101
|
Purg M, Pabis A, Baier F, Tokuriki N, Jackson C, Kamerlin SCL. Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0150. [PMID: 27698033 PMCID: PMC5052733 DOI: 10.1098/rsta.2016.0150] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 05/27/2023]
Abstract
Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates, the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal-metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
Collapse
Affiliation(s)
- Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Anna Pabis
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Florian Baier
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Colin Jackson
- Research School of Chemistry, Building 138, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| |
Collapse
|
102
|
Casalino L, Magistrato A. Structural, dynamical and catalytic interplay between Mg2+ ions and RNA. Vices and virtues of atomistic simulations. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
103
|
Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Proc Natl Acad Sci U S A 2016; 113:10310-5. [PMID: 27573840 DOI: 10.1073/pnas.1607734113] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Natural resistance-associated macrophage protein (Nramp) family transporters catalyze uptake of essential divalent transition metals like iron and manganese. To discriminate against abundant competitors, the Nramp metal-binding site should favor softer transition metals, which interact either covalently or ionically with coordinating molecules, over hard calcium and magnesium, which interact mainly ionically. The metal-binding site contains an unusual, but conserved, methionine, and its sulfur coordinates transition metal substrates, suggesting a vital role in their transport. Using a bacterial Nramp model system, we show that, surprisingly, this conserved methionine is dispensable for transport of the physiological manganese substrate and similar divalents iron and cobalt, with several small amino acid replacements still enabling robust uptake. Moreover, the methionine sulfur's presence makes the toxic metal cadmium a preferred substrate. However, a methionine-to-alanine substitution enables transport of calcium and magnesium. Thus, the putative evolutionary pressure to maintain the Nramp metal-binding methionine likely exists because it-more effectively than any other amino acid-increases selectivity for low-abundance transition metal transport in the presence of high-abundance divalents like calcium and magnesium.
Collapse
|
104
|
Jiang Y, Zhang H, Tan T. Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model. J Chem Theory Comput 2016; 12:3250-60. [DOI: 10.1021/acs.jctc.6b00223] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
105
|
The good, the bad and the user in soft matter simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2529-2538. [PMID: 26862882 DOI: 10.1016/j.bbamem.2016.02.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/21/2022]
Abstract
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
|
106
|
Kenion RL, Ananth N. Direct simulation of electron transfer in the cobalt hexammine(ii/iii) self-exchange reaction. Phys Chem Chem Phys 2016; 18:26117-26124. [DOI: 10.1039/c6cp04882j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an atomistic simulation of electron transfer in a transition metal complex system using path integral methods.
Collapse
Affiliation(s)
- Rachel L. Kenion
- Robert Frederick Smith School of Chemical and Biomolecular Engineering
- Cornell University
- Ithaca
- USA
| | - Nandini Ananth
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| |
Collapse
|
107
|
Sessa F, D’Angelo P, Guidoni L, Migliorati V. Hidden Hydration Structure of Halide Ions: an Insight into the Importance of Lone Pairs. J Phys Chem B 2015; 119:15729-37. [DOI: 10.1021/acs.jpcb.5b10636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesco Sessa
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paola D’Angelo
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Leonardo Guidoni
- Dipartimento
di Scienze Fisiche e Chimiche, Università degli Studi Dell’Aquila, Via Vetoio, L’Aquila, Italy
| | - Valentina Migliorati
- Dipartimento
di Chimica, “La Sapienza” Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| |
Collapse
|
108
|
Jiang Y, Zhang H, Feng W, Tan T. Refined Dummy Atom Model of Mg2+ by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy. J Chem Inf Model 2015; 55:2575-86. [DOI: 10.1021/acs.jcim.5b00286] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
109
|
Barrozo A, Duarte F, Bauer P, Carvalho ATP, Kamerlin SCL. Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2015; 137:9061-76. [PMID: 26091851 PMCID: PMC4513756 DOI: 10.1021/jacs.5b03945] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.
Collapse
Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| |
Collapse
|
110
|
Liao Q, Kamerlin SCL, Strodel B. Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect. J Phys Chem Lett 2015; 6:2657-62. [PMID: 26167255 PMCID: PMC4493862 DOI: 10.1021/acs.jpclett.5b01122] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/18/2015] [Indexed: 05/26/2023]
Abstract
Metal ions are both ubiquitous to and crucial in biology. In classical simulations, they are typically described as simple van der Waals spheres, making it difficult to provide reliable force field descriptions for them. An alternative is given by nonbonded dummy models, in which the central metal atom is surrounded by dummy particles that each carry a partial charge. While such dummy models already exist for other metal ions, none is available yet for Cu(2+) because of the challenge to reproduce the Jahn-Teller distortion. This challenge is addressed in the current study, where, for the first time, a dummy model including a Jahn-Teller effect is developed for Cu(2+). We successfully validate its usefulness by studying metal binding in two biological systems: the amyloid-β peptide and the mixed-metal enzyme superoxide dismutase. We believe that our parameters will be of significant value for the computational study of Cu(2+)-dependent biological systems using classical models.
