1
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Montgomery JM, Lemkul JA. Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer. J Phys Chem B 2024. [PMID: 39038441 DOI: 10.1021/acs.jpcb.4c01634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The cell membrane functions as a semipermeable barrier that governs the transport of materials into and out of cells. The bilayer features a distinct dielectric gradient due to the amphiphilic nature of its lipid components. This gradient influences various aspects of small molecule permeation and the folding and functioning of membrane proteins. Here, we employ polarizable molecular dynamics simulations to elucidate the impact of the electronic environment on the permeation process. We simulated eight distinct amino-acid side chain analogs within a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer using the Drude polarizable force field (FF). Our approach includes both unbiased and umbrella sampling simulations. By using a polarizable FF, we sought to investigate explicit dipole responses in relation to local electric fields along the membrane normal. We evaluate molecular dipole moments, which exhibit variation based on their localization within the membrane, and compare the outcomes with analogous simulations using the nonpolarizable CHARMM36 FF. This comparative analysis aims to discern characteristic differences in the free energy surfaces of permeation for the various amino-acid analogs. Our results provide the first systematic quantification of the impact of employing an explicitly polarizable FF in this context compared to the fixed-charge convention inherent to nonpolarizable FFs, which may not fully capture the influence of the membrane dielectric gradient.
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Affiliation(s)
- Julia M Montgomery
- Department of Biochemistry, Virginia Tech, Blacksburg ,Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg ,Virginia 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg ,Virginia 24061, United States
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2
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Paul A, Chakrabarti J. Dynamics of an aqueous suspension of short hyaluronic acid chains near a DPPC bilayer. Phys Chem Chem Phys 2024. [PMID: 39021115 DOI: 10.1039/d4cp01088d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The synergy between hyaluronic acid (HA) and lipid molecules plays a crucial role in synovial fluids, cell coatings, etc. Diseased cells in cancer and arthritis show changes in HA concentration and chain size, impacting the viscoelastic and mechanical properties of the cells. Although the solution behavior of HA is known in experiments, a molecular-level understanding of the role of HA in the dynamics at the interface of HA-water and the cellular boundary is lacking. Here, we perform atomistic molecular dynamics simulation of short HA chains in an explicit water solvent in the presence of a DPPC bilayer, relevant in pathological cases. We identify a stable interface between HA-water and the bilayer where the water molecules are in contact with the bilayer and the HA chains are located away without any direct contact. Both translation and rotation of the interfacial waters in contact with the lipid bilayer and translation of the HA chains exhibit subdiffusive behavior. The diffusive behavior sets in slightly away from the bilayer, where the diffusion coefficients of water and HA decrease monotonically with increase in HA concentration. On the contrary, the dependence on HA chain size is only marginal due to enhanced chain flexibility as their size increases.
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Affiliation(s)
- Anirban Paul
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block JD, Sector - III, Salt Lake, Kolkata 700106, India.
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block JD, Sector - III, Salt Lake, Kolkata 700106, India.
- Department of Chemical and Biological Sciences and the Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
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3
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Zhong Z, Ulmschneider MB, Lorenz CD. Unraveling the Molecular Dance: Insights into TREM2/DAP12 Complex Formation in Alzheimer's Disease through Molecular Dynamics Simulations. ACS OMEGA 2024; 9:28715-28725. [PMID: 38973875 PMCID: PMC11223195 DOI: 10.1021/acsomega.4c03060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024]
Abstract
Alzheimer's disease (AD) is a widespread neurodegenerative condition affecting millions globally. Recent research has implicated variants of the triggering receptor expressed in myeloid cells 2 (TREM2) as risk factors for AD. TREM2, an immunomodulatory receptor on microglial surfaces, plays a pivotal role in regulating microglial activation by association with DNAX-activation protein 12 (DAP12). Despite its significance, the mechanism underlying the formation of the complex between the transmembrane domains (TMDs) of TREM2 and DAP12 remains unclear. This study employs multiscale molecular dynamics (MD) simulations to investigate three TMD complex models, including two derived from experiments and one generated by AlphaFold2. Conducted within a lipid membrane consisting of an 80:20 mixture of phosphatidylcholine (POPC) and cholesterol, our analysis reveals hydrogen-bonding interactions between K26 of TREM2 and D16 of DAP12 in all three models, consistent with previous experimental findings. Our results elucidate the different spatial conformations observed in the models and offer insights into the structure of the TREM2/DAP12 TMD complex. Furthermore, we elucidate the role of charged residues in the assembly structure of the complex within the lipid membrane. These findings enhance our understanding of the molecular mechanism governing TREM2/DAP12 complex formation, providing a foundation for designing novel therapeutic strategies to address AD and other neurodegenerative diseases.
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Affiliation(s)
- Zhiwen Zhong
- Biological
Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K.
- Department
of Chemistry, King’s College London, London SE1 1DB, U.K.
| | | | - Christian D. Lorenz
- Biological
Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K.
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4
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Dettmann LF, Kühn O, Ahmed AA. Martini-Based Coarse-Grained Soil Organic Matter Model Derived from Atomistic Simulations. J Chem Theory Comput 2024; 20:5291-5305. [PMID: 38831535 DOI: 10.1021/acs.jctc.4c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The significance of soil organic matter (SOM) in environmental contexts, particularly its role in pollutant adsorption, has prompted an increased utilization of molecular simulations to understand microscopic interactions. This study introduces a coarse-grained SOM model, parametrized within the framework of the versatile Martini 3 force field. Utilizing models generated by the Vienna Soil Organic Matter Modeler 2, which constructs humic substance systems from a fragment database, we employed Swarm-CG to parametrize the fragments and subsequently assembled them into macromolecules. Direct Boltzmann inversion (DBI) facilitated the determination of bonded parameters between fragments. The parametrization yielded favorable agreement in the radius of gyration and solvent-accessible surface area. Transfer free energies exhibited a strong correlation with hexadecane-water and chloroform-water values, albeit deviations were noted for octanol-water values. Comparing densities of modeled Leonardite humic acid systems at coarse-grained and atomistic levels revealed promising agreement, particularly at higher water concentrations. The DBI approach effectively reproduced average values of bonded interactions between fragments. Radial distribution functions between carboxylate groups and calcium ions showed partial agreement, however, reproducing certain peaks was challenging due to fixed bead sizes. Detailed analysis of atomistic systems revealed different configurations between the groups, explaining discrepancies. The present contribution provides a comprehensive insight into the properties, strengths, and weaknesses of the coarse-grained SOM model, serving as a foundation for future investigations encompassing pollutant interactions and varied SOM compositions.
