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Tatulian SA. Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy. Phys Chem Chem Phys 2024; 26:21930-21953. [PMID: 39108200 DOI: 10.1039/d4cp01136h] [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: 08/23/2024]
Abstract
The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA.
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2
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Vásquez E, Oresti GM, Paez MD, Callegari EA, Masone D, Muñoz EM. Impact of aging on the GABA B receptor-mediated connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606013. [PMID: 39131332 PMCID: PMC11312617 DOI: 10.1101/2024.07.31.606013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
GABA B receptors (GABABRs) are heterodimeric seven-transmembrane receptors that interact with a range of proteins and form large protein complexes on cholesterol-rich membrane microdomains. As the brain ages, membrane cholesterol levels exhibit alterations, although it remains unclear how these changes impact protein-protein interactions and downstream signaling. Herein, we studied the structural bases for the interaction between GABABR and the KCC2 transporter, including their protein expression and distribution, and we compared data between young and aged rat cerebella. Also, we analyzed lipid profiles for both groups, and we used molecular dynamics simulations on three plasma membrane systems with different cholesterol concentrations, to further explore the GABABR-transporter interaction. Based on our results, we report that a significant decrease in GABAB2 subunit expression occurs in the aged rat cerebella. After performing a comparative co-immunoprecipitation analysis, we confirm that GABABR and KCC2 form a protein complex in adult and aged rat cerebella, although their interaction levels are reduced substantially as the cerebellum ages. On the other hand, our lipid analyses reveal a significant increase in cholesterol and sphingomyelin levels of the aged cerebella. Finally, we used the Martini coarse-grained model to conduct molecular dynamics simulations, from which we observed that membrane cholesterol concentrations can dictate whether the GABABR tail domains physically establish G protein-independent contacts with a transporter, and the timing when those associations eventually occur. Taken together, our findings illustrate how age-related alterations in membrane cholesterol levels affect protein-protein interactions, and how they could play a crucial role in regulating GABABR's interactome-mediated signaling. Significance Statement This study elucidates age-related changes in cerebellar GABAB receptors (GABABRs), KCC2, and plasma membrane lipids, shedding light on mechanisms underlying neurological decline. Molecular dynamics simulations reveal how membrane lipids influence protein-protein interactions, offering insights into age-related neurodegeneration. The findings underscore the broader impact of cerebellar aging on motor functions, cognition, and emotional processing in the elderly. By elucidating plasma membrane regulation and GABAergic dynamics, this research lays the groundwork for understanding aging-related neurological disorders and inspires further investigation into therapeutic interventions.
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Affiliation(s)
- Elena Vásquez
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza, Argentina
| | - Gerardo M. Oresti
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - María D. Paez
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD, USA
| | - Eduardo A. Callegari
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD, USA
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza, Argentina
| | - Estela M. Muñoz
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza, Argentina
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Azevedo AMO, Nunes C, Moniz T, Pérez RL, Ayala CE, Rangel M, Reis S, Santos JLM, Warner IM, Saraiva MLMFS. Studies of Protein Binding to Biomimetic Membranes Using a Group of Uniform Materials Based on Organic Salts Derived From 8-Anilino-1-naphthalenesulfonic Acid. APPLIED SPECTROSCOPY 2024; 78:806-814. [PMID: 38747750 DOI: 10.1177/00037028241249768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Tuning the 8-anilino-1-naphthalenesulfonic acid (ANS) structure usually requires harsh conditions and long reaction times, which can result in low yields. Herein, ANS was modified to form an ANS group of uniform materials based on organic salts (GUMBOS), prepared with simple metathesis reactions and distinct cations, namely tetrabutylammonium (N4444), tetrahexylammonium (N6666), and tetrabutylphosphonium (P4444). These ANS-based GUMBOS were investigated as fluorescent probes for membrane binding studies with four proteins having distinct physicochemical properties. Liposomes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine were employed as membrane models as a result of their ability to mimic the structure and chemical composition of cell membranes. Changes in fluorescence intensity were used to monitor protein binding to liposomes, and adsorption data were fitted to a Freundlich-like isotherm. It was determined that [N4444][ANS] and [P4444][ANS] GUMBOS have enhanced optical properties and lipophilicity as compared to parent ANS. As a result, these two GUMBOS were selected for subsequent protein-membrane binding studies. Both [N4444][ANS] and [P4444][ANS] GUMBOS and parent ANS independently reached membrane saturation within the same concentration range. Furthermore, distinct fluorescence responses were observed upon the addition of proteins to each probe, which demonstrates the impact of properties such as lipophilicity on the binding process. The relative maintenance of binding cooperativity and maximum fluorescence intensity suggests that proteins compete with ANS-based probes for the same membrane binding sites. Finally, this GUMBOS-based approach is simple, rapid, and involves relatively small amounts of reagents, making it attractive for high-throughput purposes. These results presented herein can also provide relevant information for designing GUMBOS with ameliorated properties.
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Affiliation(s)
- Ana M O Azevedo
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Cláudia Nunes
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Tânia Moniz
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- LAQV, REQUIMTE, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Rocío L Pérez
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
- Department of Chemistry and Biochemistry, Georgia Southern University, Statesboro, Georgia, USA
| | - Caitlan E Ayala
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Maria Rangel
- LAQV, REQUIMTE, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Salette Reis
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - João L M Santos
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - M Lúcia M F S Saraiva
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Hasdemir HS, Pozzi N, Tajkhorshid E. Atomistic characterization of β2-glycoprotein I domain V interaction with anionic membranes. J Thromb Haemost 2024:S1538-7836(24)00427-6. [PMID: 39047943 DOI: 10.1016/j.jtha.2024.07.010] [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: 03/20/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Interaction of β2-glycoprotein I (β2GPI) with anionic membranes is crucial in antiphospholipid syndrome (APS), implicating the role of its membrane-binding domain, domain V (DV). The mechanism of DV binding to anionic lipids is not fully understood. OBJECTIVES This study aimed to elucidate the molecular details of β2GPI DV binding to anionic membranes. METHODS We utilized molecular dynamics simulations to investigate the structural basis of anionic lipid recognition by DV. To corroborate the membrane-binding mode identified in the highly mobile membrane mimetic simulations, we conducted additional simulations using a full membrane model. RESULTS The study identified critical regions in DV, namely the lysine-rich loop and the hydrophobic loop, which are essential for membrane association via electrostatic and hydrophobic interactions, respectively. A novel lysine pair contributing to membrane binding was also discovered, providing new insights into β2GPI's membrane interaction. Simulations revealed 2 distinct binding modes of DV to the membrane, with mode 1 characterized by the insertion of the hydrophobic loop into the lipid bilayer, suggesting a dominant mechanism for membrane association. This interaction is pivotal for the pathogenesis of APS, as it facilitates the recognition of β2GPI by antiphospholipid antibodies. CONCLUSION The study advances our understanding of the molecular interactions between β2GPI's DV and anionic membranes, which are crucial for APS pathogenesis. It highlights the importance of specific regions in DV for membrane binding and reveals a predominant binding mode. These findings have significant implications for APS diagnostics and therapeutics, offering a deeper insight into the molecular basis of the syndrome.
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Affiliation(s)
- Hale S Hasdemir
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA. https://www.twitter.com/LabPozzi
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.
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Arango AS, Park H, Tajkhorshid E. Topological Learning Approach to Characterizing Biological Membranes. J Chem Inf Model 2024; 64:5242-5252. [PMID: 38912752 DOI: 10.1021/acs.jcim.4c00552] [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: 06/25/2024]
Abstract
Biological membranes play key roles in cellular compartmentalization, structure, and its signaling pathways. At varying temperatures, individual membrane lipids sample from different configurations, a process that frequently leads to higher-order phase behavior and phenomena. Here, we present a persistent homology (PH)-based method for quantifying the structural features of individual and bulk lipids, providing local and contextual information on lipid tail organization. Our method leverages the mathematical machinery of algebraic topology and machine learning to infer temperature-dependent structural information on lipids from static coordinates. To train our model, we generated multiple molecular dynamics trajectories of dipalmitoyl-phosphatidylcholine membranes at varying temperatures. A fingerprint was then constructed for each set of lipid coordinates by PH filtration, in which interaction spheres were grown around the lipid atoms while tracking their intersections. The sphere filtration formed a simplicial complex that captures enduring key topological features of the configuration landscape using homology, yielding persistence data. Following fingerprint extraction for physiologically relevant temperatures, the persistence data were used to train an attention-based neural network for assignment of effective temperature values to selected membrane regions. Our persistence homology-based method captures the local structural effects, via effective temperature, of lipids adjacent to other membrane constituents, e.g., sterols and proteins. This topological learning approach can predict lipid effective temperatures from static coordinates across multiple spatial resolutions. The tool, called MembTDA, can be accessed at https://github.com/hyunp2/Memb-TDA.
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Affiliation(s)
- Andres S Arango
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hyun Park
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Fang Y, Zhang Y, Bi S, Peng B, Wang C, Ju H, Liu Y. Securing LYTAC with Logic-Identification System for Cancer Cell-Selective Membrane Protein Degradation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310039. [PMID: 38431928 DOI: 10.1002/smll.202310039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/18/2024] [Indexed: 03/05/2024]
Abstract
Lysosome-targeting chimera (LYTAC) links proteins of interest (POIs) with lysosome-targeting receptors (LTRs) to achieve membrane protein degradation, which is becoming a promising therapeutic modality. However, cancer cell-selective membrane protein degradation remains a big challenge considering expressions of POIs in both cancer cells and normal cells, as well as broad tissue distribution of LTRs. Here a logic-identification system is designed, termed Logic-TAC, based on cell membrane-guided DNA calculations to secure LYTAC selectively for cancer cells. Logic-TAC is designed as a duplex DNA structure, with both POI and LTR recognition regions sealed to avoid systematic toxicity during administration. MCF-7 and MCF-10A are chosen as sample cancer cell and normal cell respectively. As input 1 for logic-identification, membrane proteins EpCAM, which is highly expressed by MCF-7 but barely by MCF-10A, reacts with Logic-TAC to expose POI recognition region. As input 2 for logic-identification, Logic-TAC binds to POI, membrane protein MUC1, to expose LTR recognition region. As output, MUC1 is connected to LTR and degraded via lysosome pathway selectively for cancer cell MCF-7 with little side effect on normal cell MCF-10A. The logic-identification system also demonstrated satisfactory in vivo therapeutic results, indicating its promising potential in precise targeted therapy.
