Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease

Gruia, Andreea D.; Fischer, Stefan; Smith, Jeremy C.

doi:10.1002/prot.10312

Cited by 27 publications

(25 citation statements)

References 67 publications

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“…Transport studies coupled with site directed mutagenesis are currently being utilized to understand which of the negatively charged residues are most important for transport of ferrichrome. This could be accompanied by MD simulations similar to what Gruia et al performed on the enzyme Staphylococcal nuclease to understand the kinetics of breaking an Arg-Glu salt bridge (Gruia et al 2003). Because the structures of the PBP (BtuF) and the inner membrane ABC transporter structure (BtuCD) have been solved , its coordinates could be used in these MD studies along with steered MD to understand what conformational changes are relevant for the transport of siderophores into the cytoplasm (Oloo & Tieleman 2004).…”

Section: Discussionmentioning

confidence: 96%

Molecular Dynamics Simulations of the Periplasmic Ferric-hydroxamate Binding Protein FhuD

2005

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FhuD is a periplasmic binding protein (PBP) that, under iron-limiting conditions, transports various hydroxamate-type siderophores from the outer membrane receptor (FhuA) to the inner membrane ATP-binding cassette transporter (FhuBC). Unlike many other PBPs, FhuD possesses two independently folded domains that are connected by an alpha-helix rather than two or three central beta-strands. Crystal structures of FhuD with and without bound gallichrome have provided some insight into the mechanism of siderophore binding as well as suggested a potential mechanism for FhuD binding to FhuB. Since the alpha-helix connecting the two domains imposes greater rigidity on the structure relative to the beta-strands in other 'classical' PBPs, these structures reveal no large conformational change upon binding a hydroxamate-type siderophore. Therefore, it is difficult to explain how the inner membrane transporter FhuB can distinguish between ferrichrome-bound and ferrichrome-free FhuD. In the current study, we have employed a 30 ns molecular dynamics simulation of FhuD with its bound siderophore removed to explore the dynamic behavior of FhuD in the substrate-free state. The MD simulation suggests that FhuD is somewhat dynamic with a C-terminal domain closure of 6 degrees upon release of its siderophore. This relatively large motion suggests differences that would allow FhuB to distinguish between ferrichrome-bound and ferrichrome-free FhuD.

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Section: Discussionmentioning

confidence: 96%

Molecular Dynamics Simulations of the Periplasmic Ferric-hydroxamate Binding Protein FhuD

2005

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“…However, a salt bridge is also present throughout the transition (Fig. 2 Left), and the breaking of interdomain salt bridges can involve large free-energy barriers (24), thus contributing to stabilize domain junctions.…”

Section: Discussionmentioning

confidence: 99%

Structural mechanism of the recovery stroke in the Myosin molecular motor

Fischer

Windshügel

Horák

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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171

227

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The power stroke pulling myosin along actin filaments during muscle contraction is achieved by a large rotation (Ϸ60°) of the myosin lever arm after ATP hydrolysis. Upon binding the next ATP, myosin dissociates from actin, but its ATPase site is still partially open and catalytically off. Myosin must then close and activate its ATPase site while returning the lever arm for the next power stroke. A mechanism for this coupling between the ATPase site and the distant lever arm is determined here by generating a continuous series of optimized intermediates between the crystallographic end-states of the recovery stroke. This yields a detailed structural model for communication between the catalytic and the force-generating regions that is consistent with experimental observations. The coupling is achieved by an amplifying cascade of conformational changes along the relay helix lying between the ATPase and the domain carrying the lever arm.chemo-mechanical coupling ͉ conformational transition ͉ Conjugate Peak Refinement ͉ muscle contraction ͉ power stroke T he myosin II head is a molecular motor that transforms chemical energy derived from the hydrolysis of ATP into mechanical work. The myosin head (or cross bridge) contains the catalytic activity, but the release of hydrolysis products is inhibited unless actin is bound. Lymn and Taylor (1) first proposed the cyclic scheme for the interaction between myosin and actin that produces motion (Fig. 1A). Underlying this cycle is myosin's ability to couple small changes in its catalytic ATPase site to large conformational changes in both the actin-binding and the distant force-generating domains with well defined communication mechanisms, which ensure that these changes are correlated so as to efficiently produce mechanical work. For instance, the communication mechanism between the ATP and actinbinding regions has been illuminated recently by crystal structures of the unconventional myosin V (2, 3). Here, we focus on one of the other essential communication pathways, the one for passing structural information between the ATPase site and the distant force-generating domain during the recovery stroke of the contractile cycle (i.e., going from states II to III in Fig. 1 A).The presence of that coupling first becomes apparent when comparing the crystallographic structures of the two end-states of the recovery-stroke ( Fig. 1 B and C) (4,5). As expected, the largest difference between these structures is in the orientation of the ''converter'' domain, which carries the lever arm and which is rotated by Ϸ60°relative to the rest of the head (referred to hereafter as the ''main body''). The other significant difference is in the ATP binding site, which is partially open before the recovery stroke, rendering the ATPase catalytically inactive (for example, see figure 6a in ref. 6). In contrast, after the recovery stroke, the ATP site is fully closed and the ␥-phosphate (␥P) group of the ATP forms an additional hydrogen bond with the amide of Gly-457 (Dictyostelium discoideum numberi...

