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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. [PMID: 38985993 DOI: 10.1021/acs.jctc.4c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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Liao Q, Ren H, Xu J, Wang P, Yuan B, Zhang H. Combined experiments and molecular simulations for understanding the thermo-responsive behavior and gelation of methylated glucans with different glycosidic linkages. J Colloid Interface Sci 2024; 674:315-325. [PMID: 38936088 DOI: 10.1016/j.jcis.2024.06.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
HYPOTHESIS Elucidation of the micro-mechanisms of sol-gel transition of gelling glucans with different glycosidic linkages is crucial for understanding their structure-property relationship and for various applications. Glucans with distinct molecular chain structures exhibit unique gelation behaviors. The disparate gelation phenomena observed in two methylated glucans, methylated (1,3)-β-d-glucan of curdlan (MECD) and methylated (1,4)-β-d-glucan of cellulose (MC), notwithstanding their equivalent degrees of substitution, are intricately linked to their unique molecular architectures and interactions between glucan and water. EXPERIMENTS Density functional theory and molecular dynamics simulations focused on the electronic property distinctions between MECD and MC, alongside conformational variations during thermal gelation. Inline attenuated total reflection Fourier transform infrared spectroscopy tracked secondary structure alterations in MECD and MC. To corroborate the simulation results, additional analyses including circular dichroism, rheology, and micro-differential scanning calorimetry were performed. FINDINGS Despite having similar thermally induced gel networks, MECD and MC display distinct physical gelation patterns and molecular-level conformational changes during gelation. The network of MC gel was formed via a "coil-to-ring" transition, followed by ring stacking. In contrast, the MECD gel comprised compact irregular helices accompanied by notable volume shrinkage. These variations in gelation behavior are ascribed to heightened hydrophobic interactions and diminished hydrogen bonding in both systems upon heating, resulting in gelation. These findings provide valuable insights into the microstructural changes during gelation and the thermo-gelation mechanisms of structurally similar polysaccharides.
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Affiliation(s)
- Qingyu Liao
- Advanced Rheology Institute, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huimin Ren
- Advanced Rheology Institute, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiatong Xu
- Advanced Rheology Institute, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pengguang Wang
- Advanced Rheology Institute, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Baihua Yuan
- Institute of Marine Equipment, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Hongbin Zhang
- Advanced Rheology Institute, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, Shanghai Jiao Tong University, Shanghai 200240, China.
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Anderson T, Jiang H, Cheallaigh AN, Bengtsson D, Oscarson S, Cairns C, St Michael F, Cox A, Kuttel MM. Formation and immunological evaluation of Moraxella catarrhalis glycoconjugates based on synthetic oligosaccharides. Carbohydr Polym 2024; 332:121928. [PMID: 38431400 DOI: 10.1016/j.carbpol.2024.121928] [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: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Published work has shown that glycoconjugate vaccines, based on truncated detoxified lipopolysaccharides from Moraxella catarrhalis attached through their reducing end to a carrier protein, gave good protection for all three serotypes A, B, and C in mice immunisation experiments. The (from the non-reducing end) truncated LPS structures were obtained from bacterial glycosyl transferase knock-out mutants and contained the de-esterified Lipid A, two Kdo residues and five glucose moieties. This work describes the chemical synthesis of the same outer Moraxella LPS structures, spacer-equipped and further truncated from the reducing end, i.e., without the Lipid A part and containing four or five glucose moieties or four glucose moieties and one Kdo residue, and their subsequent conjugation to a carrier protein via a five‑carbon bifunctional spacer to form glycoconjugates. Immunisation experiments both in mice and rabbits of these gave a good antibody response, being 2-7 times that of pre-immune sera. However, the sera produced only recognized the immunizing glycan immunogens and failed to bind to native LPS or whole bacterial cells. Comparative molecular modelling of three alternative antigens shows that an additional (2 → 4)-linked Kdo residue, not present in the synthetic structures, has a significant impact on the shape and volume of the molecule, with implications for antigen binding and cross-reactivity.
