1
|
Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [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: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
Collapse
Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| |
Collapse
|
2
|
Lyu Y, Chen S, Zhao Y, Yuan H, Zhang C, Zhang C, Meng Q. Effect of GM1 concentration change on plasma membrane: molecular dynamics simulation and analysis. Phys Chem Chem Phys 2024; 26:12552-12563. [PMID: 38595108 DOI: 10.1039/d3cp06161b] [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: 04/11/2024]
Abstract
Ganglioside GM1 is a class of glycolipids predominantly located in the nervous system. Comprising a ceramide anchor and an oligosaccharide chain containing sialic acid, GM1 plays a pivotal role in various cellular processes, including signal transduction, cell adhesion, and membrane organization. Moreover, GM1 has been implicated in the pathogenesis of several neurological disorders, such as Parkinson's disease, Alzheimer's disease, and stroke. In this study, by creating a neural cell model membrane simulation system and employing rigorous molecular models, we utilize a coarse-grained molecular dynamics approach to explore the structural and dynamic characteristics of multi-component neuronal plasma membranes at varying GM1 ganglioside concentrations. The simulation results reveal that as GM1 concentration increases, a greater number of hydrogen bonds form between GM1 molecules, resulting in the formation of larger clusters, which leads to reduced membrane fluidity, increased lipid ordering, decreased membrane thickness and surface area and higher levels of GM1 dissociation. Through a meticulous analysis, while considering GM1's structural attributes, we offer valuable insights into the structural and dynamic traits of the cell membrane. This study provides a robust methodology for exploring membrane characteristics and enhances our comprehension of GM1 molecules, serving as a resource for both experimental and computational researchers in this field.
Collapse
Affiliation(s)
- Yongkang Lyu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Shuo Chen
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Yu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Hongxiu Yuan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Chenyang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, People's Republic of China.
| |
Collapse
|
3
|
Shivgan AT, Marzinek JK, Krah A, Matsudaira P, Verma CS, Bond PJ. Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations. J Chem Theory Comput 2024; 20:3308-3321. [PMID: 38358378 DOI: 10.1021/acs.jctc.3c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Proteoglycans contain glycosaminoglycans (GAGs) which are negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly in governing cellular communication and attachment. Depending on their sulfonation state, acetylation, and glycosidic linkages, GAGs belong to different families. The high molecular weight, heterogeneity, and flexibility of GAGs hamper their characterization at atomic resolution, but this may be circumvented via coarse-grained (CG) approaches. In this work, we report a CG model for a library of common GAG types in their isolated or proteoglycan-linked states compatible with version 2.2 (v2.2) of the widely popular CG Martini force field. The model reproduces conformational and thermodynamic properties for a wide variety of GAGs, as well as matching structural and binding data for selected proteoglycan test systems. The parameters developed here may thus be employed to study a range of GAG-containing biomolecular systems, thereby benefiting from the efficiency and broad applicability of the Martini framework.
Collapse
Affiliation(s)
- Aishwary T Shivgan
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Alexander Krah
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Paul Matsudaira
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
| | - Chandra S Verma
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Peter J Bond
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| |
Collapse
|
4
|
Dong E, Huo Q, Zhang J, Han H, Cai T, Liu D. Advancements in nanoscale delivery systems: optimizing intermolecular interactions for superior drug encapsulation and precision release. Drug Deliv Transl Res 2024:10.1007/s13346-024-01579-w. [PMID: 38573495 DOI: 10.1007/s13346-024-01579-w] [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] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Nanoscale preparations, such as nanoparticles, micelles, and liposomes, are increasingly recognized in pharmaceutical technology for their high capability in tailoring the pharmacokinetics of the encapsulated drug within the body. These preparations have great potential in extending drug half-life, reducing dosing frequency, mitigating drug side effects, and enhancing drug efficacy. Consequently, nanoscale preparations offer promising prospects for the treatment of metabolic disorders, malignant tumors, and various chronic diseases. Nevertheless, the complete clinical potential of nanoscale preparations remains untapped due to the challenges associated with low drug loading degrees and insufficient control over drug release. In this review, we comprehensively summarize the vital role of intermolecular interactions in enhancing encapsulation and controlling drug release within nanoscale delivery systems. Our analysis critically evaluates the characteristics of common intermolecular interactions and elucidates the techniques employed to assess them. Moreover, we highlight the significant potential of intermolecular interactions in clinical translation, particularly in the screening and optimization of preparation prescriptions. By attaining a deeper understanding of intermolecular interaction properties and mechanisms, we can adopt a more rational approach to designing drug carriers, leading to substantial advancements in the application and clinical transformation of nanoscale preparations. Moving forward, continued research in this field offers exciting prospects for unlocking the full clinical potential of nanoscale preparations and revolutionizing the field of drug delivery.
Collapse
Affiliation(s)
- Enpeng Dong
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing 210009, China
| | - Qingqing Huo
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing 210009, China
| | - Jie Zhang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing 210009, China
| | - Hanghang Han
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing 210009, China
| | - Ting Cai
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing 210009, China.
| | - Dongfei Liu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing 210009, China.
