1
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Agles AA, Bourg IC. Structure and Dynamics of Water in Polysaccharide (Alginate) Solutions and Gels Explained by the Core-Shell Model. Biomacromolecules 2024. [PMID: 39228282 DOI: 10.1021/acs.biomac.4c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
In both biological and engineered systems, polysaccharides offer a means of establishing structural stiffness without altering the availability of water. Notable examples include the extracellular matrix of prokaryotes and eukaryotes, artificial skin grafts, drug delivery materials, and gels for water harvesting. Proper design and modeling of these systems require detailed understanding of the behavior of water confined in pores narrower than about 1 nm. We use molecular dynamics simulations to investigate the properties of water in solutions and gels of the polysaccharide alginate as a function of the water content and polymer cross-linking. We find that a detailed understanding of the nanoscale dynamics of water in alginate solutions and gels requires consideration of the discrete nature of water. However, we also find that the trends in tortuosity, permeability, dielectric constant, and shear viscosity can be adequately represented using the "core-shell" conceptual model that considers the confined fluid as a continuum.
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Affiliation(s)
- Avery A Agles
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Ian C Bourg
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
- High Meadows Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
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2
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Lutsyk V, Wolski P, Plazinski W. The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties. J Chem Theory Comput 2024; 20:6350-6368. [PMID: 38985993 PMCID: PMC11270825 DOI: 10.1021/acs.jctc.4c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
The conformational features of the glycosidic linkage are the most important variable to consider when studying di-, oligo-, and polysaccharide molecules using molecular dynamics (MD) simulations. The accuracy of the theoretical model describing this degree of freedom influences the quality of the results obtained from MD calculations based on this model. This article focuses on the following two issues related to the conformation of the glycosidic linkage. First, we describe the results of a comparative analysis of the predictions of three carbohydrate-dedicated classical force fields for MD simulations, namely, CHARMM, GLYCAM, and GROMOS, in the context of different parameters of structural and energetic nature related to the conformation of selected types of glycosidic linkages, α(1 → 4), β(1 → 3), and β(1 → 4), connecting glucopyranose units. This analysis revealed several differences, mainly concerning the energy levels of the secondary and tertiary conformers and the linkage flexibility within the dominant exo-syn conformation for α(1 → 4) and β(1 → 3) linkages. Some aspects of the comparative analysis also included the newly developed, carbohydrate-dedicated Martini 3 coarse-grained force field. Second, to overcome the time-scale problem associated with sampling slow degrees of freedom in polysaccharide chains during MD simulations, we developed a coarse-grained (CG) model based on the data from MD simulations and designed for Monte Carlo modeling. This model (CG MC) is based on information from simulations of short saccharide chains, effectively sampled in atomistic MD simulations, and is capable of extrapolating local conformational properties to the case of polysaccharides of arbitrary length. The CG MC model has the potential to estimate the conformations of very long polysaccharide chains, taking into account the influence of secondary and tertiary conformations of glycosidic linkages. With respect to the comparative analysis of force fields, the application of CG MC modeling showed that relatively small differences in the predictions of individual force fields with respect to a single glycosidic linkage accumulate when considering their effect on the structure of longer chains, leading to drastically different predictions with respect to parameters describing the polymer conformation, such as the persistence length.
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Affiliation(s)
- Valery Lutsyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Pawel Wolski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
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3
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Bakó I, Pusztai L, Pothoczki S. Outstanding Properties of the Hydration Shell around β-d-Glucose: A Computational Study. ACS OMEGA 2024; 9:20331-20337. [PMID: 38737074 PMCID: PMC11080014 DOI: 10.1021/acsomega.4c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Ab initio molecular dynamics (AIMD) simulations have been performed on aqueous solutions of four simple sugars, α-d-glucose, β-d-glucose, α-d-mannose, and α-d-galactose. Hydrogen-bonding (HB) properties, such as the number of donor- and acceptor-type HB-s, and the lengths and strengths of hydrogen bonds between sugar and water molecules, have been determined. Related electronic properties, such as the dipole moments of water molecules and partial charges of the sugar O atoms, have also been calculated. The hydrophilic and hydrophobic shells were characterized by means of spatial distribution functions. β-d-Glucose was found to form the highest number of hydrophilic and the smallest number of hydrophobic connections to neighboring water molecules. The average sugar-water H-bond length was the shortest for β-d-glucose, which suggests that these are the strongest such H-bonds. Furthermore, β-d-glucose appears to stand out in terms of the symmetry properties of both its hydrophilic and hydrophobic hydration shells. In summary, in all aspects considered here, there seems to be a correlation between the distinct characteristics of β-d-glucose reported here and its outstanding solubility in water. Admittedly, our findings represent only some of the important factors that influence the solubility.
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Affiliation(s)
- Imre Bakó
- HUN-REN
Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - László Pusztai
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
- International
Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Szilvia Pothoczki
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
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4
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Liu JZ, Wang L, Jiang LJ, Lyu HC, Yuan Q, Wang GF, Fu YJ, Cui Q. In sight the behavior of natural Bletilla striata polysaccharide hydrocolloids by molecular dynamics method. Int J Biol Macromol 2024; 266:131245. [PMID: 38554922 DOI: 10.1016/j.ijbiomac.2024.131245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Plant polysaccharides, distinguished by diverse glycosidic bonds and various cyclic sugar units, constitute a subclass of primary metabolites ubiquitously found in nature. Contrary to common understanding, plant polysaccharides typically form hydrocolloids upon dissolution in water, even though both excessively high and low temperatures impede this process. Bletilla striata polysaccharides (BSP), chosen for this kinetic study due to their regular repeating units, help elucidate the relationship between polysaccharide gelation and temperature. It is suggested that elevated temperatures enhance the mobility of BSP molecular chains, resulting in a notable acceleration of hydrogen bond breakage between BSP and water molecules and consequently, compromising the conformational stability of BSPs to some extent. This study unveils the unique relationship between polysaccharide dissolution processes and temperature from a kinetics perspective. Consequently, the conclusion provides a dynamical basis for comprehending the extraction and preparation of natural plant polysaccharide hydrocolloids, pharmaceuticals and related fields.
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Affiliation(s)
- Ju-Zhao Liu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China.
| | - Lu Wang
- School of Life Sciences, Westlake University, Hangzhou 310030, PR China
| | - Li-Jie Jiang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Hong-Chang Lyu
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Qiang Yuan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Guang-Fu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China
| | - Yu-Jie Fu
- College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Haidian District, Beijing 100083, PR China
| | - Qi Cui
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, PR China.