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Affiliation(s)
- Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yue Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shiyi Bi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Bo Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Caixia Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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7
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Lihan M, Tajkhorshid E. Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. J Chem Inf Model 2024; 64:4822-4834. [PMID: 38844760 DOI: 10.1021/acs.jcim.4c00619] [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: 06/25/2024]
Abstract
Cholesterol (CHL) plays an integral role in modulating the function and activity of various mammalian membrane proteins. Due to the slow dynamics of lipids, conventional computational studies of protein-CHL interactions rely on either long-time scale atomistic simulations or coarse-grained approximations to sample the process. A highly mobile membrane mimetic (HMMM) has been developed to enhance lipid diffusion and thus used to facilitate the investigation of lipid interactions with peripheral membrane proteins and, with customized in silico solvents to replace phospholipid tails, with integral membrane proteins. Here, we report an updated HMMM model that is able to include CHL, a nonphospholipid component of the membrane, henceforth called HMMM-CHL. To this end, we had to optimize the effect of the customized solvents on CHL behavior in the membrane. Furthermore, the new solvent is compatible with simulations using force-based switching protocols. In the HMMM-CHL, both improved CHL dynamics and accelerated lipid diffusion are integrated. To test the updated model, we have applied it to the characterization of protein-CHL interactions in two membrane protein systems, the human β2-adrenergic receptor (β2AR) and the mitochondrial voltage-dependent anion channel 1 (VDAC-1). Our HMMM-CHL simulations successfully identified CHL binding sites and captured detailed CHL interactions in excellent consistency with experimental data as well as other simulation results, indicating the utility of the improved model in applications where an enhanced sampling of protein-CHL interactions is desired.
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Affiliation(s)
- Muyun Lihan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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Kellogg GE. Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins. Molecules 2024; 29:2838. [PMID: 38930903 PMCID: PMC11207109 DOI: 10.3390/molecules29122838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
A method is described to deconstruct the network of hydropathic interactions within and between a protein's sidechain and its environment into residue-based three-dimensional maps. These maps encode favorable and unfavorable hydrophobic and polar interactions, in terms of spatial positions for optimal interactions, relative interaction strength, as well as character. In addition, these maps are backbone angle-dependent. After map calculation and clustering, a finite number of unique residue sidechain interaction maps exist for each backbone conformation, with the number related to the residue's size and interaction complexity. Structures for soluble proteins (~749,000 residues) and membrane proteins (~387,000 residues) were analyzed, with the latter group being subdivided into three subsets related to the residue's position in the membrane protein: soluble domain, core-facing transmembrane domain, and lipid-facing transmembrane domain. This work suggests that maps representing residue types and their backbone conformation can be reassembled to optimize the medium-to-high resolution details of a protein structure. In particular, the information encoded in maps constructed from the lipid-facing transmembrane residues appears to paint a clear picture of the protein-lipid interactions that are difficult to obtain experimentally.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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9
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Hibbard MC, Tao N, Fischer JL, Yang E, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. Nat Commun 2024; 15:5036. [PMID: 38866734 PMCID: PMC11169460 DOI: 10.1038/s41467-024-49384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | - Maddison C Hibbard
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | | | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA.
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10
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Weng Y, Gu W, Jin Y. Epoxiconazole altered hepatic metabolism in adult zebrafish based on transcriptomic analysis. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109901. [PMID: 38508352 DOI: 10.1016/j.cbpc.2024.109901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/07/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Epoxiconazole (EPX) is a triazole fungicide, which has been widely used in pest control of cereal crops. However, its extensive use has led to concerning levels of residue in water bodies, posing substantial risks to aquatic life. In this study, we characterized the toxicological effects of EPX on 6-month-old male and female zebrafish at 70 and 700 μg/L, respectively. The results revealed that EPX exposure markedly increased both body length and weight in zebrafish of both sexes, consequently elevating their condition factor. Besides, EPX exposure resulted in notable alterations in hepatic histopathology. These changes included loosened hepatocyte structure, ballooning degeneration, nucleolysis, and disappearance of cell line, with male zebrafish exhibiting more severe damage. High concentration of EPX also significantly increased hepatic lipid accumulation in male zebrafish, as well as increased hepatic triglyceride (TG) levels. Correspondingly, there was a notable alteration in the transcription of genes including cyp51, hmgcr, and PPAR-γ, which associated with cholesterol and lipid metabolism. Interestingly, with the hepatic transcriptomic analysis, high concentration of EPX produced 195 upregulated and 107 downregulated differential expression genes. Both KEGG and GO analyses identified significant enrichment of these genes in lipid and amino acid metabolism pathways. Notably, some key genes involved in the steroid synthesis pathway were marked upregulated. In addition, molecular docking study confirmed that EPX could bind CYP51 protein well (△G = -7.7 kcal/mol). Taken together, these findings demonstrated the multiple toxic effects of EPX on adult zebrafish.
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Affiliation(s)
- You Weng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Weijie Gu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China.
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11
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Rahman S, Chiou CC, Ahmad S, Islam ZU, Tanaka T, Alouffi A, Chen CC, Almutairi MM, Ali A. Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development against Bartonella henselae Strain Houston-1. Bioengineering (Basel) 2024; 11:505. [PMID: 38790371 PMCID: PMC11118080 DOI: 10.3390/bioengineering11050505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes and endothelial cells emphasize its clinical significance. Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to the B. henselae strain Houston-1. Exploring these aspects is crucial for targeted therapeutic strategies against this versatile pathogen. Using reverse-vaccinology-based subtractive proteomics, this research aimed to identify the most antigenic proteins for formulating a multi-epitope vaccine against the B. henselae strain Houston-1. One crucial virulent and antigenic protein, the PAS domain-containing sensor histidine kinase protein, was identified. Subsequently, the identification of B-cell and T-cell epitopes for the specified protein was carried out and the evaluated epitopes were checked for their antigenicity, allergenicity, solubility, MHC binding capability, and toxicity. The filtered epitopes were merged using linkers and an adjuvant to create a multi-epitope vaccine construct. The structure was then refined, with 92.3% of amino acids falling within the allowed regions. Docking of the human receptor (TLR4) with the vaccine construct was performed and demonstrated a binding energy of -1047.2 Kcal/mol with more interactions. Molecular dynamic simulations confirmed the stability of this docked complex, emphasizing the conformation and interactions between the molecules. Further experimental validation is necessary to evaluate its effectiveness against B. henselae.
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Affiliation(s)
- Sudais Rahman
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Chien-Chun Chiou
- Department of Dermatology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shabir Ahmad
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Brazil;
| | - Zia Ul Islam
- Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
- Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Abid Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
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12
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Badiee SA, Hettige J, Moradi M. Lipid-dependent conformational dynamics of bacterial ATP-binding cassette transporter Sav1866. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590185. [PMID: 38659884 PMCID: PMC11042323 DOI: 10.1101/2024.04.18.590185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Sav1866, a bacterial ATP-binding cassette (ABC) exporter, plays a crucial role in cellular processes by facilitating the efflux of a diverse range of substrates, including drugs, chemotherapeutic agents, peptides, and lipids. This efflux activity significantly impacts the effectiveness of various therapies against bacterial infections. In our recent investigation, we focused on understanding the conformational dynamics of Sav1866 within different lipid environments. Specifically, we explored its behavior in environments composed of DMPC and POPE lipids, which exhibit crucial distinctions not only in their headgroup polarity but also in the length and saturation of their hydrophobic tails. Our extensive set of equilibrium microsecond-level all-atom molecular dynamics (MD) simulations revealed significant distinctions in transporter behavior influenced by these lipid compositions. We observed a rapid transition to an occluded-inward-facing (IF-occ) conformation in POPE environments, contrasting with a channel-like behavior in DMPC environments, deviating from the expected alternating access mechanism (AAM). These findings underscore the significant impact of lipid compositions on ABC transporter function, offering new perspectives on membrane transport mechanisms.
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13
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Hutchinson K, Schlessinger A. Comprehensive Characterization of LAT1 Cholesterol-Binding Sites. J Chem Theory Comput 2024; 20:3349-3358. [PMID: 38597304 DOI: 10.1021/acs.jctc.3c01391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The human L-type amino acid transporter 1 (LAT1; SLC7A5), is an amino acid exchanger protein, primarily found in the blood-brain barrier, placenta, and testis, where it plays a key role in amino acid homeostasis. Cholesterol is an essential lipid that has been highlighted to play a role in regulating the activity of membrane transporters, such as LAT1, yet little is known about the molecular mechanisms driving this phenomenon. Here we perform a comprehensive computational analysis to investigate cholesterol's role in LAT1 structure and function, focusing on four cholesterol-binding sites (CHOL1-4) identified in a recent LAT1-apo inward-open conformation cryo-EM structure. Through a series of independent molecular dynamics (MD) simulations, molecular docking, MM/GBSA free energy calculations, and other analysis tools, we explored the interactions between LAT1 and cholesterol. Our findings suggest that CHOL3 forms the most stable and favorable interactions with LAT1. Principal component analysis (PCA) and center of mass (COM) distance assessments show that CHOL3 binding stabilizes the inward-open state of LAT1 by preserving the spatial arrangement of the hash and bundle domains. Additionally, we propose an alternative cholesterol-binding site for originally assigned CHOL1. Overall, this study improves the understanding of cholesterol's modulatory effect on LAT1 and proposes candidate sites for the discovery of future allosteric ligands with rational design.