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
5
|
Lin Y, Tao E, Champion JP, Corry B. A binding site for phosphoinositides described by multiscale simulations explains their modulation of voltage-gated sodium channels. eLife 2024; 12:RP91218. [PMID: 38465747 DOI: 10.7554/elife.91218] [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] [Indexed: 03/12/2024] Open
Abstract
Voltage-gated sodium channels (Naᵥ) are membrane proteins which open to facilitate the inward flux of sodium ions into excitable cells. In response to stimuli, Naᵥ channels transition from the resting, closed state to an open, conductive state, before rapidly inactivating. Dysregulation of this functional cycle due to mutations causes diseases including epilepsy, pain conditions, and cardiac disorders, making Naᵥ channels a significant pharmacological target. Phosphoinositides are important lipid cofactors for ion channel function. The phosphoinositide PI(4,5)P2 decreases Naᵥ1.4 activity by increasing the difficulty of channel opening, accelerating fast inactivation and slowing recovery from fast inactivation. Using multiscale molecular dynamics simulations, we show that PI(4,5)P2 binds stably to inactivated Naᵥ at a conserved site within the DIV S4-S5 linker, which couples the voltage-sensing domain (VSD) to the pore. As the Naᵥ C-terminal domain is proposed to also bind here during recovery from inactivation, we hypothesize that PI(4,5)P2 prolongs inactivation by competitively binding to this site. In atomistic simulations, PI(4,5)P2 reduces the mobility of both the DIV S4-S5 linker and the DIII-IV linker, responsible for fast inactivation, slowing the conformational changes required for the channel to recover to the resting state. We further show that in a resting state Naᵥ model, phosphoinositides bind to VSD gating charges, which may anchor them and impede VSD activation. Our results provide a mechanism by which phosphoinositides alter the voltage dependence of activation and the rate of recovery from inactivation, an important step for the development of novel therapies to treat Naᵥ-related diseases.
Collapse
Affiliation(s)
- Yiechang Lin
- Research School of Biology, Australian National University, Canberra, Australia
| | - Elaine Tao
- Research School of Biology, Australian National University, Canberra, Australia
| | - James P Champion
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, Australia
| |
Collapse
|
6
|
Garay PG, Machado MR, Verli H, Pantano S. SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation. J Chem Theory Comput 2024; 20:963-976. [PMID: 38175797 DOI: 10.1021/acs.jctc.3c00783] [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: 01/06/2024]
Abstract
Glycans constitute one of the most complex families of biological molecules. Despite their crucial role in a plethora of biological processes, they remain largely uncharacterized because of their high complexity. Their intrinsic flexibility and the vast variability associated with the many combination possibilities have hampered their experimental determination. Although theoretical methods have proven to be a valid alternative to the study of glycans, the large size associated with polysaccharides, proteoglycans, and glycolipids poses significant challenges to a fully atomistic description of biologically relevant glycoconjugates. On the other hand, the exquisite dependence on hydrogen bonds to determine glycans' structure makes the development of simplified or coarse-grained (CG) representations extremely challenging. This is particularly the case when glycan representations are expected to be compatible with CG force fields that include several molecular types. We introduce a CG representation able to simulate a wide variety of polysaccharides and common glycosylation motifs in proteins, which is fully compatible with the CG SIRAH force field. Examples of application to N-glycosylated proteins, including antibody recognition and calcium-mediated glycan-protein interactions, highlight the versatility of the enlarged set of CG molecules provided by SIRAH.
Collapse
Affiliation(s)
- Pablo G Garay
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Matias R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Hugo Verli
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Goncalves, 9500, Porto Alegre 91509-900, Brazil
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
| |
Collapse
|
7
|
Soto P, Thalhuber DT, Luceri F, Janos J, Borgman MR, Greenwood NM, Acosta S, Stoffel H. Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches. FRONTIERS IN BIOINFORMATICS 2024; 3:1321287. [PMID: 38250434 PMCID: PMC10796588 DOI: 10.3389/fbinf.2023.1321287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/06/2023] [Indexed: 01/23/2024] Open
Abstract
The Prion protein is the molecular hallmark of the incurable prion diseases affecting mammals, including humans. The protein-only hypothesis states that the misfolding, accumulation, and deposition of the Prion protein play a critical role in toxicity. The cellular Prion protein (PrPC) anchors to the extracellular leaflet of the plasma membrane and prefers cholesterol- and sphingomyelin-rich membrane domains. Conformational Prion protein conversion into the pathological isoform happens on the cell surface. In vitro and in vivo experiments indicate that Prion protein misfolding, aggregation, and toxicity are sensitive to the lipid composition of plasma membranes and vesicles. A picture of the underlying biophysical driving forces that explain the effect of Prion protein - lipid interactions in physiological conditions is needed to develop a structural model of Prion protein conformational conversion. To this end, we use molecular dynamics simulations that mimic the interactions between the globular domain of PrPC anchored to model membrane patches. In addition, we also simulate the Doppel protein anchored to such membrane patches. The Doppel protein is the closest in the phylogenetic tree to PrPC, localizes in an extracellular milieu similar to that of PrPC, and exhibits a similar topology to PrPC even if the amino acid sequence is only 25% identical. Our simulations show that specific protein-lipid interactions and conformational constraints imposed by GPI anchoring together favor specific binding sites in globular PrPC but not in Doppel. Interestingly, the binding sites we found in PrPC correspond to prion protein loops, which are critical in aggregation and prion disease transmission barrier (β2-α2 loop) and in initial spontaneous misfolding (α2-α3 loop). We also found that the membrane re-arranges locally to accommodate protein residues inserted in the membrane surface as a response to protein binding.
Collapse
Affiliation(s)
- Patricia Soto
- Department of Physics, Creighton University, Omaha, NE, United States
| | | | - Frank Luceri
- Omaha Central High School, Omaha, NE, United States
| | - Jamie Janos
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, United States
| | - Mason R. Borgman
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, United States
| | - Noah M. Greenwood
- Department of Physics, Creighton University, Omaha, NE, United States
| | - Sofia Acosta
- Omaha North High School, Omaha, NE, United States
| | | |
Collapse
|
8
|
Hryc J, Markiewicz M, Pasenkiewicz-Gierula M. Stacks of monogalactolipid bilayers can transform into a lattice of water channels. iScience 2023; 26:107863. [PMID: 37766978 PMCID: PMC10520361 DOI: 10.1016/j.isci.2023.107863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/17/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The lipid matrix of thylakoid membranes is a lamellar bilayer, but under a certain condition it can convert locally into a nonlamellar structure. This is possible because one of the main membrane lipids, MGDG, promotes the formation of an inverse hexagonal phase. Here, the spontaneous transformation of aligned hydrated MGDG bilayers into nonlamellar structures is investigated using all-atom molecular dynamics simulation. Previous studies have demonstrated that MGDG polar head groups connect vertically across the interface. In this study, the evolution of the system's initial structure into a lattice of water channels and contacted surfaces created by numerous vertical MGDG connections depended on the width of the hydrating water layers. These widths controlled the bilayers' ability to bend, which was a prerequisite for channel formation. Locally, an intensive exchange of MGDG molecules between apposing bilayer leaflets occurred, although a stable semi-toroidal stalk did not develop.