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5
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Zhao K, Zhang S, Piao C, Xu F, Zhang Y, Wang X, Zhang J, Zhao C, You SG, Zhang Y. Investigation of the formation mechanism of the pepper starch-piperine complex. Int J Biol Macromol 2024; 268:131777. [PMID: 38663710 DOI: 10.1016/j.ijbiomac.2024.131777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/08/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024]
Abstract
In this study, a new carrier for loading piperine was prepared using pepper starch, and its interaction mechanism was investigated. The porous pepper starch-piperine complex (PPS-PIP) showed higher loading efficiency (76.15 %) compared to the porous corn starch-piperine complex (PCS-PIP (52.34 %)). This may be ascribed to the hemispherical shell structure of porous pepper starch (PPS) compared to the porous structure of porous corn starch (PCS) based on the SEM result. PPS-PIP had smaller particle size (10.53 μm), higher relative crystallinity (38.95 %), and better thermal stability (87.45 °C) than PCS-PIP (17.37 μm, 32.17 %, 74.35 °C). Fourier transform infrared spectroscopy (FTIR) results implied that piperine not only forms a complex with amylose but may also be physically present in porous starch. This was demonstrated by the short-range order and X-ray type. Molecular dynamics simulations confirmed that hydrogen bonding is the primary interaction between amylose and piperine. Besides the formation of the amylose-piperine complex, some of the piperine is also present in physical form.
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Affiliation(s)
- Kangyun Zhao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China
| | - Siwei Zhang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China
| | - Chunhong Piao
- School of Food and Pharmaceutical Engineering (Guangxi Liubao Tea Modern Industry College), Wuzhou University, Wuzhou 543002, China
| | - Fei Xu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China
| | - Yutong Zhang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China
| | - Xu Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China
| | - Jiyue Zhang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China
| | - Chunxia Zhao
- The second middle school of bachu county, Kashgar 843899, China
| | - Sang Guan You
- Department of Marine Food Science and Technology, East Coast Life Sciences Institute, Gangneung-Wonju National University, 120, Gangneung, Gangwon 210-702, Republic of Korea
| | - Yanjun Zhang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China; Key Laboratory of Processing Suitability and Quality Control of the Special Tropical Crops of Hainan Province, Hainan 571533, China; National Tropical Plant Germplasm Resource Bank Sub-bank of Woody Grain Germplasm Resources, Hainan 571533, China.
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6
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Sandilya AA, Priya MH. The counteracting influence of 2-hydroxypropyl substitution and the presence of a guest molecule on the shape and size of the β-cyclodextrin cavity. Phys Chem Chem Phys 2024; 26:11531-11544. [PMID: 38323885 DOI: 10.1039/d3cp05354g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The aqueous solubility of β-cyclodextrin (β-CD), a cyclic carbohydrate comprising seven α-D-glucose molecules, is enhanced by 2-hydroxypropyl (2-HP) substitution of the hydroxyl groups at the CD rims. Our thorough analysis of the structural and solvation properties with different degrees of 2-hydroxypropyl substitution on β-CD using molecular dynamics simulations reveals that the solubility is enhanced at the cost of the structural distortion of the CD cyclic structure. Substitution at the secondary rim predominantly enhances the favourable interactions between CD and water by decreasing CD-CD hydrogen bonding and promoting CD-water hydrogen bonding. However, the effect of substitution at the primary rim on the CD-water interactions is minimal; the hydrogen bonds between water and the primary hydroxyl group in native CD merely get replaced by those between water and 2-HP, since the substitution makes the primary hydroxyl oxygen (O6 atom) inaccessible to water. In contrast, substitution at the primary rim maintains the structural integrity of CD, while substitution at the secondary rim results in structural distortion due to the disruption of the intramolecular hydrogen bond belt, even leading to cavity closure. Certain strategic substitutions of the primary hydroxyl groups can help in the reduction of structural distortion, depending upon the degree of substitution at the secondary hydroxyl rim. A detailed inspection of the simulation trajectory revealed that the tilting of glucose units with the primary hydroxyl oxygen (O6) pointing inward is the primary driver for cavity closure. Even though the dynamics of glucose tilting can influence the kinetics of host-guest complex formation, once the guest is well incorporated into the cavity, glucose tilting is inhibited and the cavity opens up as in native β-CD.
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Affiliation(s)
- Avilasha A Sandilya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai-600036, India.
| | - M Hamsa Priya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai-600036, India.
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7
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Lutsyk V, Plazinski W. Exploring Ring Conformation in Uronate Monosaccharides: Insights from Ab Initio Calculations and Classical Molecular Dynamics Simulations. J Phys Chem B 2024; 128:472-491. [PMID: 38170925 DOI: 10.1021/acs.jpcb.3c06556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The study focuses on the conformational properties of biologically relevant monosaccharides belonging to the group of uronates: α-l-iduronate, O2-sulfated-α-l-iduronate, and O2-sulfated-α-l-guluronate, either unfunctionalized or O1-methylated. We applied the previously proposed two-step methodology, combining classical MD simulations and subsequent ab initio (QM) calculations, performed on a rationally subsampled set of molecular configurations. We found that, regardless of the number of molecular configurations considered, the level of theory, and the weighting scheme applied, none of the QM approaches is capable of predicting the correct conformational equilibrium of sulfated iduronates as long as the tight counterion binding is not considered. Multicenter, ring-shape-specific binding of either Na+ or Ca2+ ions drastically shifts the conformational equilibrium of the pyranose ring in sulfated iduronates toward 1C4 but does not significantly affect the conformation of non-sulfated compounds. A similar shift is observed upon the protonation of carboxyl groups in all iduronates. In addition, we report a set of average J-coupling constant values related to vicinal protons bound to the pyranose ring of iduronates and corresponding to each of the three main groups of ring conformers, i.e., 4C1, B/S (boat/skew boat), and 1C4. In combination with the conformational energies or with the experimental data, these values allowed the relative proportions of the ring conformers to be estimated and the Karplus-type equations linking the 3JHH-coupling constants to the torsion angles within the pyranose ring to be refined.
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Affiliation(s)
- Valery Lutsyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
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8
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Agles AA, Bourg IC. Structure-Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca). J Phys Chem B 2023; 127:1828-1841. [PMID: 36791328 PMCID: PMC10159261 DOI: 10.1021/acs.jpcb.2c07129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities─and their impacts on environmental processes─requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca-Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ∼0.6 nm between alginate strands.
