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Journal articles on the topic 'Carbohydrate force field'

Author: Grafiati

Published: 5 June 2025

Last updated: 15 July 2025

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1

Guvench, Olgun, Devon Martin, and Megan Greene. "Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins." International Journal of Molecular Sciences 23, no. 1 (2021): 473. http://dx.doi.org/10.3390/ijms23010473.

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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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2

Jaya, krishna Koneru, and Mondal Jagannath. "Quantitative assessment of amylose dimerization process across force fields." Journal of Indian Chemical Society Vol. 96, Jul 2019 (2019): 949–56. https://doi.org/10.5281/zenodo.5644752.

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Tata Institute of Fundamental Research, Centre for Interdisciplinary Science, 36/P Gopanapalli Village, Serillingampally, Hyderabad-500 107, Telangana, India <em>E-mail</em>: jmondal@tifrh.res.in <em>Manuscript received online 10 May 2019, revised and accepted 23 May 2019</em> Despite being a key biomacromolecule, carbohydrate has received much less attention from computational community, compared to protein and lipids. This is majorly because of slow development of classical force fields for carbohydrate due to associated complexity in sampling its intrinsic flexibility and lack of an extensive assessment of existing carbohydrate force fields. Towards this end, the current work provides a robust comparison of four carbohydrate force fields (CHARMM36, GROMOS53A6<sub>CARBO_R</sub>, OPLS-AA, GLYCAM36) by evaluating their ability to simulate the dimerization process of a pair of amylose chain, the key ingredient of starch. The microsecond long molecular dynamics simulations on each of the four force fields capture spontaneous formation of double-helical self-assembled morphology from a pair of well-separated conformations. However, geometrical clustering of the trajectories reveal that these force fields mutually differ in sampling diverse array of conformations ranging from non-helical to partially open helical structures in addition to double-helical structures. Notably, the simulations reveal that relative to CHARMM36 and GLYCAM06 force field, GROMOS53A6<sub>CARBO_R</sub> over stabilizes the double-helical self-assembled morphology. CHARMM36 force field predicts significant transition between double-helical and partially open helical structure. The force fields differ in the relative propensity of parallel and anti-parallel double-helical formations. Overall by comparing all force fields in equal footing, this work provides a guided benchmark for carbohydrate simulation.

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3

Spiwok, Vojtěch, Petra Lipovová, Tereza Skálová, et al. "Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance." Journal of Computer-Aided Molecular Design 19, no. 12 (2006): 887–901. http://dx.doi.org/10.1007/s10822-005-9033-z.

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4

Grootenhuis, Peter D. J., and Cornelis A. G. Haasnoot. "A CHARMm Based Force Field for Carbohydrates Using the CHEAT Approach: Carbohydrate Hydroxyl Groups Represented by Extended Atoms." Molecular Simulation 10, no. 2-6 (1993): 75–95. http://dx.doi.org/10.1080/08927029308022160.

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5

Guvench, Olgun, Sairam S. Mallajosyula, E. Prabhu Raman, et al. "CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling." Journal of Chemical Theory and Computation 7, no. 10 (2011): 3162–80. http://dx.doi.org/10.1021/ct200328p.

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6

Stroylov, Victor, Maria Panova, and Philip Toukach. "Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations." International Journal of Molecular Sciences 21, no. 20 (2020): 7626. http://dx.doi.org/10.3390/ijms21207626.

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Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE accuracy with newer GLYCAM-06, and ultimately PBE0-D3/def2-TZVP (Triple-Zeta Valence Polarized) Density Functional Theory (DFT) simulations. For seven of eleven molecules, at least one empirical force field with explicit solvent outperformed DFT in NOE prediction. The aggregate of characteristics (accuracy, speed, and compatibility) made MM3 dynamics with explicit solvent at 300 K the most favorable method for bulk generation of disaccharide conformation maps for massive database filling.

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7

Chen, Yanan, Harindra Vedala, Gregg P. Kotchey, et al. "Detection of Lectins using Glyco-Functionalized Nanosensors." MRS Proceedings 1451 (2012): 191–96. http://dx.doi.org/10.1557/opl.2012.1291.