Collapse
Affiliation(s)
- Qinghua Liao
- Institute of Complex
Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | | | - Birgit Strodel
- Institute of Complex
Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| |
Collapse
|
111
|
Antipina AY, Gurtovenko AA. Molecular Mechanism of Calcium-Induced Adsorption of DNA on Zwitterionic Phospholipid Membranes. J Phys Chem B 2015; 119:6638-45. [DOI: 10.1021/acs.jpcb.5b01256] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandra Yu. Antipina
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg 199004, Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg 198504, Russia
| | - Andrey A. Gurtovenko
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg 199004, Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg 198504, Russia
| |
Collapse
|
112
|
Li P, Song LF, Merz KM. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J Chem Theory Comput 2015; 11:1645-57. [PMID: 26574374 DOI: 10.1021/ct500918t] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
Collapse
Affiliation(s)
- Pengfei Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| |
Collapse
|
113
|
Ben-David M, Sussman JL, Maxwell CI, Szeler K, Kamerlin SCL, Tawfik DS. Catalytic stimulation by restrained active-site floppiness--the case of high density lipoprotein-bound serum paraoxonase-1. J Mol Biol 2015; 427:1359-1374. [PMID: 25644661 DOI: 10.1016/j.jmb.2015.01.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 11/28/2022]
Abstract
Despite the abundance of membrane-associated enzymes, the mechanism by which membrane binding stabilizes these enzymes and stimulates their catalysis remains largely unknown. Serum paraoxonase-1 (PON1) is a lipophilic lactonase whose stability and enzymatic activity are dramatically stimulated when associated with high-density lipoprotein (HDL) particles. Our mutational and structural analyses, combined with empirical valence bond simulations, reveal a network of hydrogen bonds that connect HDL binding residues with Asn168--a key catalytic residue residing >15Å from the HDL contacting interface. This network ensures precise alignment of N168, which, in turn, ligates PON1's catalytic calcium and aligns the lactone substrate for catalysis. HDL binding restrains the overall motion of the active site and particularly of N168, thus reducing the catalytic activation energy barrier. We demonstrate herein that disturbance of this network, even at its most far-reaching periphery, undermines PON1's activity. Membrane binding thus immobilizes long-range interactions via second- and third-shell residues that reduce the active site's floppiness and pre-organize the catalytic residues. Although this network is critical for efficient catalysis, as demonstrated here, unraveling these long-rage interaction networks is challenging, let alone their implementation in artificial enzyme design.
Collapse
Affiliation(s)
- Moshe Ben-David
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christopher I Maxwell
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-754 21 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-754 21 Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-754 21 Uppsala, Sweden.
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
114
|
Vazquez DS, Agudelo WA, Yone A, Vizioli N, Arán M, González Flecha FL, González Lebrero MC, Santos J. A helix–coil transition induced by the metal ion interaction with a grafted iron-binding site of the CyaY protein family. Dalton Trans 2015; 44:2370-9. [DOI: 10.1039/c4dt02796e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An iron-binding motif EExxED from the first α-helical stretch of frataxin was grafted on a foreign peptide scaffold:KD= 1.9 ± 0.2 μM and 1 : 1 stoichiometry.
Collapse
Affiliation(s)
- Diego S. Vazquez
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - William A. Agudelo
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Angel Yone
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Nora Vizioli
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Martín Arán
- Fundación Instituto Leloir and IIBBA – CONICET
- 1405 Buenos Aires
- Argentina
| | - F. Luis González Flecha
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Mariano C. González Lebrero
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Javier Santos
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| |
Collapse
|
115
|
Lu X, Gaus M, Elstner M, Cui Q. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B 2014; 119:1062-82. [PMID: 25178644 PMCID: PMC4306495 DOI: 10.1021/jp506557r] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report the parametrization of
the approximate density functional
theory, DFTB3, for magnesium and zinc for chemical and biological
applications. The parametrization strategy follows that established
in previous work that parametrized several key main group elements
(O, N, C, H, P, and S). This 3OB set of parameters can thus be used
to study many chemical and biochemical systems. The parameters are
benchmarked using both gas-phase and condensed-phase systems. The
gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization
(MIO). The results indicate that DFTB3/3OB is particularly successful
at predicting structures, including rather complex dinuclear metalloenzyme
active sites, while being semiquantitative (with a typical mean absolute
deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point
calculations with high-level quantum mechanics (QM) methods generally
lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic
properties. DFTB3/MM simulations for solution and two enzyme systems
also lead to encouraging structural and energetic properties in comparison
to available experimental data. The remaining limitations of DFTB3,
such as the treatment of interaction between metal ions and highly
charged/polarizable ligands, are also discussed.
Collapse
Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | | | | | | |
Collapse
|
116
|
Li P, Song LF, Merz KM. Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J Phys Chem B 2014; 119:883-95. [PMID: 25145273 PMCID: PMC4306492 DOI: 10.1021/jp505875v] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Highly charged metal ions act as
catalytic centers and structural
elements in a broad range of chemical complexes. The nonbonded model
for metal ions is extensively used in molecular simulations due to
its simple form, computational speed, and transferability. We have
proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded
model for divalent metal ions in previous work, which showed a marked
improvement over the 12-6 LJ nonbonded model. In the present study,
by treating the experimental hydration free energies and ion–oxygen
distances of the first solvation shell as targets for our parametrization,
we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions
for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6
LJ nonbonded model increases dramatically for the highly charged metal
ions. We then parametrized the 12-6-4 LJ-type nonbonded model for
these metal ions with the three water models. The final parameters
reproduced the target values with good accuracy, which is consistent
with our previous experience using this potential. Finally, tests
were performed on a protein system, and the obtained results validate
the transferability of these nonbonded model parameters.
Collapse
Affiliation(s)
- Pengfei Li
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | | | | |
Collapse
|
117
|
Yang ZZ, Wang JJ, Zhao DX. Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field. J Comput Chem 2014; 35:1690-706. [DOI: 10.1002/jcc.23676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/01/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Jian-Jiang Wang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| |
Collapse
|