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Affiliation(s)
- Avery A Agles
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Ian C Bourg
- Department of Civil and Environmental Engineering and High Meadows Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
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9
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J N C, Mallajosyula SS. Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides. J Chem Inf Model 2023; 63:208-223. [PMID: 36475659 DOI: 10.1021/acs.jcim.2c01286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of crystal structures of hexose monosaccharides α-d-mannose (α-MAN), β-d-mannose (β-MAN), α-d-glucose (α-GLC), β-d-glucose (β-GLC), α-d-galactose (α-GAL), β-d-galactose (β-GAL), α-d-altrose (α-ALT), β-d-altrose (β-ALT), α-d-idose (α-IDO), and β-d-idose (β-IDO) reveals that the monosaccharide ring adopts multiple ring conformations. These ring conformations can be broadly classified as chair, half-chair, envelope, boat, and skew-boat conformations. The ability of the monosaccharide ring to adopt multiple conformations has been closely tied with their bioactivity. However, it has been difficult to capture the dynamic information of these conformations from experimental studies. Even from simulations, capturing these different conformations is challenging because of the energy barriers involved in the transitions between the stable 4C1 and 1C4 chair forms. In this study, we analyze the influence of the polarizable force field on the ring dynamics of five major types of unsubstituted aldohexoses─glucose, mannose, galactose, altrose, and idose─and their anomers. We simulate microsecond trajectories to capture the influence of the CHARMM36 additive and polarizable carbohydrate force fields on the ring dynamics. The microsecond trajectories allow us to comment on the issues associated with equilibrium molecular dynamics simulations. Further, we use the extended system adaptive biasing force (eABF) method to compare the conformational sampling efficiencies of the additive and polarizable force fields. Our studies reveal that inclusion of polarization enhances the sampling of ring conformations and lowers the energy barriers between the 4C1 and 1C4 conformations. Overall, the CHARMM36 additive force field is observed to be rigid and favor the 4C1 conformations. Although the inclusion of polarizability results in enhancing ring flexibility, we observe sampling that does not agree with experimental results, warranting a revision of the polarizable Drude parameters.
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Affiliation(s)
- Chythra J N
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat382355, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat382355, India
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10
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Guvench O. Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes. Molecules 2022; 27:7276. [PMID: 36364098 PMCID: PMC9658939 DOI: 10.3390/molecules27217276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2023] Open
Abstract
This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
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11
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Lutsyk V, Wolski P, Plazinski W. Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates. J Chem Theory Comput 2022; 18:5089-5107. [PMID: 35904547 PMCID: PMC9367002 DOI: 10.1021/acs.jctc.2c00553] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Carbohydrates play an essential role in a large number of chemical and biochemical processes. High structural diversity and conformational heterogeneity make it problematic to link their measurable properties to molecular features. Molecular dynamics simulations carried out at the level of classical force fields are routinely applied to study the complex processes occurring in carbohydrate-containing systems, while the usefulness of such simulations relies on the accuracy of the underlying theoretical model. In this article, we present the coarse-grained force field dedicated to glucopyranose-based carbohydrates and compatible with the recent version of the Martini force field (v. 3.0). The parameterization was based on optimizing bonded and nonbonded parameters with a reference to the all-atom simulation results and the experimental data. Application of the newly developed coarse-grained carbohydrate model to oligosaccharides curdlan and cellulose displays spontaneous formation of aggregates of experimentally identified features. In contact with other biomolecules, the model is capable of recovering the protective effect of glucose monosaccharides on a lipid bilayer and correctly identifying the binding pockets in carbohydrate-binding proteins. The features of the newly proposed model make it an excellent candidate for further extensions, aimed at modeling more complex, functionalized, and biologically relevant carbohydrates.
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Affiliation(s)
- Valery Lutsyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Pawel Wolski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland.,Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
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12
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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13
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Fadda E. Molecular simulations of complex carbohydrates and glycoconjugates. Curr Opin Chem Biol 2022; 69:102175. [PMID: 35728307 DOI: 10.1016/j.cbpa.2022.102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that carbohydrates cover is a direct consequence of the variety of 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging in sizes, and with the highest diversity of building blocks of any other natural biopolymer. Despite this unparalleled complexity, a common denominator can be found in the glycans' inherent flexibility, which hinders experimental characterization, but that can be addressed by high-performance computing (HPC)-based molecular simulations. In this short review, I present and discuss the state-of-the-art of molecular simulations of complex carbohydrates and glycoconjugates, highlighting methodological strengths and weaknesses, important insights through emblematic case studies, and suggesting perspectives for future developments.
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Affiliation(s)
- Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Ireland.
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14
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Poier PP. Variational Formulation of the Bond Capacity Charge Polarization Model. J Chem Phys 2022; 156:104101. [DOI: 10.1063/5.0082680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Lazar RD, Akher FB, Ravenscroft N, Kuttel MM. Carbohydrate Force Fields: The Role of Small Partial Atomic Charges in Preventing Conformational Collapse. J Chem Theory Comput 2022; 18:1156-1172. [PMID: 35015958 DOI: 10.1021/acs.jctc.1c00534] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although the quality of current additive all-atom force fields for carbohydrates has been demonstrated in many applications, occasional significant differences reported for the hydrodynamic behavior of specific polysaccharides modeled with different force fields is a cause for concern. In particular, irreversible conformational collapse has been noted for some polysaccharide simulations with the GLYCAM06j force field. Here, we investigate the cause of this phenomenon through comparative simulations of a range of saccharides with both the GLYCAM06j and the CHARMM36 carbohydrate force fields. We find that conformational collapse in GLYCAM06j occurs for saccharide chains containing the deoxy sugar α-l-rhamnose after relatively long simulation intervals. Further, we explore the mechanism of conformational collapse and show that this phenomenon arises because of the anomalous low energy in GLYCAM06j (as compared to quantum mechanical calculations) of a specific orientation of α-l-Rha to α-l-Rha glycosidic linkages, which are subsequently sustained by intramolecular interactions in the saccharide chain. We identify the lack of partial charges on aliphatic hydrogens in GLYCAM as the source of this anomaly, demonstrating that addition of small partial atomic charges on the aliphatic protons in rhamnose removes the conformational collapse phenomenon. This work reveals the large cumulative impact that small partial charges may have on the dynamic behavior of polysaccharides and indicates that future reparameterization of the GLYCAM06j force field should investigate the addition of partial charges on all aliphatic hydrogens.
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Affiliation(s)
- Ryan D Lazar
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Farideh B Akher
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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16
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Guvench O, Martin D, Greene M. Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins. Int J Mol Sci 2021; 23:473. [PMID: 35008898 PMCID: PMC8745717 DOI: 10.3390/ijms23010473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA; (D.M.); (M.G.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Devon Martin
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA; (D.M.); (M.G.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Megan Greene
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA; (D.M.); (M.G.)