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Affiliation(s)
- Lorenz F Dettmann
- Institute of Physics, University of Rostock, Albert-Einstein-Street 23-24, Rostock D-18059, Germany
| | - Oliver Kühn
- Institute of Physics, University of Rostock, Albert-Einstein-Street 23-24, Rostock D-18059, Germany
- Department of Life, Light and Matter (LLM), University of Rostock, Albert-Einstein-Street 25, Rostock D-18059, Germany
| | - Ashour A Ahmed
- Department of Life, Light and Matter (LLM), University of Rostock, Albert-Einstein-Street 25, Rostock D-18059, Germany
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5
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Latham AP, Zhu L, Sharon DA, Ye S, Willard AP, Zhang X, Zhang B. Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.30.534967. [PMID: 37034777 PMCID: PMC10081284 DOI: 10.1101/2023.03.30.534967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences to the physical properties of condensates, i.e., the molecular grammar, are hampered by a lack of effective approaches for probing high-resolution structural details. Using a combination of multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored a series of systems consisting of diblock elastin-like polypeptides (ELP). The simulations succeeded in reproducing the variation of condensate stability upon amino acid substitution and revealed different microenvironments within a single condensate, which we verified with environmentally sensitive fluorophores. The interspersion of hydrophilic and hydrophobic residues and a lack of secondary structure formation result in an interfacial environment, which explains both the strong correlation between ELP condensate stability and interfacial hydrophobicity scales, as well as the prevalence of protein-water hydrogen bonds. Our study uncovers new mechanisms for condensate stability and organization that may be broadly applicable.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Longchen Zhu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Dina A Sharon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Songtao Ye
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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6
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Chisholm LO, Jaeger NM, Murawsky HE, Harms MJ. S100A9 interacts with a dynamic region on CD14 to activate Toll-like receptor 4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594416. [PMID: 38798518 PMCID: PMC11118535 DOI: 10.1101/2024.05.15.594416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
S100A9 is a Damage Associated Molecular Pattern (DAMP) that activates inflammatory pathways via Toll-like receptor 4 (TLR4). This activity plays important homeostatic roles in tissue repair, but can also contribute to inflammatory diseases. The mechanism of activation is unknown. Here, we follow up on a previous observation that the protein CD14 is an important co-receptor that enables S100A9 to activate TLR4. Using cell-based functional assays and a combination of mutations and pharmocological perturbations, we found that CD14 must be membrane bound to potentiate TLR4 activation by S100A9. Additionally, S100A9 is sensitive to inhibitors of pathways downstream of TLR4 internalization. Together, this suggests that S100A9 induces activity via CD14-dependent internalization of TLR4. We then used mutagenesis, structural modeling, and in vitro binding experiments to establish that S100A9 binds to CD14's N-terminus in a region that overlaps with, but is not identical to, the region where CD14 binds its canonical ligand, lipopolysaccharide (LPS). In molecular dynamics simulations, this region of the protein is dynamic, allowing it to reorganize to recognize both S100A9 (a soluble protein) and LPS (a small hydrophobic molecule). Our work is the first attempt at a molecular characterization of the S100A9/CD14 interaction, bringing us one step closer to unraveling the full mechanism by which S100A9 activates TLR4/MD-2.
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7
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Zhuang Y, Quirk S, Stover ER, Bureau HR, Allen CR, Hernandez R. Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes. J Phys Chem B 2024; 128:2100-2113. [PMID: 38412510 PMCID: PMC10926100 DOI: 10.1021/acs.jpcb.3c08199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The ability of antimicrobial peptides to efficiently kill their bacterial targets depends on the efficiency of their binding to the microbial membrane. In the case of enterocins, there is a three-part interaction: initial binding, unpacking of helices on the membrane surface, and permeation of the lipid bilayer. Helical unpacking is driven by disruption of the peptide hydrophobic core when in contact with membranes. Enterocin 7B is a leaderless enterocin antimicrobial peptide produced from Enterococcus faecalis that functions alone, or with its cognate partner enterocin 7A, to efficiently kill a wide variety of Gram-stain positive bacteria. To better characterize the role that tertiary structural plasticity plays in the ability of enterocin 7B to interact with the membranes, a series of arginine single-site mutants were constructed that destabilize the hydrophobic core to varying degrees. A series of experimental measures of structure, stability, and function, including CD spectra, far UV CD melting profiles, minimal inhibitory concentrations analysis, and release kinetics of calcein, show that decreased stabilization of the hydrophobic core is correlated with increased efficiency of a peptide to permeate membranes and in killing bacteria. Finally, using the computational technique of adaptive steered molecular dynamics, we found that the atomistic/energetic landscape of peptide mechanical unfolding leads to free energy differences between the wild type and its mutants, whose trends correlate well with our experiment.
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Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, United States
| | - Erica R Stover
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hailey R Bureau
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Caley R Allen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science & Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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Guo SC, Shen R, Roux B, Dinner AR. Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP. Nat Commun 2024; 15:1408. [PMID: 38360718 PMCID: PMC10869754 DOI: 10.1038/s41467-024-45514-6] [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: 12/19/2022] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
The Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) is a membrane protein containing a voltage-sensing domain (VSD) that is homologous to VSDs from voltage-gated ion channels responsible for cellular excitability. Previously published crystal structures of Ci-VSD in putative resting and active conformations suggested a helical-screw voltage sensing mechanism in which the S4 helix translocates and rotates to enable exchange of salt-bridge partners, but the microscopic details of the transition between the resting and active conformations remained unknown. Here, by combining extensive molecular dynamics simulations with a recently developed computational framework based on dynamical operators, we elucidate the microscopic mechanism of the resting-active transition at physiological membrane potential. Sparse regression reveals a small set of coordinates that distinguish intermediates that are hidden from electrophysiological measurements. The intermediates arise from a noncanonical helical-screw mechanism in which translocation, rotation, and side-chain movement of the S4 helix are only loosely coupled. These results provide insights into existing experimental and computational findings on voltage sensing and suggest ways of further probing its mechanism.
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Affiliation(s)
- Spencer C Guo
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Rong Shen
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Benoît Roux
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
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9
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Bronkhorst AW, Lee CY, Möckel MM, Ruegenberg S, de Jesus Domingues AM, Sadouki S, Piccinno R, Sumiyoshi T, Siomi MC, Stelzl L, Luck K, Ketting RF. An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. EMBO J 2023; 42:e114072. [PMID: 37984437 PMCID: PMC10711660 DOI: 10.15252/embj.2023114072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) direct PIWI proteins to transposons to silence them, thereby preserving genome integrity and fertility. The piRNA population can be expanded in the ping-pong amplification loop. Within this process, piRNA-associated PIWI proteins (piRISC) enter a membraneless organelle called nuage to cleave their target RNA, which is stimulated by Gtsf proteins. The resulting cleavage product gets loaded into an empty PIWI protein to form a new piRISC complex. However, for piRNA amplification to occur, the new RNA substrates, Gtsf-piRISC, and empty PIWI proteins have to be in physical proximity. In this study, we show that in silkworm cells, the Gtsf1 homolog BmGtsf1L binds to piRNA-loaded BmAgo3 and localizes to granules positive for BmAgo3 and BmVreteno. Biochemical assays further revealed that conserved residues within the unstructured tail of BmGtsf1L directly interact with BmVreteno. Using a combination of AlphaFold modeling, atomistic molecular dynamics simulations, and in vitro assays, we identified a novel binding interface on the BmVreteno-eTudor domain, which is required for BmGtsf1L binding. Our study reveals that a single eTudor domain within BmVreteno provides two binding interfaces and thereby interconnects piRNA-loaded BmAgo3 and BmGtsf1L.
