A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase.

Abstract:

:Aminoacyl tRNA synthetases are enzymes that specifically attach amino acids to cognate tRNAs for use in the ribosomal stage of translation. For many aminoacyl tRNA synthetases, the required level of amino acid specificity is achieved either by specific hydrolysis of misactivated aminoacyl-adenylate intermediate (pre-transfer editing) or by hydrolysis of the mischarged aminoacyl-tRNA (post-transfer editing). To investigate the mechanism of post-transfer editing of alanine by prolyl-tRNA synthetase from the pathogenic bacteria Enterococcus faecalis, we used molecular modeling, molecular dynamic simulations, quantum mechanical (QM) calculations, site-directed mutagenesis of the enzyme, and tRNA modification. The results support a new tRNA-assisted mechanism of hydrolysis of misacylated Ala-tRNAPro. The most important functional element of this catalytic mechanism is the 2'-OH group of the terminal adenosine 76 of Ala-tRNAPro, which forms an intramolecular hydrogen bond with the carbonyl group of the alanine residue, strongly facilitating hydrolysis. Hydrolysis was shown by QM methods to proceed via a general acid-base catalysis mechanism involving two functionally distinct water molecules. The transition state of the reaction was identified. Amino acid residues of the editing active site participate in the coordination of substrate and both attacking and assisting water molecules, performing the proton transfer to the 3'-O atom of A76.

journal_name

J Biomol Struct Dyn

authors

Boyarshin KS,Priss AE,Rayevskiy AV,Ilchenko MM,Dubey IY,Kriklivyi IA,Yaremchuk AD,Tukalo MA

doi

10.1080/07391102.2016.1155171

subject

Has Abstract

pub_date

2017-02-01 00:00:00

pages

669-682

issue

3

eissn

0739-1102

issn

1538-0254

journal_volume

35

pub_type

杂志文章
  • Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain-human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2.

    abstract::SARS-CoV-2 has become a pandemic causing a serious global health concern. The absence of effective drugs for treatment of the disease has caused its rapid spread on a global scale. Similarly to the SARS-CoV, the SARS-CoV-2 is also involved in a complex interplay with the host cells. This infection is characterized by ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1841681

    authors: Gollapalli P,B S S,Rimac H,Patil P,Nalilu SK,Kandagalla S,Shetty P

    更新日期:2020-11-04 00:00:00

  • In-silico analysis of Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum through molecular modeling, docking, and dynamics simulation study.

    abstract::Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egr...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1790036

    authors: Dhal AK,Pani A,Yun SI,Mahapatra RK

    更新日期:2020-07-07 00:00:00

  • In silico identification of angiotensin-1 converting enzyme inhibitors using text mining and virtual screening.

    abstract::Cardiovascular diseases are the world's leading cause of death. Hypertension is an important risk factor for cardiovascular and renal diseases. Angiotensin-converting enzyme (ACE) can be a possible therapeutic target for managing angiotensin I conversion to angiotensin II and ultimately controlling hypertension. Indol...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1827038

    authors: Sahin K

    更新日期:2020-10-05 00:00:00

  • Probing the binding sites of resveratrol, genistein, and curcumin with milk β-lactoglobulin.

    abstract::We determined the binding sites of curcumin (cur), resveratrol (res), and genistein (gen) with milk β-lactoglobulin (β-LG) at physiological conditions. Fourier transform infrared spectroscopy, circular dichroism, and fluorescence spectroscopic methods as well as molecular modeling were used to determine the binding of...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.742461

    authors: Kanakis CD,Tarantilis PA,Polissiou MG,Tajmir-Riahi HA

    更新日期:2013-12-01 00:00:00

  • Electric birefringence of dilute agarose solutions.

    abstract::The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting p...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1990.10507830

    authors: Stellwagen NC,Stellwagen D

    更新日期:1990-12-01 00:00:00

  • Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

    abstract::The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, a...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2013.832384

    authors: Usha S,Selvaraj S

    更新日期:2014-01-01 00:00:00

  • The size of the topological domain modulates the B-Z transition of a (TG)n containing repeat.

    abstract::Under negative superhelical stress, long (TG)n containing repeats experience a stepwise multiple B-Z transitions. We have investigated the effect of the plasmid size on this transitional behavior. A 66-bp (TG)n containing repeat from the 5'-untranscribed region of mouse ribosomal DNA was inserted in a 3-kb, a 6.5-kb a...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1995.10508820

    authors: Albert AC,Leng M,Rahmouni AR

    更新日期:1995-08-01 00:00:00

  • Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes.