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17
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Plazinski W, Roslund MU, Säwén E, Engström O, Tähtinen P, Widmalm G. Tautomers of N-acetyl-d-allosamine: an NMR and computational chemistry study. Org Biomol Chem 2021; 19:7190-7201. [PMID: 34382051 DOI: 10.1039/d1ob01139a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
d-Allosamine is a rare sugar in Nature but its pyranoid form has been found α-linked in the core region of the lipopolysaccharide from the Gram-negative bacterium Porphyromonas gingivalis and in the chitanase inhibitor allosamidin, then β-linked and N-acetylated. In water solution the monosaccharide N-acetyl-d-allosamine (d-AllNAc) shows a significant presence of four tautomers arising from pyranoid and furanoid ring forms and anomeric configurations. The furanoid ring forms both showed 3JH1,H2≈ 4.85 Hz and to differentiate the anomeric configurations a series of chemical shift anisotropy/dipole-dipole cross-correlated relaxation NMR experiments was performed in which the α-anomeric form showed notable different relaxation rates for its components of the H1 doublet, thereby making it possible to elucidate the anomeric configuration of each of the furanoses. The conformational preferences of the different forms of d-AllNAc were investigated by 3JHH, 2JCH and 3JCH coupling constants from NMR experiments, molecular dynamics simulations and density functional theory calculations. The pyranose form resides in the 4C1 conformation and the furanose ring form has the majority of its conformers located on the South-East region of the pseudorotation wheel, with a small population in the Northern hemisphere. The tautomeric equilibrium was quite sensitive to changes in temperature, where the β-anomer of the pyranoid ring form decreased upon a temperature increase while the other forms increased.
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Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
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18
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Gesteira TF, Marforio TD, Mueller JW, Calvaresi M, Coulson-Thomas VJ. Structural Determinants of Substrate Recognition and Catalysis by Heparan Sulfate Sulfotransferases. ACS Catal 2021; 11:10974-10987. [PMID: 37799563 PMCID: PMC10550706 DOI: 10.1021/acscatal.1c03088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Heparan sulfate (HS) and heparin contain imprinted "sulfation codes", which dictate their diverse physiological and pathological functions. A group of orchestrated biosynthetic enzymes cooperate in polymerizing and modifying HS chains. The biotechnological development of enzymes that can recreate this sulfation pattern on synthetic heparin is challenging, primarily due to the paucity of quantitative data for sulfotransferase enzymes. Herein, we identified critical structural characteristics that determine substrate specificity and shed light on the catalytic mechanism of sugar sulfation of two HS sulfotransferases, 2-O-sulfotransferase (HS2ST) and 6-O-sulfotransferase (HS6ST). Two sets of molecular clamps in HS2ST recognize appropriate substrates; these clamps flank the acceptor binding site on opposite sides. The hexuronic epimers, and not their puckers, have a critical influence on HS2ST selectivity. In contrast, HS6ST recognizes a broader range of substrates. This promiscuity is granted by a conserved tryptophan residue, W210, that positions the acceptor within the active site for catalysis by means of strong electrostatic interactions. Lysines K131 and K132 act in concert with a second tryptophan, W153, shedding water molecules from within the active site, thus providing HS6ST with a binding preference toward 2-O-sulfated substrates. QM/MM calculations provided valuable mechanistic insights into the catalytic process, identifying that the sulfation of both HS2ST and HS6ST follows a SN2-like mechanism. When they are taken together, our findings reveal the molecular basis of how these enzymes recognize different substrates and catalyze sugar sulfation, enabling the generation of enzymes that could create specific heparin epitopes.
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Affiliation(s)
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Bologna 40126, Italy
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, U.K
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Bologna 40126, Italy
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19
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Gieroba B, Kalisz G, Sroka-Bartnicka A, Płazińska A, Płaziński W, Starek M, Dąbrowska M. Molecular Structure of Cefuroxime Axetil Complexes with α-, β-, γ-, and 2-Hydroxypropyl-β-Cyclodextrins: Molecular Simulations and Raman Spectroscopic and Imaging Studies. Int J Mol Sci 2021; 22:ijms22105238. [PMID: 34063471 PMCID: PMC8156438 DOI: 10.3390/ijms22105238] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022] Open
Abstract
The formation of cefuroxime axetil+cyclodextrin (CA+CD) complexes increases the aqueous solubility of CA, improves its physico-chemical properties, and facilitates a biomembrane-mediated drug delivery process. In CD-based tablet formulations, it is crucial to investigate the molecular details of complexes in final pharmaceutical preparation. In this study, Raman spectroscopy and mapping were applied for the detection and identification of chemical groups involved in α-, β-, γ-, and 2-hydroxypropyl-β-CD (2-HP- β-CD)+CA complexation process. The experimental studies have been complemented by molecular dynamics-based investigations, providing additional molecular details of CA+CD interactions. It has been demonstrated that CA forms the guest–host type inclusion complexes with all studied CDs; however, the nature of the interactions is slightly different. It seems that both α- and β-CD interact with furanyl and methoxy moieties of CA, γ-CD forms a more diverse pattern of interactions with CA, which are not observed in other CDs, whereas 2HP-β-CD binds CA with the contribution of hydrogen bonding. Apart from supporting this interpretation of the experimental data, molecular dynamics simulations allowed for ordering the CA+CD binding affinities. The obtained results proved that the molecular details of the host–guest complexation can be successfully predicted from the combination of Raman spectroscopy and molecular modeling.
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Affiliation(s)
- Barbara Gieroba
- Department of Biopharmacy, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland; (G.K.); (A.S.-B.); (A.P.)
- Correspondence: (B.G.); (W.P.)
| | - Grzegorz Kalisz
- Department of Biopharmacy, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland; (G.K.); (A.S.-B.); (A.P.)
| | - Anna Sroka-Bartnicka
- Department of Biopharmacy, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland; (G.K.); (A.S.-B.); (A.P.)
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland
| | - Anita Płazińska
- Department of Biopharmacy, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland; (G.K.); (A.S.-B.); (A.P.)
| | - Wojciech Płaziński
- Jerzy Haber Institute of Catalysis and Surface Chemistry, ul. Niezapominajek 8, 30-239 Krakow, Poland
- Correspondence: (B.G.); (W.P.)
| | - Małgorzata Starek
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, ul. Medyczna 9, 30-688 Kraków, Poland; (M.S.); (M.D.)
| | - Monika Dąbrowska
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, ul. Medyczna 9, 30-688 Kraków, Poland; (M.S.); (M.D.)