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Affiliation(s)
| | - Chop Y Lee
- International PhD Programme on Gene Regulation, Epigenetics & Genome StabilityMainzGermany
- Integrative Systems Biology GroupInstitute of Molecular BiologyMainzGermany
| | - Martin M Möckel
- Protein Production Core FacilityInstitute of Molecular BiologyMainzGermany
| | - Sabine Ruegenberg
- Protein Production Core FacilityInstitute of Molecular BiologyMainzGermany
| | - Antonio M de Jesus Domingues
- Biology of Non‐coding RNA GroupInstitute of Molecular BiologyMainzGermany
- Present address:
Dewpoint Therapeutics GmbHDresdenGermany
| | - Shéraz Sadouki
- Biology of Non‐coding RNA GroupInstitute of Molecular BiologyMainzGermany
| | - Rossana Piccinno
- Microscopy Core FacilityInstitute of Molecular BiologyMainzGermany
| | - Tetsutaro Sumiyoshi
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- Present address:
Department of Medical Innovations, Osaka Research Center for Drug DiscoveryOtsuka Pharmaceutical Co., Ltd.OsakaJapan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Lukas Stelzl
- Faculty of BiologyJohannes Gutenberg University MainzMainzGermany
- KOMET 1, Institute of PhysicsJohannes Gutenberg University MainzMainzGermany
| | - Katja Luck
- Integrative Systems Biology GroupInstitute of Molecular BiologyMainzGermany
| | - René F Ketting
- Biology of Non‐coding RNA GroupInstitute of Molecular BiologyMainzGermany
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg UniversityMainzGermany
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10
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Vuković F, Garcia NA, Perera S, Turchi M, Andersson MP, Solvang M, Raiteri P, Walsh TR. Atomistic simulations of calcium aluminosilicate interfaced with liquid water. J Chem Phys 2023; 159:104704. [PMID: 37694746 DOI: 10.1063/5.0164817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
The dissolution behavior of calcium aluminosilicate based glass fibers, such as stone wool fibers, is an important consideration in mineral wool applications for both the longevity of the mineral wool products in humid environments and limiting the health impacts of released and inhaled fibers from the mineral wool product. Balancing these factors requires a molecular-level understanding of calcium aluminosilicate glass dissolution mechanisms, details that are challenging to resolve with experiment alone. Molecular dynamics simulations are a powerful tool capable of providing complementary atomistic insights regarding dissolution; however, they require force fields capable of describing not-only the calcium aluminosilicate surface structure but also the interactions relevant to dissolution phenomena. Here, a new force field capable of describing amorphous calcium aluminosilicate surfaces interfaced with liquid water is developed by fitting parameters to experimental and first principles simulation data of the relevant oxide-water interfaces, including ab initio molecular dynamics simulations performed for this work for the wüstite and periclase interfaces. Simulations of a calcium aluminosilicate surface interfaced with liquid water were used to test this new force field, suggesting moderate ingress of water into the porous glass interface. This design of the force field opens a new avenue for the further study of calcium and network-modifier dissolution phenomena in calcium aluminosilicate glasses and stone wool fibers at liquid water interfaces.
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Affiliation(s)
- F Vuković
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - N A Garcia
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - S Perera
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - M Turchi
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - M P Andersson
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - M Solvang
- Group Research and Development, ROCKWOOL A/S, 2640 Hedehusene, Denmark
| | - P Raiteri
- Curtin Institute for Computation/The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, Perth, Western Australia 6845, Australia
| | - T R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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11
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Thota N, Quirk S, Zhuang Y, Stover ER, Lieberman RL, Hernandez R. Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin. Biophys J 2023; 122:2921-2937. [PMID: 36461639 PMCID: PMC10398266 DOI: 10.1016/j.bpj.2022.11.2941] [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: 08/23/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The actin filament network is in part remodeled by the action of a family of filament severing proteins that are responsible for modulating the ratio between monomeric and filamentous actin. Recent work on the protein actophorin from the amoeba Acanthamoeba castellani identified a series of site-directed mutations that increase the thermal stability of the protein by 22°C. Here, we expand this observation by showing that the mutant protein is also significantly stable to both equilibrium and kinetic chemical denaturation, and employ computer simulations to account for the increase in thermal or chemical stability through an accounting of atomic-level interactions. Specifically, the potential of mean force (PMF) can be obtained from steered molecular dynamics (SMD) simulations in which a protein is unfolded. However, SMD can be inefficient for large proteins as they require large solvent boxes, and computationally expensive as they require increasingly many SMD trajectories to converge the PMF. Adaptive steered molecular dynamics (ASMD) overcomes the second of these limitations by steering the particle in stages, which allows for convergence of the PMF using fewer trajectories compared with SMD. Use of the telescoping water scheme within ASMD partially overcomes the first of these limitations by reducing the number of waters at each stage to only those needed to solvate the structure within a given stage. In the PMFs obtained from ASMD, the work of unfolding Acto-2 was found to be higher than the Acto-WT by approximately 120 kCal/mol and reflects the increased stability seen in the chemical denaturation experiments. The evolution of the average number of hydrogen bonds and number of salt bridges during the pulling process provides a mechanistic view of the structural changes of the actophorin protein as it is unfolded, and how it is affected by the mutation in concert with the energetics reported through the PMF.
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Affiliation(s)
- Nikhil Thota
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | | | - Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Erica R Stover
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Rigoberto Hernandez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland; Department of Chemistry, Johns Hopkins University, Baltimore, Maryland; Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland.
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12
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Murphy EJ, Fehrenbach GW, Abidin IZ, Buckley C, Montgomery T, Pogue R, Murray P, Major I, Rezoagli E. Polysaccharides-Naturally Occurring Immune Modulators. Polymers (Basel) 2023; 15:polym15102373. [PMID: 37242947 DOI: 10.3390/polym15102373] [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: 03/04/2023] [Revised: 05/06/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The prevention of disease and infection requires immune systems that operate effectively. This is accomplished by the elimination of infections and abnormal cells. Immune or biological therapy treats disease by either stimulating or inhibiting the immune system, dependent upon the circumstances. In plants, animals, and microbes, polysaccharides are abundant biomacromolecules. Due to the intricacy of their structure, polysaccharides may interact with and impact the immune response; hence, they play a crucial role in the treatment of several human illnesses. There is an urgent need for the identification of natural biomolecules that may prevent infection and treat chronic disease. This article addresses some of the naturally occurring polysaccharides of known therapeutic potential that have already been identified. This article also discusses extraction methods and immunological modulatory capabilities.
