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Jou IA, Yoo AS, Dionne EV, Brady JW. Potential of mean force conformational energy maps for disaccharide linkages of the Burkholderia multivorans exopolysaccharide C1576 in aqueous solution. Carbohydr Res 2023; 524:108741. [PMID: 36716692 PMCID: PMC9974804 DOI: 10.1016/j.carres.2023.108741] [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: 09/30/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
Potential of Mean Force Ramachandran energy maps in aqueous solution have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide from the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian complex that was isolated from a cystic fibrosis patient. C1576 is a rhamnomannan with a tetrasaccharide repeat unit. In general, for the four linkage types in this polymer, hydration did not produce dramatic changes in the Ramachandran energy surfaces, with the 3-methyl-α-d-rhamnopyranose-(1→3)-α-d-rhamnopyranose case exhibiting the greatest hydration change, with the global minimum energy conformation shifting by more than 80° in ψ. However, hydration did reduce the rigidity of all the linkages, increasing the overall flexibility of this polysaccharide.
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Affiliation(s)
- Ining A Jou
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew S Yoo
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Elyssa V Dionne
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
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Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
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Bernardino K, de Moura AF. Aggregation Thermodynamics of Sodium Octanoate Micelles Studied by Means of Molecular Dynamics Simulations. J Phys Chem B 2013; 117:7324-34. [DOI: 10.1021/jp312840y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kalil Bernardino
- Departamento de Química,
Centro de Ciências
Exatas e de Tecnologia, Universidade Federal de São Carlos, Rodovia Washington Luiz km 235, CP 676, CEP
13.565-905, São Carlos, São Paulo, Brazil
| | - André F. de Moura
- Departamento de Química,
Centro de Ciências
Exatas e de Tecnologia, Universidade Federal de São Carlos, Rodovia Washington Luiz km 235, CP 676, CEP
13.565-905, São Carlos, São Paulo, Brazil
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Snyder JA, Abramyan T, Yancey JA, Thyparambil AA, Wei Y, Stuart SJ, Latour RA. Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass. Biointerphases 2012; 7:56. [PMID: 22941539 PMCID: PMC3819814 DOI: 10.1007/s13758-012-0056-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/13/2012] [Indexed: 12/01/2022] Open
Abstract
Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.
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Affiliation(s)
- James A Snyder
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, SC 29634, USA
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Vellore NA, Yancey JA, Collier G, Latour RA, Stuart SJ. Assessment of the transferability of a protein force field for the simulation of peptide-surface interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:7396-404. [PMID: 20222735 PMCID: PMC2868960 DOI: 10.1021/la904415d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (DeltaG(ads)) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host-guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. DeltaG(ads) was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent DeltaG(ads) within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results clearly show that improvements in force field parameterization are needed in order to accurately represent interactions between amino acid residues and functional groups of a surface and they provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior.
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Affiliation(s)
- Nadeem A Vellore
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA
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Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC. ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent. J Chem Theory Comput 2010; 6:1753-68. [DOI: 10.1021/ct100086j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daria B. Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Stefano Corni
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Peter J. Winn
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Martin Hoefling
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Kay E. Gottschalk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
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Latour RA. Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions. Biointerphases 2008; 3:FC2-12. [PMID: 19809597 PMCID: PMC2756768 DOI: 10.1116/1.2965132] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field molecular simulation methods have enormous potential to address this problem by providing an approach to directly investigate the adsorption behavior of peptides and proteins at the atomic level. As with any type of technology, however, these methods must be appropriately developed and applied if they are to provide realistic and useful results. Three issues that are particularly important for the accurate simulation of protein adsorption behavior are the selection of a valid force field to represent the atomic-level interactions involved, the accurate representation of solvation effects, and system sampling. In this article, each of these areas is addressed and future directions for continued development are presented.
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Affiliation(s)
- Robert A Latour
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA.
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Suzuki T, Kawashima H, Kotoku H, Sota T. Structural Fluctuation and Dynamics of Ribose Puckering in Aqueous Solution from First Principles. J Phys Chem B 2005; 109:12997-3005. [PMID: 16852613 DOI: 10.1021/jp050475i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of beta-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm(-1). Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of beta-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of beta-ribofuranose puckering between two hydroxymethyl rotamers.
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Affiliation(s)
- Teppei Suzuki
- Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.
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