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ABSTRACTWe have used single-walled carbon nanotube field-effect transistor (SWNT-FET) and chemically converted graphene field-effect transistor (CCG-FET) devices to probe the interactions between carbohydrates and their recognition lectins. Porphyrin- and pyrene-based glycoconjugates were used as receptor molecules and the target lectins were two bacterial lectins that present different carbohydrate preference, namely PA-IL, PA-IIL from Pseudomonas aeruginosa and a plant lectin Concanavalin A. The specific binding between lectin and carbohydrate can be transduced to the change in FET device conductance. An initial study with SWNT-FET noncovalently functionalized with porphyrin-based glycoconjugates showed both good selectivity and sensitivity. To compare SWNT and CCG performance, pyrene- and porphyrin-based glycoconjugates were functionalized noncovalently on the surface of CCG-FET and SWNT-FET devices, which were then treated with non-specific and specific lectins. The responses were compared and rationalized using computer-aided models of carbon nanostructure/glycoconjugate interactions. Fluorescence microscopy, atomic force microscopy, UV-vis-NIR spectroscopy and Isothermal titration microcalorimetry (ITC) measurements were used to confirm the electrical results.

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8

Balogh, Gábor, Tamás Gyöngyösi, István Timári, et al. "Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides." Journal of Chemical Information and Modeling 59, no. 11 (2019): 4855–67. http://dx.doi.org/10.1021/acs.jcim.9b00666.

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9

Pandey, Poonam, Asaminew H. Aytenfisu, Alexander D. MacKerell, and Sairam S. Mallajosyula. "Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives." Journal of Chemical Theory and Computation 15, no. 9 (2019): 4982–5000. http://dx.doi.org/10.1021/acs.jctc.9b00327.

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10

Panczyk, Tomasz, Wojciech Plazinski, François-Yves Dupradeau, Agnieszka Brzyska, and Pawel Wolski. "Interaction of Chondroitin and Hyaluronan Glycosaminoglycans with Surfaces of Carboxylated Carbon Nanotubes Studied Using Molecular Dynamics Simulations." Molecules 28, no. 2 (2023): 826. http://dx.doi.org/10.3390/molecules28020826.

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Interaction of β-D-glucopyranuronic acid (GlcA), N-acetyl-β-D-glucosamine (GlcNAc), N-acetyl-β-D-galactosamine (GalNAc) and two natural decameric glycosaminoglycans, hyaluronic acid (HA) and Chondroitin (Ch) with carboxylated carbon nanotubes, were studied using molecular dynamics simulations in a condensed phase. The force field used for carbohydrates was the GLYCAM-06j version, while functionalized carbon nanotubes (fCNT) were described using version two of the general amber force field. We found a series of significant differences in carbohydrate-fCNT adsorption strength depending on the monosaccharide molecule and protonation state of surface carboxyl groups. GlcNAc and GalNAc reveal a strong adsorption on fCNT with deprotonated carboxyl groups, and a slightly weaker adsorption on the fCNT with protonated carboxyl groups. On the contrary, GlcA weakly adsorbs on fCNT. The change in protonation state of surface carboxyl groups leads to the reversal orientation of GlcNAc and GalNAc in reference to the fCNT surface, while GlcA is not sensitive to that factor. Adsorption of decameric oligomers on the surface of fCNT weakens with the increasing number of monosaccharide units. Chondroitin adsorbs weaker than hyaluronic acid and incorporation of four Ch molecules leads to partial detachment of them from the fCNT surface. The glycan–fCNT interactions are strong enough to alter the conformation of carbohydrate backbone; the corresponding conformational changes act toward a more intensive contact of glycan with the fCNT surface. Structural and energetic features of the adsorption process suggest the CH-π interaction-driven mechanism.

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11

Spieser, Stéphane A. H., J. Albert van Kuik, Loes M. J. Kroon-Batenburg, and Jan Kroon. "Improved carbohydrate force field for gromos: ring and hydroxymethyl group conformations and exo-anomeric effect." Carbohydrate Research 322, no. 3-4 (1999): 264–73. http://dx.doi.org/10.1016/s0008-6215(99)00228-1.

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12

Coxon, Edward E., James M. Coxon, and D. Ross Boswell. "The Correlation of Carbohydrate Molecular Motion with N.O.E. Buildup Spectra." Australian Journal of Chemistry 51, no. 5 (1998): 397. http://dx.doi.org/10.1071/c97131.

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The rates of buildup of the n.O.e. (nuclear Overhauser effect) including the effects of conformational averaging, anisotropic tumbling and internal motion were calculated for methyl O-α-L-fucopyranosyl-(1→2)-β-D-galactopyranoside. This methodology is found to effectively distinguish between different computational models of carbohydrate solution behaviour, providing a new tool for the evaluation of molecular modelling predictions in solution. These studies support the MM2* force field, continuum solvent treatment (GB/SA) and molecular dynamic (MD) integration, and reinforce the concept of flexibility about the glycosidic linkage.