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Affiliation(s)
- Emma J Murphy
- Shannon Applied Biotechnology Centre, Midwest Campus, Technological University of the Shannon, V94EC5T Limerick, Ireland
- LIFE-Health and Biosciences Research Institute, Midwest Campus, Technological University of the Shannon, V94EC5T Limerick, Ireland
- PRISM, Research Institute, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
| | - Gustavo Waltzer Fehrenbach
- PRISM, Research Institute, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- Applied Polymer Technologies, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
| | - Ismin Zainol Abidin
- PRISM, Research Institute, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- Applied Polymer Technologies, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
| | - Ciara Buckley
- PRISM, Research Institute, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- Applied Polymer Technologies, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
| | - Therese Montgomery
- School of Science and Computing, Atlantic Technological University, H91 T8NW Galway, Ireland
| | - Robert Pogue
- Universidade Católica de Brasilia, QS 7 LOTE 1-Taguatinga, Brasília 71680-613, DF, Brazil
| | - Patrick Murray
- Shannon Applied Biotechnology Centre, Midwest Campus, Technological University of the Shannon, V94EC5T Limerick, Ireland
- LIFE-Health and Biosciences Research Institute, Midwest Campus, Technological University of the Shannon, V94EC5T Limerick, Ireland
| | - Ian Major
- PRISM, Research Institute, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
- Applied Polymer Technologies, Midlands Campus, Technological University of the Shannon, N37 HD68 Athlone, Ireland
| | - Emanuele Rezoagli
- Department of Emergency and Intensive Care, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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13
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Hasan MR, Niebuur BJ, Siebrecht M, Kuttich B, Schweins R, Widmer-Cooper A, Kraus T. The Colloidal Stability of Apolar Nanoparticles in Solvent Mixtures. ACS NANO 2023; 17:9302-9312. [PMID: 37163685 DOI: 10.1021/acsnano.3c00812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Solvent engineering is a powerful and versatile method to tune colloidal stability. Here, we link the molecular structure of apolar ligand shells on gold nanoparticles with their colloidal stability in solvent mixtures. The agglomeration temperature of the particles was measured with small-angle X-ray scattering. It depended on solvent composition and changed linearly for hexane-hexadecane mixtures, but nonlinearly for cyclohexane-hexadecane and hexanol-hexadecane mixtures. Molecular dynamics (MD) simulations indicate that agglomeration is dominated by temperature-dependent ligand order in the alkane mixtures and that the temperature at which the ligand shell orders depends on the solvent composition near the ligands, which can differ substantially from the bulk composition. Small-angle neutron scattering confirmed that, at intermediate solvent compositions above the agglomeration temperature, the fraction of cyclohexane near the ligands was larger than in the bulk. The enrichment of cyclohexane near the ligands stabilized their disordered state, which, consequently, led to the experimentally observed nonlinear trend of the agglomeration temperature. In contrast, hexanol was depleted from the ligand shell at all temperatures. This again stabilized the disordered state. Furthermore, we found that agglomeration at high hexanol fractions was driven by a solvophobic effect that exceeded the influence of ligand order. The results show that strong nonlinearities in the colloidal stability of nanoparticle dispersions in solvent mixtures are directly linked to the molecular details of ligand-solvent and solvent-solvent interactions, which can be used to precisely tune stability.
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Affiliation(s)
- Mohammad Rashedul Hasan
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bart-Jan Niebuur
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Martin Siebrecht
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Björn Kuttich
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Ralf Schweins
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, 66123 Sydney, New South Wales, Australia
| | - Tobias Kraus
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
- Colloid and Interface Chemistry, Saarland University, Campus D2 2, 66123 Saarbrücken, Germany
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14
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Sun K, Shoaib T, Rutland MW, Beller J, Do C, Espinosa-Marzal RM. Insight into the assembly of lipid-hyaluronan complexes in osteoarthritic conditions. Biointerphases 2023; 18:021005. [PMID: 37041102 DOI: 10.1116/6.0002502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Interactions between molecules in the synovial fluid and the cartilage surface may play a vital role in the formation of adsorbed films that contribute to the low friction of cartilage boundary lubrication. Osteoarthritis (OA) is the most common degenerative joint disease. Previous studies have shown that in OA-diseased joints, hyaluronan (HA) not only breaks down resulting in a much lower molecular weight (MW), but also its concentration is reduced ten times. Here, we have investigated the structural changes of lipid-HA complexes as a function of HA concentration and MW to simulate the physiologically relevant conditions that exist in healthy and diseased joints. Small angle neutron scattering and dynamic light scattering were used to determine the structure of HA-lipid vesicles in bulk solution, while a combination of atomic force microscopy and quartz crystal microbalance was applied to study their assembly on a gold surface. We infer a significant influence of both MW and HA concentrations on the structure of HA-lipid complexes in bulk and assembled on a gold surface. Our results suggest that low MW HA cannot form an amorphous layer on the gold surface, which is expected to negatively impact the mechanical integrity and longevity of the boundary layer and could contribute to the increased wear of the cartilage that has been reported in joints diseased with OA.
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Affiliation(s)
- Kangdi Sun
- Materials Science and Engineering Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Tooba Shoaib
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | - Mark W Rutland
- KTH Royal Institute of Technology, Department of Chemistry, Stockholm SE-100 44, Sweden; School of Chemistry, University of New South Wales, Sydney 2052, Australia; Laboratoire de Tribologie et Dynamique des Systèmes, École Centrale de Lyon, Lyon 69130, France; and Bioeconomy and Health, Materials and Surface Design, RISE Research Institutes of Sweden, Stockholm, Sweden
| | | | - Changwoo Do
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | - Rosa M Espinosa-Marzal
- Materials Science and Engineering Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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15
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Jiao M, Dai L, Ren HR, Zhang M, Xiao X, Wang B, Yang J, Liu B, Zhou G, Cheng HM. A Polarized Gel Electrolyte for Wide-Temperature Flexible Zinc-Air Batteries. Angew Chem Int Ed Engl 2023; 62:e202301114. [PMID: 36869006 DOI: 10.1002/anie.202301114] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/05/2023]
Abstract
The development of flexible zinc-air batteries (FZABs) has attracted broad attention in the field of wearable electronic devices. Gel electrolyte is one of the most important components in FZABs, which is urgent to be optimized to match with Zn anode and adapt to severe climates. In this work, a polarized gel electrolyte of polyacrylamide-sodium citric (PAM-SC) is designed for FZABs, in which the SC molecules contain large amount of polarized -COO- functional groups. The polarized -COO- groups can form an electrical field between gel electrolyte and Zn anode to suppress Zn dendrite growth. Besides, the -COO- groups in PAM-SC can fix H2 O molecules, which prevents water from freezing and evaporating. The polarized PAM-SC hydrogel delivers a high ionic conductivity of 324.68 mS cm-1 and water retention of 96.85 % after being exposed for 96 h. FZABs with the PAM-SC gel electrolyte exhibit long cycling life of 700 cycles at -40 °C, showing the application prospect under extreme conditions.