Collapse
Affiliation(s)
- Jakub Hryc
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| |
Collapse
|
9
|
Das T, Mukhopadhyay C. Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1. J Phys Chem B 2023; 127:6940-6948. [PMID: 37523476 DOI: 10.1021/acs.jpcb.3c02286] [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: 08/02/2023]
Abstract
SARS-CoV-2 spike glycoprotein is anchored by gangliosides. The sialic acid in the ganglioside headgroup is responsible for virus attachment and entry into host cells. We used coarse-grained (CG) molecular dynamics simulations to expand on our previous study of GM1 interaction with two different orientations of the SARS-CoV-2 S1 subunit N-terminal domain (NTD) and to confirm the role of sialic acid receptors in driving the viral receptor; GM3 was used as another ganglioside on the membrane. Because of the smaller headgroup, sialic acid is crucial in GM3 interactions, whereas GM1 interacts with NTD via both the sialic acid and external galactose. In line with our previous findings for NTD orientations in GM1 binding, we identified two orientations, "compact" and "distributed", comprising sugar receptor-interacting residues in GM3-embedded lipid bilayers. Gangliosides in closer proximity to the compact NTD orientation might cause relatively greater restrictions to penetrate the bilayer. However, the attachment of a distributed NTD orientation with more negative interaction energies appears to facilitate GM1/GM3 to move quickly across the membrane. Our findings likely shed some light on the orientations that the NTD receptor acquires during the early phases of interaction with GM1 and GM3 in a membrane environment.
Collapse
Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| |
Collapse
|
10
|
John LH, Naughton FB, Sansom MSP, Larsen AH. The Role of C2 Domains in Two Different Phosphatases: PTEN and SHIP2. MEMBRANES 2023; 13:408. [PMID: 37103835 PMCID: PMC10146288 DOI: 10.3390/membranes13040408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Phosphatase and tensin homologue (PTEN) and SH2-containing inositol 5'-phosphatase 2 (SHIP2) are structurally and functionally similar. They both consist of a phosphatase (Ptase) domain and an adjacent C2 domain, and both proteins dephosphorylate phosphoinositol-tri(3,4,5)phosphate, PI(3,4,5)P3; PTEN at the 3-phophate and SHIP2 at the 5-phosphate. Therefore, they play pivotal roles in the PI3K/Akt pathway. Here, we investigate the role of the C2 domain in membrane interactions of PTEN and SHIP2, using molecular dynamics simulations and free energy calculations. It is generally accepted that for PTEN, the C2 domain interacts strongly with anionic lipids and therefore significantly contributes to membrane recruitment. In contrast, for the C2 domain in SHIP2, we previously found much weaker binding affinity for anionic membranes. Our simulations confirm the membrane anchor role of the C2 domain in PTEN, as well as its necessity for the Ptase domain in gaining its productive membrane-binding conformation. In contrast, we identified that the C2 domain in SHIP2 undertakes neither of these roles, which are generally proposed for C2 domains. Our data support a model in which the main role of the C2 domain in SHIP2 is to introduce allosteric interdomain changes that enhance catalytic activity of the Ptase domain.
Collapse
Affiliation(s)
- Laura H. John
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Fiona B. Naughton
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark
| |
Collapse
|
11
|
Hilpert C, Beranger L, Souza PCT, Vainikka PA, Nieto V, Marrink SJ, Monticelli L, Launay G. Facilitating CG Simulations with MAD: The MArtini Database Server. J Chem Inf Model 2023; 63:702-710. [PMID: 36656159 DOI: 10.1021/acs.jcim.2c01375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.
Collapse
Affiliation(s)
- Cécile Hilpert
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Louis Beranger
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Paulo C T Souza
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Vincent Nieto
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Luca Monticelli
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Guillaume Launay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| |
Collapse
|
12
|
Das T, Mukhopadhyay C. Identification of possible binding modes of SARS-CoV-2 spike N-terminal domain for ganglioside GM1. Chem Phys Lett 2023; 812:140260. [PMID: 36532818 PMCID: PMC9744490 DOI: 10.1016/j.cplett.2022.140260] [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: 08/25/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Coarse-grained molecular dynamics simulations of the lipid bilayer mixture of POPC and cholesterol were carried out in the presence and absence of ganglioside monosialo 1 (GM1) with N - terminal domain (NTD) of SARS-CoV-2 spike glycoprotein. The interactions of GM1 with two different NTD orientations were compared. NTD orientation I compactly bind GM1 predominantly through the sialic acid and the external galactose moieties providing more restriction to GM1 mobility whereas orientation II is more distributed on the lipid surface and due to the relaxed mobility of GM1 there, presumably, the NTD receptor penetrates more through the membrane.