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20
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Tang P, Liu Y, Gao Y, Wang Y, Zhang H, Liu Y, Wu D. Molecular simulation, characteristics and mechanism of thermal-responsive acetylated amylose V-type helical complexes. J Mater Chem B 2021; 9:3389-3400. [PMID: 33881436 DOI: 10.1039/d1tb00102g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To explore the thermal-responsive characteristics of acetylated amylose-guest V-type helical complexes (AAGHCs) and their potential use as thermal-responsive drug carriers, different types of AAGHCs were built, in which acetylated amylose was used as a host, and iodine, propofol, or hexane was utilized as the guest molecule. Their thermal-responsive characteristics were investigated through molecular dynamic (MD) simulation and corresponding experiments. MD simulation showed that the thermal-responsive helix-unfolding and guest-release behavior in AAGHCs, and the complete unfolding of AAGHC could be divided into brewing, triggering and collapsing periods. Energy analysis revealed that the Lana-Jones potential is an important binding energy that bridges host and guest molecules and enhances the stability of the helix. The various types or number of guests showed different binding energies. The stronger the binding energy, higher is the temperature required to trigger the unfolding of the helix and the releasing of guests. FT-IR and X-ray diffraction analyses confirmed the structures of AAGHCs. The change in hydrated size, and UV-VIS absorption of AAGHCs at high temperatures both confirmed the thermal-responsiveness of AAGHCs. The fluorescence fluctuation of loaded 7-hydroxycoumarin reflected the same thermal-responsive process and mechanism as MD simulation. This study provides meaningful theoretical guidance for the design of thermal-responsive drug carriers based on acetylated amylose-guest V-type helical complexes.
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Affiliation(s)
- Peng Tang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China.
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21
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Plazinska A, Plazinski W. Comparison of Carbohydrate Force Fields in Molecular Dynamics Simulations of Protein-Carbohydrate Complexes. J Chem Theory Comput 2021; 17:2575-2585. [PMID: 33703894 DOI: 10.1021/acs.jctc.1c00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this paper, we present the results of molecular dynamics simulations aimed at critical comparison of classical, biomolecular force fields (FFs) in the context of their capabilities to describe the structural and thermodynamic features of carbohydrate-protein interactions. We have considered the three main families of FFs (CHARMM, GROMOS, and GLYCAM/AMBER) by applying them to investigate the seven different carbohydrate-protein complexes. The results indicate that although the qualitative pattern of several structural descriptors (intermolecular hydrogen bonding, ligand dynamic location, etc.) is conserved among the compared FFs, there also exists a number of significant divergences (mainly the patterns of contacts between particular amino acid residues and bound carbohydrate). The carbohydrate-protein unbinding free energies also vary from one FF to another, displaying diversified trends in deviations from the experimental data. The magnitude of those deviations is not negligible and indicates the need for refinement in the currently existing combinations of carbohydrate- and protein-dedicated biomolecular force fields. In spite of the lack of explicit functional terms responsible for the corresponding intermolecular forces, all tested FFs are capable of adequately reproducing the CH-π interactions, crucial for carbohydrate-protein binding.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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22
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Yusupov M, Privat-Maldonado A, Cordeiro RM, Verswyvel H, Shaw P, Razzokov J, Smits E, Bogaerts A. Oxidative damage to hyaluronan-CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy. Redox Biol 2021; 43:101968. [PMID: 33895486 PMCID: PMC8099558 DOI: 10.1016/j.redox.2021.101968] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/20/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44-HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44-HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44-HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
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Affiliation(s)
- Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - Angela Privat-Maldonado
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal Do ABC, Avenida Dos Estados 5001, CEP 09210-580, Santo André, SP, Brazil
| | - Hanne Verswyvel
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Priyanka Shaw
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium; Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, Kori Niyoziy 39, 100000, Tashkent, Uzbekistan; Institute of Material Sciences, Uzbek Academy of Sciences, Chingiz Aytmatov 2b, 100084, Tashkent, Uzbekistan
| | - Evelien Smits
- Solid Tumor Immunology Group, Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
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23
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Miao L, Xu Y, Jia C, Zhang B, Niu M, Zhao S. Structural changes of rice starch and activity inhibition of starch digestive enzymes by anthocyanins retarded starch digestibility. Carbohydr Polym 2021; 261:117841. [PMID: 33766339 DOI: 10.1016/j.carbpol.2021.117841] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/21/2023]
Abstract
The effects of anthocyanins on in vitro and in vivo digestibility of rice starch were evaluated in this study. Then, the effects of anthocyanins on physicochemical properties of rice starch and on starch digestive enzymes (α-amylase and α-glucosidase) were investigated to understand the mechanism of the effects of anthocyanins on starch digestibility. Characterization of physicochemical properties of rice starch indicates a structural change due to the presence of anthocyanins, hindering its access to starch digestive enzymes. Besides, anthocyanins inhibited the activities of starch digestive enzymes by binding to their active sites, competing with the substrates and changing the secondary structure of the enzymes. The above stated changes of rice starch and starch digestive enzymes due to the presence of anthocyanins both contributed to retarding the digestibility of rice starch. This study could offer some theoretical guidance to the development of new type rice-based food with low glycemic index.
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Affiliation(s)
- Lange Miao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
| | - Yan Xu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
| | - Caihua Jia
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
| | - Binjia Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
| | - Meng Niu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
| | - Siming Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
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24
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Peesapati S, Sajeevan KA, Patel SK, Roy D. Relation between glycosidic linkage, structure and dynamics of α- and β-glucans in water. Biopolymers 2021; 112:e23423. [PMID: 33572006 DOI: 10.1002/bip.23423] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 11/09/2022]
Abstract
In a molecular dynamics simulation study of several oligosaccharides comprising of the very basic building block of carbohydrate, the α- or β-d glucopyranose units, linked by any one of the 1-3/1-4 or 1-6 glycosidic linkages, we compare and contrast their structural and dynamical properties. Results indicate that the litheness of the oligosaccharide chain is noticeably controlled by the composition, anomeric nature and glycosidic linkage type of the units. In mixed β 1-4/1-3 d-glucopyranosides, as those found in oats and barley, the ratio of the β 1-4 and β 1-3 linked residues is crucial in determining the structural and dynamical attributes. Principal component analysis (PCA) using the internal coordinates of torsion angles subtended by glycosidic oxygen atoms and subsequent K-means clustering of the dynamical space spanned by PC1 to PC2 point to the dynamical and structural disparity in the various types of oligosaccharides studied. The properties simulated in this work are meant to provide a systematic yet comparative understanding of the importance of linkage and anomericity on the oligosaccharide chain properties and are in line with some experimental structural attributes.
