Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase

Тип документаJournal Article
Дата публикации2018-02-01
Название журналаJournal of Physical Chemistry B
  • Materials Chemistry
  • Surfaces, Coatings and Films
  • Physical and Theoretical Chemistry
Краткое описание
The transient absorption spectroscopy of hydrolysis of the chromogenic substrate nitrocefin by the L1 metallo-β-lactamase (MβL), a bacterial enzyme responsible for destruction of β-lactam antibiotics molecules, showed formation and decay of a plausible red-shifted reaction intermediate. We propose a mechanism of this important reaction consistent with the transient kinetic data. Quantum mechanics/molecular mechanics (QM/MM) simulations of the reaction pathway revealed occurrence of two reaction intermediates (I1, I2) between the enzyme-substrate (ES) and enzyme-product (EP) complexes. The vertical S0-S1 transition energies calculated at the minimum energy structures (ES, I1, I2, EP) using the time dependent DFT (TD-DFT) method allowed us to assign the experimental absorption bands to all reacting species. We numerically solved the equations of chemical kinetics with the rate constants of all elementary steps evaluated with the transition state theory and simulated the kinetic curves as well as the evolution of the absorption bands of ES, I2, and EP. Direct comparison to the experimental data allowed us to identify the I2 intermediate as the transient red-shifted species detected experimentally. In agreement with the experimental observations, the recomputed energy profiles for the D120N and D120C mutants of L1 reacting with nitrocefin showed absence of a stable intermediate I2. According to the consistent experimental and theoretical results, the breakdown of the intermediate I2 corresponds to the rate-limiting stage of the chemical transformations in the active site of the L1 metallo-β-lactamase. On this basis, we established a QSAR-type correlation between the observed reaction rates (kcat) of three cephalosporin antibiotics (cefotixin, nitrocefin, cefepime) showing different hydrolysis rates by the L1 metallo-β-lactamase and different structures of the corresponding intermediates of the I2 type. This correlation can be employed for a rational design of novel antibiotics, which are not decomposed by metallo-β-lactamases.
Пристатейные ссылки: 53
Цитируется в публикациях: 15
Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2
Vasilevskaya T., Khrenova M.G., Nemukhin A.V., Thiel W.
Journal of computational chemistry 2016 цитирований: 17
Single-molecule enzymology of steroid transforming enzymes: Transient kinetic studies and what they tell us
Penning T.M.
Q1 Journal of Steroid Biochemistry and Molecular Biology 2016 цитирований: 1
Refined models of New Delhi metallo-beta-lactamase-1 with inhibitors: an QM/MM modeling study
Wang Y., Cheng T.
Q3 Journal of Biomolecular Structure and Dynamics 2016 цитирований: 5
Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme
Khrenova M.G., Grigorenko B.L., Kolomeisky A.B., Nemukhin A.V.
Journal of Physical Chemistry B 2015 цитирований: 40
Overcoming differences: The catalytic mechanism of metallo-β-lactamases
Meini M., Llarrull L.I., Vila A.J.
Q2 FEBS Letters 2015 цитирований: 88
Open Access
Open access
Mechanism of Meropenem Hydrolysis by New Delhi Metallo β-Lactamase
Tripathi R., Nair N.N.
Q1 ACS Catalysis 2015 цитирований: 27
A variety of roles for versatile zinc in metallo-β-lactamases
Karsisiotis A.I., Damblon C.F., Roberts G.C.
Q1 Metallomics 2014 цитирований: 54
Steady-state, Pre-steady-state, and Single-turnover Kinetic Measurement for DNA Glycosylase Activity
Sassa A., Beard W.A., Shock D.D., Wilson S.H.
Q3 Journal of Visualized Experiments 2013 цитирований: 6
A century of enzyme kinetic analysis, 1913 to 2013
Johnson K.A.
Q2 FEBS Letters 2013 цитирований: 99
A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1
Zhu K., Lu J., Liang Z., Kong X., Ye F., Jin L., Geng H., Chen Y., Zheng M., Jiang H., Li J., Luo C.
Q1 Journal of Computer-Aided Molecular Design 2013 цитирований: 29
Metallo-β-lactamase structure and function
Palzkill T.
Q1 Annals of the New York Academy of Sciences 2012 цитирований: 275
QM/MM Studies of Monozinc β-Lactamase CphA Suggest That the Crystal Structure of an Enzyme−Intermediate Complex Represents a Minor Pathway
Wu S., Xu D., Guo H.
Q1 Journal of the American Chemical Society 2010 цитирований: 47
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
Valiev M., Bylaska E.J., Govind N., Kowalski K., Straatsma T.P., Van Dam H.J., Wang D., Nieplocha J., Apra E., Windus T.L., de Jong W.A.
Q1 Computer Physics Communications 2010 цитирований: 3573
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
Vanommeslaeghe K., Hatcher E., Acharya C., Kundu S., Zhong S., Shim J., Darian E., Guvench O., Lopes P., Vorobyov I., Mackerell A.D.
Q1 Journal of Computational Chemistry 2009 цитирований: 1373
QM/MM Methods for Biomolecular Systems
Senn H.M., Thiel W.
Q1 Angewandte Chemie - International Edition 2009 цитирований: 1685
1. Khrenova M.G., Nemukhin A.V. Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase // The Journal of Physical Chemistry B. 2018. Т. 122. № 4. С. 1378–1386.


DO - 10.1021/acs.jpcb.7b10188

UR -

TI - Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase

T2 - The Journal of Physical Chemistry B

AU - Khrenova, Maria G.

AU - Nemukhin, Alexander V.

PY - 2018

DA - 2018/01/22

PB - American Chemical Society (ACS)

SP - 1378-1386

IS - 4

VL - 122

SN - 1520-6106

SN - 1520-5207

ER -

BibTex |


doi = {10.1021/acs.jpcb.7b10188},

url = {},

year = 2018,

month = {jan},

publisher = {American Chemical Society ({ACS})},

volume = {122},

number = {4},

pages = {1378--1386},

author = {Maria G. Khrenova and Alexander V. Nemukhin},

title = {Modeling the Transient Kinetics of the L1 Metallo-$\upbeta$-Lactamase}


Khrenova, Maria G., and Alexander V. Nemukhin. “Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase.” The Journal of Physical Chemistry B 122.4 (2018): 1378–1386. Crossref. Web.