Humidity-controlled reversible structure transition of disodium adenosine 5'-triphosphate between dihydrate and trihydrate in a single crystal state

Sugawara, Yoko; Kamiya, Nobuo; Iwasaki, Hitoshi; Ito, Tsugutaka; Satow, Yoshinori

doi:10.1021/ja00014a041

Cited by 59 publications

(74 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The analysis for 1 and 2 from new data sets (namely DS2, DS3 and DS5) showed that changes on hydration of crystals cause significant alteration of conformation at the triphosphate chain and at the ribose system as well as of the pattern of M(II)-triphosphate interactions. The effects from hydration on M-O and P-O bonds are weaker than those found and reported on the corresponding moieties of Na 2 H 2 ATP·xH 2 O species [10]. The higher affinity of Mg(II) towards phosphates when compared to Na(I), and K(I) is such to link the divalent cation just to the triphosphate backbone and exclude any inner sphere interaction to the base and sugar moieties as well as to DPA molecules in 1.…”

Section: Resultscontrasting

confidence: 63%

“…In fact, among the available metallomacronutrients, Na(I), K(I), Mg(II) and Ca(II), in living systems, nature selected Mg(II) as the cofactor for the vast majority of enzymes that catalyze the breakage of (P)O-P(O) bonds. It appears important that experimental studies via XRD, MQMAS, ESIMS, Raman crystallography like those reported in Refs [10,[39][40][41][42], as well as theoretical studies like those reported in Refs 11,[43][44][45], are more and more performed on Mg(II)-NTPs and -NDPs species with the aim to shed light on the mobility of the metal on (di)triphosphate chain, on the role of free and metal bound water molecules, on the role of third molecules (mostly aminoacid residues) able to interact with the metal ions proximal to nucleotides and with nucleotides themselves. The structural role of the second divalent cation in biological systems that catalyze reactions on nucleotides (see for example Refs [46][47][48][49]), are worthy of more efforts too, on the basis of structure for 1 and 2 and of recent structures deposited in the PDB.…”

Section: Resultsmentioning

confidence: 99%

“…The accuracy for the present analysis is significantly improved on the basis of conventional agreement factors and of esds for geometrical parameters ( Table 4). The small change of the overall number of free water molecules can be probably related to differences in the humidity of the two laboratories in which DS4 and DS5 were collected [10]. In fact, the Ca-O(P) bond distance trend, the conformation of triphosphate moiety do not change significantly (the values are equal within 2σ) (see Table 4).…”

Section: (A) (B)mentioning

confidence: 98%

“…[9,10]. Nowadays, computational methods suitable for simulating molecular dynamics of small metalnucleotide molecules, at high reliability levels [11], are accessible to most inorganic chemistry laboratories.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Tamasi¹,

Berrettini²,

Hursthouse³

et al. 2010

TOCRYJ

View full text Add to dashboard Cite

Abstract:The X-ray diffraction (XRD) structures for new isoforms of [M(H 2 O) 6 ]·[M(HATP) 2 ]·2(HDPA)·xH 2 O, ATP = adenosine 5'-triphosphate, DPA = 2,2'-dipyridylamine, M = Mg(II), x = 6H 2 O, 1, M = Ca(II), x = 8H 2 O, 2 were determined by using rotating anode on molybdenum target X-ray source and Kappa CCD with confocal focusing mirror. The accuracy of the presently refined structure for 1 is the highest reported so far based on agreement factors (R1 = 0.0579) and estimated standard deviations (esds) on geometrical parameters. The comparative analysis was extended to the structures of other low molecular weight metal-triphosphate complexes, to the structures of metal-triphosphate-protein systems as well as to computed models of metal-triphosphate complexes. The structures of 1 and 2 reported in this work show that on changing the number of co-crystallized water molecules, the interaction of the metal to the phosphate chain (for 1) and the conformation of ribose (for 2) undergo subtle but significant changes. Interestingly, the vast majority of Mg-nucleoside triphosphate (NTP)-enzyme systems have similar pattern of coordination to the phosphate chain when compared to 1 and 2. The three phosphate groups have variable M-O bond distances, depending on the systems. The structures for 1 and 2 have a high significance as general model compounds for experimental solid state and computations for these types of biological systems.

show abstract

Section: Resultscontrasting

confidence: 63%

Section: Resultsmentioning

confidence: 99%

Section: (A) (B)mentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Tamasi¹,

Berrettini²,

Hursthouse³

et al. 2010

TOCRYJ

View full text Add to dashboard Cite

show abstract

“…11,12) Here, we report the dehydration process of the hydrous crystal of CS-834, with the change in the RH and the structural changes in the transformation observed by single-crystal X-ray analysis.…”

mentioning

confidence: 91%

In Situ Observation of the Four-step Dehydration Process of the 1.BETA.-Methylcarbapenem Antibiotic CS-834 Crystal by X-Rays

