1
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J N C, Guvench O, MacKerell AD, Yamaguchi T, Mallajosyula SS. Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy. J Chem Theory Comput 2024. [PMID: 39383338 DOI: 10.1021/acs.jctc.4c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
Abstract
We present a revised version of the Drude polarizable carbohydrate force field (FF), focusing on refining the ring and exocyclic torsional parameters for hexopyranose monosaccharides. This refinement addresses the previously observed discrepancies between calculated and experimental NMR 3J coupling values, particularly in describing ring dynamics and exocyclic rotamer populations within major hexose monosaccharides and their anomers. Specifically, α-MAN, β-MAN, α-GLC, β-GLC, α-GAL, β-GAL, α-ALT, β-ALT, α-IDO, and β-IDO were targeted for optimization. The optimization process involved potential energy scans (PES) of the ring and exocyclic dihedral angles computed using quantum mechanical (QM) methods. The target data for the reoptimization included PES of the inner ring dihedrals (C1-C2-C3-C4, C2-C3-C4-C5, C5-O5-C1-C2, C4-C5-O5-C1, O5-C1-C2-C3, C3-C4-C5-O5) and the exocyclic torsions, other than the pseudo ring dihedrals (O1-C1-O5-C5, O2-C2-C1-O5, and O4-C4-C5-O5) and hydroxyl torsions used in the previous parametrization efforts. These parameters, in conjunction with previously developed Drude parameters for hexopyranose monosaccharides, were validated against experimental observations, including NMR data and conformational energetics, in aqueous environments. The resulting polarizable model is shown to be in good agreement with a range of QM data, experimental NMR data, and conformational energetics of monosaccharides in aqueous solutions. This offers a significant improvement of the Drude carbohydrate force field, wherein the refinement enhances the accuracy of accessing the conformational dynamics of carbohydrates in biomolecular simulations.
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Affiliation(s)
- Chythra J N
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat India - 382355
| | - Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, University of New England, 716 Stevens Avenue, Portland, Maine 04103, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Takumi Yamaguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat India - 382355
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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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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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6
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Yang W, Chen Y, Li K, Jin W, Zhang Y, Liu Y, Ren Z, Li Y, Chen P. Optimization of microwave-expanding pretreatment and microwave-assisted extraction of hemicellulose from bagasse cells with the exploration of the extracting mechanism. Carbohydr Polym 2024; 330:121814. [PMID: 38368097 DOI: 10.1016/j.carbpol.2024.121814] [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: 07/20/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 02/19/2024]
Abstract
Hemicellulose is mainly distributed in the tightly packed S2 layer of the plant cell wall and the middle lamella. This rigid microstructure of wood and interactions among hemicellulose, lignin, and cellulose jointly restrict the separation and transformation of hemicellulose in the wood matrix. To address this issue, a method combined with microwave-expanding pretreatment (MEP) and microwave-assisted extraction (MAE) with a NaOH solution was carried out. We found that the MEP could effectively create new pathways for bagasse cells in mass transferring. More specifically, 195 % of the specific surface area (m2/g) with 193 % of the pores (>50 nm) increased after MEP; the SEM images also confirmed that the microstructure of bagasse was modified. MAE could considerably exfoliate hemicellulose from cellulose fiber and accelerate mass transfer. Additionally, we optimized MEP and MAE by using response surface methodology (RSM). The optimal parameters were 370 K, 3.7 min, 1081 W microwave power, and 9.9 wt% NH4HCO3 consumption for the MEP and 1100 W microwave power, 2.5 wt% NaOH concentration, 34.6 min reaction time for MAE, respectively. Moreover, molecular dynamics (MD) simulation suggests that NaOH could significantly lower the work needed to peel off the xylan chain from cellulose nanofibril.
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Affiliation(s)
- Wenjin Yang
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China
| | - Yu Chen
- School of Materials Science & Engineering, Beijing Institute of Technology, 100081, Beijing, China
| | - Kai Li
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China
| | - Wen Jin
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China
| | - Ya Zhang
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China
| | - Yuxin Liu
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China.
| | - Zixing Ren
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China
| | - Yuke Li
- Faculty of Chemical Engineering, Kunming University of Science and Technology, 650500, Kunming, China
| | - Pan Chen
- School of Materials Science & Engineering, Beijing Institute of Technology, 100081, Beijing, China.
