Common mechanisms of catalysis in small and heterotrimeric GTPases and their respective GAPs

Gerwert, Klaus; Mann, Daniel; Kötting, Carsten

doi:10.1515/hsz-2016-0314

Cited by 19 publications

(18 citation statements)

References 90 publications

(103 reference statements)

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“…To avoid a futile NTP hydrolysis, P-loop fold NTPases are initiated before each turnover by activating moieties provided either by other proteins or by domains of the same protein [100][101][102][103][104]. The activating moiety interacts with the triphosphate chain and triggers the hydrolysis.…”

Section: The Dnab Helicase and The Abc Transporter Bmramentioning

confidence: 99%

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

et al. 2020

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Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically obtained by adding stable, nonhydrolyzable adenosine triphosphate (ATP) -analogues to the proteins, with the goal to arrest a state that mimics as closely as possible a physiologically relevant state, e.g., the pre-hydrolytic, transition and post-hydrolytic states. We here present the lessons learned on two distinct ATPases on the best use and unexpected pitfalls observed for different analogues. The proteins investigated are the bacterial DnaB helicase from Helicobacter pylori and the multidrug ATP binding cassette (ABC) transporter BmrA from Bacillus subtilis, both belonging to the same division of P-loop fold NTPases. We review the magnetic-resonance strategies which can be of use to probe the binding of the ATP-mimics, and present carbon-13, phosphorus-31, and vanadium-51 solid-state nuclear magnetic resonance (NMR) spectra of the proteins or the bound molecules to unravel conformational and dynamic changes upon binding of the ATP-mimics. Electron paramagnetic resonance (EPR), and in particular W-band electron-electron double resonance (ELDOR)-detected NMR, is of complementary use to assess binding of vanadate. We discuss which analogues best mimic the different hydrolysis states for the DnaB helicase and the ABC transporter BmrA. These might be relevant also to structural and functional studies of other NTPases.

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Section: The Dnab Helicase and The Abc Transporter Bmramentioning

confidence: 99%

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

et al. 2020

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“…By means of a GTP–GDP-mediated activation cycle (91), these proteins are involved in numerous biological processes, with dramatic impact on cell biology. Most functions of GTPases depend on their association with cellular membranes.…”

Section: Role Of Large and Small Gtpases In The Regulation Of Cytoskementioning

confidence: 99%

Interplay of GTPases and Cytoskeleton in Cellular Barrier Defects during Gut Inflammation

2017

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An essential role of the intestine is to build and maintain a barrier preventing the luminal gut microbiota from invading the host. This involves two coordinated physical and immunological barriers formed by single layers of intestinal epithelial and endothelial cells, which avoid the activation of local immune responses or the systemic dissemination of microbial agents, and preserve tissue homeostasis. Accordingly, alterations of epithelial and endothelial barrier functions have been associated with gut inflammation, for example during inflammatory bowel disease (IBD). The discriminative control of nutriment uptake and sealing toward potentially pathological microorganisms requires a profound regulation of para- and transcellular permeability. On the subcellular level, the cytoskeleton exerts key regulatory functions in the maintenance of cellular barriers. Increased epithelial/endothelial permeability occurs primarily as a result of a reorganization of cytoskeletal–junctional complexes. Pro-inflammatory mediators such as cytokines can induce cytoskeletal rearrangements, causing inflammation-dependent defects in gut barrier function. In this context, small GTPases of the Rho family and large GTPases from the Dynamin superfamily appear as major cellular switches regulating the interaction between intercellular junctions and actomyosin complexes, and in turn cytoskeleton plasticity. Strikingly, some of these proteins, such as RhoA or guanylate-binding protein-1 (GBP-1) have been associated with gut inflammation and IBD. In this review, we will summarize the role of small and large GTPases for cytoskeleton plasticity and epithelial/endothelial barrier in the context of gut inflammation.

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“…Using time‐resolved Fourier transformed infrared (FTIR) difference spectroscopy, it is possible to study the structural transitions and reaction steps in proteins in short time periods. This already enabled a deeper understanding of various reaction mechanisms, such as the light‐driven proton pump bacteriorhodopsin or the GTPase mechanism of the Ras protein . To eliminate the irrelevant absorptions, FTIR difference spectroscopy is utilized.…”

Section: Introductionmentioning

confidence: 99%

“…This already enabled a deeper understanding of various reaction mechanisms, such as the light-driven proton pump bacteriorhodopsin 13 or the GTPase mechanism of the Ras protein. 14 LMA is now publicly accessible as a python-based software tool, which can be downloaded at https://github.com/MatthiasMa/Local-Mode-Analysis and up-to-date information are available at http:// www.bph.rub.de/link_software_en.htm. In this publication, we give an overview of the LMA features including their theoretical background.…”

Section: Introductionmentioning

confidence: 99%

Monitoring transient events in infrared spectra using local mode analysis

et al. 2018

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Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.

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Common mechanisms of catalysis in small and heterotrimeric GTPases and their respective GAPs

Cited by 19 publications

References 90 publications

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

Interplay of GTPases and Cytoskeleton in Cellular Barrier Defects during Gut Inflammation

Monitoring transient events in infrared spectra using local mode analysis

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