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Affiliation(s)
- Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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14
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Sadeghi M, Rosenberger D. Dynamic framework for large-scale modeling of membranes and peripheral proteins. Methods Enzymol 2024; 701:457-514. [PMID: 39025579 DOI: 10.1016/bs.mie.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In this chapter, we present a novel computational framework to study the dynamic behavior of extensive membrane systems, potentially in interaction with peripheral proteins, as an alternative to conventional simulation methods. The framework effectively describes the complex dynamics in protein-membrane systems in a mesoscopic particle-based setup. Furthermore, leveraging the hydrodynamic coupling between the membrane and its surrounding solvent, the coarse-grained model grounds its dynamics in macroscopic kinetic properties such as viscosity and diffusion coefficients, marrying the advantages of continuum- and particle-based approaches. We introduce the theoretical background and the parameter-space optimization method in a step-by-step fashion, present the hydrodynamic coupling method in detail, and demonstrate the application of the model at each stage through illuminating examples. We believe this modeling framework to hold great potential for simulating membrane and protein systems at biological spatiotemporal scales, and offer substantial flexibility for further development and parametrization.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
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15
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Jandu RS, Yu H, Zhao Z, Le HT, Kim S, Huan T, Duong van Hoa F. Capture of endogenous lipids in peptidiscs and effect on protein stability and activity. iScience 2024; 27:109382. [PMID: 38577106 PMCID: PMC10993126 DOI: 10.1016/j.isci.2024.109382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/17/2023] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
Compared to protein-protein and protein-nucleic acid interactions, our knowledge of protein-lipid interactions remains limited. This is primarily due to the inherent insolubility of membrane proteins (MPs) in aqueous solution. The traditional use of detergents to overcome the solubility barrier destabilizes MPs and strips away certain lipids that are increasingly recognized as crucial for protein function. Recently, membrane mimetics have been developed to circumvent the limitations. In this study, using the peptidisc, we find that MPs in different lipid states can be isolated based on protein purification and reconstitution methods, leading to observable effects on MP activity and stability. Peptidisc also enables re-incorporating specific lipids to fine-tune the protein microenvironment and assess the impact on downstream protein associations. This study offers a first look at the illusive protein-lipid interaction specificity, laying the path for a systematic evaluation of lipid identity and contributions to membrane protein function.
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Affiliation(s)
- Rupinder Singh Jandu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Huaxu Yu
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hai Tuong Le
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sehyeon Kim
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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16
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Smith JW, Carnevale LN, Das A, Chen Q. Electron videography of a lipid-protein tango. SCIENCE ADVANCES 2024; 10:eadk0217. [PMID: 38630809 PMCID: PMC11023515 DOI: 10.1126/sciadv.adk0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Lauren N. Carnevale
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Aditi Das
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Materials Research Laboratory, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
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17
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Zhao J, Zhao L, Xu W, Lu Z, Xu S. Fabrication of High-Negatively Charged Bicelle-Mediated Supported Lipid Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8083-8093. [PMID: 38572682 DOI: 10.1021/acs.langmuir.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Supported lipid bilayers (SLBs), two-dimensional lipid films formed on a solid-supporting substrate, serve as models for biomembranes and exhibit remarkable potential in chemistry, biology, and medicine. However, preparing SLBs with highly negatively charged contents on the negatively charged surface by overcoming electrostatic repulsion remains a challenge. Here, a creative bicelle-mediated and divalent cation-free SLB preparation method with the assistance of phosphate-buffered saline (PBS) solution was proposed, which can form the SLBs containing 50% DOPS or 30% CL on the silica surface monitored by a quartz crystal microbalance with dissipation (QCM-D). Results of molecular dynamics (MD) simulation indicate that electrostatic repulsion can be overcome by the increased number of hydrogen bonds caused by the adsorption of dihydrogen phosphate ions onto the headgroups of lipids. In addition, the negatively charged SLB formation was identified to be a three-step kinetic process, which differs from a two-step mechanism in the case of amphoteric SLB. The extra kinetic step can be attributed to the reduction in the number of intermolecular hydrogen bonds and the ordering of water molecules in the hydration layer. This investigation resolves the challenge of fabricating SLB over negatively charged surfaces and offers a fresh perspective on the SLB assembly methodology.
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Affiliation(s)
- Junyi Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Li Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Weiqing Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Zhongyuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory of Material Simulation Methods and Software of Ministry of Education, Changchun 130012, China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
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18
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Szczepaniak F, Dehez F, Roux B. Configurational Sampling of All-Atom Solvated Membranes Using Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations. J Phys Chem Lett 2024; 15:3796-3804. [PMID: 38557030 DOI: 10.1021/acs.jpclett.4c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
All-atom simulations are a powerful approach to study the structure and dynamics of biological membranes. However, sampling the atomic configurations of inhomogeneous membranes can be challenging due to the slow lateral diffusion of the various constituents. To address this issue, a hybrid nonequilibrium molecular dynamics Monte Carlo (neMD/MC) simulation method is proposed in which randomly chosen lipid molecules are swapped to generate configurations that are subsequently accepted or rejected according to a Metropolis criterion based on the alchemical work for the attempted swap calculated via a short trajectory. A dual-topology framework constraining the common atoms of the exchanging molecules yields a good acceptance probability using switching trajectories as short as 10 ps. The performance of the hybrid neMD/MC algorithm and its ability to sample the distribution of lipids near a transmembrane helix carrying a net charge are illustrated for a binary mixture of charged and zwitterionic lipids.
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Affiliation(s)
- Florence Szczepaniak
- CNRS, LPCT, Université de Lorraine, F-54000 Nancy, France
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637,United States
| | - François Dehez
- CNRS, LPCT, Université de Lorraine, F-54000 Nancy, France
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Université de Lorraine, LPCT, F-54000 Nancy, France
| | - Benoît Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637,United States
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19
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Ananchenko A, Gao RY, Dehez F, Baenziger JE. State-dependent binding of cholesterol and an anionic lipid to the muscle-type Torpedo nicotinic acetylcholine receptor. Commun Biol 2024; 7:437. [PMID: 38600247 PMCID: PMC11006840 DOI: 10.1038/s42003-024-06106-8] [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: 08/28/2023] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
The ability of the Torpedo nicotinic acetylcholine receptor (nAChR) to undergo agonist-induced conformational transitions requires the presence of cholesterol and/or anionic lipids. Here we use recently solved structures along with multiscale molecular dynamics simulations to examine lipid binding to the nAChR in bilayers that have defined effects on nAChR function. We examine how phosphatidic acid and cholesterol, lipids that support conformational transitions, individually compete for binding with phosphatidylcholine, a lipid that does not. We also examine how the two lipids work synergistically to stabilize an agonist-responsive nAChR. We identify rapidly exchanging lipid binding sites, including both phospholipid sites with a high affinity for phosphatidic acid and promiscuous cholesterol binding sites in the grooves between adjacent transmembrane α-helices. A high affinity cholesterol site is confirmed in the inner leaflet framed by a key tryptophan residue on the MX α-helix. Our data provide insight into the dynamic nature of lipid-nAChR interactions and set the stage for a detailed understanding of the mechanisms by which lipids facilitate nAChR function at the neuromuscular junction.
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Affiliation(s)
- Anna Ananchenko
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Rui Yan Gao
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - François Dehez
- CNRS, LPCT, Université de Lorraine, F-54000 Nancy, France.
| | - John E Baenziger
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
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20
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Hasdemir HS, Pozzi N, Tajkhorshid E. Atomistic Characterization of Beta-2-Glycoprotein I Domain V Interaction with Anionic Membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585743. [PMID: 38562685 PMCID: PMC10983932 DOI: 10.1101/2024.03.19.585743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Interaction of beta-2-glycoprotein I ( β 2 GPI) with anionic membranes is crucial in antiphospholipid syndrome (APS), implicating the role of it's membrane bind-ing domain, Domain V (DV). The mechanism of DV binding to anionic lipids is not fully understood. Objectives This study aims to elucidate the mechanism by which DV of β 2 GPI binds to anionic membranes. Methods We utilized molecular dynamics (MD) simulations to investigate the struc-tural basis of anionic lipid recognition by DV. To corroborate the membrane-binding mode identified in the HMMM simulations, we conducted additional simulations using a full mem-brane model. Results The study identified critical regions in DV, namely the lysine-rich loop and the hydrophobic loop, essential for membrane association via electrostatic and hydrophobic interactions, respectively. A novel lysine pair contributing to membrane binding was also discovered, providing new insights into β 2 GPI's membrane interaction. Simulations revealed two distinct binding modes of DV to the membrane, with mode 1 characterized by the insertion of the hydrophobic loop into the lipid bilayer, suggesting a dominant mechanism for membrane association. This interaction is pivotal for the pathogenesis of APS, as it facilitates the recognition of β 2 GPI by antiphospholipid antibodies. Conclusion The study advances our understanding of the molecular interactions be-tween β 2 GPI's DV and anionic membranes, crucial for APS pathogenesis. It highlights the importance of specific regions in DV for membrane binding and reveals a predominant bind-ing mode. These findings have significant implications for APS diagnostics and therapeutics, offering a deeper insight into the molecular basis of the syndrome.
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21
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Chen M. Rendering protein structures inside cells at the atomic level with Unreal Engine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.08.570879. [PMID: 38496473 PMCID: PMC10942390 DOI: 10.1101/2023.12.08.570879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
While the recent development of cryogenic electron tomography (CryoET) makes it possible to identify various macromolecules inside cells and determine their structure at near-atomic resolution, it remains challenging to visualize the complex cellular environment at the atomic level. One of the main hurdles in cell visualization is to render the millions of molecules in real time computationally. Here, using a video game engine, we demonstrate the capability of rendering massive biological macromolecules at the atomic level within their native environment. To facilitate the visualization, we also provide tools that help the interactive navigation inside the cells, as well as software that converts protein structures identified using CryoET to a scene that can be explored with the game engine.