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7
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Angelescu DG. Molecular modeling of the carbohydrate corona formation on a polyvinyl chloride nanoparticle and its impact on the adhesion to lipid bilayers. J Chem Phys 2024; 160:144901. [PMID: 38591687 DOI: 10.1063/5.0198254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
The pervasive presence of nanoplastics (NPs) in the environment has gained increasing attention due to their accumulation in living organisms. These emerging contaminants inevitably interact with extracellular polymeric substances along respiratory or gastrointestinal tracts, and diverse organic coating on the surface of NPs, known as bio- or eco-corona, is formed. Although its impact on altering the NP properties and potential cell internalization has been extensively examined, studies on its role in NP partitioning in the cell membrane are elusive yet. In this work, molecular dynamics is used to investigate the formation of chitosan (CT) corona centered on a polyvinyl chloride (PVC) nanoparticle and the uptake of the resulting complex onto lipid membranes. Coarse-grained models compatible with the newly developed Martini 3.0 force field are implemented for the two polymers employing the atomistic properties as targets in the parameterization. The reliability of the coarse-grained polymer models is demonstrated by reproducing the structural properties of the PVC melt and of solvated CT strands, as well as by determining the conformation adopted by the latter at the NP surface. Results show that the spontaneous binding of CT chains of high and intermediate protonation degrees led to the formation of soft and hard corona that modulates the interaction of PVC core with model membranes. The structural changes of the corona adsorbed at the lipid-water interface enable a subsequent transfer of the NP to the center of the saturated lipid membranes and a complete or partial transition to a snorkel conformation depending on the hydrophilic/hydrophobic balance in the CT-PVC complex. Overall, the computational investigation of the coarse-grained model system provides implications for understanding how the eco-corona development influences the uptake and implicit toxicology of NPs.
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Affiliation(s)
- Daniel G Angelescu
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania
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8
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Wu Z, Collins AM, Jayaraman A. Understanding Self-Assembly and Molecular Packing in Methylcellulose Aqueous Solutions Using Multiscale Modeling and Simulations. Biomacromolecules 2024; 25:1682-1695. [PMID: 38417021 DOI: 10.1021/acs.biomac.3c01209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
We present a multiscale molecular dynamics (MD) simulation study on self-assembly in methylcellulose (MC) aqueous solutions. First, using MD simulations with a new coarse-grained (CG) model of MC chains in implicit water, we establish how the MC chains self-assemble to form fibrils and fibrillar networks and elucidate the MC chains' packing within the assembled fibrils. The CG model for MC is extended from a previously developed model for unsubstituted cellulose and captures the directionality of H-bonding interactions between the -OH groups. The choice and placement of the CG beads within each monomer facilitates explicit modeling of the exact degree and position of methoxy substitutions in the monomers along the MC chain. CG MD simulations show that with increasing hydrophobic effect and/or increasing H-bonding strength, the commercial MC chains (with degree of methoxy substitution, DS, ∼1.8) assemble from a random dispersed configuration into fibrils. The assembled fibrils exhibit consistent fibril diameters regardless of the molecular weight and concentration of MC chains, in agreement with past experiments. Most MC chains' axes are aligned with the fibril axis, and some MC chains exhibit twisted conformations in the fibril. To understand the molecular driving force for the twist, we conduct atomistic simulations of MC chains preassembled in fibrils (without any chain twists) in explicit water at 300 and 348 K. These atomistic simulations also show that at DS = 1.8, MC chains adopt twisted conformations, with these twists being more prominent at higher temperatures, likely as a result of shielding of hydrophobic methyl groups from water. For MC chains with varying DS, at 348 K, atomistic simulations show a nonmonotonic effect of DS on water-monomer contacts. For 0.0 < DS < 0.6, the MC monomers have more water contacts than at DS = 0.0 or DS > 0.6, suggesting that with few methoxy substitutions, the MC chains are effectively hydrophilic, letting the water molecules diffuse into the fibril to participate in H-bonds with the MC chains' remaining -OH groups. At DS > 0.6, the MC monomers become increasingly hydrophobic, as seen by decreasing water contacts around each monomer. We conclude based on the atomistic observations that MC chains with lower degrees of substitutions (DS ≤ 0.6) should exhibit solubility in water over broader temperature ranges than DS ∼ 1.8 chains.
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Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Audrey M Collins
- Department of Chemistry and Biochemistry, University of Delaware, 102 Brown Laboratory, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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9
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Xi S, Ban X, Kong H, Li C, Gu Z, Li Z. Conserved residues at the family and subfamily levels determine enzyme activity and substrate binding in glycoside hydrolase family 13. Int J Biol Macromol 2023; 253:126980. [PMID: 37729992 DOI: 10.1016/j.ijbiomac.2023.126980] [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: 05/11/2023] [Revised: 08/24/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023]
Abstract
Site-directed mutagenesis is a valuable strategy for modifying enzymes, but the lack of understanding of conserved residues regulating glycosidase function hinders enzyme design. We analyzed 1662 enzyme sequences to identify conserved amino acids in maltohexaose-forming amylase at both family and subfamily levels. Several conserved residues at the family level (G37, P45, R52, Y57, D101, V103, H106, G230, R232, D234, E264, H330, D331, and G360) were found, mutations of which resulted in reduced enzyme activity or inactivation. At the subfamily level, several conserved residues (L65, E67, F68, D111, E114, R126, R147, F154, W156, F161, G163, D165, W218H, V342, W345, and F346) were identified, which primarily facilitate substrate binding in the enzyme's active site, as shown by molecular dynamics and kinetic assays. Our findings provide critical insights into conserved residues essential for catalysis and can inform targeted enzyme design in protein engineering.
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Affiliation(s)
- Shixia Xi
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Haocun Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China.
