scholarly journals Water as a reactant in the first step of triosephosphate isomerase catalysis

2021 ◽  
Author(s):  
Max Yates ◽  
Patrik R. Callis
Keyword(s):  
Electric Fields ◽  
Triosephosphate Isomerase ◽  
Initial Step ◽  
Dihydroxyacetone Phosphate ◽  
Alternative Mechanism ◽  
General Base ◽  
Carboxylate Oxygen ◽  
Strong Electric Fields ◽  
High Electric Fields ◽  
Dynamics Simulations

ABSTRACTThe enzyme triosephosphate isomerase (TIM) performs a crucial role in the extraction of energy from glucose, doing so by converting dihydroxyacetone phosphate (DHAP) into glyceraldehyde phosphate, thereby doubling the yield of ATP molecules during glycolysis. The initial step of the mechanism is the seemingly unlikely abstraction of the pro-R methylene hydrogen from C1 by a conserved glutamate (Glu165), an assignment that has been both universally accepted yet a much-studied phenomenon for decades. In this work we introduce an alternative mechanism in which water as a strong general base abstracts the carbon proton acting effectively as hydroxide. We posit that strong electric fields associated with the substrate phosphate promote facile autoionization of water trapped near the phosphate dianion of DHAP and Glu165, an example of substrate assisted catalysis. Classical molecular dynamics simulations assert that the closest water oxygen atom is consistently closer to the pro-R H than the carboxylate oxygen atoms of the accepted base Glu165. Our proposal is further supported by quantum computations that confirm the implausibility of abstraction of the methylene hydrogen by glutamate and the ease with which it is abstracted by hydroxide. The necessity of Glu165 for efficient catalysis is attributed to its crucial involvement in trapping the vital water in an environment of high electric fields which promote ionization far more rapidly than in bulk solvent.

scholarly journals Quantum Kinetic Transport under High Electric Fields

VLSI Design ◽  
1998 ◽  
Vol 6 (1-4) ◽  
pp. 3-7 ◽  
Author(s):  
Nobuyuki Sano ◽  
Akira Yoshii
Keyword(s):  
Electric Fields ◽  
Field Effect ◽  
Quantum Wires ◽  
Marked Contrast ◽  
One Dimensional ◽  
The Monte Carlo Method ◽  
Strong Electric Fields ◽  
Moderate Electric Field ◽  
High Electric Fields ◽  
Low Dimensional

Quantum kinetic transport under high electric fields is investigated with emphasis on the intracollisional field effect (ICFE) in low-dimensional structures. It is shown that the ICFE in GaAs one-dimensional quantum wires is already significant under moderate electric field strengths (≥ a few hundreds V/cm). This is a marked contrast to the cases in bulk, where the ICFE is expected to be significant under extremely strong electric fields (≥ MV/cm). Employing the Monte Carlo method including the ICFE, the electron drift velocity in quantum wires is shown to be much smaller than that expected from earlier investigations.

Atomic Spectroscopy in the FIM

1986 ◽  
Vol 44 ◽  
pp. 758-761
Author(s):  
J. J. Hren ◽  
S. D. Walck
Keyword(s):  
Electron Microscope ◽  
Electric Fields ◽  
Atom Probe ◽  
Atomic Spectroscopy ◽  
Single Atom ◽  
Statistical Sampling ◽  
Commercial Instrument ◽  
Available Technology ◽  
High Electric Fields ◽  
Field Ion Microscope

The field ion microscope (FIM) has had the ability to routinely image the surface atoms of metals since Mueller perfected it in 1956. Since 1967, the TOF Atom Probe has had single atom sensitivity in conjunction with the FIM. “Why then hasn't the FIM enjoyed the success of the electron microscope?” The answer is closely related to the evolution of FIM/Atom Probe techniques and the available technology. This paper will review this evolution from Mueller's early discoveries, to the development of a viable commercial instrument. It will touch upon some important contributions of individuals and groups, but will not attempt to be all inclusive. Variations in instrumentation that define the class of problems for which the FIM/AP is uniquely suited and those for which it is not will be described. The influence of high electric fields inherent to the technique on the specimens studied will also be discussed. The specimen geometry as it relates to preparation, statistical sampling and compatibility with the TEM will be examined.

Tuning the Electric Field Response of MOFs by Rotatable Dipolar Linkers

2019 ◽  
Author(s):  
Johannes P. Dürholt ◽  
Babak Farhadi Jahromi ◽  
Rochus Schmid
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Structural Changes ◽  
Dielectric Behavior ◽  
Two Dimensions ◽  
Dielectric Constants ◽  
Electric Response ◽  
Dipole Strength ◽  
Metal Organic ◽  
Dynamics Simulations

Recently the possibility of using electric fields as a further stimulus to trigger structural changes in metal-organic frameworks (MOFs) has been investigated. In general, rotatable groups or other types of mechanical motion can be driven by electric fields. In this study we demonstrate how the electric response of MOFs can be tuned by adding rotatable dipolar linkers, generating a material that exhibits paralectric behavior in two dimensions and dielectric behavior in one dimension. The suitability of four different methods to compute the relative permittivity κ by means of molecular dynamics simulations was validated. The dependency of the permittivity on temperature T and dipole strength μ was determined. It was found that the herein investigated systems exhibit a high degree of tunability and substantially larger dielectric constants as expected for MOFs in general. The temperature dependency of κ obeys the Curie-Weiss law. In addition, the influence of dipolar linkers on the electric field induced breathing behavior was investigated. With increasing dipole moment, lower field strength are required to trigger the contraction. These investigations set the stage for an application of such systems as dielectric sensors, order-disorder ferroelectrics or any scenario where movable dipolar fragments respond to external electric fields.

Medical and Veterinary Importance of the Moonlighting Functions of Triosephosphate Isomerase

2019 ◽  
Vol 20 (4) ◽  
pp. 304-315 ◽  
Author(s):  
Mónica Rodríguez-Bolaños ◽  
Ruy Perez-Montfort
Keyword(s):  
Cell Cycle ◽  
Immune Response ◽  
Triosephosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Canonical Function ◽  
Moonlighting Protein ◽  
Veterinary Importance ◽  
Moonlighting Functions

Triosephosphate isomerase is the fifth enzyme in glycolysis and its canonical function is the reversible isomerization of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Within the last decade multiple other functions, that may not necessarily always involve catalysis, have been described. These include variations in the degree of its expression in many types of cancer and participation in the regulation of the cell cycle. Triosephosphate isomerase may function as an auto-antigen and in the evasion of the immune response, as a factor of virulence of some organisms, and also as an important allergen, mainly in a variety of seafoods. It is an important factor to consider in the cryopreservation of semen and seems to play a major role in some aspects of the development of Alzheimer's disease. It also seems to be responsible for neurodegenerative alterations in a few cases of human triosephosphate isomerase deficiency. Thus, triosephosphate isomerase is an excellent example of a moonlighting protein.

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