Collapse
Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| |
Collapse
|
13
|
Rodríguez-Moraga N, Ramos-Martín F, Buchoux S, Rippa S, D'Amelio N, Sarazin C. The effect of rhamnolipids on fungal membrane models as described by their interactions with phospholipids and sterols: An in silico study. Front Chem 2023; 11:1124129. [PMID: 36895318 PMCID: PMC9989204 DOI: 10.3389/fchem.2023.1124129] [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: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Introduction: Rhamnolipids (RLs) are secondary metabolites naturally produced by bacteria of the genera Pseudomonas and Burkholderia with biosurfactant properties. A specific interest raised from their potential as biocontrol agents for crop culture protection in regard to direct antifungal and elicitor activities. As for other amphiphilic compounds, a direct interaction with membrane lipids has been suggested as the key feature for the perception and subsequent activity of RLs. Methods: Molecular Dynamics (MD) simulations are used in this work to provide an atomistic description of their interactions with different membranous lipids and focusing on their antifungal properties. Results and discussion: Our results suggest the insertion of RLs into the modelled bilayers just below the plane drawn by lipid phosphate groups, a placement that is effective in promoting significant membrane fluidification of the hydrophobic core. This localization is promoted by the formation of ionic bonds between the carboxylate group of RLs and the amino group of the phosphatidylethanolamine (PE) or phosphatidylserine (PS) headgroups. Moreover, RL acyl chains adhere to the ergosterol structure, forming a significantly higher number of van der Waals contact with respect to what is observed for phospholipid acyl chains. All these interactions might be essential for the membranotropic-driven biological actions of RLs.
Collapse
Affiliation(s)
- Nely Rodríguez-Moraga
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Sébastien Buchoux
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, CNRS UMR 7025, Sorbonne Universités, Université de Technologie de Compiègne, Compiègne, France
| | - Nicola D'Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| |
Collapse
|
14
|
Grünewald F, Punt MH, Jefferys EE, Vainikka PA, König M, Virtanen V, Meyer TA, Pezeshkian W, Gormley AJ, Karonen M, Sansom MSP, Souza PCT, Marrink SJ. Martini 3 Coarse-Grained Force Field for Carbohydrates. J Chem Theory Comput 2022; 18:7555-7569. [PMID: 36342474 DOI: 10.1021/acs.jctc.2c00757] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.
Collapse
Affiliation(s)
- Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Mats H Punt
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Elizabeth E Jefferys
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Valtteri Virtanen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Travis A Meyer
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.,The Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Adam J Gormley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Maarit Karonen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon 69367, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| |
Collapse
|
15
|
Bolik S, Albrieux C, Schneck E, Demé B, Jouhet J. Sulfoquinovosyldiacylglycerol and phosphatidylglycerol bilayers share biophysical properties and are good mutual substitutes in photosynthetic membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184037. [PMID: 36041508 DOI: 10.1016/j.bbamem.2022.184037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/22/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Stéphanie Bolik
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France; Institut Laue-Langevin, 38000 Grenoble, France
| | - Catherine Albrieux
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, TU Darmstadt, 64289 Darmstadt, Germany
| | - Bruno Demé
- Institut Laue-Langevin, 38000 Grenoble, France.
| | - Juliette Jouhet
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France.
| |
Collapse
|
16
|
Shamaprasad P, Frame CO, Moore TC, Yang A, Iacovella CR, Bouwstra JA, Bunge AL, McCabe C. Using molecular simulation to understand the skin barrier. Prog Lipid Res 2022; 88:101184. [PMID: 35988796 PMCID: PMC10116345 DOI: 10.1016/j.plipres.2022.101184] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022]
Abstract
Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.
Collapse
Affiliation(s)
- Parashara Shamaprasad
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Chloe O Frame
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Alexander Yang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Joke A Bouwstra
- Division of BioTherapeutics, LACDR, Leiden University, 2333 CC Leiden, the Netherlands
| | - Annette L Bunge
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, United States of America
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America; School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, United Kingdom.
| |
Collapse
|
17
|
Hryc J, Szczelina R, Markiewicz M, Pasenkiewicz-Gierula M. Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases. Front Mol Biosci 2022; 9:958537. [PMID: 36046609 PMCID: PMC9423040 DOI: 10.3389/fmolb.2022.958537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, carried out using computational methods, the organisation of the lipid/water interface of bilayers composed of galactolipids with both α-linolenoyl acyl chains is analysed and compared in three different lyotropic liquid-crystalline phases. These systems include the monogalactosyldiglyceride (MGDG) and digalactosyldiglyceride (DGDG) bilayers in the lamellar phase, the MGDG double bilayer during stalk phase formation and the inverse hexagonal MGDG phase. For each system, lipid-water and direct and water-mediated lipid-lipid interactions between the lipids of one bilayer leaflet and those of two apposing leaflets at the onset of new phase (stalk) formation, are identified. A network of interactions between DGDG molecules and its topological properties are derived and compared to those for the MGDG bilayer.
Collapse
Affiliation(s)
- Jakub Hryc
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Szczelina
- Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | |
Collapse
|
18
|
Lutsyk V, Wolski P, Plazinski W. Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates. J Chem Theory Comput 2022; 18:5089-5107. [PMID: 35904547 PMCID: PMC9367002 DOI: 10.1021/acs.jctc.2c00553] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Carbohydrates play an essential role in a large number of chemical and biochemical processes. High structural diversity and conformational heterogeneity make it problematic to link their measurable properties to molecular features. Molecular dynamics simulations carried out at the level of classical force fields are routinely applied to study the complex processes occurring in carbohydrate-containing systems, while the usefulness of such simulations relies on the accuracy of the underlying theoretical model. In this article, we present the coarse-grained force field dedicated to glucopyranose-based carbohydrates and compatible with the recent version of the Martini force field (v. 3.0). The parameterization was based on optimizing bonded and nonbonded parameters with a reference to the all-atom simulation results and the experimental data. Application of the newly developed coarse-grained carbohydrate model to oligosaccharides curdlan and cellulose displays spontaneous formation of aggregates of experimentally identified features. In contact with other biomolecules, the model is capable of recovering the protective effect of glucose monosaccharides on a lipid bilayer and correctly identifying the binding pockets in carbohydrate-binding proteins. The features of the newly proposed model make it an excellent candidate for further extensions, aimed at modeling more complex, functionalized, and biologically relevant carbohydrates.