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10
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Gracia Carmona O, Oostenbrink C. Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling. J Chem Theory Comput 2023; 19:6521-6531. [PMID: 37649349 PMCID: PMC10536968 DOI: 10.1021/acs.jctc.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Indexed: 09/01/2023]
Abstract
Molecular dynamics simulations often struggle to obtain sufficient sampling to study complex molecular events due to high energy barriers separating the minima of interest. Multiple enhanced sampling techniques have been developed and improved over the years to tackle this issue. Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that works by adding a biasing potential, lifting the energy landscape up, and decreasing the height of its barriers. GaMD allows one to increase the sampling of events of interest without the need of a priori knowledge of the system or the relevant coordinates. All required acceleration parameters can be obtained from a previous search run. Upon its development, several improvements for the methodology have been proposed, among them selective GaMD in which the boosting potential is selectively applied to the region of interest. There are currently four selective GaMD methods that have shown promising results. However, all of these methods are constrained on the number, location, and scenarios in which this selective boosting potential can be applied to ligands, peptides, or protein-protein interactions. In this work, we showcase a GROMOS implementation of the GaMD methodology with a fully flexible selective GaMD approach that allows the user to define, in a straightforward way, multiple boosting potentials for as many regions as desired. We show and analyze the advantages of this flexible selective approach on two previously used test systems, the alanine dipeptide and the chignolin peptide, and extend these examples to study its applicability and potential to study conformational changes of glycans and glycosylated proteins.
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Affiliation(s)
- Oriol Gracia Carmona
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna. Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna. Muthgasse 18, 1190 Vienna, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna. Muthgasse 18, 1190 Vienna, Austria
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11
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Tian Y, Kong H, Ban X, Li C, Gu Z, Li Z. Distribution of Aromatic Amino Acid Residues in Substrate-Binding Regions Modulates Substrate Specificity of Microbial Debranching Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37463425 DOI: 10.1021/acs.jafc.3c02979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Debranching enzymes (DBEs) directly hydrolyze α-1,6-glucosidic linkages in glycogen, starch, and related polysaccharides, making them important in the starch processing industry. However, the ambiguous substrate specificity usually restricts synergistic catalysis with other amylases for improving starch utilization. Herein, a glycogen-debranching enzyme from Saccharolobus solfataricus (SsGDE) and two isoamylases from Pseudomonas amyloderamosa (PaISO) and Chlamydomonas reinhardtii (CrISO) were used to investigate the molecular mechanism of substrate specificity. Along with the structure-based computational analysis, the aromatic residues in the substrate-binding region of DBEs played an important role in binding substrates. The aromatic residues in SsGDE appeared clustered, contributing to a small substrate-binding region. In contrast, the aromatic residues in isoamylase were distributed dispersedly, forming a large active site. The distinct characteristics of substrate-binding regions in SsGDE and isoamylase might explain their substrate preferences for maltodextrin and amylopectin, respectively. By modulating the substrate-binding region of SsGDE, variants Y323F and V375F were obtained with significantly enhanced activities, and the activities of Y323F and V375F increased by 30 and 60% for amylopectin, and 20 and 23% for DE4 maltodextrin, respectively. This study revealed the molecular mechanisms underlying the substrate specificity for SsGDE and isoamylases, providing a route for engineering enzymes to achieve higher catalytic performance.
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Affiliation(s)
- Yixiong Tian
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
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12
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Solhi L, Guccini V, Heise K, Solala I, Niinivaara E, Xu W, Mihhels K, Kröger M, Meng Z, Wohlert J, Tao H, Cranston ED, Kontturi E. Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset. Chem Rev 2023; 123:1925-2015. [PMID: 36724185 PMCID: PMC9999435 DOI: 10.1021/acs.chemrev.2c00611] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.
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Affiliation(s)
- Laleh Solhi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Valentina Guccini
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Katja Heise
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Iina Solala
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Elina Niinivaara
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - Wenyang Xu
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Laboratory of Natural Materials Technology, Åbo Akademi University, TurkuFI-20500, Finland
| | - Karl Mihhels
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Marcel Kröger
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Zhuojun Meng
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou325001, China
| | - Jakob Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10044Stockholm, Sweden
| | - Han Tao
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Emily D Cranston
- Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Eero Kontturi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
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13
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Chen Y, Nishiyama Y, Lu A, Fang Y, Shao Z, Hu T, Ye D, Qi H, Li X, Wohlert J, Chen P. The thermodynamics of enhanced dope stability of cellulose solution in NaOH solution by urea. Carbohydr Polym 2023; 311:120744. [PMID: 37028854 DOI: 10.1016/j.carbpol.2023.120744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/07/2023]
Abstract
The addition of urea in pre-cooled alkali aqueous solution is known to improve the dope stability of cellulose solution. However, its thermodynamic mechanism at a molecular level is not fully understood yet. By using molecular dynamics simulation of an aqueous NaOH/urea/cellulose system using an empirical force field, we found that urea was concentrated in the first solvation shell of the cellulose chain stabilized mainly by dispersion interaction. When adding a glucan chain into the solution, the total solvent entropy reduction is smaller if urea is present. Each urea molecule expelled an average of 2.3 water molecules away from the cellulose surface, releasing water entropy that over-compensates the entropy loss of urea and thus maximizing the total entropy. Scaling the Lennard-Jones parameter and atomistic partial charge of urea revealed that direct urea/cellulose interaction was also driven by dispersion energy. The mixing of urea solution and cellulose solution in the presence or absence of NaOH are both exothermic even after correcting for the contribution from dilution.
