Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution

Müller, Christoph W.; Schulz, Georg E.

doi:10.1016/0022-2836(92)90582-5

Cited by 497 publications

(495 citation statements)

References 49 publications

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“…The second condition should be satisfied, too. For this particular case, electrostatic and dipolar interactions are involved in the stabilization of the complex [43,44] forces that are expected to increase upon solvent removal (unlike hydrophobic interactions that will decrease or even vanish in the gas phase).…”

Section: Resultsmentioning

confidence: 99%

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors

Daniel

McCombie

Wendt

et al. 2003

J. Am. Soc. Mass Spectrom.

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Noncovalent complexes between chicken muscle adenylate kinase and two inhibitors, P 1 ,P 4 -di(adenosine-5')tetraphosphate (Ap4A) and P 1 ,P 5 -di(adenosine-5') pentaphosphate (Ap5A), were investigated with electrospray ionization mass spectrometry under non-denaturing conditions. The nonconvalent nature and the specificity of the complexes are demonstrated with a number of control experiments. Titration experiments allowed the association constants for inhibitor binding to be determined. Problems with concentration dependent ion yields are circumvented by a data evaluation method that is insensitive to the overall ionization efficiency. The K a values found were 9.0 ϫ 10 4 M Ϫ1 (Ap4A) and 4.0 ϫ S oft ionization mass spectrometry (MS), in particular matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), is well known for its ability to bring high molecular weight biomolecules into the gase phase and to even preserve noncovalent complexes [1][2][3][4][5][6][7][8][9][10]. Besides its established applications, a recurring question concerns the applicability of mass spectrometry to measuring noncovalent interaction strengths [11]. There are different approaches to measure the interaction strengths in the gas phase as well as in the liquid phase. In the former case, the mass spectra should ideally directly represent the solution phase chemistry. Gas-phase methods include cone voltage driven dissociation (called the "VC 50 " method) [12,13], collision-induced dissociation [14,15], guided ion beam tandem mass spectrometry [16,17], blackbody infrared radiative dissociation [18,19] and heated capillary dissocation [20,21].Some mass spectrometric studies have been reported in the literature for the determination of noncovalent interaction strengths. There are three basic methods to determine association constants that are reflective of those in solution: first, it is possible to record "melting curves" by raising the temperature of the analyte solution and to use MS to determine the percentage of intact complexes. Cheng et al. analyzed complementary DNA strands [22] and Fändrich et al. studied the chaperone GimC/prefolding homologue complex [13] with this method. Second, competition experiments can be used to evaluate the stability of noncovalent complexes. In Jørgensen's method [23,24], the relative intensities of the free host and the different complexes were used, whereas Kempen et al. employed the known concentration of a reference complex to determine the concentration of an unknown complex [25]. Third, a titration of a host with a guest (or vice versa) can be used. In this case, the mass spectrometric signals should accurately represent the concentrations of the species in solution. The titration method is documented in a number of publications, all of them convincingly showing the successful use of mass spectrometry for the quantitative determination of noncovalent binding constants of proteins and small molecules [26 -33]. This aspect was the main focus in most previous research; th...

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Section: Resultsmentioning

confidence: 99%

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors

Daniel

McCombie

Wendt

et al. 2003

J. Am. Soc. Mass Spectrom.

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“…Basic discoveries are shown in red and are followed in order of prismatic colors by increasingly specific findings, which have led to the experimental setups used presently. (Müller et al 1996;Müller & Schulz, 1992;Sawaya & Kraut, 1997). In such cases, data from dynamic experiments can be interpreted in terms of interconversions between these states.…”

Section: Integration Of Nmr With Other Analytical Methodsmentioning

confidence: 99%

“…Adk undergoes a large conformational change in response to ligand binding that shuttles the protein into a closed and active conformation where phosphoryl transfer occurs (Rhoads & Lowenstein, 1968). Because of its favorable properties -specifically, its tendency to yield excellent NMR spectra (Ådén & Wolf-Watz, 2007;Schrank et al 2009), catalysis of a reversible reaction, and large conformational changes (Müller et al 1996;Müller & Schulz, 1992) -Adk has emerged as one of the principal model systems for analyzing the linkage between dynamics and enzymatic turnover (Arora & Brooks, 2007;Hanson et al 2007;Nagarajan et al 2011;Schrank et al 2009;Shapiro et al 2009Shapiro et al , 2000Shapiro & Meirovitch, 2006). In an extensive multi-approach effort, the Kern laboratory has shown that substrate-free Adk from the hyperthermophilic bacterium Aquifex aeolicus samples 'closed like' structures (Henzler-Wildman et al 2007).…”

Section: Adkmentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

148

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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“…AK are a/b proteins (a five-stranded b-sheet surrounded by several a-helices) [3][4][5]. They are composed of three main domains: LID, core and AMP binding.…”

Section: Introductionmentioning

confidence: 99%

“…AK are divided into two groups: the short and the long forms, which differ in a 20-30 amino acid residue insertion in the LID domain [3,4]. Mammalian AK (both cytosolic and nuclear) are usually of the short form, whereas the long AK are found in most bacteria, yeast, and mitochondria.…”

Section: Introductionmentioning

confidence: 99%

Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria

et al. 2010

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Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn 2? , Zn-AK; Co 2? , Co-AK; and Fe 2? , Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 Å , respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.

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Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution

Cited by 497 publications

References 49 publications

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors

Protein dynamics and function from solution state NMR spectroscopy

Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria

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