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Affiliation(s)
- Sruthi Peesapati
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
| | - Karuna Anna Sajeevan
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
| | - Siddhant Kumar Patel
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
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25
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Pedebos C, Smith IPS, Boags A, Khalid S. The hitchhiker's guide to the periplasm: Unexpected molecular interactions of polymyxin B1 in E. coli. Structure 2021; 29:444-456.e2. [PMID: 33577754 DOI: 10.1016/j.str.2021.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/11/2020] [Accepted: 01/21/2021] [Indexed: 12/19/2022]
Abstract
The periplasm of Gram-negative bacteria is a complex, highly crowded molecular environment. Little is known about how antibiotics move across the periplasm and the interactions they experience. Here, atomistic molecular dynamics simulations are used to study the antibiotic polymyxin B1 within models of the periplasm, which are crowded to different extents. We show that PMB1 is likely to be able to "hitchhike" within the periplasm by binding to lipoprotein carriers-a previously unreported passive transport route. The simulations reveal that PMB1 forms both transient and long-lived interactions with proteins, osmolytes, lipids of the outer membrane, and the cell wall, and is rarely uncomplexed when in the periplasm. Furthermore, it can interfere in the conformational dynamics of native proteins. These are important considerations for interpreting its mechanism of action and are likely to also hold for other antibiotics that rely on diffusion to cross the periplasm.
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Affiliation(s)
- Conrado Pedebos
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Iain Peter Shand Smith
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Alister Boags
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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26
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Hammond RG, Schormann N, McPherson RL, Leung AKL, Deivanayagam CCS, Johnson MA. ADP-ribose and analogues bound to the deMARylating macrodomain from the bat coronavirus HKU4. Proc Natl Acad Sci U S A 2021; 118:e2004500118. [PMID: 33397718 PMCID: PMC7812796 DOI: 10.1073/pnas.2004500118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Macrodomains are proteins that recognize and hydrolyze ADP ribose (ADPR) modifications of intracellular proteins. Macrodomains are implicated in viral genome replication and interference with host cell immune responses. They are important to the infectious cycle of Coronaviridae and Togaviridae viruses. We describe crystal structures of the conserved macrodomain from the bat coronavirus (CoV) HKU4 in complex with ligands. The structures reveal a binding cavity that accommodates ADPR and analogs via local structural changes within the pocket. Using a radioactive assay, we present evidence of mono-ADPR (MAR) hydrolase activity. In silico analysis presents further evidence on recognition of the ADPR modification for hydrolysis. Mutational analysis of residues within the binding pocket resulted in diminished enzymatic activity and binding affinity. We conclude that the common structural features observed in the macrodomain in a bat CoV contribute to a conserved function that can be extended to other known macrodomains.
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Affiliation(s)
- Robert G Hammond
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Norbert Schormann
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287
| | - Champion C S Deivanayagam
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Margaret A Johnson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294;
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27
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Schahl A, Gerber IC, Réat V, Jolibois F. Diversity of the Hydrogen Bond Network and Its Impact on NMR Parameters of Amylose B Polymorph: A Study Using Molecular Dynamics and DFT Calculations Within Periodic Boundary Conditions. J Phys Chem B 2020; 125:158-168. [PMID: 33356276 DOI: 10.1021/acs.jpcb.0c08631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Classical molecular dynamics simulations have been combined with quantum (DFT) calculations of 13C NMR parameters in order to relate the experimental spectrum of the double-helix form of the amylose B-polymorph in highly crystalline conditions not only to its 3D structure but also to the arrangement of atoms in the crystal lattice. Structures obtained from these simulations or from geometry optimization procedures at the DFT level have shown the presence of hydrogen bond networks between sugars of the same helix or between residues of the two chains of the double helix. 13C NMR parameter calculations have revealed the impact of such a network on the chemical shifts of carbon atoms. In addition, DFT calculations using periodic boundary conditions were compulsory to highlight the presence of two types of sugar within the crystal sample. It allows us to confirm, theoretically, the experimental hypothesis that the existence of two distinct sugar types in the NMR spectrum is a consequence of crystal packing.
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Affiliation(s)
- Adrien Schahl
- LPCNO, CNRS UMR 5215, Université de Toulouse-INSA-UPS, 135 av. Rangueil, F-31077 Toulouse, France.,Institut de Pharmacologie et Biologie Structurale, UMR 5089, CNRS-Université de Toulouse-UPS BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex 04, France
| | - Iann C Gerber
- LPCNO, CNRS UMR 5215, Université de Toulouse-INSA-UPS, 135 av. Rangueil, F-31077 Toulouse, France
| | - Valérie Réat
- Institut de Pharmacologie et Biologie Structurale, UMR 5089, CNRS-Université de Toulouse-UPS BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex 04, France
| | - Franck Jolibois
- LPCNO, CNRS UMR 5215, Université de Toulouse-INSA-UPS, 135 av. Rangueil, F-31077 Toulouse, France
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28
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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29
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Sandilya A, Natarajan U, Priya MH. Molecular View into the Cyclodextrin Cavity: Structure and Hydration. ACS OMEGA 2020; 5:25655-25667. [PMID: 33073091 PMCID: PMC7557249 DOI: 10.1021/acsomega.0c02760] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/14/2020] [Indexed: 05/21/2023]
Abstract
We find, through atomistic molecular dynamics simulation of native cyclodextrins (CDs) in water, that although the outer surface of a CD appears like a truncated cone, the inner cavity resembles a conical hourglass because of the inward protrusion of the glycosidic oxygens. Furthermore, the conformations of the constituent α-glucose molecules are found to differ significantly from a free monomeric α-glucose molecule. This is the first computational study that maps the conformational change to the preferential hydrogen bond donating capacity of one of the secondary hydroxyl groups of CD, in consensus with an NMR experiment. We have developed a simple and novel geometry-based technique to identify water molecules occupying the nonspherical CD cavity, and the computed water occupancies are in close agreement with the experimental and density functional theory studies. Our analysis reveals that a water molecule in CD cavity loses out about two hydrogen bonds and remains energetically frustrated but possesses higher orientational degree of freedom compared to bulk water. In the context of CD-drug complexation, these imply a nonclassical, that is, enthalpically driven hydrophobic association of a drug in CD cavity.