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Affiliation(s)
- Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hao Jiang
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Ní Cheallaigh
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dennis Bengtsson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Chantelle Cairns
- Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada
| | - Frank St Michael
- Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada
| | - Andrew Cox
- Vaccine Program, Human Health Therapeutics Portfolio, National Research Council, Ottawa, Ontario K1A 0R6, Canada
| | - Michelle M Kuttel
- Department of Computer Science, University of Cape Town, Cape Town 7701, South Africa
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Brown CM, Marrink SJ. Modeling membranes in situ. Curr Opin Struct Biol 2024; 87:102837. [PMID: 38744147 DOI: 10.1016/j.sbi.2024.102837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, in situ, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.
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Affiliation(s)
- Chelsea M Brown
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. https://twitter.com/chelseabrowncg
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. s.j.marrinkrug.nl
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Liu X, Wang Y, Zhang R, Gao Y, Chen H, Dong S, Hu X. Insights into the transcriptomic mechanism and characterization of endoglucanases from Aspergillus terreus in cellulose degradation. Int J Biol Macromol 2024; 263:130340. [PMID: 38387642 DOI: 10.1016/j.ijbiomac.2024.130340] [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: 11/18/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Filamentous fungi are the main industrial source of cellulases which are important in the process of converting cellulose to fermentable sugars. In this study, transcriptome analysis was conducted on Aspergillus terreus NEAU-7 cultivated using corn stover and glucose as carbon sources. Four putative endoglucanases (EG5A, EG7A, EG12A, and EG12C) from A. terreus NEAU-7 were efficiently expressed in Pichia pastoris. Among them, EG7A exhibited the highest enzyme activity (75.17 U/mg) with an optimal temperature of 40 °C and pH 5.0. EG5A and EG12A displayed specific activities of 19.92 U/mg and 14.62 U/mg, respectively, at 50 °C. EG12C showed acidophilic characteristics with an optimal pH of 3.0 and a specific activity of 12.21 U/mg at 40 °C. With CMC-Na as the substrate, the Km value of EG5A, EG7A, EG12A or, EG12C was, 11.08 ± 0.87 mg/mL, 6.82 ± 0.74 mg/mL, 7.26 ± 0.64 mg/mL, and 9.88 ± 0.86 mg/mL, with Vmax values of 1258.23 ± 51.62 μmol∙min-1∙mg-1, 842.65 ± 41.53 μmol∙min-1∙mg-1, 499.38 ± 20.42 μmol∙min-1∙mg-1, and 681.41 ± 30.08 μmol∙min-1∙mg-1, respectively. The co-treatment of EG7A with the commercial cellulase increased the yield of reducing sugar by 155.77 % (filter paper) and 130.49 % (corn stover). Molecular docking assay showed the interaction energy of EG7A with cellotetraose at -10.50 kcal/mol, surpassing EG12A (-10.43 kcal/mol), EG12C (-10.28 kcal/mol), and EG5A (-9.00 kcal/mol). Root Mean Square Deviation (RMSD) and Solvent Accessible Surface Area (SASA) values revealed that the presence of cellotetraose stabilized the molecular dynamics simulation of the cellotetraose-protein complex over a 100 ns time scale. This study provides valuable insights for developing recombinant enzymes and biomass degradation technologies.
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Affiliation(s)
- Xin Liu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanbo Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Rui Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yunfei Gao
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Heshu Chen
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | | | - Xiaomei Hu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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SureshKumar H, Appadurai R, Srivastava A. Glycans modulate lipid binding in Lili-Mip lipocalin protein: insights from molecular simulations and protein network analyses. Glycobiology 2024; 34:cwad094. [PMID: 38015986 DOI: 10.1093/glycob/cwad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, a lipid-binding glycoprotein that crystallises in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterised the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilise spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of the ligand. However, we find that either deglycosylation or glycosylation with high-mannose and paucimannose on the core glycans, which better mimic the natural insect glycosylation state, significantly affects the conformation and dynamics. A simple but effective distance- and correlation-based network analysis of the protein also reveals the key residues regulating the barrel's architecture and ligand binding characteristics in response to glycosylation.