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Affiliation(s)
- Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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22
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Yong J, Shu H, Zhang X, Yang K, Luo G, Yu L, Li J, Huang H. Natural Products-Based Inhaled Formulations for Treating Pulmonary Diseases. Int J Nanomedicine 2024; 19:1723-1748. [PMID: 38414528 PMCID: PMC10898359 DOI: 10.2147/ijn.s451206] [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: 11/22/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Given the unique physiological and pathological characteristics of the lung, the direct, inhalable route is more conducive to pulmonary drug delivery and disease control than traditional systemic drug delivery, significantly circumventing drug loss, off-target effects, systemic and organ toxicity, etc., and is widely regarded as the preferred regimen for pulmonary drug delivery. However, very few lung diseases are currently treated with the preferred inhaled formulations, such as asthma, chronic obstructive pulmonary disease and pulmonary hypertension. And there is a lack of appropriate inhaled formulations for other critical lung diseases, such as lung cancer and pulmonary fibrosis, due to the fact that the physicochemical properties of the drugs and their pharmacokinetic profiles do not match the physiology of the lung, and conventional inhalation devices are unable to deliver them to the specific parts of the lung. Phytochemicals of natural origin, due to their wide availability and clear safety profile, hold great promise for the preparation of inhalable formulations to improve the current dilemma in the treatment of lung diseases. In particular, the preparation of inhalable formulations based on nano- and microparticulate carriers for drug delivery to deep lung tissues, which overcome the shortcomings of conventional inhalation therapies while targeting the drug activity directly to a specific part of the lung, may be the best approach to change the current dilemma of lung disease treatment. In this review, we discuss recent advances in nano- and micron-carrier-based inhalation formulations for the delivery of natural products for the treatment of pulmonary diseases, which may represent an opportunity for practical clinical translation of natural products.
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Affiliation(s)
- Jiangyan Yong
- Department of Clinical Laboratory, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610072, People’s Republic of China
| | - Hongli Shu
- Department of Clinical Laboratory, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610072, People’s Republic of China
| | - Xiao Zhang
- Department of Clinical Laboratory, Chengdu Children Special Hospital, Chengdu, Sichuan, 610031, People’s Republic of China
| | - Kun Yang
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People’s Republic of China
| | - Guining Luo
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People’s Republic of China
| | - Lu Yu
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People’s Republic of China
| | - Jiaqi Li
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People’s Republic of China
| | - Hong Huang
- Department of Clinical Laboratory, the People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, 401121, People’s Republic of China
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23
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Moura ACM, Asare IK, Cruz MF, Aguado AJF, Tuck KD, Campbell CC, Scheyer MW, Obaseki I, Alston S, Kravats AN, Sanders CR, Lorigan GA, Sahu ID. Studying Conformational Properties of Transmembrane Domain of KCNE3 in a Lipid Bilayer Membrane Using Molecular Dynamics Simulations. MEMBRANES 2024; 14:45. [PMID: 38392672 PMCID: PMC10890134 DOI: 10.3390/membranes14020045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
KCNE3 is a single-pass integral membrane protein that regulates numerous voltage-gated potassium channel functions such as KCNQ1. Previous solution NMR studies suggested a moderate degree of curved α-helical structure in the transmembrane domain (TMD) of KCNE3 in lyso-myristoylphosphatidylcholine (LMPC) micelles and isotropic bicelles with the residues T71, S74 and G78 situated along the concave face of the curved helix. During the interaction of KCNE3 and KCNQ1, KCNE3 pushes its transmembrane domain against KCNQ1 to lock the voltage sensor in its depolarized conformation. A cryo-EM study of KCNE3 complexed with KCNQ1 in nanodiscs suggested a deviation of the KCNE3 structure from its independent structure in isotropic bicelles. Despite the biological significance of KCNE3 TMD, the conformational properties of KCNE3 are poorly understood. Here, all atom molecular dynamics (MD) simulations were utilized to investigate the conformational dynamics of the transmembrane domain of KCNE3 in a lipid bilayer containing a mixture of POPC and POPG lipids (3:1). Further, the effect of the interaction impairing mutations (V72A, I76A and F68A) on the conformational properties of the KCNE3 TMD in lipid bilayers was investigated. Our MD simulation results suggest that the KCNE3 TMD adopts a nearly linear α helical structural conformation in POPC-POPG lipid bilayers. Additionally, the results showed no significant change in the nearly linear α-helical conformation of KCNE3 TMD in the presence of interaction impairing mutations within the sampled time frame. The KCNE3 TMD is more stable with lower flexibility in comparison to the N-terminal and C-terminal of KCNE3 in lipid bilayers. The overall conformational flexibility of KCNE3 also varies in the presence of the interaction-impairing mutations. The MD simulation data further suggest that the membrane bilayer width is similar for wild-type KCNE3 and KCNE3 containing mutations. The Z-distance measurement data revealed that the TMD residue site A69 is close to the lipid bilayer center, and residue sites S57 and S82 are close to the surfaces of the lipid bilayer membrane for wild-type KCNE3 and KCNE3 containing interaction-impairing mutations. These results agree with earlier KCNE3 biophysical studies. The results of these MD simulations will provide complementary data to the experimental outcomes of KCNE3 to help understand its conformational dynamic properties in a more native lipid bilayer environment.
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Affiliation(s)
| | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mateo Fernandez Cruz
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Kaeleigh Dyan Tuck
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner C Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Ikponwmosa Obaseki
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Steve Alston
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Andrea N Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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24
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Hall AR, Choi YK, Im W, Vavylonis D. Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study. Structure 2024; 32:242-252.e2. [PMID: 38103546 PMCID: PMC10872332 DOI: 10.1016/j.str.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
Cytokinesis of animal and fungi cells depends crucially on the anillin scaffold proteins. Fission yeast anillin-related Mid1 anchors cytokinetic ring precursor nodes to the membrane. However, it is unclear if both of its Pleckstrin Homology (PH) and C2 C-terminal domains bind to the membrane as monomers or dimers, and if one domain plays a dominant role. We studied Mid1 membrane binding with all-atom molecular dynamics near a membrane with yeast-like lipid composition. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the disordered L3 loop of C2 in a vertical orientation, with the PH away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. Simulations of C2-PH dimers show extensive asymmetric membrane contacts. These multiple modes of binding may reflect Mid1's multiple interactions with membranes, node proteins, and ability to sustain mechanical forces.
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Affiliation(s)
- Aaron R Hall
- Department of Physics, Lehigh University, Bethlehem, PA 18017, USA
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18017, USA
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18017, USA
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA 18017, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA.
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25
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Hu X, Chi H, Fu X, Chen J, Dong L, Jiang S, Li Y, Chen J, Cheng M, Min Q, Tian Y, Zhang P. Tunable Multivalent Aptamer-Based DNA Nanostructures To Regulate Multiheteroreceptor-Mediated Tumor Recognition. J Am Chem Soc 2024; 146:2514-2523. [PMID: 38247135 DOI: 10.1021/jacs.3c10704] [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: 01/23/2024]
Abstract
Precise mapping and regulation of cell surface receptors hold immense significance in disease treatment, such as cancer, infection, and neurodisorders, but also face enormous challenges. In this study, we designed a series of adjustable multivalent aptamer-based DNA nanostructures to precisely control their interaction with receptors in tumor cells. By profiling surface receptors on 12 cell lines using 10 different aptamers, we generated a heatmap that accurately distinguished between various tumor types based on multiple markers. We then incorporated these aptamers onto DNA origami structures to regulate receptor recognition, with patch-like structures demonstrating a tendency to be trapped on the cell surface and with tube-like structures showing a preference for internalization. Through precise control of aptamer species, valence, and geometric patterns, we found that multiheteroreceptor-mediated recognition not only favored the specific binding of nanostructures to tumor cells but also greatly enhanced intracellular uptake by promoting clathrin-dependent endocytosis. Specifically, we achieved over 5-fold uptake in different tumor cells versus normal cells using tube-like structures modified with different diheteroaptamer pairs, facilitating targeted drug delivery. Moreover, patch-like structures with triheteroaptamers guided specific interactions between macrophages and tumor cells, leading to effective immune clearance. This programmable multivalent system allows for the precise regulation of cell recognition using multiple parameters, demonstrating great potential for personalized tumor treatment.
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Affiliation(s)
- Xiaoxue Hu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Hongli Chi
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Xiaoyi Fu
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jinling Chen
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Linying Dong
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shiqi Jiang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yan Li
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jingyi Chen
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ming Cheng
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Qianhao Min
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Penghui Zhang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
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26
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Steck TL, Ali Tabei SM, Lange Y. Estimating the Cholesterol Affinity of Integral Membrane Proteins from Experimental Data. Biochemistry 2024; 63:19-26. [PMID: 38099740 PMCID: PMC10765374 DOI: 10.1021/acs.biochem.3c00567] [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: 10/16/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
The cholesterol affinities of many integral plasma membrane proteins have been estimated by molecular computation. However, these values lack experimental confirmation. We therefore developed a simple mathematical model to extract sterol affinity constants and stoichiometries from published isotherms for the dependence of the activity of such proteins on the membrane cholesterol concentration. The binding curves for these proteins are sigmoidal, with strongly lagged thresholds attributable to competition for the cholesterol by bilayer phospholipids. The model provided isotherms that matched the experimental data using published values for the sterol association constants and stoichiometries of the phospholipids. Three oligomeric transporters were found to bind cholesterol without cooperativity, with dimensionless association constants of 35 for Kir3.4* and 100 for both Kir2 and a GAT transporter. (The corresponding ΔG° values were -8.8, -11.4, and -11.4 kJ/mol, respectively). These association constants are significantly lower than those for the phospholipids, which range from ∼100 to 6000. The BK channel, the nicotinic acetylcholine receptor, and the M192I mutant of Kir3.4* appear to bind multiple cholesterol molecules cooperatively (n = 2 or 4), with subunit affinities of 563, 950, and 700, respectively. The model predicts that the three less avid transporters are approximately half-saturated in their native plasma membranes; hence, they are sensitive to variations in cholesterol in vivo. The more avid proteins would be nearly saturated in vivo. The method can be applied to any integral protein or other ligands in any bilayer for which there are reasonable estimates of the sterol affinities and stoichiometries of the phospholipids.
