Evidence for Proton Shuffling in a Thioredoxin-Like Protein during Catalysis

Narzi, Daniele; Si, Yain-Whar; Stirnimann, Christian U.; Grimshaw, John P.A.; Glockshuber, Rudi; Capitani, Guido; Böckmann, Rainer A.

doi:10.1016/j.jmb.2008.07.061

Cited by 11 publications

(11 citation statements)

References 56 publications

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“…After a ligand binds to the EGFR complex, the signal is ultimately propagated in the membrane through GTP binding to RAS [12]. Activated RAS then “recruits” RAF to the cell membrane and adds multiple phosphates [13].…”

Section: Methodsmentioning

confidence: 99%

Coulomb Interactions between Cytoplasmic Electric Fields and Phosphorylated Messenger Proteins Optimize Information Flow in Cells

Gatenby

Frieden

2010

PLoS ONE

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BackgroundNormal cell function requires timely and accurate transmission of information from receptors on the cell membrane (CM) to the nucleus. Movement of messenger proteins in the cytoplasm is thought to be dependent on random walk. However, Brownian motion will disperse messenger proteins throughout the cytosol resulting in slow and highly variable transit times. We propose that a critical component of information transfer is an intracellular electric field generated by distribution of charge on the nuclear membrane (NM). While the latter has been demonstrated experimentally for decades, the role of the consequent electric field has been assumed to be minimal due to a Debye length of about 1 nanometer that results from screening by intracellular Cl− and K+. We propose inclusion of these inorganic ions in the Debye-Huckel equation is incorrect because nuclear pores allow transit through the membrane at a rate far faster than the time to thermodynamic equilibrium. In our model, only the charged, mobile messenger proteins contribute to the Debye length.FindingsUsing this revised model and published data, we estimate the NM possesses a Debye-Huckel length of a few microns and find this is consistent with recent measurement using intracellular nano-voltmeters. We demonstrate the field will accelerate isolated messenger proteins toward the nucleus through Coulomb interactions with negative charges added by phosphorylation. We calculate transit times as short as 0.01 sec. When large numbers of phosphorylated messenger proteins are generated by increasing concentrations of extracellular ligands, we demonstrate they generate a self-screening environment that regionally attenuates the cytoplasmic field, slowing movement but permitting greater cross talk among pathways. Preliminary experimental results with phosphorylated RAF are consistent with model predictions.ConclusionThis work demonstrates that previously unrecognized Coulomb interactions between phosphorylated messenger proteins and intracellular electric fields will optimize information transfer from the CM to the NM in cells.

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Section: Methodsmentioning

confidence: 99%

Coulomb Interactions between Cytoplasmic Electric Fields and Phosphorylated Messenger Proteins Optimize Information Flow in Cells

Gatenby

Frieden

2010

PLoS ONE

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“…For example, Salmonella enterica serovar Typhimurium contains, in addition to a DsbA and a DsbB, a second pair of homologues in DsbL and DsbI (with, respectively, 27% and 30% homology to DsbA and DsbB) together in an operon with an aryl sulfate-sulfotransferase, assT, which is dependent on oxidation by DsbL/I for activity. A similar DsbL/DsbI pair was found in uropathogenic E. coli strain CFT073, which is also highly divergent from DsbA/B (19/24% sequence identity) but clearly paralogous in function (93,94). DsbL is more oxidizing than DsbA (redox potential of -95 mV) and differs in the substrate-binding groove harboring basic residues instead of the hydrophobic patch of DsbA, suggesting narrower substrate specificity.…”

Section: Diversity Of Disulfide Bond Formation Pathways In Bacteriamentioning

confidence: 66%

Disulfide Bond Formation in the Periplasm of Escherichia coli

2019

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The formation of disulfide bonds is critical to the folding of many extracytoplasmic proteins in all domains of life. With the discovery in the early 1990s that disulfide bond formation is catalyzed by enzymes, the field of oxidative folding of proteins was born. Escherichia coli played a central role as a model organism for the elucidation of the disulfide bond-forming machinery. Since then, many of the enzymatic players and their mechanisms of forming, breaking, and shuffling disulfide bonds have become understood in greater detail. This article summarizes the discoveries of the past 3 decades, focusing on disulfide bond formation in the periplasm of the model prokaryotic host E. coli.

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“…The computational cost of such methods is, however, at variance with the need for high throughput, e.g., in protein design or protein–ligand docking and in the pK a analysis of titratable sites as well. The latter problem requires the accurate estimation of the free energy differences between protonated and de-protonated states of all titratable groups in proteins, either on crystal structures or on trajectories obtained from molecular dynamics simulations to better grasp the protein flexibility (Narzi et al, 2008a ). Protonation or pK changes are, e.g., important during the function of enzymes (Narzi et al, 2008a ), or in protein–ligand binding (Narzi et al, 2008b ; Onufriev and Alexov, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules

Bertelshofer

Sun

Greiner

et al. 2015

Front. Bioeng. Biotechnol.

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Knowledge about the electrostatic potential on the surface of biomolecules or biomembranes under physiological conditions is an important step in the attempt to characterize the physico-chemical properties of these molecules and, in particular, also their interactions with each other. Additionally, knowledge about solution electrostatics may also guide the design of molecules with specified properties. However, explicit water models come at a high computational cost, rendering them unsuitable for large design studies or for docking purposes. Implicit models with the water phase treated as a continuum require the numerical solution of the Poisson–Boltzmann equation (PBE). Here, we present a new flexible program for the numerical solution of the PBE, allowing for different geometries, and the explicit and implicit inclusion of membranes. It involves a discretization of space and the computation of the molecular surface. The PBE is solved using finite differences, the resulting set of equations is solved using a Gauss–Seidel method. It is shown for the example of the sucrose transporter ScrY that the implicit inclusion of a surrounding membrane has a strong effect also on the electrostatics within the pore region and, thus, needs to be carefully considered, e.g., in design studies on membrane proteins.

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Evidence for Proton Shuffling in a Thioredoxin-Like Protein during Catalysis

Cited by 11 publications

References 56 publications

Coulomb Interactions between Cytoplasmic Electric Fields and Phosphorylated Messenger Proteins Optimize Information Flow in Cells

Coulomb Interactions between Cytoplasmic Electric Fields and Phosphorylated Messenger Proteins Optimize Information Flow in Cells

Disulfide Bond Formation in the Periplasm of Escherichia coli

GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules

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