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Journal ArticleDOI

Effect of the SH3-SH2 domain linker sequence on the structure of Hck kinase.

01 Aug 2011-Journal of Molecular Modeling (Springer-Verlag)-Vol. 17, Iss: 8, pp 1927-1934

TL;DR: Comparison molecular dynamics simulations of wildtype Hck and of a mutant Hck in which the SH3-SH2 domain linker is replaced by the corresponding sequence from the homologous kinase Lck reveal that linker replacement not only affects the orientation of theSH3 domain itself, but also leads to an alternative conformation of the activation segment in the Hck kinase domain.

AbstractThe coordination of activity in biological systems requires the existence of different signal transduction pathways that interact with one another and must be precisely regulated. The Src-family tyrosine kinases, which are found in many signaling pathways, differ in their physiological function despite their high overall structural similarity. In this context, the differences in the SH3-SH2 domain linkers might play a role for differential regulation, but the structural consequences of linker sequence remain poorly understood. We have therefore performed comparative molecular dynamics simulations of wildtype Hck and of a mutant Hck in which the SH3-SH2 domain linker is replaced by the corresponding sequence from the homologous kinase Lck. These simulations reveal that linker replacement not only affects the orientation of the SH3 domain itself, but also leads to an alternative conformation of the activation segment in the Hck kinase domain. The sequence of the SH3-SH2 domain linker thus exerts a remote effect on the active site geometry and might therefore play a role in modulating the structure of the inactive kinase or in fine-tuning the activation process itself.

Topics: SH3 domain (59%), SH2 domain (56%), Protein kinase domain (54%), Src family kinase (54%), Linker (52%)

Summary (2 min read)

Introduction

  • The SH2 and SH3 domains bind specific phosphotyrosine and proline-rich motifs, respectively.
  • The catalytic domain consists of two lobes, which form a cleft that serves as a docking site for ATP and other substrates representing the active site of the kinase.
  • The crystal structures of the inactive („closed‟) forms of c-Src [6-8] and Hck [9, 10] reveal that intramolecular interactions involving the SH2 and SH3 domains are essential for suppression of kinase activity despite being far away from the active site.
  • In Hck and most other SFKs the connecting linker stabilizes the SH3-SH2 domain orientation by a salt-bridge between a conserved glutamate of the linker (E147 in Hck) and a lysine (K104 in Hck) of the SH3 domain.

Preparation of starting structures

  • The crystal structures of inactive Hck complexed with the nucleoside analog PP1 (Protein Data Bank ID 1QCF, [10]), was used to generate the starting structures.
  • The force field parameters for PP1, which are not available in the AMBER package, were obtained as follows: ArgusLab [21] was utilized to add missing hydrogen atoms.
  • Then, the structure was subjected to two consecutive geometry optimizations with Gaussian03 [22] using the ab initio methods HF/MIDI!, and HF/6-31G(d).

Molecular dynamics (MD) simulations

  • The parameters for the phosphotyrosine present in the C-terminal kinase tail were assigned according to Homeyer et al. [30].
  • All structures were minimized in a three-step procedure by using the SANDER module of AMBER following a previously established protocol [32].
  • Subsequently, 30-ns MD simulations with standard NPT conditions were performed for data collection.
  • All bonds involving hydrogen atoms were constrained using the SHAKE procedure [35].

Results and discussion

  • Influence of the SH3-SH2 linker sequence on the global structure and dynamics of PP1inhibited Hck To determine the effect of the SH3-SH2 linker on the global structure of Src kinases, 30-ns molecular dynamics simulations of wildtype Hck and of Hck with a mutated SH3-SH2 linker (Hck*) were carried out.
  • This rigidity is also consistent with the structural overlay showing that the geometry of the kinase domain is almost unaffected by the SH3-SH2 linker sequence (Fig. 4).
  • All starting structures of the present simulations correspond to the “DFG-in” conformation, which is also retained in the simulations of PP1-bound Hck/Hck* as well as in the simulation of uninhibited wildtype Hck.
  • Since their results indicate that mutations of the SH3-SH2 linker affect the active site geometry of Hck, the authors have checked the literature, whether remote effects of mutations on the active site conformation have already been reported for other SFKs in the past.
  • This is reflected in the low affinity of c-Src for the drug imatinib, which exclusively binds the DFGout conformation.

Acknowledgments

  • The authors thank Pia Rücker and Dr. Holger Dinkel for fruitful discussions, and A. Jens Meiselbach-Wilke for critically reading the manuscript.
  • This work was supported by grants from the Deutsche Forschungsgemeinschaft.