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Affiliation(s)
- Theodore L. Steck
- Department
of Biochemistry and Molecular Biology, University
of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - S. M. Ali Tabei
- Department
of Physics, University of Northern Iowa, Cedar Falls, Iowa 50614, United States
| | - Yvonne Lange
- Department
of Pathology, Rush University Medical Center, Chicago, Illinois 60612, United States
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27
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Rout M, Mishra S, Panda S, Dehury B, Pati S. Lipid and cholesterols modulate the dynamics of SARS-CoV-2 viral ion channel ORF3a and its pathogenic variants. Int J Biol Macromol 2024; 254:127986. [PMID: 37944718 DOI: 10.1016/j.ijbiomac.2023.127986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
SARS-CoV-2 accessory protein, ORF3a is a putative ion channel which immensely contributes to viral pathogenicity by modulating host immune responses and virus-host interactions. Relatively high expression of ORF3a in diseased individuals and implication with inflammasome activation, apoptosis and autophagy inhibition, ratifies as an effective target for developing vaccines and therapeutics. Herein, we present the elusive dynamics of ORF3a-dimeric state using all-atoms molecular dynamics (MD) simulations at μ-seconds scale in a heterogeneous lipid-mimetic system in multiple replicates. Additionally, we also explore the effect of non-synonymous pathogenic mutations on ORF3a ion channel activity and viral pathogenicity in different SARS-CoV-2 variants using various structure-based protein stability (ΔΔG) tools and computational saturation mutagenesis. Our study ascertains the role of phosphatidylcholines and cholesterol in modulating the structure of ORF3a, which perturbs the size and flexibility of the polar cavity that allows permeation of large cations. Discrete trend in ion channel pore radius and area per lipid arises the premise that presence of lipids might also affect the overall conformation of ORF3a. MD structural-ensembles, in some replicates rationalize the crucial role of TM2 in maintaining the native structure of ORF3a. We also infer that loss of structural stability primarily grounds for pathogenicity in more than half of the pathogenic variants of ORF3a. Overall, the effect of mutation on alteration of ion permeability of ORF3a, proposed in this study brings mechanistic insights into variant consequences on viral membrane proteins of SARS-CoV-2, which can be utilized for the development of novel therapeutics to treat COVID-19 and other coronavirus diseases.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
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28
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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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29
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Duan XY, Qian ZH, Tuo YX, Gong L, Zhu CY. Atomistic Insights into the Effect of Functional Groups on the Adsorption of Water by Activated Carbon for Heat Energy Storage. Molecules 2023; 29:11. [PMID: 38202594 PMCID: PMC10780261 DOI: 10.3390/molecules29010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Adsorption heat storage holds great promise for solar energy applications. The development of new adsorbent materials is currently the research focus in this area. The present work designs several activated carbon models with different functional groups, including -OH, -NH2, -COOH, and -SO3H, and explores the influence of functional groups' categories and numbers on the water adsorption capacity of the activated carbon using the GCMC method. The adsorption mechanism between functional groups and water molecules is analyzed using density functional theory. The results show that the functional groups could significantly improve the water adsorption capacity of activated carbon due to the hydrogen bond between functional groups and water molecules. In the scope of this paper, under low pressure, the activated carbon with -SO3H exhibits the best adsorption capacity, followed by the activated carbon with -COOH. Under low and medium pressure, increasing the number of -SO3H functional groups could increase the water adsorption capacity; however, when the pressure is high, increasing the functional group numbers might decrease the water adsorption capacity. As the temperature increases, the water adsorption capacity of activated carbons decreases, and the activated carbon with -SO3H is proven to have excellent application prospects in heat energy storage.
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Affiliation(s)
| | | | | | | | - Chuan-Yong Zhu
- College of New Energy, China University of Petroleum (East China), Qingdao 266580, China; (X.-Y.D.); (Z.-H.Q.); (Y.-X.T.); (L.G.)
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30
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Yamada T, Miyazaki Y, Harada S, Kumar A, Vanni S, Shinoda W. Improved Protein Model in SPICA Force Field. J Chem Theory Comput 2023; 19:8967-8977. [PMID: 37989551 DOI: 10.1021/acs.jctc.3c01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and the stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was overstabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study, we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and reoptimize almost all nonbonded parameters for amino acids. The improved FF proposed here successfully reproduces the radii of gyration of various IDPs, the binding sensitivity of several peripheral membrane proteins, and the dimerization free energies of several transmembrane helices. The new model also shows improved agreement with experiments on the free energy of peptide association in water. In addition, an extensive library of nonbonded interactions between proteins and lipids, including various glycerophospholipids, sphingolipids, and cholesterol, allows the study of specific interactions between lipids and peripheral and transmembrane proteins. Hence, the new SPICA FF (version 2) proposed herein is applicable with high accuracy for simulating a wide range of protein systems.
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Affiliation(s)
- Teppei Yamada
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Shogo Harada
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Ashutosh Kumar
- Department of Biology and National Center of Competence in Research Bio-inspired Materials, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology and National Center of Competence in Research Bio-inspired Materials, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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31
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Arango AS, Park H, Tajkhorshid E. Topological Learning Approach to Characterizing Biological Membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569053. [PMID: 38076911 PMCID: PMC10705453 DOI: 10.1101/2023.11.28.569053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Biological membranes play key roles in cellular compartmentalization, structure, and its signaling pathways. At varying temperatures, individual membrane lipids sample from different configurations, a process that frequently leads to higher-order phase behavior and phenomena. Here we present a persistent homology-based method for quantifying the structural features of individual and bulk lipids, providing local and contextual information on lipid tail organization. Our method leverages the mathematical machinery of algebraic topology and machine learning to infer temperature-dependent structural information of lipids from static coordinates. To train our model, we generated multiple molecular dynamics trajectories of DPPC membranes at varying temperatures. A fingerprint was then constructed for each set of lipid coordinates by a persistent homology filtration, in which interactions spheres were grown around the lipid atoms while tracking their intersections. The sphere filtration formed a simplicial complex that captures enduring key topological features of the configuration landscape, using homology, yielding persistence data. Following fingerprint extraction for physiologically relevant temperatures, the persistence data were used to train an attention-based neural network for assignment of effective temperature values to selected membrane regions. Our persistence homology-based method captures the local structural effects, via effective temperature, of lipids adjacent to other membrane constituents, e.g. sterols and proteins. This topological learning approach can predict lipid effective temperatures from static coordinates across multiple spatial resolutions. The tool, called MembTDA, can be accessed at https://github.com/hyunp2/Memb-TDA.
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Affiliation(s)
- Andres S Arango
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hyun Park
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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32
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Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA. Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. Nat Commun 2023; 14:7570. [PMID: 37989735 PMCID: PMC10663523 DOI: 10.1038/s41467-023-43008-5] [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: 05/12/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
ADP-ribosylation factor 1 (Arf1) interacts with multiple cellular partners and membranes to regulate intracellular traffic, organelle structure and actin dynamics. Defining the dynamic conformational landscape of Arf1 in its active form, when bound to the membrane, is of high functional relevance and key to understanding how Arf1 can alter diverse cellular processes. Through concerted application of nuclear magnetic resonance (NMR), neutron reflectometry (NR) and molecular dynamics (MD) simulations, we show that, while Arf1 is anchored to the membrane through its N-terminal myristoylated amphipathic helix, the G domain explores a large conformational space, existing in a dynamic equilibrium between membrane-associated and membrane-distal conformations. These configurational dynamics expose different interfaces for interaction with effectors. Interaction with the Pleckstrin homology domain of ASAP1, an Arf-GTPase activating protein (ArfGAP), restricts motions of the G domain to lock it in what seems to be a conformation exposing functionally relevant regions.
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Affiliation(s)
- Yue Zhang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Ring Therapeutics, Inc., Cambridge, MA, USA
| | - Olivier Soubias
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Loxo Oncology at Lilly, Louisville, CO, USA
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Jess Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Yifei Li
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA
- Vonsun Pharmatech Co., Ltd., Suzhou, China
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK
| | - Sebastian Daum
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Kirsten Bacia
- Institute for Chemistry, Department of Biophysical Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3A, 06120, Halle, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, 04107, Leipzig, Germany
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- NIST Center for Neutron Research, Gaithersburg, MD, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
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33
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Navarro C, Majewski M, De Fabritiis G. Top-Down Machine Learning of Coarse-Grained Protein Force Fields. J Chem Theory Comput 2023; 19:7518-7526. [PMID: 37874270 PMCID: PMC10777392 DOI: 10.1021/acs.jctc.3c00638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 10/25/2023]
Abstract
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended time scales. Our methodology involves simulating proteins with molecular dynamics and utilizing the resulting trajectories to train a neural network potential through differentiable trajectory reweighting. Remarkably, this method requires only the native conformation of proteins, eliminating the need for labeled data derived from extensive simulations or memory-intensive end-to-end differentiable simulations. Once trained, the model can be employed to run parallel molecular dynamics simulations and sample folding events for proteins both within and beyond the training distribution, showcasing its extrapolation capabilities. By applying Markov state models, native-like conformations of the simulated proteins can be predicted from the coarse-grained simulations. Owing to its theoretical transferability and ability to use solely experimental static structures as training data, we anticipate that this approach will prove advantageous for developing new protein force fields and further advancing the study of protein dynamics, folding, and interactions.