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13

Dai, Hongcui, Hui Zhang, Zongxin Li, Kaichang Liu, and Kazem Zamanian. "Tillage Practice Impacts on the Carbon Sequestration Potential of Topsoil Microbial Communities in an Agricultural Field." Agronomy 11, no. 1 (2020): 60. http://dx.doi.org/10.3390/agronomy11010060.

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Soil microorganisms are the core force driving the conversion of plant residues into soil organic carbon (SOC). Identifying the changes in soil microorganism responses to tillage practices is a key step in understanding the SOC sequestration potential. The aim of this study is to assess the impacts of different tillage practices on microbial communities and functions in agricultural soils. A field experiment involving no tillage (NT), rotary tillage (RT), and deep tillage (DT) in winter wheat-summer maize double cropping was performed to determine the structure of the microbial community and its functions using metagenomics. We found that tillage practices changed the composition of soil microbial communities and their functions related to the C cycle. The relative abundance of fungi in DT was significantly higher than that of the NT and RT treatments and primarily facilitated the growth of the fungi community. Moreover, DT treatment increased the relative abundance of genes involved in carbohydrate transport and metabolism genes and carbohydrate metabolism pathway genes, in addition to those encoding carbohydrate-binding modules. Therefore, we concluded that DT increases the transformation potential of straw-C to SOC in the North China Plain where large amounts of wheat and maize straw are returned to the field every year.

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14

Kuttel, Michelle, J. W. Brady, and Kevin J. Naidoo. "Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations." Journal of Computational Chemistry 23, no. 13 (2002): 1236–43. http://dx.doi.org/10.1002/jcc.10119.

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15

Glennon, Timothy M., and Kenneth M. Merz. "A carbohydrate force field for amber and its application to the study of saccharide to surface adsorption." Journal of Molecular Structure: THEOCHEM 395-396 (May 1997): 157–71. http://dx.doi.org/10.1016/s0166-1280(96)04949-4.

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16

Mallajosyula, Sairam S., Olgun Guvench, and Alexander D. MacKerell. "CHARMM Additive All-Atom Force Field for O-Glycan and N-Glycan Linkages in Carbohydrate-Protein Modeling." Biophysical Journal 100, no. 3 (2011): 526a. http://dx.doi.org/10.1016/j.bpj.2010.12.3077.

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17

Ferrari, Nicola, Cecilia Ada Maestri, Paolo Bettotti, Mario Grassi, Michela Abrami, and Marina Scarpa. "Effect of Process Conditions and Colloidal Properties of Cellulose Nanocrystals Suspensions on the Production of Hydrogel Beads." Molecules 26, no. 9 (2021): 2552. http://dx.doi.org/10.3390/molecules26092552.

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The influence of the physical, rheological, and process parameters on the cellulose nanocrystal (CNC) drops before and after external gelation in a CaCl2 solution was investigated. The dominant role of the CNC’s colloidal suspension properties, such as the viscous force, inertial, and surface tension forces in the fluid dynamics was quantitatively evaluated in the formation of drops and jellified beads. The similarity and difference between the behavior of carbohydrate polymers and rod-like crystallites such as CNC were enlightened. Pump-driven and centrifugally-driven external gelation approaches were followed to obtain CNC hydrogel beads with tunable size and regular shape. A superior morphological control—that is, a more regular shape and smaller dimension of the beads—were obtained by centrifugal force-driven gelation. These results suggest that even by using a simple set-up and a low-speed centrifuge device, the extrusion of a colloidal solution through a small nozzle under a centrifugal field is an efficient approach for the production of CNC hydrogel beads with good reproducibility, control over the bead morphology and size monodispersion.

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18

Re, Suyong, Shigehisa Watabe, Wataru Nishima, and Yuji Sugita. "3P049 Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans(01A. Protein: Structure,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S220. http://dx.doi.org/10.2142/biophys.53.s220_1.

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19

GLENNON, T. M., and K. M. JUN MERZ. "ChemInform Abstract: A Carbohydrate Force Field for AMBER and Its Application to the Study of Saccharide to Surface Adsorption." ChemInform 28, no. 45 (2010): no. http://dx.doi.org/10.1002/chin.199745349.

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20

Kochan, Kamila, David Perez-Guaita, Julia Pissang, et al. "In vivo atomic force microscopy–infrared spectroscopy of bacteria." Journal of The Royal Society Interface 15, no. 140 (2018): 20180115. http://dx.doi.org/10.1098/rsif.2018.0115.