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Affiliation(s)
- Harini SureshKumar
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, KA 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, KA 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, KA 560012, India
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Widmalm G. Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy. JACS AU 2024; 4:20-39. [PMID: 38274261 PMCID: PMC10807006 DOI: 10.1021/jacsau.3c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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Affiliation(s)
- Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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Grothaus IL, Bussi G, Colombi Ciacchi L. Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. J Chem Inf Model 2022; 62:4992-5008. [PMID: 36179122 DOI: 10.1021/acs.jcim.2c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite their fundamental biological relevance, structure-property relationships in N-glycans are fundamentally lacking, and their highly multidimensional compositional and conformational phase spaces remain largely unexplored. The torsional flexibility of the glycosidic linkages and the ring dynamics result in wide, rugged free-energy landscapes that are difficult to sample in molecular dynamics simulations. We show that a novel enhanced-sampling scheme combining replica exchange with solute and collective-variable tempering, enabling transitions over all relevant energy barriers, delivers converged distributions of solvated N-glycan conformers. Several dimensionality-reduction algorithms are compared and employed to generate conformational free-energy maps in two dimensions. Together with an originally developed conformation-based nomenclature scheme that uniquely identifies glycan conformers, our modeling procedure is applied to reveal the effect of chemical substitutions on the conformational ensemble of selected high-mannose-type and complex glycans. Moreover, the structure-prediction capabilities of two commonly used glycan force fields are assessed via the theoretical prediction of experimentally available nuclear magnetic resonance J-coupling constants. The results especially confirm the key role of ω and ψ torsion angles in discriminating between different conformational states and suggest an intriguing correlation between the torsional and ring-puckering degrees of freedom that may be biologically relevant.
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Affiliation(s)
- Isabell Louise Grothaus
- Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136Trieste, Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany
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Kogut MM, Danielsson A, Ricard-Blum S, Samsonov SA. Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis. Comput Biol Chem 2022; 99:107727. [PMID: 35841830 DOI: 10.1016/j.compbiolchem.2022.107727] [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: 05/12/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022]
Abstract
Heparin (HP) belongs to glycosaminoglycans (GAGs), anionic linear polysaccharides composed of repetitive disaccharide units. They are key players in many biological processes occurring in the extracellular matrix and at the cell surface. GAGs are challenging molecules for computational research due to their high chemical heterogeneity, flexibility, periodicity, pseudosymmetry, predominantly electrostatics-driven nature of interactions with their protein partners and potential multipose binding. The molecular mechanisms underlying GAG interactions mediated by divalent ions, which are important for GAG binding to several proteins, are not well understood. The goal of this study was to characterize the binding of Ca2+ to two HP oligosaccharides of different lengths (dp10 and dp18, dp: degree of polymerization) and their impact on HP conformational space and their dynamic behavior with the use of molecular dynamics (MD)-based approaches with two Ca2+ parameter sets. MD data suggested that the flexibility of the monosaccharides, the glycosidic linkages and ring puckering were not affected by the presence of Ca2+, in contrast to H-bond propensities and the calculated Rg for a fraction of the oligosaccharide populations in both dp10 and dp18. Moreover, the essential differences in the data obtained by using two Ca2+ parameter sets were reported.
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Affiliation(s)
- Małgorzata M Kogut
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, Villeurbanne CEDEX F-69622, France
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland.
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Fadda E. Molecular simulations of complex carbohydrates and glycoconjugates. Curr Opin Chem Biol 2022; 69:102175. [PMID: 35728307 DOI: 10.1016/j.cbpa.2022.102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that carbohydrates cover is a direct consequence of the variety of 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging in sizes, and with the highest diversity of building blocks of any other natural biopolymer. Despite this unparalleled complexity, a common denominator can be found in the glycans' inherent flexibility, which hinders experimental characterization, but that can be addressed by high-performance computing (HPC)-based molecular simulations. In this short review, I present and discuss the state-of-the-art of molecular simulations of complex carbohydrates and glycoconjugates, highlighting methodological strengths and weaknesses, important insights through emblematic case studies, and suggesting perspectives for future developments.
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Affiliation(s)
- Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Ireland.
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