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Affiliation(s)
- Miaolun Jiao
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Lixin Dai
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Hong-Rui Ren
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Mengtian Zhang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xiao Xiao
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Boran Wang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Jinlong Yang
- College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Bilu Liu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Guangmin Zhou
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Hui-Ming Cheng
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Shenyang, 110016, China
- Institute of Technology for Carbon Neutrality, Faculty of Materials Science and Energy Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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16
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Dorgan B, Liu Y, Wang S, Aduse-Opoku J, Whittaker SBM, Roberts MAJ, Lorenz CD, Curtis MA, Garnett JA. Structural Model of a Porphyromonas gingivalis type IX Secretion System Shuttle Complex. J Mol Biol 2022; 434:167871. [PMID: 36404438 DOI: 10.1016/j.jmb.2022.167871] [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: 05/28/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Porphyromonas gingivalis is a gram-negative oral anaerobic pathogen and is one of the key causative agents of periodontitis. P. gingivalis utilises a range of virulence factors, including the cysteine protease RgpB, to drive pathogenesis and these are exported and attached to the cell surface via the type IX secretion system (T9SS). All cargo proteins possess a conserved C-terminal signal domain (CTD) which is recognised by the T9SS, and the outer membrane β-barrel protein PorV (PG0027/LptO) can interact with cargo proteins as they are exported to the bacterial surface. Using a combination of solution nuclear magnetic resonance (NMR) spectroscopy, biochemical analyses, machine-learning-based modelling and molecular dynamics (MD) simulations, we present a structural model of a PorV:RgpB-CTD complex from P. gingivalis. This is the first structural insight into CTD recognition by the T9SS and shows how the conserved motifs in the CTD are the primary sites that mediate binding. In PorV, interactions with extracellular surface loops are important for binding the CTD, and together these appear to cradle and lock RgpB-CTD in place. This work provides insight into cargo recognition by PorV but may also have important implications for understanding other aspects of type-IX dependent secretion.
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Affiliation(s)
- Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yichao Liu
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Joseph Aduse-Opoku
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sara B-M Whittaker
- Institute of Cancer & Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mark A J Roberts
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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17
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Bełdowski P, Przybyłek M, Bełdowski D, Dedinaite A, Sionkowska A, Cysewski P, Claesson PM. Collagen type II-hyaluronan interactions - the effect of proline hydroxylation: a molecular dynamics study. J Mater Chem B 2022; 10:9713-9723. [PMID: 36413305 DOI: 10.1039/d2tb01550a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Hyaluronan-collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents the results from molecular dynamics calculations of HA-collagen type II interactions with hyaluronan. The applied protocol employed docking and geometry optimization of complexes built using collagen structures with different numbers of hydroxyl groups attached to proline moieties. It was established that the hydroxyproline/proline ratio affects both structural and energetic features of the collagen-hyaluronan complex. Proline hydroxylation was found to significantly influence the number of all identified types of molecular forces, hydrophobic interactions, water bridges and hydrogen bonds, which can be formed between collagen and hyaluronan. Importantly, an increase in the hydroxyproline/proline ratio in the collagen chain increases the binding affinity for hyaluronan. This is illustrated by the linear correlation between the binding free energy and the hydroxylation degree. A comparison of the results obtained for 3 and 4 hydroxylation of proline indicates that the hydroxyl group attachment position plays a minor role in complex stabilization. However, a slightly stronger affinity was observed for 4 hydroxylation. In order to evaluate the effect of the aqueous environment on the collagen-hyaluronan complex stability, the enthalpic and entropic contributions to the free energy of solvation were analyzed.
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Affiliation(s)
- Piotr Bełdowski
- Institute of Mathematics and Physics, Bydgoszcz University of Science and Technology, al. Kaliskiego 7, 85-796 Bydgoszcz, Poland.
| | - Maciej Przybyłek
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
| | - Damian Bełdowski
- Institute of Mathematics, Jagiellonian University, Lukasiewicza 6, 30-348 Kraków, Poland
| | - Andra Dedinaite
- Division of Surface and Corrosion Science, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.,KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Engineering Pedagogics, SE-100 44 Stockholm, Sweden
| | - Alina Sionkowska
- Department of Biomaterials and Cosmetics Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarin 7, 87-100 Toruń, Poland
| | - Piotr Cysewski
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
| | - Per M Claesson
- Division of Surface and Corrosion Science, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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18
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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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19
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Paul D, Paul A, Mukherjee D, Saroj S, Ghosal M, Pal S, Senapati D, Chakrabarti J, Pal SK, Rakshit T. A Mechanoelastic Glimpse on Hyaluronan-Coated Extracellular Vesicles. J Phys Chem Lett 2022; 13:8564-8572. [PMID: 36069730 DOI: 10.1021/acs.jpclett.2c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cancer cells secrete extracellular vesicles (EVs) covered with a carbohydrate polymer, hyaluronan (HA), linked to tumor malignancy. Herein, we have unravelled the contour lengths of HA on a single cancer cell-derived EV surface using single-molecule force spectroscopy (SMFS), which divulges the presence of low molecular weight HA (LMW-HA < 200 kDa). We also discovered that these LMW-HA-EVs are significantly more elastic than the normal cell-derived EVs. This intrinsic elasticity of cancer EVs could be directly allied to the LMW-HA abundance and associated labile water network on EV surface as revealed by correlative SMFS, hydration dynamics with fluorescence spectroscopy, and molecular dynamics simulations. This method emerges as a molecular biosensor of the cancer microenvironment.