Collapse
Affiliation(s)
- Valery Lutsyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Pawel Wolski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland.,Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| |
Collapse
|
19
|
Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
Collapse
Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
| |
Collapse
|
20
|
Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| |
Collapse
|
21
|
Shamaprasad P, Moore TC, Xia D, Iacovella CR, Bunge AL, McCabe C. Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7496-7511. [PMID: 35671175 PMCID: PMC9309713 DOI: 10.1021/acs.langmuir.2c00471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C24 lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.
Collapse
Affiliation(s)
- Parashara Shamaprasad
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA, 37235-1604
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN, USA, 37235-1604
| | - Timothy C. Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA, 37235-1604
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN, USA, 37235-1604
| | - Donna Xia
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA, 37235-1604
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN, USA, 37235-1604
| | - Christopher R. Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA, 37235-1604
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN, USA, 37235-1604
| | - Annette L. Bunge
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA, 80401
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA, 37235-1604
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN, USA, 37235-1604
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA, 37235-1604
| |
Collapse
|
22
|
Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
Collapse
Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
| |
Collapse
|
23
|
Podewitz M, Wang Y, Gkeka P, von Grafenstein S, Liedl KR, Cournia Z. Correction to "Phase Diagram of a Stratum Corneum Lipid Mixture". J Phys Chem B 2022; 126:3193-3195. [PMID: 35435660 DOI: 10.1021/acs.jpcb.2c02015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
24
|
Guo L, Morin EE, Yu M, Mei L, Fawaz MV, Wang Q, Yuan Y, Zhan CG, Standiford TJ, Schwendeman A, Li XA. Replenishing HDL with synthetic HDL has multiple protective effects against sepsis in mice. Sci Signal 2022; 15:eabl9322. [PMID: 35290084 PMCID: PMC9825056 DOI: 10.1126/scisignal.abl9322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sepsis is a major health issue with mortality exceeding 30% and few treatment options. We found that high-density lipoprotein cholesterol (HDL-C) abundance was reduced by 45% in septic patients compared to that in nonseptic patients. Furthermore, HDL-C abundance in nonsurviving septic patients was substantially lower than in those patients who survived. We therefore hypothesized that replenishing HDL might be a therapeutic approach for treating sepsis and found that supplementing HDL with synthetic HDL (sHDL) provided protection against sepsis in mice. In mice subjected to cecal ligation and puncture (CLP), infusing the sHDL ETC-642 increased plasma HDL-C amounts and improved the 7-day survival rate. Septic mice treated with sHDL showed improved kidney function and reduced inflammation, as indicated by marked decreases in the plasma concentrations of blood urea nitrogen (BUN) and the cytokines interleukin-6 (IL-6) and IL-10, respectively. We found that sHDL inhibited the ability of the endotoxins LPS and LPA to activate inflammatory pathways in RAW264.7 cells and HEK-Blue cells expressing the receptors TLR4 or TLR2 and NF-κB reporters. In addition, sHDL inhibited the activation of HUVECs by LPS, LTA, and TNF-α. Together, these data indicate that sHDL treatment protects mice from sepsis in multiple ways and that it might be an effective therapy for patients with sepsis.
Collapse
Affiliation(s)
- Ling Guo
- Saha Cardiovascular Research Center and Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Emily E. Morin
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Minzhi Yu
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Ling Mei
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Maria V. Fawaz
- Department of Medicinal Chemistry, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Qian Wang
- Saha Cardiovascular Research Center and Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Yaxia Yuan
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, USA
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, USA
| | - Theodore J. Standiford
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, Ann Arbor, MI 48198, USA
| | - Xiang-An Li
- Saha Cardiovascular Research Center and Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
- Lexington VA Health Care System, Lexington, KY 40502, USA
| |
Collapse
|
25
|
Chng CP, Wang K, Ma W, Hsia KJ, Huang C. Chloroplast membrane lipid remodeling protects against dehydration by limiting membrane fusion and distortion. PLANT PHYSIOLOGY 2022; 188:526-539. [PMID: 34730798 PMCID: PMC8774810 DOI: 10.1093/plphys/kiab512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Dehydration damages the structural integrity of the chloroplast membrane and, consequently, the normal photosynthetic function of this organelle. Remodeling of galactolipids by converting monogalactosyl-diacylglycerol (MGDG) to digalactosyl-diacylglycerol (DGDG) and oligo-galactolipids is an effective adaptation strategy for protecting against dehydration damage to the chloroplast membrane. However, detailed molecular mechanisms are missing. In this study, by performing molecular-level simulations of bi-lamellar membranes under various dehydration conditions, we find that MGDG-to-DGDG remodeling protects the chloroplast membrane in a unique manner by simultaneously dictating both the extent and the pattern of fusion stalks formed with the apposed membrane. Specifically, MGDG-rich membranes form elongated stalks at a moderate dehydration level, whereas DGDG-rich membranes form smaller, rounded stalks. Simulations of wild-type and mutant Arabidopsis (Arabidopsis thaliana) outer chloroplast membranes further confirm that the mutant membrane without galactolipid remodeling is more susceptible to membrane fusion due to its higher MGDG content. Our work reveals the underlying physical mechanisms that govern the pattern and extent of membrane fusion structures, paving the way for rational genetic engineering of crops with improved dehydration tolerance.