    abstract::Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have n...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1798812

    authors: Elmezayen AD,Yelekçi K

    更新日期:2020-07-27 00:00:00

  • Molecular dynamics simulations of a calmodulin-peptide complex in solution.

    abstract::We have performed an 4-ns MD simulation of calmodulin complexed with a target peptide in explicit water, under realistic conditions of constant temperature and pressure, in the presence of a physiological concentration of counterions and using Ewald summation to avoid truncation of long-range electrostatic forces. Dur...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2002.10506834

    authors: Yang C,Kuczera K

    更新日期:2002-10-01 00:00:00

  • Digestion of the lambda cI repressor with various serine proteases and correlation with its three dimensional structure.

    abstract::Partial proteolysis of the lambda cI repressor has been carried out systematically with trypsin, chymotrypsin, elastase, endoproteinase Glu-C, kallikrein, and thrombin. The cleavage sites have been determined by (i) comparison of fragments produced and observed in SDS-polyacrylamide gel with known fragments and plots ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507249

    authors: Pal A,Chattopadhyaya R

    更新日期:2008-12-01 00:00:00

  • Distribution of unselectively bound ligands along DNA.

    abstract::Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L bin...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507234

    authors: Lando DY,Nechipurenko YD

    更新日期:2008-10-01 00:00:00

  • Density functional geometry optimization and energy calculations of calcium(II)-triphosphate complexes. Polyphosphates as possible dissolving agents for calcium pyrophosphate dihydrate crystals in chondrocalcinosis disease.

    abstract::Geometry optimizations and energy calculations have been carried out via molecular orbital methods at the density functional B3LYP/LANL2DZ level on the molecules PO3-, OPO3(3-), HOPO3(2-), CH3OPO3(2-), H(CH3OPO3)-, O(PO3)2(4-), HO(PO3)2(3-), CH2(PO3)2(4-), (CH3OPO2)O(PO3)3-, O(PO3)3(5-), HO(PO3)3(4-), (PO3)3(3-), (CH3...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506655

    authors: Cini R,Chindamo D,Catenaccio M,Lorenzini S,Marcolongo R

    更新日期:2000-08-01 00:00:00

  • Pharmacophore model and atom-based 3D quantitative structure activity relationship (QSAR) of human immunodeficiency virus-1 (HIV-1) capsid assembly inhibitors.

    abstract::A potential anti-Human Immunodeficiency Virus (HIV) agent with novel mode of action is urgently needed to fight against drug resistance HIV. The HIV capsid protein is important for both late and early stages of the viral replication cycle and emerged as a promising target for the developing of small molecule inhibitor...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1715258

    authors: Bhole RP,Bonde CG,Bonde SC,Chikhale RV,Wavhale RD

    更新日期:2021-02-01 00:00:00

  • Structural clones of UAG decoding RNA.

    abstract::Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gya...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507324

    authors: Das S,Mukherjee R,Sahoo S,Thakkar R,Chakrabarti J

    更新日期:2009-12-01 00:00:00

  • Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

    abstract::DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) and nucleosomebinding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章,评审

    doi:10.1080/07391102.1995.10508842

    authors: Brukner I,Sánchez R,Suck D,Pongor S

    更新日期:1995-10-01 00:00:00

  • Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1507839

    authors: Kovalchuk MV,Boikova AS,Dyakova YA,Ilina KB,Konarev PV,Kryukova AE,Marchenkova MA,Pisarevsky YV,Timofeev VI

    更新日期:2019-08-01 00:00:00

  • Density functional theory based probe of the affinity interaction of saccharide ligands with extra-cellular sialic acid residues.

    abstract::Changes in glycosylation pattern leads to malignant transformations among the cells. In combination with upregulated actions of sialyltransferases, it ultimately leads to differential expression of sialic acid (SA) at cell surface. Given its negative charge and localization to extracellular domain, SA has been exploit...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1461690

    authors: Patel A,Tiwari S,Jha PK

    更新日期:2019-04-01 00:00:00

  • Reversible crystal transition of guanosine between the dihydrate and anhydrous states coupled with adsorption-desorption process.