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A new experimental platform for probing nanoscale molecular changes in living bacteria using atomic force microscopy–infrared (AFM–IR) spectroscopy is demonstrated. This near-field technique is eminently suited to the study of single bacterial cells. Here, we report its application to monitor dynamical changes occurring in the cell wall during cell division in Staphylococcus aureus using AFM to demonstrate the division of the cell and AFM–IR to record spectra showing the thickening of the septum . This work was followed by an investigation into single cells, with particular emphasis on cell-wall signatures, in several bacterial species. Specifically, mainly cell wall components from S. aureus and Escherichia coli containing complex carbohydrate and phosphodiester groups, including peptidoglycans and teichoic acid, could be identified and mapped at nanometre spatial resolution. Principal component analysis of AFM–IR spectra of six living bacterial species enabled the discrimination of Gram-positive from Gram-negative bacteria based on spectral bands originating mainly from the cell wall components. The ability to monitor in vivo molecular changes during cellular processes in bacteria at the nanoscale opens a new platform to study environmental influences and other factors that affect bacterial chemistry.

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21

Gouin, Sébastien G., Enguerran Vanquelef, José Manuel García Fernández, Carmen Ortiz Mellet, François-Yves Dupradeau, and José Kovensky. "Multi-Mannosides Based on a Carbohydrate Scaffold: Synthesis, Force Field Development, Molecular Dynamics Studies, and Binding Affinities for Lectin Con A." Journal of Organic Chemistry 72, no. 24 (2007): 9032–45. http://dx.doi.org/10.1021/jo071248a.

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22

Uslupehlivan, Muhammet, and Ecem Şener Uslupehlivan. "GLYCOINFORMATICS APPROACH FOR IDENTIFYING TARGET POSITIONS TO INHIBIT INITIAL BINDING OF SARS-COV-2 S1 PROTEIN TO THE HOST CELL." Journal of Applied Biological Sciences 16, no. 1 (2022): 89–101. https://doi.org/10.71336/jabs.950.

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COVID-19 outbreak is still threatening the public health. Therefore, in the middle of the pandemic, all kind of knowledge on SARS-CoV-2 may help us to find the solution. Determining the 3D structures of the proteins involved in host-pathogen interactions are of great importance in the fight against infection. Besides, post-translational modifications of the protein on 3D structure should be revealed in order to understand the protein function since these modifications are responsible for the host-pathogen interaction. Based on these, we predicted O-glycosylation and phosphorylation positions using full amino acid sequence of S1 protein. Candidate positions were further analyzed with enzyme binding activity, solvent accessibility, surface area parameters and the positions determined with high accuracy rate were used to design 3D O-glycoprotein structure of the S1 protein using carbohydrate force field. In addition, the interaction between the C-type lectin CD209L and α-mannose residues was examined and carbohydrate recognition positions were predicted. We suggest these positions as a potential target for the inhibition of the initial binding of SARS-CoV-2 S1 protein to the host cell.

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23

Uslupehlivan and Uslupehlivan. "GLYCOINFORMATICS APPROACH FOR IDENTIFYING TARGET POSITIONS TO INHIBIT INITIAL BINDING OF SARS-COV-2 S1 PROTEIN TO THE HOST CELL." Journal of Applied Biological Sciences 16, no. 1 (2022): 89–101. https://doi.org/10.5281/zenodo.5826179.

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COVID-19 outbreak is still threatening the public health. Therefore, in the middle of the pandemic, all kind of knowledge on SARS-CoV-2 may help us to find the solution. Determining the 3D structures of the proteins involved in host-pathogen interactions are of great importance in the fight against infection. Besides, post-translational modifications of the protein on 3D structure should be revealed in order to understand the protein function since these modifications are responsible for the host-pathogen interaction. Based on these, we predicted O-glycosylation and phosphorylation positions using full amino acid sequence of S1 protein. Candidate positions were further analyzed with enzyme binding activity, solvent accessibility, surface area parameters and the positions determined with high accuracy rate were used to design 3D O-glycoprotein structure of the S1 protein using carbohydrate force field. In addition, the interaction between the C-type lectin CD209L and α-mannose residues was examined and carbohydrate recognition positions were predicted. We suggest these positions as a potential target for the inhibition of the initial binding of SARS-CoV-2 S1 protein to the host cell.