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Affiliation(s)
- Yu Chen
- Beijing Engineering Research Centre of Cellulose and Its Derivatives, School of Materials Science and Engineering, Beijing Institute of Technology, 100081 Beijing, PR China
| | | | - Ang Lu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yan Fang
- Fujian Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, Fujian 350007, PR China
| | - Ziqiang Shao
- Beijing Engineering Research Centre of Cellulose and Its Derivatives, School of Materials Science and Engineering, Beijing Institute of Technology, 100081 Beijing, PR China
| | - Tao Hu
- School of Materials Science and Engineering, State Key Laboratory of Advanced Special Steels, Shanghai University, Shanghai 200444, China
| | - Dongdong Ye
- School of Textile Materials and Engineering, Wuyi University, Jiangmen 529020, PR China
| | - Haisong Qi
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Xiaodong Li
- School of Materials Science and Engineering, Beijing Institute of Technology, 100081 Beijing, PR China
| | - Jakob Wohlert
- Wallenberg Wood Science Center, Department of Fiber and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, SE-10044 Stockholm, Sweden.
| | - Pan Chen
- Beijing Engineering Research Centre of Cellulose and Its Derivatives, School of Materials Science and Engineering, Beijing Institute of Technology, 100081 Beijing, PR China.
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14
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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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15
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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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16
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Walker B, Liu C, Wait E, Ren P. Automation of AMOEBA polarizable force field for small molecules: Poltype 2. J Comput Chem 2022; 43:1530-1542. [PMID: 35778723 PMCID: PMC9329217 DOI: 10.1002/jcc.26954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022]
Abstract
A next-generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using SMILES, robust torsion fitting, non-aromatic ring torsion parameterization, coupled torsion-torsion parameterization, Van der Waals parameter refinement using ab initio dimer data and an intelligent fragmentation scheme that produces parameters with dramatically reduced ab initio computational cost. Additional improvements include better local frame assignment for atomic multipoles, automated formal charge assignment, Zwitterion detection, smart memory resource defaults, parallelized fragment job submission, incorporation of Psi4 quantum package, ab initio error handling, ionization state enumeration, hydration free energy prediction and binding free energy prediction. For validation, we have applied Poltype 2 to ~1000 FDA approved drug molecules from DrugBank. The ab initio molecular dipole moments and electrostatic potential values were compared with Poltype 2 derived AMOEBA counterparts. Parameters were further substantiated by calculating hydration free energy (HFE) on 40 small organic molecules and were compared with experimental data, resulting in an RMSE error of 0.59 kcal/mol. The torsion database has expanded to include 3543 fragments derived from FDA approved drugs. Poltype 2 provides a convenient utility for applications including binding free energy prediction for computational drug discovery. Further improvement will focus on automated parameter refinement by experimental liquid properties, expansion of the Van der Waals parameter database and automated parametrization of modified bio-fragments such as amino and nucleic acids.
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Affiliation(s)
- Brandon Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Elizabeth Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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17
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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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18
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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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19
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Kolaříková A, Kutálková E, Buš V, Witasek R, Hrnčiřík J, Ingr M. Salt-dependent intermolecular interactions of hyaluronan molecules mediate the formation of temporary duplex structures. Carbohydr Polym 2022; 286:119288. [DOI: 10.1016/j.carbpol.2022.119288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/02/2022]
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20
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Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations. J Biomol Struct Dyn 2022; 41:3305-3320. [PMID: 35262462 DOI: 10.1080/07391102.2022.2047109] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the current study, we have investigated the conformational dynamics of a triantennary (N-glycan1) and tetraantennary (N-glycan2) hybrid N-glycans found on the surface of the HIV glycoprotein using 20 μs long all-atom molecular dynamics (MD) simulations. The main objective of the present study is to elucidate the influence of adding a complex branch on the overall glycan structural dynamics. Our investigation suggests that the average RMSD value increases when a complex branch is added to N-glycan1. However, the RMSD distribution is relatively wider in the case of N-glycan1 compared to N-glycan2, which indicates that multiple complex branches restrict the conformational variability of glycans. A similar observation is obtained from the principal component analysis of both glycans. All the puckering states (4C1 to 1C4) of each monosaccharide except mannose are sampled in our simulations, although the 4C1 chair form is energetically more favorable than 1C4. In N-glycan1, the 1-6 linkage in the mannose branch [Man(9)-α(1-6)-Man(5)] stays in the gauche-gauche cluster, whereas it moves towards trans-gauche in N-glycan2. For both glycans, mannose branches are more flexible than the complex branches, and adding a complex branch does not influence the dynamics of the mannose branches. We have noticed that the end-to-end distance of the complex branch shortens by ∼ 10 Å in the presence of another complex branch. This suggests that in the presence of an additional complex branch, the other complex branch adopts a close folded structure. All these conformational changes involve the selective formation of inter-residue and water-mediated hydrogen-bond networks.