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“…Our data demonstrating that GABA activation of the receptor results in an increase in the negative electrostatic potentials near ␤ 2 K215 and ␤ 2 K213 (Table 3) as well as previous data in the GABA A R ␣ 1 subunit demonstrating interactions between charged residues in loop 2, loop 7, and the M2-M3 loop (Kash et al, 2003) are consistent with this idea. The kinetics of salt bridge breaking is estimated to be ϳ200 ns (Sheldahl and Harvey, 1999;Gruia et al, 2003), and thus, the breaking and forming of salt bridges is potentially a fast enough mechanism for transducing movements from the binding site to the channel domain.…”

Section: Electrostatic Network Of Interactionsmentioning

confidence: 99%

Charged Residues in the α₁and β₂Pre-M1 Regions Involved in GABA_AReceptor Activation

Mercado¹,

Czajkowski²

2006

J. Neurosci.

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For Cys-loop ligand-gated ion channels (LGIC), the protein movements that couple neurotransmitter binding to channel gating are not well known. The pre-M1 region, which links the extracellular agonist-binding domain to the channel-containing transmembrane domain, is in an ideal position to transduce binding site movements to gating movements. A cluster of cationic residues in this region is observed in all LGIC subunits, and in particular, an arginine residue is absolutely conserved. We mutated charged pre-M1 residues in the GABA A receptor ␣ 1 (K219, R220, K221) and ␤ 2 (K213, K215, R216) subunits to cysteine and expressed the mutant subunits with wild-type ␤ 2 or ␣ 1 in Xenopus oocytes. Cysteine substitution of ␤ 2 R216 abolished channel gating by GABA without altering the binding of the GABA agonist [3 H]muscimol, indicating that this residue plays a key role in coupling GABA binding to gating. Tethering thiol-reactive methanethiosulfonate (MTS) reagents onto ␣ 1 K219C, ␤ 2 K213C, and ␤ 2 K215C increased maximal GABA-activated currents, suggesting that structural perturbations of the pre-M1 regions affect channel gating. GABA altered the rates of sulfhydryl modification of ␣ 1 K219C, ␤ 2 K213C, and ␤ 2 K215C, indicating that the pre-M1 regions move in response to channel activation. A positively charged MTS reagent modified ␤ 2 K213C and ␤ 2 K215C significantly faster than a negatively charged reagent, and GABA activation eliminated modification of ␤ 2 K215C by the negatively charged reagent. Overall, the data indicate that the pre-M1 region is part of the structural machinery coupling GABA binding to gating and that the transduction of binding site movements to channel movements is mediated, in part, by electrostatic interactions.

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Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease

Cited by 27 publications

References 67 publications

Molecular Dynamics Simulations of the Periplasmic Ferric-hydroxamate Binding Protein FhuD

Molecular Dynamics Simulations of the Periplasmic Ferric-hydroxamate Binding Protein FhuD

Structural mechanism of the recovery stroke in the Myosin molecular motor

Charged Residues in the α₁and β₂Pre-M1 Regions Involved in GABA_AReceptor Activation

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Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease

Cited by 27 publications

References 67 publications

Molecular Dynamics Simulations of the Periplasmic Ferric-hydroxamate Binding Protein FhuD

Molecular Dynamics Simulations of the Periplasmic Ferric-hydroxamate Binding Protein FhuD

Structural mechanism of the recovery stroke in the Myosin molecular motor

Charged Residues in the α1and β2Pre-M1 Regions Involved in GABAAReceptor Activation

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Charged Residues in the α₁and β₂Pre-M1 Regions Involved in GABA_AReceptor Activation