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24

David, Ivona. "Analysis of Physiological and Biochemical Parameters in the Radish (Raphanus sativus L.) Obtained in Different Cultivation Systems." Grassroots Journal of Natural Resources 7, no. 2 (2024): 41–62. http://dx.doi.org/10.33002/nr2581.6853.070202.

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This paper presents the results obtained from the analysis of physiological and biochemical parameters in the radish, species Raphanus sativus L., variety Rond Ecarlate, which was grown in three different systems (in the field, in the solarium and in the climate chamber). Several parameters necessary for the evaluation of biomass, physiological processes and nutritional values were determined. Regarding the biometric parameters, it was noticed that in the field cultivation the plants formed 11-12 leaves, in the solarium average 12-13 leaves, and in the climatic chamber the analyzed plants formed 7-9 leaves, on an average. The total biomass of the plant was recorded with the following average values: in the field 70.05 grams, in the solarium 92.3 grams and in the climate chamber 32.9 grams. Regarding the circumference of the tuberous hypocotyl axis, the values are higher in plants grown in solarium (16.9 cm), with the smallest dimensions being recorded in plants grown in the climate chamber (7.2 cm). The highest average pulp firmness value was observed in plants grown in the solarium (0.27 kg force), and the lowest values were seen in plants grown in the climate chamber (0.14 kg force). Regarding the amount of water lost through perspiration by the leaves of radish plants, the highest average values were recorded at plants grown in the solarium, and the lowest at plants grown in the climatic chamber. The average soluble dry matter content was higher (over 4%) in plants grown in the climate chamber compared to other harvesting systems. The analysis of the average carbohydrate content shows that the total soluble carbohydrates were present only in the hypocotyl axis and glucose was found both in the hypocotyl axis of the studied plants and in the leaves. Vitamin C was present in variable amounts, both in the hypocotyl axis and in the leaves. The average amino acid content (expressed in amino nitrogen) was between 0.003% and 0.006%. The anthocyanin was present with highest values (54.5 mg) in field-grown plants, and catalase activity was present both in the hypocotyl axis and in the leaves and roots. Air humidity and temperature had a high influence on the development of plant biomass, on the content of dry matter and on the loss of water through transpiration. The biometric, physiological and biochemical parameters varied depending on the cultivation system.

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25

Foley, B. Lachele, Matthew B. Tessier, and Robert J. Woods. "Carbohydrate force fields." Wiley Interdisciplinary Reviews: Computational Molecular Science 2, no. 4 (2011): 652–97. http://dx.doi.org/10.1002/wcms.89.

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26

Ahunun, I. Frances. "Investigation of the Effect of Thiols on the Size of Nanoparticles." Trends in Pharmaceuticals and Nanotechnology 1, no. 2 (2019): 22–26. https://doi.org/10.5281/zenodo.3247280.

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<em>fields including biomedicine, carbohydrate – carbohydrate and carbohydrate – protein binding inclusive. These studies are relevant in the treatment of various illnesses such as asthma, atherosclerosis, cancer and arthritis where biological processes such as cell adhesion, signal transduction, host pathogen recognition and inflammation could be affected. Furthermore, the weak binding affinity between carbohydrates and proteins have made this difficult.</em> <em>In order to successfully carry out carbohydrate and protein binding studies, the carbohydrate moiety has to be presented multivalently. Gold nanoparticles functionalized with carbohydrates can be used to achieve this aim. Gold nanoparticles have been used to overcome this difficulty: these particles are negatively charged and globular presenting the carbohydrates multivalently, overcoming the weak binding affinity between carbohydrates and also between carbohydrates and proteins.</em> <em>In nanoparticle synthesis, size is of utmost importance depending on the purpose for which it is being made. For hydrophilic and lipophilic systems, the resulting forces acting on particles are a sum of the repulsive forces V<sub>R </sub>and the attractive forces V<sub>A</sub>. An electric double layer, ions of alternate charge formed around nanoparticles can confer stability to dispersion.</em> <em>There was marked increase in particle size using sodium sulphide (Na<sub>2</sub>S) as aggregating agent; Na<sub>2</sub>S containing the sulphide ion present in all thiols.</em>

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Anila, Midhun Mohan, Paweł Rogowski, and Bartosz Różycki. "Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3." Molecules 29, no. 12 (2024): 2768. http://dx.doi.org/10.3390/molecules29122768.