Collapse
Affiliation(s)
- Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Kun Wang
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston MA 02115, USA
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - K Jimmy Hsia
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| |
Collapse
|
26
|
Borges-Araújo L, Souza PCT, Fernandes F, Melo MN. Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field. J Chem Theory Comput 2021; 18:357-373. [PMID: 34962393 DOI: 10.1021/acs.jctc.1c00615] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphoinositides are a family of membrane phospholipids that play crucial roles in membrane regulatory events. As such, these lipids are often a key part of molecular dynamics simulation studies of biological membranes, in particular of those employing coarse-grain models because of the potential long times and sizes of the involved membrane processes. Version 3 of the widely used Martini coarse-grain force field has been recently published, greatly refining many aspects of biomolecular interactions. In order to properly use it for lipid membrane simulations with phosphoinositides, we put forth the Martini 3-specific parameterization of inositol, phosphatidylinositol, and seven physiologically relevant phosphorylated derivatives of phosphatidylinositol. Compared to parameterizations for earlier Martini versions, focus was put on a more accurate reproduction of the behavior seen in both atomistic simulations and experimental studies, including the signaling-relevant phosphoinositide interaction with divalent cations. The models that we develop improve upon the conformational dynamics of phosphoinositides in the Martini force field and provide stable topologies at typical Martini time steps. They are able to reproduce experimentally known protein-binding poses as well as phosphoinositide aggregation tendencies. The latter was tested both in the presence and absence of calcium and included correct behavior of PI(4,5)P2 calcium-induced clusters, which can be of relevance for regulation.
Collapse
Affiliation(s)
- Luís Borges-Araújo
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Associate Laboratory i4HB─Institute for Health and Bioeconomy, at Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Fábio Fernandes
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Associate Laboratory i4HB─Institute for Health and Bioeconomy, at Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| |
Collapse
|
27
|
Borges-Araújo L, Domingues MM, Fedorov A, Santos NC, Melo MN, Fernandes F. Acyl-chain saturation regulates the order of phosphatidylinositol 4,5-bisphosphate nanodomains. Commun Chem 2021; 4:164. [PMID: 36697613 PMCID: PMC9814227 DOI: 10.1038/s42004-021-00603-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 01/28/2023] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) plays a critical role in the regulation of various plasma membrane processes and signaling pathways in eukaryotes. A significant amount of cellular resources are spent on maintaining the dominant 1-stearoyl-2-arachidonyl PI(4,5)P2 acyl-chain composition, while less abundant and more saturated species become more prevalent in response to specific stimuli, stress or aging. Here, we report the impact of acyl-chain structure on the biophysical properties of cation-induced PI(4,5)P2 nanodomains. PI(4,5)P2 species with increasing levels of acyl-chain saturation cluster in progressively more ordered nanodomains, culminating in the formation of gel-like nanodomains for fully saturated species. The formation of these gel-like domains was largely abrogated in the presence of 1-stearoyl-2-arachidonyl PI(4,5)P2. This is, to the best of our knowledge, the first report of the impact of PI(4,5)P2 acyl-chain composition on cation-dependent nanodomain ordering, and provides important clues to the motives behind the enrichment of PI(4,5)P2 with polyunsaturated acyl-chains. We also show how Ca2+-induced PI(4,5)P2 nanodomains are able to generate local negative curvature, a phenomenon likely to play a role in membrane remodeling events.
Collapse
Affiliation(s)
- Luís Borges-Araújo
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Marco M Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Alexander Fedorov
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Fábio Fernandes
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
| |
Collapse
|
28
|
Sim SI, von Bülow S, Hummer G, Park E. Structural basis of polyamine transport by human ATP13A2 (PARK9). Mol Cell 2021; 81:4635-4649.e8. [PMID: 34715013 DOI: 10.1016/j.molcel.2021.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023]
Abstract
Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson's disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryoelectron microscopy (cryo-EM) structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand the functions and mechanisms of P5B-ATPases.
Collapse
Affiliation(s)
- Sue Im Sim
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
29
|
Caparotta M, Puiatti M, Masone D. Artificial stabilization of the fusion pore by intra-organelle styrene-maleic acid copolymers. SOFT MATTER 2021; 17:8314-8321. [PMID: 34550159 DOI: 10.1039/d1sm00978h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Styrene-maleic acid copolymers have become an advantageous detergent-free alternative for membrane protein isolation. Since their discovery, experimental membrane protein extraction and purification by keeping intact their lipid environment has become significantly easier. With the aim of identifying new applications of these interesting copolymers, their molecular binding and functioning mechanisms have recently become intense objects of study. In this work, we describe the use of styrene-maleic acid copolymers as an artificial tool to stabilize the fusion pore. We show that when these copolymers circumscribe the water channel that defines the fusion pore, they keep it from shrinking and closing. We describe how only intra-organelle copolymers have stabilizing capabilities while extra-organelle ones have negligible or even contrary effects on the fusion pore life-time.
Collapse
Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
| | - Marcelo Puiatti
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), 5016, Córdoba, Argentina
| | - Diego Masone
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina.
| |
Collapse
|
30
|
Larsen AH, Tata L, John LH, Sansom MSP. Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008807. [PMID: 34555023 PMCID: PMC8491906 DOI: 10.1371/journal.pcbi.1008807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 10/05/2021] [Accepted: 09/14/2021] [Indexed: 11/19/2022] Open
Abstract
Early Endosomal Antigen 1 (EEA1) is a key protein in endosomal trafficking and is implicated in both autoimmune and neurological diseases. The C-terminal FYVE domain of EEA1 binds endosomal membranes, which contain phosphatidylinositol-3-phosphate (PI(3)P). Although it is known that FYVE binds PI(3)P specifically, it has not previously been described of how FYVE attaches and binds to endosomal membranes. In this study, we employed both coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations to determine how FYVE binds to PI(3)P-containing membranes. CG-MD showed that the dominant membrane binding mode resembles the crystal structure of EEA1 FYVE domain in complex with inositol-1,3-diphospate (PDB ID 1JOC). FYVE, which is a homodimer, binds the membrane via a hinge mechanism, where the C-terminus of one monomer first attaches to the membrane, followed by the C-terminus of the other monomer. The estimated total binding energy is ~70 kJ/mol, of which 50-60 kJ/mol stems from specific PI(3)P-interactions. By AT-MD, we could partition the binding mode into two types: (i) adhesion by electrostatic FYVE-PI(3)P interaction, and (ii) insertion of amphipathic loops. The AT simulations also demonstrated flexibility within the FYVE homodimer between the C-terminal heads and coiled-coil stem. This leads to a dynamic model whereby the 200 nm long coiled coil attached to the FYVE domain dimer can amplify local hinge-bending motions such that the Rab5-binding domain at the other end of the coiled coil can explore an area of 0.1 μm2 in the search for a second endosome with which to interact.