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21
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Computational quantitation of the aldehyde forms of aldohexoses and disaccharides composed of d-glucose: Predictions of their reactivities in the Maillard reaction. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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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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23
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Chen Y, Fu X, Yu S, Quan K, Zhao C, Shao Z, Ye D, Qi H, Chen P. Parameterization of classical nonpolarizable force field for hydroxide toward the large‐scale molecular dynamics simulation of cellulose in pre‐cooled alkali/urea aqueous solution. J Appl Polym Sci 2021. [DOI: 10.1002/app.51477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Chen
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Xiaotong Fu
- Key Laboratory of Eco‐Textiles, Ministry of Education Jiangnan University Wuxi Jiangsu Province China
| | - Shuxian Yu
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Kun Quan
- China Institute of Marine Technology and Economy Beijing China
| | - Changjun Zhao
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Ziqiang Shao
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Dongdong Ye
- School of Textile Materials and Engineering Wuyi University Jiangmen Guangdong Province China
| | - Haisong Qi
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou Guangdong Province China
| | - Pan Chen
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
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24
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Ruda A, Widmalm G, Wohlert J. O-Methylation in Carbohydrates: An NMR and MD Simulation Study with Application to Methylcellulose. J Phys Chem B 2021; 125:11967-11979. [PMID: 34704449 PMCID: PMC8573740 DOI: 10.1021/acs.jpcb.1c07293] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Methylated carbohydrates
are important from both biological and
technical perspectives. Specifically, methylcellulose is an interesting
cellulose derivative that has applications in foods, materials, cosmetics,
and many other fields. While the molecular dynamics simulation technique
has the potential for both advancing the fundamental understanding
of this polymer and aiding in the development of specific applications,
a general drawback is the lack of experimentally validated interaction
potentials for the methylated moieties. In the present study, simulations
using the GROMOS 56 carbohydrate force field are compared to NMR spin–spin
coupling constants related to the conformation of the exocyclic torsion
angle ω in d-glucopyranose and derivatives containing
a 6-O-methyl substituent and a 13C-isotopologue thereof.
A 3JCC Karplus-type relationship
is proposed for the C5–C6–O6–CMe torsion
angle. Moreover, solvation free energies are compared to experimental
data for small model compounds. Alkylation in the form of 6-O-methylation
affects exocyclic torsion only marginally. Computed solvation free
energies between nonmethylated and methylated molecules were internally
consistent, which validates the application of these interaction potentials
for more specialized purposes.
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Affiliation(s)
- Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jakob Wohlert
- Department of Fiber and Polymer Technology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.,Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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25
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Visan RM, Leonties AR, Aricov L, Chihaia V, Angelescu DG. Polymorphism of chitosan-based networks stabilized by phytate investigated by molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:22601-22612. [PMID: 34591050 DOI: 10.1039/d1cp02961d] [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
Chitosan can associate in the presence of polyphosphates into insoluble hydrogels capable of drug encapsulation and safe and efficient release. On the one hand, chitosan hydrogels were synthesized using the phytate anion as a crosslinking agent and were characterized by employing dynamic light scattering (DLS) and Fourier transform infrared spectroscopy (FTIR). On the other hand, an effective chitosan-phytate model with atomistic details was created to examine the underlying physical crosslinking pattern, and the structure and dynamics of the chitosan-phytate complex were systematically investigated by using molecular dynamics (MD) simulations. To harbor the crosslinker potential for obtaining chitosan-based hydrogels, the impact of the phytate concentration and the functional groups of the chitosan on the reticulation process was addressed. The phytate association was determined by the phosphates' capacity for H-bonding to the amine and hydroxyl groups belonging to two consecutive glucosidic units. The physical crosslinking pattern was determined by the number of chitosan chains bound by one phytate anion and the phytate orientation relative to the glucopyranose neighbors. Cross-linking of two up to six chitosan chains mediated by a phytate anion represented favorable states, and the number distribution of cross-linked chains depended on the phytate concentration. The circular distribution of the cross-linkable phosphates regulated the nearly isotropic orientation of the chitosan chains and phytate at the junction, and the variety of topological crosslinking demonstrated the phytate ion's potential for developing chitosan-based hydrogels with improved structural attributes.