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Galectin-3 is a protein involved in many intra- and extra-cellular processes. It has been identified as a diagnostic or prognostic biomarker for certain types of heart disease, kidney disease and cancer. Galectin-3 comprises a carbohydrate recognition domain (CRD) and an N-terminal domain (NTD), which is unstructured and contains eight collagen-like Pro-Gly-rich tandem repeats. While the structure of the CRD has been solved using protein crystallography, current knowledge about conformations of full-length galectin-3 is limited. To fill in this knowledge gap, we performed molecular dynamics (MD) simulations of full-length galectin-3. We systematically re-scaled the solute–solvent interactions in the Martini 3 force field to obtain the best possible agreement between available data from SAXS experiments and the ensemble of conformations generated in the MD simulations. The simulation conformations were found to be very diverse, as reflected, e.g., by (i) large fluctuations in the radius of gyration, ranging from about 2 to 5 nm, and (ii) multiple transient contacts made by amino acid residues in the NTD. Consistent with evidence from NMR experiments, contacts between the CRD and NTD were observed to not involve the carbohydrate-binding site on the CRD surface. Contacts within the NTD were found to be made most frequently by aromatic residues. Formation of fuzzy complexes with unspecific stoichiometry was observed to be mediated mostly by the NTD. Taken together, we offer a detailed picture of the conformational ensemble of full-length galectin-3, which will be important for explaining the biological functions of this protein at the molecular level.

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Reiling, Stephan, Michael Schlenkrich, and J�rgen Brickmann. "Force field parameters for carbohydrates." Journal of Computational Chemistry 17, no. 4 (1996): 450–68. http://dx.doi.org/10.1002/(sici)1096-987x(199603)17:4<450::aid-jcc6>3.0.co;2-t.

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Foley, B. Lachele, Matthew B. Tessier, and Robert J. Woods. "ChemInform Abstract: Carbohydrate Force Fields." ChemInform 44, no. 10 (2013): no. http://dx.doi.org/10.1002/chin.201310273.

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Edi Wibowo, Dwi, and Benny Diah Madusari. "Legal Protection for Consumers on Unlabelled Processed Food from Seaweed in Brebes Regency." SHS Web of Conferences 54 (2018): 06010. http://dx.doi.org/10.1051/shsconf/20185406010.

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Some certain types of seaweed, such as Euchema, Cottoni, Gracelaria, are also cultivated by people who live at coastal areas in Java. They make seaweed as a processed food like candies and solid porridge (dodol) because seaweed contains many nutrient substances, such as water (27,8%), protein (5,4%), carbohydrate (33,3%), fat (8,6%), coarse fiber (3%) and ashes (22,25%). Government should convince or guarantee with legal certainties, that people who consume goods and services, especially food products are safe, so that the existing of Rules as well as the regulations and other law for products set up and launched by the government, for giving protection to the people who use or consume the goods and products, will possibly bring a sense of security and improve welfare. The question is how is the legal protection for consumers on unlabelled processed food from seaweed? The Approach method used is empirical-juridical method which is used to solve problems by conducting research on primary data in the field. Juridical itself is a kind of research method referring to the law, the currently in force laws and regulations, and the theory of law.The regulations used in this research are Regulation No 8 / 1999 concerning Customers’ protection that is Regulation No.18 / 2012 concerning food.

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Lopez, Cesar A. "Martini Force Field: Extension To Carbohydrates." Biophysical Journal 96, no. 3 (2009): 405a. http://dx.doi.org/10.1016/j.bpj.2008.12.2062.

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STUIKE-PRILL, Rainer, and Bernd MEYER. "A new force-field program for the calculation of glycopeptides and its application to a heptacosapeptide-decasaccharide of immunoglobulin G1. Importance of 1-6-glycosidic linkages in carbohydrate . peptide interactions." European Journal of Biochemistry 194, no. 3 (1990): 903–13. http://dx.doi.org/10.1111/j.1432-1033.1990.tb19485.x.

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STUIKE-PRILL, Rainer, and Bernd MEYER. "A new force-field program for the calculation of glycopeptides and its application to a heptacosapeptide-decasaccharide of immunoglobulin G1. Importance of 1-6-glycosidic linkages in carbohydrate . peptide interactions." European Journal of Biochemistry 194, no. 3 (1990): 914–19. http://dx.doi.org/10.1111/j.1432-1033.1990.tb19486.x.

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Harcourt, Bernard André, Michalis Panagiotopoulos, Stavros Sardelis, Gerasimos Terzis, and Gregory C. Bogdanis. "The Effect of Dehydration on Vertical Jump, Muscle Strength and Sprint Performance." Proceedings 25, no. 1 (2019): 10. http://dx.doi.org/10.3390/proceedings2019025010.