Kobayashi

Fukuhara²,

Hata

et al. 2003

CHEMICAL & PHARMACEUTICAL BULLETIN

View full text Add to dashboard Cite

Bulk drug substances frequently can be obtained as crystalline hydrates rather than as anhydrates, because they can crystallize more easily, 1) or are transformed into hydrates by contact with water molecules from hydrate excipients in the formulation process.2) The hydrate crystals often transform into different solids such as amorphous or dehydrate form in the process of drying or storage under low relative humidity (RH). [3][4][5][6] Generally, the resulting dehydrate crystals can be converted to the different hydrate forms depending on the surrounding RH and temperature. It is also well known that different hydrate drugs show different physicochemical properties, 7,8) such as bioavailability, phase stability, and dissolution rate. For the development of pharmaceuticals using hydrous bulk drug substances, many efforts have been made to investigate the changes in the physicochemical properties in the process of phase transformation to different hydrate states. The prediction of hydration properties has therefore been a long-standing subject of great interest in pharmaceutical science.A compound of pivaloyloxymethyl (1R,5S,6S)-6-[(R)-1-hydroxyethyl]-1-methyl-2-[[(R)-5-oxo-pyrrolidin-3-yl]thio]-1-carbapen-2-em-3-carboxylate, CS-834, was developed as an orally effective 1b-methylcarbapenem antibiotic agent possessing potent and broad-spectrum antibacterial activities and excellent stability against dehydropeptidase-I (Fig. 1). 9)It crystallizes as an anhydrate form (A-form) from anhydrous solutions and as a dihydrate (B2-form) from an aqueous solution. The B2-form undergoes the multistep transformation following the loss of water molecules upon heating, as shown in Fig. 2.10) This figure indicates that the B2-form is transformed to the dehydrate form (B0-form) through the B2Ј-, B1-, and B1Ј-forms, where the B1-form was the monohydrate form whereas the B2Ј-and B1Ј-forms were intermediate ones between the B2-and B1-forms, and between the B1-and B0-forms, respectively. The possible crystal transformation of CS-834 is summarized in Fig. 3.It was reported that the hydrate crystals of disodium adenosine 5Ј-triphophate (Na 2 ATP) and disodium cytidine 5Ј-monophophate (Na 2 CMP) also underwent reversible humidity-dependent structural transformation between the higher hydrate and the lower hydrate forms as observed by X-ray crystal structure analysis.11,12) Here, we report the dehydration process of the hydrous crystal of CS-834, with the change in the RH and the structural changes in the transformation observed by single-crystal X-ray analysis. ExperimentalPreparation of Different Crystal Forms. Materials CS-834 of pharmaceutical grade was synthesized in the Process Development Laboratories of Sankyo Co., Ltd.Preparation of the Dihydrate (B2-Form) The A-form crystals were dissolved in a 3% aqueous ethyl acetate solution at 40°C. The solution was filtrated, evaporated, cooled to about 0°C, and kept at 0°C overnight. The crystals were collected by filtration and washed with 3% aqueous ethyl acetate. The crystals were kept ...

show abstract

Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments

Arnez¹,

Flanagan²,

Moras³

et al. 1998

Proteins

View full text Add to dashboard Cite

Histidyl-tRNA synthetase (HisRS) differs from other class II aminoacyl-tRNA synthetases (aaRS) in that it harbors an arginine at a position where the others bind a catalytic Mg2+ ion. In computer experiments, four mutants of HisRS from Escherichia coli were engineered by removing the arginine and introducing a Mg2+ ion and residues from seryl-tRNA synthetase (SerRS) that are involved in Mg2+ binding. The mutants recreate an active site carboxylate pair conserved in other class II aaRSs, in two possible orders: Glu-Asp or Asp-Glu, replacing Glu-Thr in native HisRS. The mutants were simulated by molecular dynamics in complex with histidyl-adenylate. As controls, the native HisRS was simulated in complexes with histidine, histidyl-adenylate, and histidinol. The native structures sampled were in good agreement with experimental structures and biochemical data. The two mutants with the Glu-Asp sequence showed significant differences in active site structure and Mg2+ coordination from SerRS. The others were more similar to SerRS, and one of them was analyzed further through simulations in complex with histidine, and His+ATP. The latter complex sampled two Mg2+ positions, depending on the conformation of a loop anchoring the second carboxylate. The lowest energy conformation led to an active site geometry very similar to SerRS, with the principal Mg2+ bridging the alpha- and beta-phosphates, the first carboxylate (Asp) coordinating the ion through a water molecule, and the second (Glu) coordinating it directly. This mutant is expected to be catalytically active and suggests a basis for the previously unexplained conservation of the active site Asp-Glu pair in class II aaRSs other than HisRS.

show abstract

Humidity-controlled reversible structure transition of disodium adenosine 5'-triphosphate between dihydrate and trihydrate in a single crystal state

Cited by 59 publications

References 0 publications

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

Effect of Free Water Molecules on the Structure of Mg-ATPDipyridylamine and Overview on Selected Metal-Adenosine Triphosphate Structures in Model Compounds and in Enzymes~!2009-08-29~!2009-12-08~!2010-02-08~!

In Situ Observation of the Four-step Dehydration Process of the 1.BETA.-Methylcarbapenem Antibiotic CS-834 Crystal by X-Rays

Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments

Contact Info

Product

Resources

About