Collapse
Affiliation(s)
| | - Lilya Tata
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
31
|
Islam S, Mukhopadhyay C. Aggregation of Lysozyme in the Presence of a Mixed Bilayer of POPC and POPG. ACS OMEGA 2021; 6:17861-17869. [PMID: 34308021 PMCID: PMC8295997 DOI: 10.1021/acsomega.1c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/30/2021] [Indexed: 05/04/2023]
Abstract
Understanding the molecular mechanisms by which amyloidogenic proteins interact with membranes is a challenging task. Amyloid accumulates from many human diseases have been observed to contain membrane lipids. In this work, coarse-grained molecular dynamics simulations have been used to inspect hen egg white lysozyme (HEWL) aggregation and membrane association in the presence of a pure POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) bilayer and a POPC and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol) mixed bilayer. It was observed that, in both cases, two HEWLs formed aggregates. In the presence of a mixed bilayer, after aggregation, the aggregated system started to interact with the membrane. It has been found that one of the lysozymes which came closer to the mixed bilayer unfolded more. The process of the initial insertion of an aggregated system in the mixed bilayer has been analyzed. The structural rearrangements of the protein and lipids were analyzed as well along the course of the simulation. Although with a pure POPC bilayer, aggregation was observed, the aggregated system moved away from the membrane. We believe that our study will provide considerable insights into lysozyme aggregation in the presence of a membrane environment.
Collapse
Affiliation(s)
- Shahee Islam
- Department of Chemistry, University
of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University
of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| |
Collapse
|
32
|
Larsen AH, Sansom MSP. Binding of Ca 2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study. Structure 2021; 29:1200-1213.e2. [PMID: 34081910 PMCID: PMC8507603 DOI: 10.1016/j.str.2021.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 01/17/2023]
Abstract
C2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins. Binding of Ca2+-independent C2 domains to membranes was explored by MD simulation C2 domains from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2 were compared C2 domains formed longer-lived interactions with lipid bilayers containing PIP2 For PTEN and SHIP2, simulations of their phosphatase plus C2 domains were performed
Collapse
Affiliation(s)
- Andreas Haahr Larsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
33
|
Souza PCT, Alessandri R, Barnoud J, Thallmair S, Faustino I, Grünewald F, Patmanidis I, Abdizadeh H, Bruininks BMH, Wassenaar TA, Kroon PC, Melcr J, Nieto V, Corradi V, Khan HM, Domański J, Javanainen M, Martinez-Seara H, Reuter N, Best RB, Vattulainen I, Monticelli L, Periole X, Tieleman DP, de Vries AH, Marrink SJ. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat Methods 2021; 18:382-388. [PMID: 33782607 DOI: 10.1038/s41592-021-01098-3] [Citation(s) in RCA: 474] [Impact Index Per Article: 158.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023]
Abstract
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.
Collapse
Affiliation(s)
- Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands. .,Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France.
| | - Riccardo Alessandri
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands.,Intangible Realities Laboratory, University of Bristol, School of Chemistry, Bristol, UK
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands.,Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Ignacio Faustino
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Bart M H Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Peter C Kroon
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Vincent Nieto
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hanif M Khan
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Chemistry and Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Jan Domański
- Department of Biochemistry, University of Oxford, Oxford, UK.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Nathalie Reuter
- Department of Chemistry and Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, Tampere, Finland.,Department of Physics, University of Helsinki, Helsinki, Finland
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
| | - Xavier Periole
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
34
|
Kanduč M, Schneck E, Stubenrauch C. Intersurfactant H-bonds between head groups of n-dodecyl-β-d-maltoside at the air-water interface. J Colloid Interface Sci 2021; 586:588-595. [DOI: 10.1016/j.jcis.2020.10.125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
|
35
|
Wan M, Song J, Yang Y, Gao L, Fang W. Development of coarse-grained force field for alcohols: an efficient meta-multilinear interpolation parameterization algorithm. Phys Chem Chem Phys 2021; 23:1956-1966. [PMID: 33464253 DOI: 10.1039/d0cp05503d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coarse-grained (CG) molecular dynamics are powerful tools to access a mesoscopic phenomenon and simultaneously record microscopic details, but currently the CG force fields (FFs) are still limited by low parameterization efficiency and poor accuracy especially for polar molecules. In this work, we developed a Meta-Multilinear Interpolation Parameterization (Meta-MIP) algorithm to optimize the CG FFs for alcohols. This algorithm significantly boosts parameterization efficiency by constructing on-the-fly local databases to cover the global optimal parameterization path. In specific, an alcohol molecule is mapped to a heterologous model composed of an OH bead and a hydrocarbon portion which consists of alkane beads representing two to four carbon atoms. Non-bonded potentials are described by soft Morse functions that have no tail-corrections but can still retain good continuities at truncation distance. Nearly all of the properties in terms of density, heat of vaporization, surface tension, and solvation free energy for alcohols predicted by the current FFs deviate from experimental values by less than 7%. This Meta-MIP algorithm can be readily applied to force field development for a wide variety of molecules or functional groups, in many situations including but not limited to CG FFs.
Collapse
Affiliation(s)
- Mingwei Wan
- Institution of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | | | | | | | | |
Collapse
|
36
|
Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes. J Membr Biol 2021; 254:157-173. [PMID: 33427943 DOI: 10.1007/s00232-020-00162-x] [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: 07/17/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.