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Affiliation(s)
- Avilasha
A. Sandilya
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Upendra Natarajan
- Department
of Chemical Engineering, Indian Institute
of Technology Madras, Chennai 600036, India
| | - M. Hamsa Priya
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- . Phone: +91-44-22574132
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30
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Pieczywek PM, Płaziński W, Zdunek A. Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations. Sci Rep 2020; 10:14691. [PMID: 32895471 PMCID: PMC7477560 DOI: 10.1038/s41598-020-71820-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/19/2020] [Indexed: 12/23/2022] Open
Abstract
In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.
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Affiliation(s)
- P M Pieczywek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-270, Lublin, Poland.
| | - W Płaziński
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Cracow, Poland
| | - A Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-270, Lublin, Poland
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31
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Nester K, Plazinski W. Deciphering the conformational preferences of furanosides. A molecular dynamics study. J Biomol Struct Dyn 2020; 38:3359-3370. [DOI: 10.1080/07391102.2019.1656670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
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32
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Poier PP, Jensen F. Polarizable charges in a generalized Born reaction potential. J Chem Phys 2020; 153:024111. [DOI: 10.1063/5.0012022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Pier Paolo Poier
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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33
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Pieczywek P, Kozioł A, Płaziński W, Cybulska J, Zdunek A. Resolving the nanostructure of sodium carbonate extracted pectins (DASP) from apple cell walls with atomic force microscopy and molecular dynamics. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2020.105726] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Nester K, Plazinski W. Conformational properties of inulin, levan and arabinan studied by molecular dynamics simulations. Carbohydr Polym 2020; 240:116266. [PMID: 32475556 DOI: 10.1016/j.carbpol.2020.116266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
Inulin, levan and arabinan are the polysaccharides that consist of exclusively furanose units. To date, their conformational features studied at the molecular scale have remained largely unexplained. To tackle this issue, we have performed a series of explicit-solvent molecular dynamics simulations, carried out within the furanose-dedicated force field. None of the polysaccharides exhibits a single, dominating structure type. Instead, they create a large number of separated conformational states originating from the intensive rotation around the φ and ω glycosidic angles. 21-helices are the preferential conformational forms for all compounds but they appear only locally, at the length of several consecutive residues. The flexibility of all three furanose-based polysaccharides is much greater in relation to the (1-4)-linked pyranose polysaccharides and is comparable to that of (1-6)-linked pyranoses. The dynamic geometries of both furanose rings and glycosidic linkages are nearly unchanged independently if considering them at the level of mono-, di- or polysaccharides.
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Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Ul. Niezapominajek 8, 30-239 Cracow, Poland.
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35
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Ferreira RJ, Kasson PM. Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics. ACS Infect Dis 2019; 5:2096-2104. [PMID: 31593635 DOI: 10.1021/acsinfecdis.9b00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crossing the Gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay of outer membrane vesicle swelling. Parallel molecular dynamics simulations of compound uptake through Escherichia coli (E. coli) OmpF are used to successfully and quantitatively predict experimental permeabilities measured via either outer membrane swelling or prior liposome-swelling measurements. These simulations are analyzed using an inhomogeneous solubility-diffusion model to yield predictions of permeability. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer membrane permeability.
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Affiliation(s)
- Ricardo J. Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Peter M. Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Departments of Biomedical Engineering and Molecular Physiology and Biological Physics, University of Virginia, Box 800886, Charlottesville, Virginia 22908, United States
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36
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Alibay I, Bryce RA. Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:4729-4741. [PMID: 31609614 DOI: 10.1021/acs.jcim.9b00529] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformational flexibility of the glycosaminoglycans (GAGs) is known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucuronate and iduronate. These calculations indicate that in some cases, an excess of 15 μs is required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm-enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for 15 further monosaccharides related to GAGs; this includes to our knowledge the first simulation study of sulfation effects on β-GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of β-GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the 1C4 ring conformation; this observation may have implications for understanding the structural basis of the biological function of β-GalNAc-containing glycosaminoglycans such as dermatan sulfate.
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Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K.,Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K
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37
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Koneru JK, Zhu X, Mondal J. Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields. J Chem Theory Comput 2019; 15:6203-6212. [DOI: 10.1021/acs.jctc.9b00630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jaya Krishna Koneru
- Tata Institute of Fundamental Research, Centre For Interdisciplinary Sciences, Hyderabad 500107, India
| | - Xiao Zhu
- Department of Agricultural and Biological Engineering, Research Computing, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Centre For Interdisciplinary Sciences, Hyderabad 500107, India
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38
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Poier PP, Lagardère L, Piquemal JP, Jensen F. Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model. J Chem Theory Comput 2019; 15:6213-6224. [DOI: 10.1021/acs.jctc.9b00721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Pier Paolo Poier
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Louis Lagardère
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, 75005, Paris, France
- Sorbonne Université, Institut des Sciences du Calcul et des Données, 75005, Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, 75005, Paris, France
- Sorbonne Université, Institut Universitaire de France, 75005, Paris, France
- University of Texas, Department of Biomedical Engineering, Austin, Texas, United States
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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39
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Pandey P, Aytenfisu AH, MacKerell AD, Mallajosyula SS. Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives. J Chem Theory Comput 2019; 15:4982-5000. [PMID: 31411469 PMCID: PMC6852669 DOI: 10.1021/acs.jctc.9b00327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of d-glucuronate, l-iduronate, N-acetyl-d-glucosamine (GlcNAc), and N-acetyl-d-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of d-glucuronate and N-acetyl-d-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.
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Affiliation(s)
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
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40
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Cheng L, Zhu X, Hamaker BR, Zhang H, Campanella OH. Complexation process of amylose under different concentrations of linoleic acid using molecular dynamics simulation. Carbohydr Polym 2019; 216:157-166. [DOI: 10.1016/j.carbpol.2019.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 02/09/2023]
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41
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Dayhoff GW, Rogers DM. Hydration and Dispersion Forces in Hydroxypropylcellulose Phase Behavior. J Phys Chem B 2019; 123:4976-4985. [PMID: 31082228 DOI: 10.1021/acs.jpcb.9b01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many-body polarization and hydration forces can strongly affect the equilibrium structure and energetics of mixed phases. Accurately reproducing both forces presents a challenge to force field models because it requires balancing hydrogen bonding at short range with many-body orientational order and dispersive attraction at long range. This work reports the first comparison of experimental measurements of the pressure-area isotherm for hydroxypropylcellulose (HPC) against molecular dynamics results with four different force field models-united-atom, all-atom (OPLS and CHARMM), and Drude oscillator models. All force fields exhibit the experimentally determined, exponentially shaped repulsive force at short range. Above a critical temperature of about 40 °C and a lattice spacing of around 14 Å, HPC experiments show a reversible, heat-induced polymer aggregation into an ordered phase driven by loss of water. The nonpolarizable force fields do not display the critical point and instead show biphasic behavior at all temperatures tested. This indicates net attractive forces at intermediate lattice spacings. In contrast, the Drude polarizable force field shows positive osmotic pressure and a single, homogeneous phase over all temperatures and spacings tested. Analysis of structural data from our simulations provides several clues to help interpret these findings. Although all force fields show similar water-water hydrogen bond numbers in the mixed phase, the polarizable model predicts that water-HPC hydrogen bonds are much more favorable than HPC-HPC hydrogen bonds when polymers are dispersed. At high density, water is driven out and replaced by HPC-HPC hydrogen bonds. The polarizable force field shows that both effects have a stronger dependence on polymer density than any of the nonpolarizable models. Our observations support the conclusion that hydration forces are coupled to the polymer coordination number by local, structural waters and that long-range dispersive attraction is overestimated by pairwise additive models.
