1
|
Arodola OA, Kanchi S, Hloma P, Bisetty K, Asiri AM, Inamuddin. An in-silico layer-by-layer adsorption study of the interaction between Rebaudioside A and the T1R2 human sweet taste receptor: modelling and biosensing perspectives. Sci Rep 2020; 10:18391. [PMID: 33110140 PMCID: PMC7591876 DOI: 10.1038/s41598-020-75123-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/28/2020] [Indexed: 12/03/2022] Open
Abstract
The human sweet taste receptor (T1R2) monomer-a member of the G-protein coupled receptor family that detects a wide variety of chemically and structurally diverse sweet tasting molecules, is known to pose a significant threat to human health. Protein that lack crystal structure is a challenge in structure-based protein design. This study focused on the interaction of the T1R2 monomer with rebaudioside A (Reb-A), a steviol glycoside with potential use as a natural sweetener using in-silico and biosensing methods. Herein, homology modelling, docking studies, and molecular dynamics simulations were applied to elucidate the interaction between Reb-A and the T1R2 monomer. In addition, the electrochemical sensing of the immobilised T1R2-Reb-A complex with zinc oxide nanoparticles (ZnONPs) and graphene oxide (GO) were assessed by testing the performance of multiwalled carbon nanotube (MWCNT) as an adsorbent experimentally. Results indicate a strong interaction between Reb-A and the T1R2 receptor, revealing the stabilizing interaction of the amino acids with the Reb-A by hydrogen bonds with the hydroxyl groups of the glucose moieties, along with a significant amount of hydrophobic interactions. Moreover, the presence of the MWCNT as an anchor confirms the adsorption strength of the T1R2-Reb-A complex onto the GO nanocomposite and supported with electrochemical measurements. Overall, this study could serve as a cornerstone in the development of electrochemical immunosensor for the detection of Reb-A, with applications in the food industry.
Collapse
Affiliation(s)
- Olayide A Arodola
- Department of Chemistry, Durban University of Technology, P.O Box 1334, Durban, 4000, South Africa.
| | - Suvardhan Kanchi
- Department of Chemistry, Durban University of Technology, P.O Box 1334, Durban, 4000, South Africa
| | - Phathisanani Hloma
- Department of Chemistry, Durban University of Technology, P.O Box 1334, Durban, 4000, South Africa
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, P.O Box 1334, Durban, 4000, South Africa.
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Inamuddin
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
- Advanced Functional Materials Laboratory, Department of Applied Chemistry, Faculty of Engineering and Technology, Aligarh Muslim University, Aligarh, 202 002, India.
| |
Collapse
|
2
|
Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. J Am Chem Soc 2020; 142:17966-17980. [PMID: 32959658 DOI: 10.1021/jacs.0c02148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ∼18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme-substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
Collapse
Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Jerry M Parks
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| |
Collapse
|
3
|
Li P, Zhang C, Xu D. Molecular dynamics investigations of cello-oligosaccharide recognition by Cel9G-CBM3c from Clostridium cellulovorans. Phys Chem Chem Phys 2018; 20:5235-5245. [PMID: 29399685 DOI: 10.1039/c7cp07175b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The processive mechanism of cellulases against cellulose represents one of the key mechanisms in the conversion of biomass. A reliable model of substrate binding in a multidomain cellulase is a prerequisite for fully understanding this mechanism. In this study, the specificity of the recognition of the polysaccharide by the multidomain endoglucanase Cel9G from Clostridium cellulovorans was investigated by molecular dynamics simulations. Aromatic ring-containing residues were found to be critical for stabilizing the substrate. The calculated subtotal contributions of polar residues close to the active site, e.g., D58, E244, R315 and D420, also have some critical functions in substrate binding. Unlike other members of the carbohydrate-binding module family, CBM3c alone is shown not to bind cellulose very well, which is also consistent with experimental conclusions.