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Affiliation(s)
- Carles Navarro
- Acellera
Labs, Doctor Trueta 183, 08005 Barcelona, Spain
| | | | - Gianni De Fabritiis
- Computational
Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Acellera
Ltd., Devonshire House
582, Middlesex HA7 1JS, United Kingdom
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
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34
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Gahtori P, Gunwant V, Pandey R. How Does pH Affect the Adsorption of Human Serum Protein in the Presence of Hydrophobic and Hydrophilic Nanoparticles at Air-Water and Lipid-Water Interfaces? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15487-15498. [PMID: 37878019 DOI: 10.1021/acs.langmuir.3c01755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
This study investigates interaction between hydrophilic (11-mercaptoundecanoic acid (MUA)) and hydrophobic (1-undecanethiol (UDT)) gold nanoparticles (GNPs) with human serum albumin (HSA) protein on air-water and lipid-water interfaces at pH 3 and 7. Vibrational sum frequency generation (VSFG) spectroscopy is used to analyze changes in the intensity of interfacial water molecules and the C-H group of the protein. At the air-water interface, the hydrophobic interaction between the HSA protein and hydrophobic GNPs at pH 3 leads to their accumulation at the interface, resulting in an increased C-H intensity of the protein with a slight decrease in water intensity. Whereas, at pH 7, where the negative charge of the protein results in the reduced surface activity of the HSA compared to pH 3, the interaction between alkyl chain of the hydrophobic GNPs and alkyl group of the protein results in the adsorption of the protein-capped GNPs at the interface. This leads to an increased intensity of the C-H group of protein and water molecules. However, negatively charged hydrophilic GNPs do not induce significant changes in the interfacial water structure or the C-H group of the protein due to the electrostatic force of repulsion with the negatively charged HSA at pH 7. In contrast, at the lipid-water interface, both hydrophobic and hydrophilic GNPs interact with HSA protein, causing disordering of interfacial water molecules at pH 3 and ordering at pH 7. Interestingly, similar behavior of the protein with both types of GNPs results in comparable ordering/disordering at the interface depending on the pH of solution. Furthermore, the VSFG results obtained with the deuterated lipid suggest that changes in ordering and disorder occur due to increased protein adsorption in the presence of GNPs, causing alterations in the membrane structure. These findings give a better understanding of the mechanisms that govern protein-nanoparticle interaction and their consequential effects on the structure, function, and behavior of molecules at the biological membrane interface, which is crucial for developing safe and effective nanoparticle-based therapeutics.
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Affiliation(s)
- Preeti Gahtori
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Vineet Gunwant
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ravindra Pandey
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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35
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Satoh I, Gotou K, Nagatsuma S, Nagashima KVP, Kobayashi M, Yu LJ, Madigan MT, Kimura Y, Wang-Otomo ZY. Selective expression of light-harvesting complexes alters phospholipid composition in the intracytoplasmic membrane and core complex of purple phototrophic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:149001. [PMID: 37527691 DOI: 10.1016/j.bbabio.2023.149001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Phospholipid-protein interactions play important roles in regulating the function and morphology of photosynthetic membranes in purple phototrophic bacteria. Here, we characterize the phospholipid composition of intracytoplasmic membrane (ICM) from Rhodobacter (Rba.) sphaeroides that has been genetically altered to selectively express light-harvesting (LH) complexes. In the mutant strain (DP2) that lacks a peripheral light-harvesting (LH2) complex, the phospholipid composition was significantly different from that of the wild-type strain; strain DP2 showed a marked decrease in phosphatidylglycerol (PG) and large increases in cardiolipin (CL) and phosphatidylcholine (PC) indicating preferential interactions between the complexes and specific phospholipids. Substitution of the core light-harvesting (LH1) complex of Rba. sphaeroides strain DP2 with that from the purple sulfur bacterium Thermochromatium tepidum further altered the phospholipid composition, with substantial increases in PG and PE and decreases in CL and PC, indicating that the phospholipids incorporated into the ICM depend on the nature of the LH1 complex expressed. Purified LH1-reaction center core complexes (LH1-RC) from the selectively expressing strains also contained different phospholipid compositions than did core complexes from their corresponding wild-type strains, suggesting different patterns of phospholipid association between the selectively expressed LH1-RC complexes and those purified from native strains. Effects of carotenoids on the phospholipid composition were also investigated using carotenoid-suppressed cells and carotenoid-deficient species. The findings are discussed in relation to ICM morphology and specific LH complex-phospholipid interactions.
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Affiliation(s)
- I Satoh
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - K Gotou
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - S Nagatsuma
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - K V P Nagashima
- Research Institute for Integrated Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686, Japan
| | - M Kobayashi
- National Institute of Technology, Ariake College, Omuta, Fukuoka 836-8585, Japan
| | - L-J Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - M T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | - Y Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Z-Y Wang-Otomo
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan.
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36
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Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. J Chem Theory Comput 2023; 19:7387-7404. [PMID: 37796943 DOI: 10.1021/acs.jctc.3c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
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Affiliation(s)
- Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Ana C Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tugba Nur Ozturk
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Rúa de Jenaro de la Fuente, 15705 Santiago de Compostela, Spain
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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37
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Cheng KJ, De Lio AM, Jain R, Paul D, Morrissey JH, Pogorelov TV. Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains. Biochemistry 2023; 62:3020-3032. [PMID: 37747791 PMCID: PMC10903746 DOI: 10.1021/acs.biochem.3c00274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Protein binding to negatively charged lipids is essential for maintaining numerous vital cellular processes where its dysfunction can lead to various diseases. One such protein that plays a crucial role in this process is lactadherin, which competes with coagulation factors for membrane binding sites to regulate blood clotting. Despite identifying key binding regions of these proteins through structural and biochemical studies, models incorporating membrane dynamics are still lacking. In this study, we report on the multimodal binding of lactadherin and use it to gain insight into the binding mechanisms of its C domain homologs, factor V and factor VIII. Molecular dynamics simulations enhanced with the highly mobile mimetic model enabled the determination of lactadherin's multimodal binding on membranes that revealed critical interacting residues consistent with prior NMR and mutagenesis data. The binding occurred primarily via two dynamic structural ensembles: an inserted state and an unreported, highly conserved side-lying state driven by a cationic patch. We utilized these findings to analyze the membrane binding domains of coagulation factors V and VIII and identified their preferred membrane-bound conformations. Specifically, factor V's C domains maintained an inserted state, while factor VIII preferred a tilted, side-lying state that permitted antibody binding. Insight into lactadherin's atomistically resolved membrane interactions from a multistate perspective can guide new therapeutic opportunities in treating diseases related to blood coagulation.
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Affiliation(s)
- Kevin J Cheng
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ashley M De Lio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- National Center for Supercomputer Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Riya Jain
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Divyani Paul
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - James H Morrissey
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Taras V Pogorelov
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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38
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Fu T, Zeng S, Zheng Q, Zhu F. The Important Role of Transporter Structures in Drug Disposition, Efficacy, and Toxicity. Drug Metab Dispos 2023; 51:1316-1323. [PMID: 37295948 DOI: 10.1124/dmd.123.001275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
The ATP-binding cassette (ABC) and solute carrier (SLC) transporters are critical determinants of drug disposition, clinical efficacy, and toxicity as they specifically mediate the influx and efflux of various substrates and drugs. ABC transporters can modulate the pharmacokinetics of many drugs via mediating the translocation of drugs across biologic membranes. SLC transporters are important drug targets involved in the uptake of a broad range of compounds across the membrane. However, high-resolution experimental structures have been reported for a very limited number of transporters, which limits the study of their physiologic functions. In this review, we collected structural information on ABC and SLC transporters and described the application of computational methods in structure prediction. Taking P-glycoprotein (ABCB1) and serotonin transporter (SLC6A4) as examples, we assessed the pivotal role of structure in transport mechanisms, details of ligand-receptor interactions, drug selectivity, the molecular mechanisms of drug-drug interactions, and differences caused by genetic polymorphisms. The data collected contributes toward safer and more effective pharmacological treatments. SIGNIFICANCE STATEMENT: The experimental structure of ATP-binding cassette and solute carrier transporters was collected, and the application of computational methods in structure prediction was described. P-glycoprotein and serotonin transporter were used as examples to reveal the pivotal role of structure in transport mechanisms, drug selectivity, the molecular mechanisms of drug-drug interactions, and differences caused by genetic polymorphisms.
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Affiliation(s)
- Tingting Fu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
| | - Su Zeng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
| | - Qingchuan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
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39
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Weesner JA, Annunziata I, van de Vlekkert D, d'Azzo A. Glycosphingolipids within membrane contact sites influence their function as signaling hubs in neurodegenerative diseases. FEBS Open Bio 2023; 13:1587-1600. [PMID: 37014126 PMCID: PMC10476575 DOI: 10.1002/2211-5463.13605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
Intracellular organelles carry out many of their functions by engaging in extensive interorganellar communication through specialized membrane contact sites (MCSs) formed where two organelles tether to each other or to the plasma membrane (PM) without fusing. In recent years, these ubiquitous membrane structures have emerged as central signaling hubs that control a multitude of cellular pathways, ranging from lipid metabolism/transport to the exchange of metabolites and ions (i.e., Ca2+ ), and general organellar biogenesis. The functional crosstalk between juxtaposed membranes at MCSs relies on a defined composite of proteins and lipids that populate these microdomains in a dynamic fashion. This is particularly important in the nervous system, where alterations in the composition of MCSs have been shown to affect their functions and have been implicated in the pathogenesis of neurodegenerative diseases. In this review, we focus on the MCSs that are formed by the tethering of the endoplasmic reticulum (ER) to the mitochondria, the ER to the endo-lysosomes and the mitochondria to the lysosomes. We highlight how glycosphingolipids that are aberrantly processed/degraded and accumulate ectopically in intracellular membranes and the PM change the topology of MCSs, disrupting signaling pathways that lead to neuronal demise and neurodegeneration. In particular, we focus on neurodegenerative lysosomal storage diseases linked to altered glycosphingolipid catabolism.
