proc Natl Acad Sci USA. 2008;105(49):19223-8.

13. Zhai Y, Martinis SA. Two conserved threonines collaborate in the Escherichia coli leucyl-tRNA synthetase amino acid editing mechanism. Biochemistry. 2005;44(47):15437-43.

14. Tan M, Zhu B, Zhou XL, He R, Chen X, Eriani G, Wang ED. tRNA-dependent pre-transfer editing by prokaryotic leucyltRNA synthetase. J Biol Chem. 2010;285(5):3235-44.

15. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem. 2005;26(16):1668-88.

24 references, page 1 of 2
Abstract
Aim. To investigate the structural bases for the amino acid selectivity of the Thermus thermophilus leucyl-tRNA synthetase (LeuRSTT) aminoacylation site and to disclose the binding pattern of pre-transfer editing substrates. Methods. Eight amino acids proposed as semi-cognate substrates for aminoacylation and eight aminoacyl-adenylates (formed from AMP and eight amino acids) were prepared in zwitterions form. The protein structure with a co-crystallized substrate in the aminoacylation site [PDBID: 1OBH] was taken from RCSB. Docking settings and evaluation of substrate efficiency were followed by twofold docking function analysis for each conformation with Gold C...
Persistent Identifiers
Subjects
free text keywords: leucyl-tRNAsynthetase, editing, amino acids, aminoacyl-adenylate, molecular docking, MD simulations, Biology (General), QH301-705.5, Genetics, QH426-470, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Biochemistry, Docking (molecular), Biology, Leucyl-tRNA synthetase, Thermus thermophilus, biology.organism_classification, Amino acid, chemistry.chemical_classification, chemistry, Molecular dynamics
24 references, page 1 of 2

1. Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617-50. [OpenAIRE]

2. Cusack S, Berthet-Colominas C, Härtlein M, Nassar N, Leberman R. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A. Nature. 1990;347(6290):249-55.

3. Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990;347(6289):203-6.

4. Yadavalli SS, Ibba M. Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol. 2012;86:1-43. [OpenAIRE]

5. Fersht AR. Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase. Biochemistry. 1977;16(5):1025-30. [OpenAIRE]

6. Cusack S, Yaremchuk A, Tukalo M. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyladenylate analogue. EMBO J. 2000;19(10):2351-61. [OpenAIRE]

7. Martinis SA, Fox GE. Non-standard amino acid recognition by Escherichia coli leucyl-tRNA synthetase. Nucleic Acids Symp Ser. 1997;36:125-8.

8. Zhu B, Yao P, Tan M, Eriani G, Wang ED. tRNA-independent pretransfer editing by class I leucyl-tRNA synthetase. J Biol Chem. 2009;284(6):3418-24.

9. Cvetesic N, Palencia A, Halasz I, Cusack S, Gruic-Sovulj I. The physiological target for LeuRS translational quality control is norvaline. EMBO J. 2014;33(15):1639-53.

10. Lincecum TL Jr, Tukalo M, Yaremchuk A, Mursinna RS, Williams AM, Sproat BS, Van Den Eynde W, Link A, Van Calenbergh S, Grøtli M, Martinis SA, Cusack S. Structural and mechanistic basis of pre- and posttransfer editing by leucyltRNA synthetase. Mol Cell. 2003;11(4):951-63.

11. Dulic M, Cvetesic N, Perona JJ, Gruic-Sovulj I. Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J Biol Chem. 2010;285(31):23799-809.

12. Boniecki MT, Vu MT, Betha AK, Martinis SA. CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase. Proc Natl Acad Sci USA. 2008;105(49):19223-8.

13. Zhai Y, Martinis SA. Two conserved threonines collaborate in the Escherichia coli leucyl-tRNA synthetase amino acid editing mechanism. Biochemistry. 2005;44(47):15437-43.

14. Tan M, Zhu B, Zhou XL, He R, Chen X, Eriani G, Wang ED. tRNA-dependent pre-transfer editing by prokaryotic leucyltRNA synthetase. J Biol Chem. 2010;285(5):3235-44.

15. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem. 2005;26(16):1668-88.

24 references, page 1 of 2
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