Figure captions

  • Fig. 1 (a) Structures of the linker between regulatory domains from the Hck kinase (left), and Lck kinase .
  • A schematic representation of Hck showing the analyzed distances Fig. 3 Distance between amino acids A403 of the activation segment and S142 located in the SH3-SH2 linker, also known as Right panel.
  • Distance between the center-of-mass of the distinct domains of the kinase without inhibitor PP1 as a function of simulation time Distance between (a) SH3 and N-lobe, (b) N-lobe and C-lobe of the catalytic domains; (c) SH2 and C-lobe, and (d) between the regulatory domains.
  • See Fig. 2 (right panel) for a schematic presentation of the analyzed distances Fig. 6 Structural changes of uninhibited Hck and Hck*.

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Eect of the SH3-SH2 domain linker sequence on the
structure of Hck kinase
Heike Meiselbach, Heinrich Sticht
To cite this version:
Heike Meiselbach, Heinrich Sticht. Eect of the SH3-SH2 domain linker sequence on the structure of
Hck kinase. Journal of Molecular Modeling, Springer Verlag (Germany), 2010, 17 (8), pp.1927-1934.
�10.1007/s00894-010-0897-z�. �hal-00645110�

1
Effect of the SH3-SH2 domain linker sequence on the structure of
Hck kinase
Received: 30.06.2010 / Accepted: 23.10.2010
Heike Meiselbach and Heinrich Sticht
Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität, Erlangen-Nürnberg,
Fahrstraße 17, D-91054 Erlangen, Germany
Tel.: +49 - 9131 / 85 24614; Fax: +49 - 9131 / 85 22485; E-Mail: h.sticht@biochem.uni-
erlangen.de
Abstract
The coordination of activity in biological systems requires the existence of different signal
transduction pathways that interact with one another and must be precisely regulated. The
Src-family tyrosine kinases, which are found in many signaling pathways, differ in their
physiological function despite their high overall structural similarity. In this context, the
differences in the SH3-SH2 domain linkers might play a role for differential regulation, but
the structural consequences of linker sequence are yet poorly understood. We have therefore
performed comparative molecular dynamics simulations of wildtype Hck and of a mutant
Hck, in which the SH3-SH2 domain linker is replaced by the sequence from the homologous
kinase Lck. The simulations reveal that linker replacement does not only affect the orientation
of the SH3 domain itself, but also leads to an alternative conformation of the activation
segment in the Hck kinase domain. The sequence of the SH3-SH2 domain linker thus exerts a
remote effect on the active site geometry and might therefore play a role in modulating the
structure of the inactive kinase or for the fine-tuning of the activation process itself.
Keywords Src-family kinases SH3 SH2 Molecular dynamics simulations Domain
motions

2
Introduction
The Src family of non-receptor tyrosine kinases to date comprises nine members (Src, Fyn,
Lck, Hck, Yes, Fgr, Yrk, Blk, and Lyn) which play critical roles in eukaryotic signal
pathways that control a diverse array of processes such as cell growth, differentiation,
activation and transformation [1-3]. These proteins have a common molecular architecture
that includes five distinct regions [4, 5]: a unique N-terminal region with sequences for lipid
attachment, the regulatory SH3 and SH2 domains and a kinase domain, followed by a
negative regulatory C-terminal tail (Fig. 1b). The SH2 and SH3 domains bind specific
phosphotyrosine and proline-rich motifs, respectively. The catalytic domain consists of two
lobes, which form a cleft that serves as a docking site for ATP and other substrates
representing the active site of the kinase.
The crystal structures of the inactive („closed‟) forms of c-Src [6-8] and Hck [9, 10] reveal
that intramolecular interactions involving the SH2 and SH3 domains are essential for
suppression of kinase activity despite being far away from the active site. In fact, these
regulatory domains are bound to the distal side of the catalytic domain, restricting its
conformational flexibility to hinder productive ATP binding. The SH3 domain is docked to
the N-terminal lobe of the kinase domain via a proline-containing motif in the SH2-kinase
linker (Fig. 1b).
Activation of Src-family kinases (SFKs) requires the disruption of the intramolecular
interactions, the dephosphorylation of the C-terminal tail by phosphatases, or the binding of
high-affinity ligands to the SH2 or the SH3 domain [9-12]. Additionally, the active
conformation becomes stabilized upon autophosphorylation of Tyr416 (in Src) in the
activation segment and is required for maximal kinase activity [13, 14]. In this case, the
phosphorylated activation segment, which contains the highly conserved aspartate-
phenylalanine-glycine (DFG) motif, becomes less ordered and moves out of the active site,
thereby allowing substrate access [15].
An additional feature, which turned out to be important for the activation process, is the
sequence of the linker that connects the SH3 and SH2 domain. In wildtype Src and Hck, a
short rigid linker joins the regulatory SH3 and SH2 domains and leads to dynamic coupling of
the two domains in the closed conformation, thereby forming a stiff clamp [16, 17].
Computational studies and site-directed mutagenesis experiments have shown that the