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Affiliation(s)
| | - Ida Annunziata
- Department of GeneticsSt. Jude Children's Research HospitalMemphisTNUSA
- Compliance OfficeSt. Jude Children's Research HospitalMemphisTNUSA
| | | | - Alessandra d'Azzo
- Department of GeneticsSt. Jude Children's Research HospitalMemphisTNUSA
- Department of Anatomy and Neurobiology, College of Graduate Health SciencesUniversity of Tennessee Health Science CenterMemphisTNUSA
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40
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Liu Z, Chen S, Wu J. Advances in ultrahigh-throughput screening technologies for protein evolution. Trends Biotechnol 2023; 41:1168-1181. [PMID: 37088569 DOI: 10.1016/j.tibtech.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023]
Abstract
Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.
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Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China.
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41
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Zheng L, Zhu Y, Sun Y, Xia S, Duan S, Yu B, Li J, Xu FJ. Flexible Modulation of Cellular Activities with Cationic Photosensitizers: Insights of Alkyl Chain Length on Reactive Oxygen Species Antimicrobial Mechanisms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302943. [PMID: 37231625 DOI: 10.1002/adma.202302943] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Cationic photosensitizers have good binding ability with negatively charged bacteria and fungi, exhibiting broad applications potential in antimicrobial photodynamic therapy (aPDT). However, cationic photosensitizers often display unsatisfactory transkingdom selectivity between mammalian cells and pathogens, especially for eukaryotic fungi. It is unclear which biomolecular sites are more efficient for photodynamic damage, owing to the lack of systematic research with the same photosensitizer system. Herein, a series of cationic aggregation-induced emission (AIE) derivatives (CABs) (using berberine (BBR) as the photosensitizers core) with different length alkyl chains are successfully designed and synthesized for flexible modulation of cellular activities. The BBR core can efficiently produce reactive oxygen species (ROS) and achieve high-performance aPDT . Through the precise regulation of alkyl chain length, different bindings, localizations, and photodynamic killing effects of CABs are achieved and investigated systematically among bacteria, fungi, and mammalian cells. It is found that intracellular active substances, not membranes, are more efficient damage sites of aPDT. Moderate length alkyl chains enable CABs to effectively kill Gram-negative bacteria and fungi with light, while still maintaining excellent mammalian cell and blood compatibility. This study is expected to provide systematic theoretical and strategic research guidance for the construction of high-performance cationic photosensitizers with good transkingdom selectivity.
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Affiliation(s)
- Liang Zheng
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yiwen Zhu
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yujie Sun
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuai Xia
- College of Medical Engineering & the Key Laboratory for Medical Functional Nanomaterials, Jining Medical University, Jining, 272067, China
| | - Shun Duan
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Bingran Yu
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jing Li
- College of Medical Engineering & the Key Laboratory for Medical Functional Nanomaterials, Jining Medical University, Jining, 272067, China
| | - Fu-Jian Xu
- State Key Laboratory of Chemical Resource Engineering, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education) and Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
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42
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Schlessinger A, Zatorski N, Hutchinson K, Colas C. Targeting SLC transporters: small molecules as modulators and therapeutic opportunities. Trends Biochem Sci 2023; 48:801-814. [PMID: 37355450 PMCID: PMC10525040 DOI: 10.1016/j.tibs.2023.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023]
Abstract
Solute carrier (SLCs) transporters mediate the transport of a broad range of solutes across biological membranes. Dysregulation of SLCs has been associated with various pathologies, including metabolic and neurological disorders, as well as cancer and rare diseases. SLCs are therefore emerging as key targets for therapeutic intervention with several recently approved drugs targeting these proteins. Unlocking this large and complex group of proteins is essential to identifying unknown SLC targets and developing next-generation SLC therapeutics. Recent progress in experimental and computational techniques has significantly advanced SLC research, including drug discovery. Here, we review emerging topics in therapeutic discovery of SLCs, focusing on state-of-the-art approaches in structural, chemical, and computational biology, and discuss current challenges in transporter drug discovery.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Nicole Zatorski
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Colas
- University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria.
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43
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Kobayashi M, Noguchi H, Sato G, Watanabe C, Fujiwara K, Yanagisawa M. Phase-Separated Giant Liposomes for Stable Elevation of α-Hemolysin Concentration in Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11481-11489. [PMID: 37531551 DOI: 10.1021/acs.langmuir.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Staphylococcus aureus α-hemolysin (αHL) is one of the most popular proteins in nanopore experiments within lipid membranes. Higher concentrations of αHL within the lipid membrane are desirable to enhance the mass transport capacity through nanopores. However, the reconstitution of αHL at high concentrations is associated with the problem of membrane lytic disruption. In this study, we present a method that effectively increases αHL concentration while maintaining membrane stability. This method is achieved by using phase-separated giant liposomes, where coexisting liquid-disordered (Ld) and liquid-ordered phases (Lo) are enriched in unsaturated lipids and saturated lipids with cholesterol (Chol), respectively. Fluorescence observation of αHL in liposomes revealed that the presence of Chol facilitates αHL insertion into the membrane. Despite the preferential localization of αHL in the Ld phase rather than the Lo phase, the coexistence of both Lo and Ld phases prevents membrane disruption in the presence of concentrated αHL. We have explained this stabilization mechanism considering the lower membrane tension exhibited by phase-separated liposomes compared to homogeneous liposomes. Under hypertonic conditions, we have successfully increased the local concentration of αHL by invagination of the lipid-only region in the Ld phase, leaving αHL behind. This method exhibits potential for the reconstitution of various nanochannels and membrane proteins that prefer the Ld phase over the Lo phase, thus enabling the production of giant liposomes at high concentrations and the replication of the membrane-crowding condition observed in cells.
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Affiliation(s)
- Mizuki Kobayashi
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Hiroshi Noguchi
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Graduate School of Science, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Gaku Sato
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama 223-8522, Japan
| | - Chiho Watanabe
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi, Hiroshima 739-8521, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama 223-8522, Japan
| | - Miho Yanagisawa
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
- Graduate School of Science, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
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44
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Dehghani-Ghahnaviyeh S, Smith M, Xia Y, Dousis A, Grossfield A, Sur S. Ionizable Amino Lipids Distribution and Effects on DSPC/Cholesterol Membranes: Implications for Lipid Nanoparticle Structure. J Phys Chem B 2023; 127:6928-6939. [PMID: 37498794 PMCID: PMC10424244 DOI: 10.1021/acs.jpcb.3c01296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/05/2023] [Indexed: 07/29/2023]
Abstract
Lipid nanoparticles (LNPs) containing ionizable aminolipids are among the leading platforms for the successful delivery of nucleic-acid-based therapeutics, including messenger RNA (mRNA). The two recently FDA-approved COVID-19 vaccines developed by Moderna and Pfizer/BioNTech belong to this category. Ionizable aminolipids, cholesterol, and DSPC lipids are among the key components of such formulations, crucially modulating physicochemical properties of these formulations and, consequently, the potency of these therapeutics. Despite the importance of these components, the distribution of these molecules in LNPs containing mRNA is not clear. In this study, we used all-atom molecular dynamics (MD) simulations to investigate the distribution and effects of the Lipid-5 (apparent pKa of the lipid nanoparticle = 6.56), a rationally designed and previously reported ionizable aminolipid by Moderna, on lipid bilayers [Mol. Ther. 2018, 26, 1509-1519]. The simulations were conducted with half of the aminolipids charged and half neutral approximately to the expected ionization in the microenvironment of the LNP surface. In all five simulated systems in this work, the cholesterol content was kept constant, whereas the DSPC and Lipid-5 concentrations were changed systematically. We found that at higher concentrations of the ionizable aminolipids, the neutral aminolipids form a disordered aggregate in the membrane interior that preferentially includes cholesterol. The rules underlying the lipid redistribution could be used to rationally choose lipids to optimize the LNP function.
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Affiliation(s)
- Sepehr Dehghani-Ghahnaviyeh
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
- Theoretical
and Computational Biophysics Group, NIH Center for Macromolecular
Modeling and Bioinformatics, Beckman Institute for Advanced Science
and Technology, Department of Biochemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61820, United States
| | - Michael Smith
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
| | - Yan Xia
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
| | | | - Alan Grossfield
- Department
of Biochemistry and Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
| | - Sreyoshi Sur
- Moderna,
Inc., Cambridge, Massachusetts 02139, United States
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45
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Zhang J, Li F, Shen S, Yang Z, Ji X, Wang X, Liao X, Zhang Y. More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review. Food Chem 2023; 416:135726. [PMID: 36893635 DOI: 10.1016/j.foodchem.2023.135726] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.
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Affiliation(s)
- Jinghao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Fangwei Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Suxia Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Zhaotian Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xingyu Ji
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Yan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China.
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46
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Ren M, Ma Z, Zhao L, Wang Y, An H, Sun F. Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection. J Chem Inf Model 2023; 63:4423-4432. [PMID: 37382878 DOI: 10.1021/acs.jcim.3c00041] [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: 06/30/2023]
Abstract
Transmissibility of SARS-CoV-2 initially relies on its trimeric Spike-RBDs to tether the ACE-2 on host cells, and enhanced self-association of ACE-2 engaged with Spike facilitates the viral infection. Two primary packing modes of Spike-ACE2 heteroproteins exist potentially due to discrepant amounts of RBDs loading on ACE-2, but the resultant self-association difference is inherently unclear. We used extensive coarse-grained dynamic simulations to characterize the self-association efficiency, the conformation relevance, and the molecular mechanism of ACE-2 with different RBD amounts. It was revealed that the ACE-2 hanging two/full RBDs (Mode-A) rapidly dimerized into the heteroprotein complex in a compact "linear" conformation, while the bare ACE-2 showed weakened self-association and a protein complex. The RBD-tethered ectodomains of ACE-2 presented a more upright conformation relative to the membrane, and the intermolecular ectodomains were predominantly packed by the neck domains, which was obligated to the rapid protein self-association in a compact pattern. Noted is the fact that the ACE-2 tethered by a single RBD (Mode-B) retained considerable self-association efficiency and clustering capability, which unravels the interrelation of ACE-2 colocalization and protein cross-linkage. The molecular perspectives in this study expound the self-association potency of ACE-2 with different RBD amounts and the viral activity implications, which can greatly enhance our comprehension of SARS-CoV-2 infection details.