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Affiliation(s)
- Guy W Dayhoff
- Department of Chemistry , University of South Florida , Tampa 33620 , United States
| | - David M Rogers
- Department of Chemistry , University of South Florida , Tampa 33620 , United States
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42
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Fierro F, Giorgetti A, Carloni P, Meyerhof W, Alfonso-Prieto M. Dual binding mode of "bitter sugars" to their human bitter taste receptor target. Sci Rep 2019; 9:8437. [PMID: 31186454 PMCID: PMC6560132 DOI: 10.1038/s41598-019-44805-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
The 25 human bitter taste receptors (hTAS2Rs) are responsible for detecting bitter molecules present in food, and they also play several physiological and pathological roles in extraoral compartments. Therefore, understanding their ligand specificity is important both for food research and for pharmacological applications. Here we provide a molecular insight into the exquisite molecular recognition of bitter β-glycopyranosides by one of the members of this receptor subclass, hTAS2R16. Most of its agonists have in common the presence of a β-glycopyranose unit along with an extremely structurally diverse aglycon moiety. This poses the question of how hTAS2R16 can recognize such a large number of "bitter sugars". By means of hybrid molecular mechanics/coarse grained molecular dynamics simulations, here we show that the three hTAS2R16 agonists salicin, arbutin and phenyl-β-D-glucopyranoside interact with the receptor through a previously unrecognized dual binding mode. Such mechanism may offer a seamless way to fit different aglycons inside the binding cavity, while maintaining the sugar bound, similar to the strategy used by several carbohydrate-binding lectins. Our prediction is validated a posteriori by comparison with mutagenesis data and also rationalizes a wealth of structure-activity relationship data. Therefore, our findings not only provide a deeper molecular characterization of the binding determinants for the three ligands studied here, but also give insights applicable to other hTAS2R16 agonists. Together with our results for other hTAS2Rs, this study paves the way to improve our overall understanding of the structural determinants of ligand specificity in bitter taste receptors.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- Department of Biotechnology, University of Verona, Verona, Italy
- JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
- VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Wolfgang Meyerhof
- Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany.
- JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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Turupcu A, Diem M, Smith LJ, Oostenbrink C. Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments. Chemphyschem 2019; 20:1527-1537. [PMID: 30920077 PMCID: PMC6563056 DOI: 10.1002/cphc.201900079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/27/2019] [Indexed: 11/26/2022]
Abstract
A powerful conformational searching and enhanced sampling simulation method, and unbiased molecular dynamics simulations have been used along with NMR spectroscopic observables to provide a detailed structural view of O-glycosylation. For four model systems, the force-field parameters can accurately predict experimental NMR observables (J couplings and NOE's). This enables us to derive conclusions based on the generated ensembles, in which O-glycosylation affects the peptide backbone conformation by forcing it towards to an extended conformation. An exception is described for β-GalNAc-Thr where the α content is increased and stabilized via hydrogen bonding between the sugar and the peptide backbone, which was not observed in the rest of the studied systems. These observations might offer an explanation for the evolutionary preference of α-linked GalNAc glycosylation instead of a β link.
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Affiliation(s)
- Aysegül Turupcu
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Matthias Diem
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | | | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
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Poier PP, Jensen F. Describing Molecular Polarizability by a Bond Capacity Model. J Chem Theory Comput 2019; 15:3093-3107. [PMID: 30920212 DOI: 10.1021/acs.jctc.8b01215] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a bond capacity model for describing molecular polarization in force field energy functions at the charge-only level. Atomic charges are calculated by allowing charge to flow between atom pairs according to a bond capacity and a difference in electrostatic potential. The bond capacity is closely related to the bond order and decays to zero as the bond distance is increased. The electrostatic potential is composed of an intrinsic potential, identified as the electronegativity, and a screened Coulomb potential from all other charges. The bond capacity model leads to integer fragment charges upon bond dissociation and displays linear scaling of the polarizability with system size. Bond capacity parameters can be derived from reference molecular polarizabilities, while electronegativity parameters can be derived from reference atomic charges or a reference molecular electrostatic potential. Out-of-plane polarization for planar systems is modeled by off-nuclei charge sites. The model is shown to be able to reproduce anisotropic reference molecular polarizabilities with an accuracy of ∼10% using a limited set of bond capacity parameters and can describe both inter- and intramolecular polarization.
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Affiliation(s)
- Pier Paolo Poier
- Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus , Denmark
| | - Frank Jensen
- Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus , Denmark
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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NMR solution geometry of saccharides containing the 6-O-(α-D-glucopyranosyl)-α/β-D-glucopyranose (isomaltose) or 6-O-(α-D-galactopyranosyl)-α/β-D-glucopyranose (melibiose) core. Carbohydr Res 2019; 473:18-35. [DOI: 10.1016/j.carres.2018.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022]
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Tautomeric and epimeric equilibria of aldo- and ketohexoses studied by the MD simulations and QM calculations. Carbohydr Res 2019; 474:8-15. [DOI: 10.1016/j.carres.2019.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/17/2022]
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Nester K, Gaweda K, Plazinski W. A GROMOS Force Field for Furanose-Based Carbohydrates. J Chem Theory Comput 2019; 15:1168-1186. [DOI: 10.1021/acs.jctc.8b00838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
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Cheng L, Feng T, Zhang B, Zhu X, Hamaker B, Zhang H, Campanella O. A molecular dynamics simulation study on the conformational stability of amylose-linoleic acid complex in water. Carbohydr Polym 2018; 196:56-65. [DOI: 10.1016/j.carbpol.2018.04.102] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/21/2018] [Accepted: 04/26/2018] [Indexed: 10/17/2022]
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