Collapse
Affiliation(s)
- Penghui Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | | | | |
Collapse
|
4
|
Xiao K, Yu H. Rationalising pK a shifts in Bacillus circulans xylanase with computational studies. Phys Chem Chem Phys 2018; 18:30305-30312. [PMID: 27485091 DOI: 10.1039/c6cp02526a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacillus circulans xylanase (BcX), a family 11 glycoside hydrolase, catalyses the hydrolysis of xylose polymers with a net retention of stereochemistry. Glu172 in BcX is believed to act as a general acid by protonating the aglycone during glycosylation, and then as a general base to facilitate the deglycosylation step. The key to the dual role of this general acid/base lies in its protonation states, which depend on its intrinsic pKa value and the specific environment which it resides within. To fully understand the detailed molecular features in BcX to establish the dual role of Glu172, we present a combined study based on both atomistic simulations and empirical models to calculate pKa shifts for the general acid/base Glu172 in BcX at different functional states. Its pKa values and those of nearby residues, obtained based on QM/MM free energy calculations, MCCE and PROPKA, show a good agreement with available experimental data. Additionally, our study provides additional insights into the effects of structural and electrostatic perturbations caused by mutations and chemical modifications, suggesting that the local solvation environment and mutagenesis of the residues adjacent to Glu172 establish its dual role during hydrolysis. The strengths and limitations of various methods for calculating pKas and pKa shifts have also been discussed.
Collapse
Affiliation(s)
- Kela Xiao
- School of Chemistry, University of Wollongong, NSW 2522, Australia.
| | - Haibo Yu
- School of Chemistry, University of Wollongong, NSW 2522, Australia. and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| |
Collapse
|
5
|
An efficient, scalable approach to hydrolyze flavonoid glucuronides via activation of glycoside bond. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.02.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
6
|
Plazinski W, Lonardi A, Hünenberger PH. Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains. J Comput Chem 2015; 37:354-65. [PMID: 26525424 DOI: 10.1002/jcc.24229] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023]
Abstract
This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.
Collapse
Affiliation(s)
- Wojciech Plazinski
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland.,J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, Cracow, 30-239, Poland
| | - Alice Lonardi
- Laboratory of Physical Chemistry, ETH Hönggerberg, HCI, Zürich, CH-8093, Switzerland
| | | |
Collapse
|
7
|
Plazinski W, Drach M. The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations. Carbohydr Res 2015; 415:17-27. [DOI: 10.1016/j.carres.2015.07.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/20/2015] [Accepted: 07/29/2015] [Indexed: 11/29/2022]
|
8
|
Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
Collapse
Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
| |
Collapse
|
9
|
Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter J. Reilly
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, United States
| | - Carme Rovira
- Departament de Química Orgànica
and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
10
|
Jitonnom J, Sattayanon C, Kungwan N, Hannongbua S. A DFT study of the unusual substrate-assisted mechanism of Serratia marcescens chitinase B reveals the role of solvent and mutational effect on catalysis. J Mol Graph Model 2015; 56:53-9. [DOI: 10.1016/j.jmgm.2014.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
|
11
|
Mhlongo NN, Ebrahim M, Skelton AA, Kruger HG, Williams IH, Soliman MES. Dynamics of the thumb-finger regions in a GH11 xylanase Bacillus circulans: comparison between the Michaelis and covalent intermediate. RSC Adv 2015. [DOI: 10.1039/c5ra16836h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure and dynamics of B. circulans β-1,4-xylanase (BCX) were comparatively studied utilizing molecular dynamics.
Collapse
Affiliation(s)
- Ndumiso N. Mhlongo
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahasin Ebrahim
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Adam A. Skelton
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| | | | - Mahmoud E. S. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences University of KwaZulu-Natal
- Durban 4001
- South Africa
| |
Collapse
|
12
|
Mhlongo NN, Skelton AA, Kruger G, Soliman ME, Williams IH. A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases. Proteins 2014; 82:1747-55. [DOI: 10.1002/prot.24528] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/20/2013] [Accepted: 01/28/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Ndumiso N. Mhlongo
- Discipline of Pharmaceutical Sciences; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Adam A. Skelton
- Discipline of Pharmaceutical Sciences; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Gert Kruger
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Mahmoud E.S. Soliman
- Discipline of Pharmaceutical Sciences; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Ian H. Williams
- Department of Chemistry; University of Bath; Bath BA2 7AY United Kingdom
| |
Collapse
|
13
|
Plazinski W, Drach M. The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach. RSC Adv 2014. [DOI: 10.1039/c4ra03410d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The transition paths corresponding to the conformational rearrangements in the ring of hexapyranose (α-d- and β-d-glucose) molecules were described by applying the transition path sampling method.