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AIM: Negative fluid balance before competition is used by some track-and-field athletes aiming to reduce body weight and increase jumping performance. However, the effects of body weight loss due to dehydration on fast and explosive muscle actions have not been fully explored. The purpose of this study was to investigate the effect of dehydration on weight-bearing and non-weight-bearing explosive movements. MATERIAL & METHOD: Nine athletes took part in this study (5 females and 4 males, 20–23 years old). Participants were familiarized with the procedures and measurements of the study, recorded their normal dietary and fluid intake for 3 days, and took part in two randomly assigned conditions. On one condition, carbohydrate intake was reduced by 70% and water intake by 50% of their habitual diet on the day preceding the measurements (dehydration). On the other condition, the habitual diet and fluid intake were followed (habitual hydration). Prior to the performance measurements in each condition, body weight (BW) and urine specific gravity were measured. After a standardized 15-min warm-up, the following assessments were performed: countermovement jump (CMJ), maximum isometric leg press force, and rate of force development (RFD), 10-, 20-, and 30-m sprint performance, and six 30-m sprints interspersed with 25 s of rest. RESULTS: Mild dehydration (1.1 ± 1.1% BW) was achieved, which was confirmed by almost two-fold higher thirst ratings compared with habitual hydration (p < 0.002) and a trend for higher urine specific gravity (habitual hydration: 1025 ± 5 vs. dehydration: 1032 ± 7 mg/mL, p = 0.054). CMJ performance, expressed as relative power, was similar in habitual hydration and dehydration (38.5 ± 4.6 vs. 39.0 ± 3.6 W/kg BW, p = 0.14). Also, 20-m, 30-m, and repeated-sprint performance were similar in the two conditions, but 10-m sprint performance was impaired by 3.2 ± 0.13% (p = 0.019) in dehydration. Moreover, although maximum isometric leg press force was unaffected, RFD was lower in dehydration at 0–150 ms (by 13.3%; p = 0.05), 0–200 ms (by 11.8%; p = 0.03), and 0–250 ms (by 11.2%; p = 0.03). CONCLUSION: Mild dehydration did not affect maximum force or power output, but decreased acceleration and RFD. The decreases in RFD may be linked with the lower acceleration ability in these athletes.

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Asensio, Juan Luis, and Jesus Jimenez-Barbero. "The use of the AMBER force field in conformational analysis of carbohydrate molecules: Determination of the solution conformation of methyl ?-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations." Biopolymers 35, no. 1 (1995): 55–73. http://dx.doi.org/10.1002/bip.360350107.

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Damm, Wolfgang, Antonio Frontera, Julian Tirado-Rives, and William L. Jorgensen. "OPLS all-atom force field for carbohydrates." Journal of Computational Chemistry 18, no. 16 (1997): 1955–70. http://dx.doi.org/10.1002/(sici)1096-987x(199712)18:16<1955::aid-jcc1>3.0.co;2-l.

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Kirschner, Karl N., Austin B. Yongye, Sarah M. Tschampel, et al. "GLYCAM06: A generalizable biomolecular force field. Carbohydrates." Journal of Computational Chemistry 29, no. 4 (2007): 622–55. http://dx.doi.org/10.1002/jcc.20820.

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Chen, Hsieh, Jason R. Cox, and Athanassios Z. Panagiotopoulos. "Force Fields for Carbohydrate–Divalent Cation Interactions." Journal of Physical Chemistry B 120, no. 23 (2016): 5203–8. http://dx.doi.org/10.1021/acs.jpcb.6b01438.

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Cai, Jiaxin, Haiming Chen, Runqiu Wang, et al. "Membrane Damage and Metabolic Disruption as the Mechanisms of Linalool against Pseudomonas fragi: An Amino Acid Metabolomics Study." Foods 13, no. 16 (2024): 2501. http://dx.doi.org/10.3390/foods13162501.