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Affiliation(s)
- Debashish Paul
- Department of Chemistry, Shiv Nadar Institute of Eminence, Delhi-NCR, Tehsil Dadri UP 201314, Uttar Pradesh, India
| | - Anirban Paul
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Dipanjan Mukherjee
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Saroj Saroj
- Department of Chemistry, Shiv Nadar Institute of Eminence, Delhi-NCR, Tehsil Dadri UP 201314, Uttar Pradesh, India
| | - Manorama Ghosal
- Chemical Science Division, Saha Institute of Nuclear Physics, HBNI, Kolkata 700064, India
| | - Suchetan Pal
- Department of Chemistry, Indian Institute of Technology, Bhilai, CG 492015, India
| | - Dulal Senapati
- Chemical Science Division, Saha Institute of Nuclear Physics, HBNI, Kolkata 700064, India
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Samir Kumar Pal
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Tatini Rakshit
- Department of Chemistry, Shiv Nadar Institute of Eminence, Delhi-NCR, Tehsil Dadri UP 201314, Uttar Pradesh, India
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20
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Lechner BD, Smith P, McGill B, Marshall S, Trick JL, Chumakov AP, Winlove CP, Konovalov OV, Lorenz CD, Petrov PG. The Effects of Cholesterol Oxidation on Erythrocyte Plasma Membranes: A Monolayer Study. MEMBRANES 2022; 12:828. [PMID: 36135847 PMCID: PMC9506283 DOI: 10.3390/membranes12090828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Cholesterol plays a key role in the molecular and mesoscopic organisation of lipid membranes and it is expected that changes in its molecular structure (e.g., through environmental factors such as oxidative stress) may affect adversely membrane properties and function. In this study, we present evidence that oxidation of cholesterol has significant effects on the mechanical properties, molecular and mesoscopic organisation and lipid-sterol interactions in condensed monolayers composed of the main species found in the inner leaflet of the erythrocyte membrane. Using a combination of experimental methods (static area compressibility, surface dilatational rheology, fluorescence microscopy, and surface sensitive X-ray techniques) and atomistic molecular dynamics simulations, we show that oxidation of cholesterol to 7-ketocholesterol leads to stiffening of the monolayer (under both static and dynamic conditions), significant changes in the monolayer microdomain organisation, disruption in the van der Waals, electrostatic and hydrophobic interactions between the sterol and the other lipid species, and the lipid membrane hydration. Surface sensitive X-ray techniques reveal that, whilst the molecular packing mode is not significantly affected by cholesterol oxidation in these condensed phases, there are subtle changes in membrane thickness and a significant decrease in the coherence length in monolayers containing 7-ketocholesterol.
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Affiliation(s)
- Bob-Dan Lechner
- Department of of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL, UK
| | - Paul Smith
- Department of Physics, King’s College London, The Strand, London WC2R 2LS, UK
| | - Beth McGill
- Department of of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL, UK
| | - Skye Marshall
- Department of of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL, UK
| | - Jemma L. Trick
- Department of Physics, King’s College London, The Strand, London WC2R 2LS, UK
| | - Andrei P. Chumakov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Charles Peter Winlove
- Department of of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL, UK
| | - Oleg V. Konovalov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Christian D. Lorenz
- Department of Physics, King’s College London, The Strand, London WC2R 2LS, UK
| | - Peter G. Petrov
- Department of of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL, UK
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21
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Zhuang Y, Thota N, Quirk S, Hernandez R. Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics. J Chem Theory Comput 2022; 18:4649-4659. [PMID: 35830368 DOI: 10.1021/acs.jctc.2c00498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jarzynski's equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the required use of very large solvent boxes. We introduce telescoping box schemes within adaptive steered molecular dynamics (ASMD) in which we adjust the solvent box between stages and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long α-helical peptide, Ala30, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost.
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Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Nikhil Thota
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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22
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23
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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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24
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Derwich M, Lassmann L, Machut K, Zoltowska A, Pawlowska E. General Characteristics, Biomedical and Dental Application, and Usage of Chitosan in the Treatment of Temporomandibular Joint Disorders: A Narrative Review. Pharmaceutics 2022; 14:pharmaceutics14020305. [PMID: 35214037 PMCID: PMC8880239 DOI: 10.3390/pharmaceutics14020305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
The aim of this narrative review was to present research investigating chitosan, including its general characteristics, properties, and medical and dental applications, and finally to present the current state of knowledge regarding the efficacy of chitosan in the treatment of temporomandibular disorders (TMDs) based on the literature. The PICO approach was used for the literature search strategy. The PubMed database was analyzed with the following keywords: (“chitosan”[MeSH Terms] OR “chitosan”[All Fields] OR “chitosans”[All Fields] OR “chitosan s”[All Fields] OR “chitosane”[All Fields]) AND (“temporomandibular joint”[MeSH Terms] OR (“tem-poromandibular”[All Fields] AND “joint”[All Fields]) OR “temporomandibular joint”[All Fields] OR (“temporomandibular”[All Fields] AND “joints”[All Fields]) OR “temporo-mandibular joints”[All Fields]). After screening 8 results, 5 studies were included in this review. Chitosan presents many biological properties and therefore it can be widely used in several branches of medicine and dentistry. Chitosan promotes wound healing, helps to control bleeding, and is used in wound dressings, such as sutures and artificial skin. Apart from its antibacterial property, chitosan has many other properties, such as antifungal, mucoadhesive, anti-inflammatory, analgesic, antioxidant, antihyperglycemic, and antitumoral properties. Further clinical studies assessing the efficacy of chitosan in the treatment of TMD are required. According to only one clinical study, chitosan was effective in the treatment of TMD; however, better clinical results were obtained with platelet-rich plasma.
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Affiliation(s)
- Marcin Derwich
- ORTODENT, Specialist Orthodontic Private Practice in Grudziadz, 86-300 Grudziadz, Poland
- Correspondence: ; Tel.: +48-660-723-164
| | - Lukasz Lassmann
- Dental Sense, Dental Private Practice in Gdansk, 80-283 Gdansk, Poland;
| | - Katarzyna Machut
- Department of Endodontic Dentistry, Medical University of Gdansk, 80-210 Gdansk, Poland; (K.M.); (A.Z.)
| | - Agata Zoltowska
- Department of Endodontic Dentistry, Medical University of Gdansk, 80-210 Gdansk, Poland; (K.M.); (A.Z.)