Collapse
Affiliation(s)
- Wojciech Plazinski
- Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- 30-239 Cracow, Poland
| | - Mateusz Drach
- Department of Theoretical Chemistry
- Faculty of Chemistry
- UMCS
- 20-031 Lublin, Poland
| |
Collapse
|
14
|
Oborský P, Tvaroška I, Králová B, Spiwok V. Toward an accurate conformational modeling of iduronic acid. J Phys Chem B 2013; 117:1003-9. [PMID: 23286518 DOI: 10.1021/jp3100552] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Iduronic acid (IdoA), unlike most other monosaccharides, can adopt different ring conformations, depending on the context of the molecular structure. Accurate modeling of this building block is essential for understanding the role of glycosaminoglycans and other glycoconjugates. Here, we use metadynamics to predict equilibria of (1)C(4), (4)C(1) and (2)S(O) conformations of α-L-IdoA-OMe and α-L-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1-4 interaction) were tested. It was found that scaling (reduction) of 1-4 electrostatic interactions significantly changes conformational preferences toward the (4)C(1) conformation. More interestingly, scaling of 1-4 van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1-4 interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments.
Collapse
Affiliation(s)
- Pavel Oborský
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Technická 3, Prague 6 166 28, Czech Republic
| | | | | | | |
Collapse
|
15
|
Pan XL, Liu W, Liu JY. Mechanism of the Glycosylation Step Catalyzed by Human α-Galactosidase: A QM/MM Metadynamics Study. J Phys Chem B 2013; 117:484-9. [DOI: 10.1021/jp308747c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiao-Liang Pan
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of
Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Wei Liu
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of
Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key
Laboratory of Theoretical and Computational Chemistry, Institute of
Theoretical Chemistry, Jilin University, Changchun 130023, China
| |
Collapse
|
16
|
Badieyan S, Bevan DR, Zhang C. Probing the Active Site Chemistry of β-Glucosidases along the Hydrolysis Reaction Pathway. Biochemistry 2012; 51:8907-18. [DOI: 10.1021/bi300675x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Somayesadat Badieyan
- Department
of Biological Systems Engineering and ‡Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
24061, United States
| | - David R. Bevan
- Department
of Biological Systems Engineering and ‡Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
24061, United States
| | - Chenming Zhang
- Department
of Biological Systems Engineering and ‡Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
24061, United States
| |
Collapse
|
17
|
QM/MM study of catalytic mechanism of Xylanase Cex from Cellulomonas fimi. J Mol Graph Model 2012; 37:67-76. [DOI: 10.1016/j.jmgm.2012.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/01/2012] [Accepted: 04/17/2012] [Indexed: 12/13/2022]
|
18
|
Mark P, Zhang Q, Czjzek M, Brumer H, Ågren H. Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucanendo-transglycosylase. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.566605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
19
|
Carneiro AS, Lameira J, Alves CN. A theoretical study of the molecular mechanism of the GAPDH Trypanosoma cruzi enzyme involving iodoacetate inhibitor. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
20
|
Jitonnom J, Lee VS, Nimmanpipug P, Rowlands HA, Mulholland AJ. Quantum Mechanics/Molecular Mechanics Modeling of Substrate-Assisted Catalysis in Family 18 Chitinases: Conformational Changes and the Role of Asp142 in Catalysis in ChiB. Biochemistry 2011; 50:4697-711. [DOI: 10.1021/bi101362g] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jitrayut Jitonnom
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Vannajan S. Lee
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Piyarat Nimmanpipug
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Heather A. Rowlands
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| |
Collapse
|
21
|
Hansen HS, Hünenberger PH. A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. J Comput Chem 2010; 32:998-1032. [PMID: 21387332 DOI: 10.1002/jcc.21675] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/12/2010] [Accepted: 08/17/2010] [Indexed: 11/07/2022]
Abstract
This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences; and (iv) the design of simulation approaches accelerating the anomerization process along an unphysical pathway.
Collapse
Affiliation(s)
- Halvor S Hansen
- Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | | |
Collapse
|
22
|
Williams IH. Catalysis: transition-state molecular recognition? Beilstein J Org Chem 2010; 6:1026-34. [PMID: 21085499 PMCID: PMC2981812 DOI: 10.3762/bjoc.6.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 10/05/2010] [Indexed: 11/23/2022] Open
Abstract
THE KEY TO UNDERSTANDING THE FUNDAMENTAL PROCESSES OF CATALYSIS IS THE TRANSITION STATE (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for S(N)2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.
Collapse
Affiliation(s)
- Ian H Williams
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom.
| |
Collapse
|
23
|
Petersen L, Ardèvol A, Rovira C, Reilly PJ. Molecular Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation. J Am Chem Soc 2010; 132:8291-300. [DOI: 10.1021/ja909249u] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Petersen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Albert Ardèvol
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Carme Rovira
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Peter J. Reilly
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|