scholarly journals A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase

2020 ◽  
Author(s):  
Yufan Wu ◽  
Stephen Fried ◽  
Steven Boxer
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Ground State ◽  
Active Site ◽  
Electrostatic Interactions ◽  
Stark Effect ◽  
Structural Changes ◽  
Enzymatic Catalysis ◽  
Ketosteroid Isomerase ◽  
Computational Enzyme Design

<div><p>Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI’s intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction’s TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems. <br></p></div>

scholarly journals A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase

2020 ◽  
Author(s):  
Yufan Wu ◽  
Stephen Fried ◽  
Steven Boxer
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Ground State ◽  
Active Site ◽  
Electrostatic Interactions ◽  
Stark Effect ◽  
Structural Changes ◽  
Enzymatic Catalysis ◽  
Ketosteroid Isomerase ◽  
Computational Enzyme Design

<div><p>Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI’s intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction’s TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems. <br></p></div>

scholarly journals Extreme electric fields power catalysis in the active site of ketosteroid isomerase

Science ◽  
2014 ◽  
Vol 346 (6216) ◽  
pp. 1510-1514 ◽  
Author(s):  
Stephen D. Fried ◽  
Sayan Bagchi ◽  
Steven G. Boxer
Keyword(s):  
Electric Field ◽  
Electric Fields ◽  
Active Site ◽  
Stark Effect ◽  
Catalytic Effect ◽  
Biomolecular Systems ◽  
Ketosteroid Isomerase ◽  
Rate Determining Step ◽  
Experimental Approaches ◽  
A Charge

Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI’s rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme’s catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.

scholarly journals An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2410 ◽  
Author(s):  
Xianwei Wang ◽  
Xiao He
Keyword(s):  
Electric Field ◽  
Ab Initio ◽  
Active Site ◽  
Md Simulation ◽  
Stark Effect ◽  
Computational Simulation ◽  
Ketosteroid Isomerase ◽  
Correlation Relationship ◽  
Amber Force Field ◽  
Electrostatic Contribution

The electric field in the hydrogen-bond network of the active site of ketosteroid isomerase (KSI) has been experimentally measured using vibrational Stark effect (VSE) spectroscopy, and utilized to study the electrostatic contribution to catalysis. A large gap was found in the electric field between the computational simulation based on the Amber force field and the experimental measurement. In this work, quantum mechanical (QM) calculations of the electric field were performed using an ab initio QM/MM molecular dynamics (MD) simulation and electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. Our results demonstrate that the QM-derived electric field based on the snapshots from QM/MM MD simulation could give quantitative agreement with the experiment. The accurate calculation of the electric field inside the protein requires both the rigorous sampling of configurations, and a QM description of the electrostatic field. Based on the direct QM calculation of the electric field, we theoretically confirmed that there is a linear correlation relationship between the activation free energy and the electric field in the active site of wild-type KSI and its mutants (namely, D103N, Y16S, and D103L). Our study presents a computational protocol for the accurate simulation of the electric field in the active site of the protein, and provides a theoretical foundation that supports the link between electric fields and enzyme catalysis.

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.

scholarly journals Origin of the enhanced structural and reorientational relaxation rates in the presence of relatively weak dc electric fields

2004 ◽  
Vol 76 (1) ◽  
pp. 215-221 ◽  
Author(s):  
A. Vegiri
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Electric Fields ◽  
Structural Relaxation ◽  
Structural Changes ◽  
Common Mechanism ◽  
Weak Electric Field ◽  
Water Molecules ◽  
Relaxation Rates ◽  
Dynamics Simulations

The origin of the dramatic increase of the reorientational and structural relaxation rates of single water molecules in clusters of size N = 16, 32, and 64 at T = 200 K, under the influence of an external, relatively weak electric field (~0.5 107 V/cm) is examined through molecular dynamics simulations. The observed effect is attributed not to any profound structural changes, but to the increase of the size of the molecular cage. The response of water to an electric field in this range shows many similarities with the dynamics of water under low pressure. By referring to simulations and experiments from the literature, we show that in both cases the observed effects are dictated by a common mechanism.

scholarly journals Separation of water–ethanol solutions with carbon nanotubes and electric fields

2016 ◽  
Vol 18 (48) ◽  
pp. 33310-33319 ◽  
Author(s):  
Winarto Winarto ◽  
Daisuke Takaiwa ◽  
Eiji Yamamoto ◽  
Kenji Yasuoka
Keyword(s):  
Carbon Nanotubes ◽  
Electric Field ◽  
Electric Fields ◽  
Electrostatic Interactions ◽  
Water Molecules ◽  
Ordered Structure

Under an electric field, water prefers to fill CNTs over ethanol, and electrostatic interactions within the ordered structure of the water molecules determine the separation effects.

scholarly journals Supramolecular Stark Effect in Host-Guest Complexes via Charge Density Analysis

2014 ◽  
Vol 70 (a1) ◽  
pp. C674-C674
Author(s):  
Sajesh Thomas ◽  
Rebecca Fuller ◽  
Alexandre Sobolev ◽  
Philip Schauer ◽  
Simon Grabowsky ◽  
...  
Keyword(s):  
Electric Field ◽  
Charge Density ◽  
Electric Fields ◽  
Active Sites ◽  
Stark Effect ◽  
Dipole Moments ◽  
Covalent Bonds ◽  
Guest Molecules ◽  
Density Mapping ◽  
Density Analysis

The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques [3]. In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.

scholarly journals The Interplay of Electrostatics and Chemical Positioning in the Evolution of Antibiotic Resistance in TEM β-Lactamases

2021 ◽  
Author(s):  
Samuel H Schneider ◽  
Jacek Kozuch ◽  
Steven G Boxer
Keyword(s):  
Antibiotic Resistance ◽  
Electric Fields ◽  
Stark Effect ◽  
Structural Changes ◽  
Fitness Landscape ◽  
Md Simulations ◽  
Penicillin G ◽  
Modulate Function ◽  
Evolutionary Trajectory ◽  
Enzyme Active Site

The interplay of enzyme active site electrostatics and chemical positioning are important for understanding the origin(s) of enzyme catalysis and the design of novel catalysts. We reconstruct the evolutionary trajectory of TEM-1 β-lactamase to TEM-52 towards extended-spectrum activity to better understand the emergence of antibiotic resistance and to provide insights into the structure-function paradigm and non-covalent interactions involved in catalysis. Utilizing a detailed kinetic analysis and the vibrational Stark effect, we quantify the changes in rate and electric fields in the Michaelis and acyl-enzyme complexes for penicillin G and cefotaxime to ascertain the evolutionary role of electric fields to modulate function. These data are combined with MD simulations to interpret and quantify the substrate-dependent structural changes during evolution. We observe that evolution utilizes a large preorganized electric field and substrate-dependent chemical positioning to facilitate catalysis. This governs the evolvability, substrate promiscuity, and protein fitness landscape in TEM β-lactamase antibiotic resistance.

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