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Affiliation(s)
- Raluca M Visan
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
| | - Anca R Leonties
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
| | - Ludmila Aricov
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
| | - Viorel Chihaia
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
| | - Daniel G Angelescu
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
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26
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Abdi F, Arkan E, Mansouri K, Shekarbeygi Z, Barzegari E. Interactions of Bevacizumab with chitosan biopolymer nanoparticles: Molecular modeling and spectroscopic study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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27
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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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28
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Abreu B, Cruz C, Oliveira ASF, Soares CM. ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK 2E importer. Sci Rep 2021; 11:10591. [PMID: 34012037 PMCID: PMC8134467 DOI: 10.1038/s41598-021-89556-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/27/2021] [Indexed: 02/03/2023] Open
Abstract
ATP binding cassette (ABC) transporters employ ATP hydrolysis to harness substrate translocation across membranes. The Escherichia coli MalFGK2E maltose importer is an example of a type I ABC importer and a model system for this class of ABC transporters. The MalFGK2E importer is responsible for the intake of malto-oligossacharides in E.coli. Despite being extensively studied, little is known about the effect of ATP hydrolysis and nucleotide exit on substrate transport. In this work, we studied this phenomenon using extensive molecular dynamics simulations (MD) along with potential of mean force calculations of maltose transport across the pore, in the pre-hydrolysis, post-hydrolysis and nucleotide-free states. We concluded that ATP hydrolysis and nucleotide exit trigger conformational changes that result in the decrease of energetic barriers to maltose translocation towards the cytoplasm, with a concomitant increase of the energy barrier in the periplasmic side of the pore, contributing for the irreversibility of the process. We also identified key residues that aid in positioning and orientation of maltose, as well as a novel binding pocket for maltose in MalG. Additionally, ATP hydrolysis leads to conformations similar to the nucleotide-free state. This study shows the contribution of ATP hydrolysis and nucleotide exit in the transport cycle, shedding light on ABC type I importer mechanisms.
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Affiliation(s)
- Bárbara Abreu
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Carlos Cruz
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - A. Sofia F. Oliveira
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal ,grid.5337.20000 0004 1936 7603School of Biochemistry and Centre for Computational Chemistry, University of Bristol, Bristol, UK
| | - Cláudio M. Soares
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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29
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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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30
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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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31
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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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32
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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: 71] [Impact Index Per Article: 17.8] [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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33
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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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34
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Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. J Chem Inf Model 2020; 60:5103-5116. [PMID: 32786708 DOI: 10.1021/acs.jcim.0c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human G protein-coupled receptors (hGPCRs) are the most frequent targets of Food and Drug Administration (FDA)-approved drugs. Structural bioinformatics, along with molecular simulation, can support structure-based drug design targeting hGPCRs. In this context, several years ago, we developed a hybrid molecular mechanics (MM)/coarse-grained (CG) approach to predict ligand poses in low-resolution hGPCR models. The approach was based on the GROMOS96 43A1 and PRODRG united-atom force fields for the MM part. Here, we present a new MM/CG implementation using, instead, the Amber 14SB and GAFF all-atom potentials for proteins and ligands, respectively. The new implementation outperforms the previous one, as shown by a variety of applications on models of hGPCR/ligand complexes at different resolutions, and it is also more user-friendly. Thus, it emerges as a useful tool to predict poses in low-resolution models and provides insights into ligand binding similarly to all-atom molecular dynamics, albeit at a lower computational cost.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Biotechnology, University of Verona, 37314 Verona, Italy.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Cecile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
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35
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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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36
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Ferreras Moreno M, Stinson CJ, Shepherd RG, Welsh ID, Altaner C, Crittenden DL. Temperature-Dependent Blue Shifting of O-H Stretching Frequencies in Crystalline Cellulose Explained. J Phys Chem B 2020; 124:4924-4930. [PMID: 32441522 DOI: 10.1021/acs.jpcb.0c02793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing the temperature of a chemical system generally causes covalent bonds to lengthen and weaken, often the first step in initiating chemical reactions. However, for some hydrogen-bonded systems, infrared (IR) spectroscopy measurements reveal that covalent O-H bonds actually strengthen and therefore shorten when heated. In 1957, Finch and Lippincott proposed a simple one-dimensional (1D) model to explain this effect, in which thermal excitation of intermolecular stretching modes leads to lengthening and weakening of intermolecular O-H···O hydrogen bonds, thereby indirectly strengthening the associated covalent O-H bonds. Taking cellulose (an infinitely repeating polymer of d-glucose) as an example, we use molecular dynamics modeling to show that the same mechanism is responsible for temperature-dependent blue shifting of O-H stretching bands in IR spectra of carbohydrate biopolymers, except that interchain hydrogen bonds are weakened by thermal excitation of chain-separation modes, while intrachain hydrogen bonds are weakened by thermally induced changes in ring puckering and orientation of ring substituents but not reorientation of glucose units relative to one another or overall twisting of the cellulose chains.