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Pseudomonas fragi (P. fragi) is usually detected in low-temperature meat products, and seriously threatens food safety and human health. Therefore, the study investigated the antibacterial mechanism of linalool against P. fragi from membrane damage and metabolic disruption. Results from field-emission transmission electron microscopy (FETEM) and atomic force microscopy (AFM) showed that linalool damage membrane integrity increases surface shrinkage and roughness. According to Fourier transform infrared (FTIR) spectra results, the components in the membrane underwent significant changes, including nucleic acid leakage, carbohydrate production, protein denaturation and modification, and fatty acid content reduction. The data obtained from amino acid metabolomics indicated that linalool caused excessive synthesis and metabolism of specific amino acids, particularly tryptophan metabolism and arginine biosynthesis. The reduced activities of glucose 6-phosphate dehydrogenase (G6PDH), malate dehydrogenase (MDH), and phosphofructokinase (PFK) suggested that linalool impair the respiratory chain and energy metabolism. Meanwhile, genes encoding the above enzymes were differentially expressed, with pfkB overexpression and zwf and mqo downregulation. Furthermore, molecular docking revealed that linalool can interact with the amino acid residues of G6DPH, MDH and PFK through hydrogen bonds. Therefore, it is hypothesized that the mechanism of linalool against P. fragi may involve cell membrane damage (structure and morphology), disturbance of energy metabolism (TCA cycle, EMP and HMP pathway) and amino acid metabolism (cysteine, glutamic acid and citrulline). These findings contribute to the development of linalool as a promising antibacterial agent in response to the food security challenge.

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Nester, Karina, Karolina Gaweda, and Wojciech Plazinski. "A GROMOS Force Field for Furanose-Based Carbohydrates." Journal of Chemical Theory and Computation 15, no. 2 (2019): 1168–86. http://dx.doi.org/10.1021/acs.jctc.8b00838.

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López, Cesar A., Andrzej J. Rzepiela, Alex H. de Vries, Lubbert Dijkhuizen, Philippe H. Hünenberger, and Siewert J. Marrink. "Martini Coarse-Grained Force Field: Extension to Carbohydrates." Journal of Chemical Theory and Computation 5, no. 12 (2009): 3195–210. http://dx.doi.org/10.1021/ct900313w.

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Kony, D., W. Damm, S. Stoll, and W. F. Van Gunsteren. "An improved OPLS-AA force field for carbohydrates." Journal of Computational Chemistry 23, no. 15 (2002): 1416–29. http://dx.doi.org/10.1002/jcc.10139.

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Xiong, Xiuming, Zhaoqiang Chen, Benjamin P. Cossins, et al. "Force fields and scoring functions for carbohydrate simulation." Carbohydrate Research 401 (January 2015): 73–81. http://dx.doi.org/10.1016/j.carres.2014.10.028.

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Lins, Roberto D., and Philippe H. Hünenberger. "A new GROMOS force field for hexopyranose-based carbohydrates." Journal of Computational Chemistry 26, no. 13 (2005): 1400–1412. http://dx.doi.org/10.1002/jcc.20275.

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Plazinska, Anita, and Wojciech Plazinski. "Comparison of Carbohydrate Force Fields in Molecular Dynamics Simulations of Protein–Carbohydrate Complexes." Journal of Chemical Theory and Computation 17, no. 4 (2021): 2575–85. http://dx.doi.org/10.1021/acs.jctc.1c00071.

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Vermaas, Josh V., Loukas Petridis, John Ralph, Michael F. Crowley, and Gregg T. Beckham. "Systematic parameterization of lignin for the CHARMM force field." Green Chemistry 21, no. 1 (2019): 109–22. http://dx.doi.org/10.1039/c8gc03209b.

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We develop a comprehensive molecular mechanics force field for lignin and evaluate its performance in terms of thermodynamics and structure with respect to experimental observables. The developed force field can be used to model lignin polymers, including their covalent linkages to carbohydrates, and their interaction with other biomolecules.

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Matthews, James F., Gregg T. Beckham, Malin Bergenstråhle-Wohlert, John W. Brady, Michael E. Himmel та Michael F. Crowley. "Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields". Journal of Chemical Theory and Computation 8, № 2 (2012): 735–48. http://dx.doi.org/10.1021/ct2007692.

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Shimada, J., H. Kaneko, H. Minagawa, T. Takada, S. Kitamura, and K. Kajiwara. "Force-field dependence found in simulations of carbohydrates and related molecules." Seibutsu Butsuri 40, supplement (2000): S51. http://dx.doi.org/10.2142/biophys.40.s51_3.

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Pol-Fachin, Laercio, Victor H. Rusu, Hugo Verli, and Roberto D. Lins. "GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates." Journal of Chemical Theory and Computation 8, no. 11 (2012): 4681–90. http://dx.doi.org/10.1021/ct300479h.

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Kamath, Ganesh, Olgun Guvench, and Alexander D. MacKerell. "CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol." Journal of Chemical Theory and Computation 4, no. 5 (2008): 765–78. http://dx.doi.org/10.1021/ct800019u.

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