| | - Elzbieta Pawlowska
- Department of Orthodontics, Medical University of Lodz, 90-419 Lodz, Poland;
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Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. SCIENCE ADVANCES 2021; 7:eabh3355. [PMID: 34433568 PMCID: PMC8386928 DOI: 10.1126/sciadv.abh3355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/02/2021] [Indexed: 05/26/2023]
Abstract
The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of the SLC15 family is their extreme substrate promiscuity, which has enabled the targeting of these transporters for the improvement of oral bioavailability for several prodrug molecules. Although recent structural and biochemical studies on bacterial homologs have identified conserved sites of proton and peptide binding, the mechanism of peptide capture and ligand promiscuity remains unclear for mammalian family members. Here, we present the cryo-electron microscopy structure of the outward open conformation of the rat peptide transporter PepT2 in complex with an inhibitory nanobody. Our structure, combined with molecular dynamics simulations and biochemical and cell-based assays, establishes a framework for understanding peptide and prodrug recognition within this pharmaceutically important transporter family.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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Yee SM, Lorenz CD. On the Structure and Flip-flop of Free Docosahexaenoic Acid in a Model Human Brain Membrane. J Phys Chem B 2021; 125:8038-8047. [PMID: 34270235 DOI: 10.1021/acs.jpcb.1c03929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among the omega-3 fatty acids, docosahexaenoic acid (DHA, sn22:6) is particularly vital in human brain cell membranes. There is considerable interest in DHA because low-level DHA has been associated with declined cognitive function and poor visual acuity. In this work, atomistic molecular dynamics simulations were used to investigate the effects of free protonated DHA (DHAP) in molar fractions of 0, 17, 30, and 38% in a realistic model of a healthy brain cell membrane comprising 26 lipid types. Numerous flip-flop events of DHAP were observed and categorized as successful or aborted. Novel use of the machine learning technique, density-based spatial clustering of applications with noise (DBSCAN), effectively identified flip-flop events by way of clustering. Our data show that increasing amounts of DHAP in the membrane disorder the bilayer packing, fluidize the membrane, and increase the rates of successful flip-flop from k = 0.2 μs-1 (17% DHAP) to 0.8 μs-1 (30% DHAP) and to 1.3 μs-1 (38% DHAP). In addition, we also provided a detailed understanding of the flip-flop mechanism of DHAP across this complex membrane. Interestingly, we noted the role of hydrogen bonds in two distinct coordinated flip-flop phenomena between two DHAP molecules: double flip-flop and assisted flip-flop. Understanding the effects of various concentrations of DHAP on the dynamics within a lipid membrane and the resulting structural properties of the membrane are important when considering the use of DHAP as a dietary supplement or as a potential therapeutic.
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Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
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27
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Rook ML, Miaro M, Couch T, Kneisley DL, Musgaard M, MacLean DM. Mutation of a conserved glutamine residue does not abolish desensitization of acid-sensing ion channel 1. THE JOURNAL OF GENERAL PHYSIOLOGY 2021; 153:212203. [PMID: 34061161 PMCID: PMC8167889 DOI: 10.1085/jgp.202012855] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/13/2021] [Indexed: 12/14/2022]
Abstract
Desensitization is a common feature of ligand-gated ion channels, although the molecular cause varies widely between channel types. Mutations that greatly reduce or nearly abolish desensitization have been described for many ligand-gated ion channels, including glutamate, GABA, glycine, and nicotinic receptors, but not for acid-sensing ion channels (ASICs) until recently. Mutating Gln276 to a glycine (Q276G) in human ASIC1a was reported to mostly abolish desensitization at both the macroscopic and the single channel levels, potentially providing a valuable tool for subsequent studies. However, we find that in both human and chicken ASIC1, the effect of Q276G is modest. In chicken ASIC1, the equivalent Q277G slightly reduces desensitization when using pH 6.5 as a stimulus but desensitizes, essentially like wild-type, when using more acidic pH values. In addition, steady-state desensitization is intact, albeit right-shifted, and recovery from desensitization is accelerated. Molecular dynamics simulations indicate that the Gln277 side chain participates in a hydrogen bond network that might stabilize the desensitized conformation. Consistent with this, destabilizing this network with the Q277N or Q277L mutations largely mimics the Q277G phenotype. In human ASIC1a, the Q276G mutation also reduces desensitization, but not to the extent reported previously. Interestingly, the kinetic consequences of Q276G depend on the human variant used. In the common G212 variant, Q276G slows desensitization, while in the rare D212 variant desensitization accelerates. Our data reveal that while the Q/G mutation does not abolish or substantially impair desensitization as previously reported, it does point to unexpected differences between chicken and human ASICs and the need for careful scrutiny before using this mutation in future studies.
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Affiliation(s)
- Matthew L Rook
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - Megan Miaro
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Tyler Couch
- Graduate Program in Cellular and Molecular Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - Dana L Kneisley
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - Maria Musgaard
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - David M MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
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28
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Wilson CJ, Chang M, Karttunen M, Choy WY. KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability. Int J Mol Sci 2021; 22:5408. [PMID: 34065616 PMCID: PMC8161161 DOI: 10.3390/ijms22105408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
We have performed 280 μs of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1) (G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim was to provide structural insight into the effects of these mutants, including a new class of ANCHOR (additionally NRF2-complexed hypomorph) mutant variants. Our work provides additional insight into the structural dynamics of mutants that could not be analyzed experimentally, painting a more complete picture of their mutagenic effects. Notably, blade-wise analysis of the Kelch domain points to stability as a possible target of cancer in KEAP1. Interestingly, structural analysis of the R470C ANCHOR mutant, the most prevalent missense mutation in KEAP1, revealed no significant change in structural stability or NRF2 binding site dynamics, possibly indicating an covalent modification as this mutant's mode of action.
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Affiliation(s)
- Carter J. Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
- Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
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A Bittersweet Computational Journey among Glycosaminoglycans. Biomolecules 2021; 11:biom11050739. [PMID: 34063530 PMCID: PMC8156566 DOI: 10.3390/biom11050739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 01/22/2023] Open
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiological and pathological processes by binding to different proteins, thus modulating their structure and function, and their concentration and availability in the microenvironment. Unfortunately, the enormous structural diversity of GAGs/PGs has hampered the development of dedicated analytical technologies and experimental models. Similarly, computational approaches (in particular, molecular modeling, docking and dynamics simulations) have not been fully exploited in glycobiology, despite their potential to demystify the complexity of GAGs/PGs at a structural and functional level. Here, we review the state-of-the art of computational approaches to studying GAGs/PGs with the aim of pointing out the “bitter” and “sweet” aspects of this field of research. Furthermore, we attempt to bridge the gap between bioinformatics and glycobiology, which have so far been kept apart by conceptual and technical differences. For this purpose, we provide computational scientists and glycobiologists with the fundamentals of these two fields of research, with the aim of creating opportunities for their combined exploitation, and thereby contributing to a substantial improvement in scientific knowledge.