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Affiliation(s)
- Manuel Ferreras Moreno
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Chris J Stinson
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Ross G Shepherd
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Ivan D Welsh
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Clemens Altaner
- New Zealand School of Forestry, University of Canterbury, Christchurch 8041, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
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37
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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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38
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Ogawa Y. Electron microdiffraction reveals the nanoscale twist geometry of cellulose nanocrystals. NANOSCALE 2019; 11:21767-21774. [PMID: 31573012 DOI: 10.1039/c9nr06044h] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanocellulose consisting of crystalline cellulose nanoparticles has high potential to serve as a building block for bio-based functional materials. The intrinsic chirality of cellulose provides them with high added values such as optical properties and chiral induction ability. At the nanoscale, this chirality is connected to the right-handed longitudinal twisting of these fibrous crystallites. However, this nanoscale fibrillar twist has been a matter of debate due to contradictory data between ultrastructural observations and molecular simulations and so far, the exact twist geometry has not been elucidated. Here, an electron microdiffraction (μED) analysis under cryogenic conditions reveals the continuous twisting of cellulose nanocrystals (CNCs) in aqueous suspension. This intrinsic regular twist is drastically modified to a discontinuous sharp twist when the CNCs are dried on a flat surface. The present μED-based analysis at the single nanoparticle level allows the establishment of the quantitative structure-property relationship of various solid and colloidal nanocellulose systems.
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Affiliation(s)
- Yu Ogawa
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.
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39
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Li Q, Chen P, Li Y, Li B, Liu S. Construction of cellulose-based Pickering stabilizer as a novel interfacial antioxidant: A bioinspired oxygen protection strategy. Carbohydr Polym 2019; 229:115395. [PMID: 31826411 DOI: 10.1016/j.carbpol.2019.115395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 11/28/2022]
Abstract
Oxygen protection/isolation is imperative to prevent the lipid oxidation since oxygen molecule is an ultimate quencher in photon conversion process. Inspired by the structural buildup of seeds from oil crops, a sustainable solid particle stabilizer with novel antioxidant activity was prepared by using cellulose and polyphenol. In this work, bacterial cellulose (BC) nanofibrils modified by tea polyphenols (TPs) was prepared and used as Pickering emulsifier for the O/W emulsion. BC nanofibirls exhibited excellent adsorption capacity up to 55 μg/mg, and the adsorption kinetics between BC and TPs were further investigated. After modification, the interfacial diffusion rate constant of BC was significantly increased to from 0.43 to 1.21 mN m-1 s-0.5. Moreover, the obtained O/W interfacial modulus of the dilatational elasticity was increased from 58 to 130 mN/m. Furthermore, the emulsions exhibited excellent free-radical scavenging activity at oil-water interface, suggesting a potential application in usage to extend the lifespan of the food containing polyunsaturated fats.
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Affiliation(s)
- Qi Li
- College of Food Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Pan Chen
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden; Beijing Engineering Research Center of Cellulose and its Derivatives, School of Materials Science and Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, China.
| | - Yan Li
- College of Food Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Li
- College of Food Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shilin Liu
- College of Food Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
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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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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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Qian L, Cai W, Xu D, Bao Y, Lu ZY, Cui S. Single-Molecule Studies Reveal That Water Is a Special Solvent for Amylose and Natural Cellulose. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lu Qian
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Wanhao Cai
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Duo Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Yu Bao
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Zhong-yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Shuxun Cui
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
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43
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Glazova I, Smirnova L, Zamyshlyayeva O, Zaitsev S, Avdoshin A, Naumov V, Ignatov S. Interpolymer interaction in insulin-chitosan complexes. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1614180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Irina Glazova
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Larisa Smirnova
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Olga Zamyshlyayeva
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Sergey Zaitsev
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Alexander Avdoshin
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Vladimir Naumov
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Stanislav Ignatov
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
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Plazinski W, Gaweda K, Plazinska A. Relation between the NMR data and the pseudorotational free-energy profile for oxolane. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conformation of five-membered furanose rings is a crucial issue for the structural analysis of many biologically-relevant molecules, including DNA and RNA. Oxolane can be treated as a prototypical furanose, composed only of saturated unsubstituted ring. In spite of its structural simplicity, providing the accurate quantitative description of the oxolane conformational features remains a great challenge for both the experimental and theoretical techniques. Here we show the method of recovering the free-energy profiles describing the conformational equilibrium in the oxolane ring (i.e. pseudorotation) based on the experimentally-inferred NMR data ([Formula: see text] coupling constants). The results remain in agreement with the quantum-mechanical-based molecular dynamics simulations and emphasize the large contributions of all ring conformers, even those located at the free-energy barriers. This includes the significant populations of limiting 3T2/2T3 and OE/EO shapes. Our findings provide another example of a poor applicability of the two-state model, which is routinely applied to analyze the NMR data in terms of population of different ring conformers.
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Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Kraków, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Kraków, Poland
| | - Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, ul. W. Chodzki 4A, PL-20093 Lublin, Poland
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Gaweda K, Plazinski W. The systematic influence of solvent on the conformational features of furanosides. Org Biomol Chem 2019; 17:2479-2485. [PMID: 30756110 DOI: 10.1039/c9ob00043g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endo- and exo-anomeric effects are the two most recognizable stereoelectronic effects exhibited by carbohydrates. Their presence relies on the interactions between ring substituent(s) and ring oxygen atoms. Here, we report the finding of a new effect that partially controls the conformational properties of furanose rings and can be ascribed to the influence of the solvent on the electronic structure of a molecule. In contrast to anomeric effects, it is not dependent on either presence or absence of ring substituents. Its origins lie in a solvent-induced flux of atomic charges that involves atoms forming the furanose ring. This systematically changes the energy of the whole molecular system and alters the ring-distortion free energies by ∼2.5-6.5 kJ mol-1, favoring the geometries close to the twist 3T2/2T3 conformers and disfavoring the envelope OE/EO-like shapes. This intriguing effect has never been reported before, although it is expected to exist in all furanose rings. Along with more recognized stereoelectronic effects, this phenomenon contributes to a wide applicability of the two-state (north vs. south) model of pseudorotation in furanosides and, in the case of extremely flexible furanose rings, may change the preferred conformation type in comparison with the gas-phase-oriented predictions.