3
disruption of the structural properties of the rigid linker by introduction of glycine mutations
reduces the strength of the clamp and facilitates activation of the kinase [17].
In Hck and most other SFKs the connecting linker stabilizes the SH3-SH2 domain orientation
by a salt-bridge between a conserved glutamate of the linker (E147 in Hck) and a lysine
(K104 in Hck) of the SH3 domain. In the homologous kinase Lck, E147 is replaced by proline
and therefore the salt-bridge cannot be formed. Accordingly, the isolated Lck SH3-SH2
domain pair shows an ill-defined domain orientation in NMR-spectroscopic studies [18, 19].
The effect of the Lck linker sequence on the intact kinase, however, is yet poorly understood
due to the lack of an intact Lck crystal structure containing both regulatory and kinase
domains.
To assess whether the differences in linker sequence also affect the structure of inactive
SFKs, we have investigated the effect of linker replacement using Hck as a model system.
Comparative molecular dynamics simulations were performed for wildtype Hck and for a
mutant Hck (Hck*), in which the SH3-SH2 domain linker was replaced by the respective
sequence from Lck. To address the effect of the inhibitor PP1 on kinase dynamics,
simulations were performed in the presence and absence of PP1 totalling up to four systems
studied. Our results show that an altered linker sequence does not only result in local changes,
but also has a remote effect on the geometry of the active site.
Materials and methods
Preparation of starting structures
The crystal structures of inactive Hck complexed with the nucleoside analog PP1 (Protein
Data Bank ID 1QCF, [10]), was used to generate the starting structures. For consistency, the
sequence numbering from entry 1QCF was also adapted in the present work. To obtain the
model of mutant Hck (termed Hck*), the wildtype SH3-SH2 linker sequence (
140
V-D-S-L-E-
T-E-E
147
) was replaced with the linker sequence form Lck (A-N-S-L-E-P-E-P) (Fig. 1a) using
the Sybyl 7 [20]. Inspection of the model revealed no steric clashed indicating that the Lck-
linker sequence can be readily accommodated in the Hck scaffold. The systems Hck and Hck*
were simulated each with and without inhibitor PP1.

4
The force field parameters for PP1, which are not available in the AMBER package, were
obtained as follows: The initial coordinates of PP1 were extracted from the 1QCF pdb file.
ArgusLab [21] was utilized to add missing hydrogen atoms. Then, the structure was subjected
to two consecutive geometry optimizations with Gaussian03 [22] using the ab initio methods
HF/MIDI!, and HF/6-31G(d). For all quantum mechanical geometry optimizations the
stationary points found were ensured to be true minima by the calculation of the vibrational
frequencies. The atomic charges for PP1 were then obtained following the established
procedure [23, 24] by fitting the charges to the HF/6-31G(d) computed electrostatic potential
using the Antechamber tool from the AMBER program suite.
Molecular dynamics (MD) simulations
All MD simulations were performed using the PMEMD module of AMBER 8.0 [25, 26] with
the parm99 force field [27, 28]. For the organic compound PP1 the general AMBER force
field (gaff) [29] was used. The parameters for the phosphotyrosine present in the C-terminal
kinase tail were assigned according to Homeyer et al. [30].
An appropriate number of Na+ counter ions was added to neutralize the system and
afterwards the molecules were solvated in a box of water using the TIP3P water model [31]
with at least 10 Å of water around every atom of the solute. All structures were minimized in
a three-step procedure by using the SANDER module of AMBER following a previously
established protocol [32].
After energy minimization, the system was equilibrated for 0.1 ns, raising the temperature
gradually to 298 K by coupling to a temperature bath with a time constant of 0.2 ps, as
described by Berendsen [33]. Subsequently, 30-ns MD simulations with standard NPT
conditions were performed for data collection. Classical equations of motion were propagated
numerically with a time step of 1 fs. A cutoff distance of 10 Å was used for the non-bonded
interactions, and the particle mesh Ewald method [34] was employed to calculate the long-
range electrostatic interactions. All bonds involving hydrogen atoms were constrained using
the SHAKE procedure [35].
The convergence of temperature, pressure, and energy of the systems, as well as the atomic
root mean square deviations of the structure, were used to verify the stability of the systems.

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TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Abstract: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.

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Q1. What are the contributions in "Effect of the sh3-sh2 domain linker sequence on the structure of hck kinase" ?

The authors have therefore performed comparative molecular dynamics simulations of wildtype Hck and of a mutant Hck, in which the SH3-SH2 domain linker is replaced by the sequence from the homologous kinase Lck.