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30
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Ziolek RM, Smith P, Pink DL, Dreiss CA, Lorenz CD. Unsupervised Learning Unravels the Structure of Four-Arm and Linear Block Copolymer Micelles. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02523] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert M. Ziolek
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
| | - Paul Smith
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
| | - Demi L. Pink
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
| | - Cécile A. Dreiss
- Institute of Pharmaceutical Science, King’s College London, London SE1 9NH, U.K
| | - Christian D. Lorenz
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
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31
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Harusawa K, Watanabe C, Kobori Y, Tomita K, Kitamura A, Kinjo M, Yanagisawa M. Membrane Surface Modulates Slow Diffusion in Small Crowded Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:437-444. [PMID: 33351626 DOI: 10.1021/acs.langmuir.0c03086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Membranes are ubiquitous structures in cells. The effects of membranes on various functional molecules have been reported, but their behaviors under macromolecular crowding and cell-sized confinement have not fully been understood. In this study, we model an intracellular environment by crowding micrometer-sized droplets and investigate the effects of membrane properties on molecular diffusion. The molecular diffusion inside small droplets covered with a lipid layer of phosphatidylcholine (PC) becomes slower compared with that of the corresponding bulk solutions under a crowding condition of polysaccharide dextran but not of its monomer unit, glucose. The addition of a poly(ethylene glycol) conjugated lipid (PEGylated lipid) to the PC membrane significantly alters the degree of slow diffusion observed inside small droplets of concentrated dextran. Interestingly, the change is not monotonic against dextran concentration; that is, the PEGylated membrane increases and decreases the degree of slow diffusion with increasing dextran concentration. We explain the nonmonotonic alternation from the increase in effective dextran concentration and the hindered temporal adsorption of dextran to the membrane. Because diffusion alteration by adding PEGylated lipid is observed for condensed small droplets of linear polymer PEG and hydrophilic protein bovine serum albumin, the phenomenon is general for other polymer systems as well. Furthermore, our findings may facilitate the understanding of intracellular molecular behaviors based on membrane effects as well as the development of numerous applications using polymer droplets.
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Affiliation(s)
- Kanae Harusawa
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Chiho Watanabe
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Yuta Kobori
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Kazuho Tomita
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Akira Kitamura
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Masataka Kinjo
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Miho Yanagisawa
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Basic Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
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32
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Vennelakanti V, Qi HW, Mehmood R, Kulik HJ. When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. Chem Sci 2021; 12:1147-1162. [PMID: 35382134 PMCID: PMC8908278 DOI: 10.1039/d0sc05084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023] Open
Abstract
Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction. Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.![]()
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Helena W. Qi
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Rimsha Mehmood
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Heather J. Kulik
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
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33
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Computer Simulation Study on Adsorption and Conformation of Polymer Chains Driven by External Force. CHINESE JOURNAL OF POLYMER SCIENCE 2020. [DOI: 10.1007/s10118-020-2491-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Smith P, Quinn PJ, Lorenz CD. Two Coexisting Membrane Structures Are Defined by Lateral and Transbilayer Interactions between Sphingomyelin and Cholesterol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9786-9799. [PMID: 32701297 DOI: 10.1021/acs.langmuir.0c01237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure of fully hydrated bilayers composed of equimolar proportions of palmitoylsphingomyelin (PSM) and cholesterol has been examined by synchrotron X-ray powder diffraction and atomistic molecular dynamics (MD) simulations. Two coexisting bilayer structures, which are distinguished by the transbilayer phosphate-phosphate distance of coupled PSM molecules, are observed by diffraction at 37 °C. The MD simulations reveal that PSM molecules in the thicker membrane are characterized by more ordered, more extended, and less interdigitated hydrocarbon tails compared to those in the thinner membrane. Intermolecular hydrogen bonds further distinguish the two bilayer structures, and we observe the disruption of a sphingomyelin intermolecular hydrogen bond network induced by the proximity of cholesterol. Through an unsupervised clustering of interatomic distances, we show for the first time that the asymmetry of phospholipids is important in driving their interactions with cholesterol. We identify four distinct modes of interaction, two of which lead to the dehydration of cholesterol. These two modes of interaction provide the first description of precise physical mechanisms underlying the umbrella model, which itself explains how phospholipids may shield cholesterol from water. The most dehydrating mode of interaction is particular to the N-acylated fatty acid moiety of PSM and thus may explain the long-held observation that cholesterol preferentially mixes with sphingomyelins over glycerophospholipids.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London, WC2R 2LS, U.K
| | - Peter J Quinn
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
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The Role of Hyaluronic Acid in Cartilage Boundary Lubrication. Cells 2020; 9:cells9071606. [PMID: 32630823 PMCID: PMC7407873 DOI: 10.3390/cells9071606] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 01/23/2023] Open
Abstract
Hydration lubrication has emerged as a new paradigm for lubrication in aqueous and biological media, accounting especially for the extremely low friction (friction coefficients down to 0.001) of articular cartilage lubrication in joints. Among the ensemble of molecules acting in the joint, phosphatidylcholine (PC) lipids have been proposed as the key molecules forming, in a complex with other molecules including hyaluronic acid (HA), a robust layer on the outer surface of the cartilage. HA, ubiquitous in synovial joints, is not in itself a good boundary lubricant, but binds the PC lipids at the cartilage surface; these, in turn, massively reduce the friction via hydration lubrication at their exposed, highly hydrated phosphocholine headgroups. An important unresolved issue in this scenario is why the free HA molecules in the synovial fluid do not suppress the lubricity by adsorbing simultaneously to the opposing lipid layers, i.e., forming an adhesive, dissipative bridge between them, as they slide past each other during joint articulation. To address this question, we directly examined the friction between two hydrogenated soy PC (HSPC) lipid layers (in the form of liposomes) immersed in HA solution or two palmitoyl-oleoyl PC (POPC) lipid layers across HA-POPC solution using a surface force balance (SFB). The results show, clearly and surprisingly, that HA addition does not affect the outstanding lubrication provided by the PC lipid layers. A possible mechanism indicated by our data that may account for this is that multiple lipid layers form on each cartilage surface, so that the slip plane may move from the midplane between the opposing surfaces, which is bridged by the HA, to an HA-free interface within a multilayer, where hydration lubrication is freely active. Another possibility suggested by our model experiments is that lipids in synovial fluid may complex with HA, thereby inhibiting the HA molecules from adhering to the lipids on the cartilage surfaces.
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Interactions of a short hyaluronan chain with a phospholipid membrane. Colloids Surf B Biointerfaces 2019; 184:110539. [PMID: 31629183 DOI: 10.1016/j.colsurfb.2019.110539] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/09/2019] [Accepted: 09/29/2019] [Indexed: 01/06/2023]
Abstract
Hyaluronic acid and phospholipids are two components that are present in the synovial fluid, and both are implicated as important facilitators of joint lubrication. In this work we aim to clarify how hyaluronic acid interacts with a phospholipid bilayer through their molecular interactions at the bilayer surface. To this end we performed molecular dynamics simulations of one hyaluronic acid molecule at a phospholipid bilayer in aqueous solution. The simulations were carried out for two aqueous solutions of equal concentrations, containing either NaCl or CaCl2. We analyzed hydrogen bonds, hydrophobic contacts and cation mediated bridges to clarify how hyaluoronic acid binds to a phospholipid bilayer. The analysis shows that calcium ions promote longer lasting bonds between the species as they create calcium ion bridges between the carboxylate group of hyaluronic acid and the phosphate group of the phospholipid. This type of additional bonding does not significantly influence the total number of contact created, but rather stabilizes the contact. The presented results can facilitate understanding of the role of hyaluronic acid and phospholipid interactions in terms of lubrication of articular cartilage.
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