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Affiliation(s)
- Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Lina Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yanjiao Wang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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47
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Tsuzuki S, Ikeda S, Shinoda W, Shigenobu K, Ueno K, Dokko K, Watanabe M. Molecular Dynamics Simulations of High-Concentration Li[TFSA] Sulfone Solution: Effect of Easy Conformation Change of Sulfolane on Fast Diffusion of Li Ion. J Phys Chem B 2023. [PMID: 37428625 DOI: 10.1021/acs.jpcb.3c02009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The parameters of the polarizable force field used for molecular dynamics simulations of Li diffusion in high-concentration lithium bis(trifluoromethanesulfonyl)amide (Li[TFSA]) sulfone (sulfolane, dimethylsulfone, ethylmethylsulfone, and ethyl-i-propylsulfone) solutions were refined. The densities of the solutions obtained by molecular dynamics simulations reproduced well the experimental values. The calculated concentration, temperature, and solvent dependencies of self-diffusion coefficients of ions and solvents in the mixtures well reproduce the experimentally observed dependencies. Ab initio calculations show that the intermolecular interactions between Li ions and four sulfones are not largely different. Conformational analyses show that sulfolane can change the conformation more easily owing to lower barrier height for pseudorotation compared to the rotational barrier heights of diethylsulfone and ethylmethylsulfone. Molecular dynamics simulations indicate that the easy conformation change of solvent affects the rotational relaxation of the solvent and the diffusion of Li ion in the mixture. The easy conformation change of sulfolane is one of the causes of faster diffusion of Li ion in the mixture of Li[TFSA] and sulfolane compared to the mixtures of smaller dimethylsulfone and ethylmethylsulfone.
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Affiliation(s)
- Seiji Tsuzuki
- Advanced Chemical Energy Research Centre (ACERC), Institute of Advanced Sciences, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shuhei Ikeda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Keisuke Shigenobu
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuhide Ueno
- Advanced Chemical Energy Research Centre (ACERC), Institute of Advanced Sciences, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kaoru Dokko
- Advanced Chemical Energy Research Centre (ACERC), Institute of Advanced Sciences, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
- Department of Chemistry and Life Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Masayoshi Watanabe
- Advanced Chemical Energy Research Centre (ACERC), Institute of Advanced Sciences, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
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48
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Liu J, Zhang T, Sun S. Molecular Dynamics Simulations of Ion Transport through Protein Nanochannels in Peritoneal Dialysis. Int J Mol Sci 2023; 24:10074. [PMID: 37373224 DOI: 10.3390/ijms241210074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
In recent decades, the development of dialysis techniques has greatly improved the survival rate of renal failure patients, and peritoneal dialysis is gradually showing dominance over hemodialysis. This method relies on the abundant membrane proteins in the peritoneum, avoiding the use of artificial semipermeable membranes, and the ion fluid transport is partly controlled by the protein nanochannels. Hence, this study investigated ion transport in these nanochannels by using molecular dynamics (MD) simulations and an MD Monte Carlo (MDMC) algorithm for a generalized protein nanochannel model and a saline fluid environment. The spatial distribution of ions was determined via MD simulations, and it agreed with that modeled via the MDMC method; the effects of simulation duration and external electronic fields were also explored to validate the MDMC algorithm. The specific atomic sequence within a nanochannel was visualized, which was the rare transport state during the ion transport process. The residence time was assessed through both methods to represent the involved dynamic process, and its values showed the temporal sequential order of different components in the nanochannel as follows: H2O > Na+ > Cl-. The accurate prediction using the MDMC method of the spatial and temporal properties proves its suitability to handle ion transport problems in protein nanochannels.
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Affiliation(s)
- Jie Liu
- Computational Transport Phenomena Laboratory, Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tao Zhang
- Computational Transport Phenomena Laboratory, Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shuyu Sun
- Computational Transport Phenomena Laboratory, Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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49
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Nguyen N, Lewis A, Pham T, Sikazwe D, Cheng KH. Exploring the Role of Anionic Lipid Nanodomains in the Membrane Disruption and Protein Folding of Human Islet Amyloid Polypeptide Oligomers on Lipid Membrane Surfaces Using Multiscale Molecular Dynamics Simulations. Molecules 2023; 28:4191. [PMID: 37241931 PMCID: PMC10223233 DOI: 10.3390/molecules28104191] [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: 04/21/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The aggregation of human Islet Amyloid Polypeptide (hIAPP) on cell membranes is linked to amyloid diseases. However, the physio-chemical mechanisms of how these hIAPP aggregates trigger membrane damage are unclear. Using coarse-grained and all-atom molecular dynamics simulations, we investigated the role of lipid nanodomains in the presence or absence of anionic lipids, phosphatidylserine (PS), and a ganglioside (GM1), in the membrane disruption and protein folding behaviors of hIAPP aggregates on phase-separated raft membranes. Our raft membranes contain liquid-ordered (Lo), liquid-disordered (Ld), mixed Lo/Ld (Lod), PS-cluster, and GM1-cluster nanosized domains. We observed that hIAPP aggregates bound to the Lod domain in the absence of anionic lipids, but also to the GM1-cluster- and PS-cluster-containing domains, with stronger affinity in the presence of anionic lipids. We discovered that L16 and I26 are the lipid anchoring residues of hIAPP binding to the Lod and PS-cluster domains. Finally, significant lipid acyl chain order disruption in the annular lipid shells surrounding the membrane-bound hIAPP aggregates and protein folding, particularly beta-sheet formation, in larger protein aggregates were evident. We propose that the interactions of hIAPP and both non-anionic and anionic lipid nanodomains represent key molecular events of membrane damage associated with the pathogenesis of amyloid diseases.
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Affiliation(s)
- Ngoc Nguyen
- Physics Department, Trinity University, San Antonio, TX 78212, USA; (N.N.); (T.P.)
| | - Amber Lewis
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA;
| | - Thuong Pham
- Physics Department, Trinity University, San Antonio, TX 78212, USA; (N.N.); (T.P.)
| | - Donald Sikazwe
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA;
| | - Kwan H. Cheng
- Physics Department, Trinity University, San Antonio, TX 78212, USA; (N.N.); (T.P.)
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA;
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50
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Malec K, Monaco S, Delso I, Nestorowicz J, Kozakiewicz-Latała M, Karolewicz B, Khimyak YZ, Angulo J, Nartowski KP. Unravelling the mechanisms of drugs partitioning phenomena in micellar systems via NMR spectroscopy. J Colloid Interface Sci 2023; 638:135-148. [PMID: 36736115 DOI: 10.1016/j.jcis.2023.01.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Despite extensive use of micelles in materials and colloidal science, their supramolecular organization as well as host-guest interactions within these dynamic assemblies are poorly understood. Small guest molecules in the presence of micelles undergo constant exchange between a micellar aggregate and the surrounding solution, posing a considerable challenge for their molecular level characterisation. In this work we reveal the interaction maps between small guest molecules and surfactants forming micelles via novel applications of NMR techniques supported with state-of-the-art analytical methods used in colloidal science. Model micelles composed of structurally distinct surfactants (block non-ionic polymer Pluronic® F-127, non-ionic surfactant Tween 20 or Tween 80, and ionic surfactant sodium lauryl sulphate, SLS) were selected and loaded with model small molecules of biological relevance (i.e. the drugs fluconazole, FLU or indomethacin, IMC) known to have different partition coefficients. Molecular level organization of FLU or IMC within hydrophilic and hydrophobic domains of micellar aggregates was established using the combination of NMR methods (1D 1H NMR, 1D 19F NMR, 2D 1H-1H NOESY and 2D 1H-19F HOESY, and the multifrequency-STD NMR) and corroborated with molecular dynamics (MD) simulations. This is the first application of multifrequency-STD NMR to colloidal systems, enabling us to elucidate intricately detailed patterns of drug/micelle interactions in a single NMR experiment within minutes. Importantly, our results indicate that flexible surfactants, such as block copolymers and polysorbates, form micellar aggregates with a surface composed of both hydrophilic and hydrophobic domains and do not follow the classical core-shell model of the micelle. We propose that the magnitude of changes in 1H chemical shifts corroborated with interaction maps obtained from DEEP-STD NMR and 2D NMR experiments can be used as an indicator of the strength of the guest-surfactant interactions. This NMR toolbox can be adopted for the analysis of broad range of colloidal host-guest systems from soft materials to biological systems.
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Affiliation(s)
- Katarzyna Malec
- Department of Drug Form Technology, Faculty of Pharmacy, Wroclaw Medical University, 211a Borowska Str, 50-556 Wroclaw, Poland
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Chancellors Drive, NR4 7TJ Norwich, UK
| | - Ignacio Delso
- School of Pharmacy, University of East Anglia, Chancellors Drive, NR4 7TJ Norwich, UK
| | - Justyna Nestorowicz
- Department of Drug Form Technology, Faculty of Pharmacy, Wroclaw Medical University, 211a Borowska Str, 50-556 Wroclaw, Poland
| | - Marta Kozakiewicz-Latała
- Department of Drug Form Technology, Faculty of Pharmacy, Wroclaw Medical University, 211a Borowska Str, 50-556 Wroclaw, Poland
| | - Bożena Karolewicz
- Department of Drug Form Technology, Faculty of Pharmacy, Wroclaw Medical University, 211a Borowska Str, 50-556 Wroclaw, Poland
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia, Chancellors Drive, NR4 7TJ Norwich, UK.
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Chancellors Drive, NR4 7TJ Norwich, UK; Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, Sevilla 41092, Spain.
| | - Karol P Nartowski
- Department of Drug Form Technology, Faculty of Pharmacy, Wroclaw Medical University, 211a Borowska Str, 50-556 Wroclaw, Poland; School of Pharmacy, University of East Anglia, Chancellors Drive, NR4 7TJ Norwich, UK.
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