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Affiliation(s)
- Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland.
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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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Ghosh MK, Howard MS, Dussan K, Dooley S. Mechanism and theory of d-glucopyranose homogeneous acid catalysis in the aqueous solution phase. Phys Chem Chem Phys 2019; 21:17993-18011. [PMID: 31386704 DOI: 10.1039/c8cp07224h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A detailed systematic theoretical study of the mechanism of the homogeneous Brønsted-acid catalysis of d-glucose in aqueous solution phase ("acid hydrolysis") is reported. G4MP2 with the SMD solvation model at B3LYP/6-31G(2df,p) are employed to compute the free energies of the molecular and ionic species pertaining to the isomerization, protonation, hydrogen cation transfer and decomposition processes of d-glucopyranose in aqueous solution phase. This information is used to hypothesise a reaction mechanism that is of improved accuracy and completeness from the existing art. It is found that rotation of the d-glucose alkyl carbon-carbon bond is a facile process and is very important to the subsequent catalytic mechanism. This rotation produces two rotameric isomers which are of notably different thermodynamic stability and reactivity, even with regard to the products of this acid catalysis. As a low energy process (ΔG‡ = ∼3.8-6.7 kcal mol-1), the alkyl carbon-carbon bond may rotate toward the hydroxyl group at the adjacent "4" position reducing the energy required to protonate that position by 3.0-7.2 kcal mol-1 (or 15-30%). The combination of two rotomeric isomers with the six structural isomers owing to the oxygen atoms, means that protonated d-glucose cations embark on a complex competition of interconversion and decomposition that is both thermodynamically and kinetically influenced. The calculations support the hypothesis that the acid-catalysed hydrolysis of d-glucose may yield a number of platform chemicals that have not previously been suggested. These include the prospect of three isomers of 5-hydroxymethylfurfural (HMF); 5-(hydroxymethyl)furan-2-carbaldehyde, 5-(hydroxymethyl)furan-3-carbaldehyde and 5-(hydroxymethyl)furan-4-carbaldehyde. Vibrational spectra of these HMF isomers are also computed and compared to experimentally determined infrared spectra of "humins". On this basis, it is cautiously speculated that the alternative HMF isomers, may be monomeric constituent of the polymeric "humins".
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Han F, Liu Y, E J, Guan S, Han W, Shan Y, Wang S, Zhang H. Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study. Biopolymers 2018; 109:e23238. [PMID: 30484856 DOI: 10.1002/bip.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Analysis of simulation results suggests that the binding free energies between the substrate and WT-Cbh9A are lower than those of Y555S and W678G mutants. The pull forces and energy barrier in Y555S and W678G mutants also reduced significantly during the steered molecular dynamics (SMD) simulation compared with that of the WT-Cbh9A. And the potential mean force calculations showed that the pulling energy barrier of Y555S and W678G mutants is much lower than that of WT-Cbh9A.
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Affiliation(s)
- Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Shanshan Guan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Yaming Shan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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Sugar-based bactericides targeting phosphatidylethanolamine-enriched membranes. Nat Commun 2018; 9:4857. [PMID: 30451842 PMCID: PMC6242839 DOI: 10.1038/s41467-018-06488-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 09/06/2018] [Indexed: 12/04/2022] Open
Abstract
Anthrax is an infectious disease caused by Bacillus anthracis, a bioterrorism agent that develops resistance to clinically used antibiotics. Therefore, alternative mechanisms of action remain a challenge. Herein, we disclose deoxy glycosides responsible for specific carbohydrate-phospholipid interactions, causing phosphatidylethanolamine lamellar-to-inverted hexagonal phase transition and acting over B. anthracis and Bacillus cereus as potent and selective bactericides. Biological studies of the synthesized compound series differing in the anomeric atom, glycone configuration and deoxygenation pattern show that the latter is indeed a key modulator of efficacy and selectivity. Biomolecular simulations show no tendency to pore formation, whereas differential metabolomics and genomics rule out proteins as targets. Complete bacteria cell death in 10 min and cellular envelope disruption corroborate an effect over lipid polymorphism. Biophysical approaches show monolayer and bilayer reorganization with fast and high permeabilizing activity toward phosphatidylethanolamine membranes. Absence of bacterial resistance further supports this mechanism, triggering innovation on membrane-targeting antimicrobials. Bacillus anthracis causes the infectious disease anthrax. Here, the authors synthesized deoxy glycosides that are effective against B. anthracis and related bacteria and found that these amphiphilic compounds kill bacteria via an unusual mechanism of action.
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