Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data - PubMed (original) (raw)

Comparative Study

. 2004 Nov 15;57(3):468-80.

doi: 10.1002/prot.20226.

Affiliations

Comparative Study

Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data

N Alpay Temiz et al. Proteins. 2004.

Abstract

The dynamics of adenylate kinase of Escherichia coli (AKeco) and its complex with the inhibitor AP(5)A, are characterized by correlating the theoretical results obtained with the Gaussian Network Model (GNM) and the anisotropic network model (ANM) with the order parameters and correlation times obtained with Slowly Relaxing Local Structure (SRLS) analysis of (15)N-NMR relaxation data. The AMPbd and LID domains of AKeco execute in solution large amplitude motions associated with the catalytic reaction Mg(+2)*ATP + AMP --> Mg(+2)*ADP + ADP. Two sets of correlation times and order parameters were determined by NMR/SRLS for AKeco, attributed to slow (nanoseconds) motions with correlation time tau( perpendicular) and low order parameters, and fast (picoseconds) motions with correlation time tau( parallel) and high order parameters. The structural connotation of these patterns is examined herein by subjecting AKeco and AKeco*AP(5)A to GNM analysis, which yields the dynamic spectrum in terms of slow and fast modes. The low/high NMR order parameters correlate with the slow/fast modes of the backbone elucidated with GNM. Likewise, tau( parallel) and tau( perpendicular) are associated with fast and slow GNM modes, respectively. Catalysis-related domain motion of AMPbd and LID in AKeco, occurring per NMR with correlation time tau( perpendicular), is associated with the first and second collective slow (global) GNM modes. The ANM-predicted deformations of the unliganded enzyme conform to the functional reconfiguration induced by ligand-binding, indicating the structural disposition (or potential) of the enzyme to bind its substrates. It is shown that NMR/SRLS and GNM/ANM analyses can be advantageously synthesized to provide insights into the molecular mechanisms that control biological function.

(c) 2004 Wiley-Liss, Inc.

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Figures

Fig. 1

Fig. 1

Ribbon diagrams of the crystal structures of (a) AKeco and (b) AKeco in complex with the two-substrate-mimic inhibitor AP5A. The figures were drawn with the program Molscript using the PDB coordinate files 4ake for AKeco and 1 ake (complex II) for AKeco*AP5A. The AMP binding domain, AMPbd, comprises helices α2 and α3, the domain LID comprises the strands β5-β8 and the intervening loops, and the CORE domain comprises the remaining part of the polypeptide chain.

Fig. 2

Fig. 2

a: Schematic of the virtual bond of the GNM theory. The chain is made of consecutive peptide planes comprising the atoms . The bond vector Ni-Hi makes an angle εi with the virtual bond, Ii, that connects the atoms .b: Diagram showing the angular change Δαi in the orientationmi(t) of the bond Ni-Hi, induced by the torsional rotation, Δφi, undergone by the virtual bond, Ii. Δαi and Δφi are related by eq 14, assuming that the angle ε between Ii andmi(t) is fixed.

Fig. 3

Fig. 3

Experimental, (---) and GNM-predicted (—) B-factors for AKeco (a) and AKeco*AP5A (b).

Fig. 4

Fig. 4

a: NMR order parameters obtained with MF analysis (open circles) and theoretical GNM order parameters (solid curve), as a function of residue number for AKeco.b: NMR order parameters obtained with SRLS analysis (open circles) and theoretical GNM order parameters calculated from the slowest N/4 modes (solid curve) and the N/4 fastest modes (dashed curve) as a function of residue number for AKeco.c: Counterpart of Figure a for AKeco*AP5A with the NMR/MF data from reference . d: Counterpart of b for AKeco*AP5A with the NMR/SRLS data from reference . (S02)2 and S2 were obtained by fitting the experimental 15N T1, T2, and15N- NOE data of the two enzyme forms obtained at 303K and at 14.1/18.8 T with SRLS, and MF, respectively, using τm = 15.1 ns for AKeco and τm= 11.6 ns for AKeco*AP5A.

Fig. 5

Fig. 5

Best-fit local motion correlation time component,τ⊥;, obtained by fitting the experimental 15N T1, T2, and15N- NOE data of AKeco obtained at 303K, and at 14.1/18.8 T (open circles). GNM correlation times τiGNM (eq 12) obtained for AKeco from the five slowest modes (solid curve) and all the modes (dashed curve). The abscissa represents residue number.

Fig. 6

Fig. 6

First slowest global GNM mode shapes for AKeco (—) and AKeco*AP5A (- - -) (a), and second slowest global GNM mode shapes for AKeco (—) and AKeco*AP5A (- - -) (b).Insets: The ribbon diagrams of AKeco and AKeco*AP5A color-coded cyan-blue-red-yellow-green in order of increasing mobility. The black boxes depict the LID and AMPbd domains. The blue dots denote residues associated by crystallographic studies with hinges.

Fig. 7

Fig. 7

Conformations I and II between which AKeco (a) and AKeco*AP5A (b) fluctuate based on the first global mode according to ANM analysis. The LID and AMPbd domains are colored red and blue, respectively, and the inhibitor is colored yellow.

Fig. 8

Fig. 8

Distribution of mean-square fluctuations determined with GNM for the AKmt solution structure and the AKeco*AP5A crystal structure as a function of the AKmt sequence.

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