    abstract::Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observe...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508028

    authors: Sugawara Y,Iimura Y,Iwasaki H,Urabe H,Saito H

    更新日期:1994-02-01 00:00:00

  • A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs.

    abstract::This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP·T(WC)↔2AP·T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1331864

    authors: Brovarets' OO,Voiteshenko IS,Pérez-Sánchez H,Hovorun DM

    更新日期:2018-05-01 00:00:00

  • Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin.

    abstract::The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subs...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1996.10508888

    authors: de Groot BL,Amadei A,van Aalten DM,Berendsen HJ

    更新日期:1996-04-01 00:00:00

  • Inhibitory effects of curcumin on aldose reductase and cyclooxygenase-2 enzymes.

    abstract::Diabetes is very much known as a wide-spread disorder all around the world with serious complications for the diabetic patient. In order to reduce these complications, inhibition the activity of aldose reductase (AR) and cyclooxygenase-2 (COX-2) enzymes is a proposed pathway. Within this work potency of curcumin (CUR)...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1800513

    authors: Mirzaei M,Harismah K,Soleimani M,Mousavi S

    更新日期:2020-07-31 00:00:00

  • BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC).

    abstract::Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1754918

    authors: Patel HM,Shaikh M,Ahmad I,Lokwani D,Surana SJ

    更新日期:2020-04-23 00:00:00

  • Characterization of the structural conformation adopted by (TTAGGG)n telomeric DNA repeats of different length in closed circular DNA.

    abstract::Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:

    authors: Huertas D,Lipps H,Azorín F

    更新日期:1994-08-01 00:00:00

  • Proton NMR and optical spectroscopic studies on the DNA triplex formed by d-A-(G-A)7-G and d-C-(T-C)7-T.

    abstract::Triplex and duplex formation of two deoxyribohexadecamers d-A-(G-A)-G (a) and d-C-(T-C)-T (b) have been studied by UV, CD, fluorescence, and proton NMR spectroscopy. Optical studies of a and b at dilute concentrations (microM range) yielded results similar to those seen for polymers of the same sequence, indicating th...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1991.10507857

    authors: Kan LS,Callahan DE,Trapane TL,Miller PS,Ts'o PO,Huang DH

    更新日期:1991-04-01 00:00:00

  • Docking and DFT studies on ligand binding to Quercetin 2,3-dioxygenase.

    abstract::Simple molecular docking calculations on quercetin, kojic acid and diethylcarbamatodithoic acid using the software package MOE are shown to be close to the geometries reported in the X-ray crystal structures of the protein co-crystallized with the respective ligands. Furthermore, DFT optimization of the docked conform...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1123190

    authors: Malkhasian AY,Howlin BJ

    更新日期:2016-11-01 00:00:00

  • Effect of neighboring bases on base-pair stacking orientation: a molecular dynamics study.

    abstract::It is generally believed that base-pair stacking interaction in DNA double helix is one of the strongest interactions that governs sequence directed structural variability. However, X-ray crystal structures of some base-paired doublet sequences have been seen to adopt different structures when flanked by different bas...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506645

    authors: Bandyopadhyay D,Bhattacharyya D

    更新日期:2000-08-01 00:00:00

  • Structure analysis of the proteins associated with polyA repeat expansion disorders.

    abstract::Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. There have been numerous studies on the most common group of re...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2021.1871957

    authors: Hernandez R,Facelli JC

    更新日期:2021-01-18 00:00:00

  • Exploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by in silico calculations.

    abstract::Binding interactions of the phenazinium dye Janus green blue (JGB) with human and bovine serum albumins (BSA - and BSA) have been explored for the first time from multi-spectroscopic and calorimetric measurements aided by in silico calculations. The formation of ground state complexes between JGB and the respective se...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1870156

    authors: Saha S,Bhattacharjee S,Chowdhury J

    更新日期:2021-01-07 00:00:00

  • Characterization of polyion counterion interactions in cartilage by 23Na NMR relaxation.

    abstract::Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1996.10508898

    authors: Dai H,McFarland EW

    更新日期:1996-04-01 00:00:00

  • Theoretical Design, Chemical Synthesis and Footprinting Analysis of a Novel Peptide Derivative of the Intercalator 7-H Pyridocarbazole Targeted Towards the Major Groove of DNA.

    abstract::Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508090

    authors: Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

    更新日期:1994-08-01 00:00:00