Collapse
|
37
|
Huang Y, Xu HC, Liao JL. Coarse-grained free-energy simulations of conformational state transitions in an adenosine 5′-triphosphate-binding cassette exporter. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp1908149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yun Huang
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Hao-chen Xu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jie-lou Liao
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| |
Collapse
|
38
|
Caparotta M, Tomes CN, Mayorga LS, Masone D. The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore. J Chem Theory Comput 2020; 16:7840-7851. [DOI: 10.1021/acs.jctc.0c00734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| | - Claudia N. Tomes
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| | - Luis S. Mayorga
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| |
Collapse
|
39
|
Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
Collapse
Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
| |
Collapse
|
40
|
Canepa E, Salassi S, de Marco AL, Lambruschini C, Odino D, Bochicchio D, Canepa F, Canale C, Dante S, Brescia R, Stellacci F, Rossi G, Relini A. Amphiphilic gold nanoparticles perturb phase separation in multidomain lipid membranes. NANOSCALE 2020; 12:19746-19759. [PMID: 32966489 DOI: 10.1039/d0nr05366j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Amphiphilic gold nanoparticles with diameters in the 2-4 nm range are promising as theranostic agents thanks to their spontaneous translocation through cell membranes. This study addresses the effects that these nanoparticles may have on a distinct feature of plasma membranes: lipid lateral phase separation. Atomic force microscopy, quartz crystal microbalance, and molecular dynamics are combined to study the interaction between model neuronal membranes, which spontaneously form ordered and disordered lipid domains, and amphiphilic gold nanoparticles having negatively charged surface functionalization. Nanoparticles are found to interact with the bilayer and form bilayer-embedded ordered aggregates. Nanoparticles also suppress lipid phase separation, in a concentration-dependent fashion. A general, yet simple thermodynamic model is developed to show that the change of lipid-lipid enthalpy is the dominant driving force towards the nanoparticle-induced destabilization of phase separation.
Collapse
Affiliation(s)
- Ester Canepa
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, 16146 Genoa, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Shivgan AT, Marzinek JK, Huber RG, Krah A, Henchman RH, Matsudaira P, Verma CS, Bond PJ. Extending the Martini Coarse-Grained Force Field to N-Glycans. J Chem Inf Model 2020; 60:3864-3883. [PMID: 32702979 DOI: 10.1021/acs.jcim.0c00495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycans play a vital role in a large number of cellular processes. Their complex and flexible nature hampers structure-function studies using experimental techniques. Molecular dynamics (MD) simulations can help in understanding dynamic aspects of glycans if the force field parameters used can reproduce key experimentally observed properties. Here, we present optimized coarse-grained (CG) Martini force field parameters for N-glycans, calibrated against experimentally derived binding affinities for lectins. The CG bonded parameters were obtained from atomistic (ATM) simulations for different glycan topologies including high mannose and complex glycans with various branching patterns. In the CG model, additional elastic networks are shown to improve maintenance of the overall conformational distribution. Solvation free energies and octanol-water partition coefficients were also calculated for various N-glycan disaccharide combinations. When using standard Martini nonbonded parameters, we observed that glycans spontaneously aggregated in the solution and required down-scaling of their interactions for reproduction of ATM model radial distribution functions. We also optimized the nonbonded interactions for glycans interacting with seven lectin candidates and show that a relatively modest scaling down of the glycan-protein interactions can reproduce free energies obtained from experimental studies. These parameters should be of use in studying the role of glycans in various glycoproteins and carbohydrate binding proteins as well as their complexes, while benefiting from the efficiency of CG sampling.
Collapse
Affiliation(s)
- Aishwary T Shivgan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Roland G Huber
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Alexander Krah
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Paul Matsudaira
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Chandra S Verma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| |
Collapse
|
42
|
Vaiwala R, Sharma P, Puranik M, Ayappa KG. Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers. J Chem Theory Comput 2020; 16:5369-5384. [DOI: 10.1021/acs.jctc.0c00539] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mrinalini Puranik
- Unilever Research & Development, 64 Main Road, Whitefield, Bangalore 560066, India
| | - K. Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
43
|
Banerjee P, Lipowsky R, Santer M. Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein. J Chem Theory Comput 2020; 16:3889-3903. [PMID: 32392421 PMCID: PMC7303967 DOI: 10.1021/acs.jctc.0c00056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/17/2023]
Abstract
Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
Collapse
Affiliation(s)
- Pallavi Banerjee
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Institute
of Biochemistry and Biology, University
of Potsdam, Potsdam 14469, Germany
| | - Reinhard Lipowsky
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Institute
of Biochemistry and Biology, University
of Potsdam, Potsdam 14469, Germany
| | - Mark Santer
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| |
Collapse
|
44
|
Roel-Touris J, Bonvin AM. Coarse-grained (hybrid) integrative modeling of biomolecular interactions. Comput Struct Biotechnol J 2020; 18:1182-1190. [PMID: 32514329 PMCID: PMC7264466 DOI: 10.1016/j.csbj.2020.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 12/23/2022] Open
Abstract
The computational modeling field has vastly evolved over the past decades. The early developments of simplified protein systems represented a stepping stone towards establishing more efficient approaches to sample intricated conformational landscapes. Downscaling the level of resolution of biomolecules to coarser representations allows for studying protein structure, dynamics and interactions that are not accessible by classical atomistic approaches. The combination of different resolutions, namely hybrid modeling, has also been proved as an alternative when mixed levels of details are required. In this review, we provide an overview of coarse-grained/hybrid models focusing on their applicability in the modeling of biomolecular interactions. We give a detailed list of ready-to-use modeling software for studying biomolecular interactions allowing various levels of coarse-graining and provide examples of complexes determined by integrative coarse-grained/hybrid approaches in combination with experimental information.
Collapse
|
45
|
Liguori N, Croce R, Marrink SJ, Thallmair S. Molecular dynamics simulations in photosynthesis. PHOTOSYNTHESIS RESEARCH 2020; 144:273-295. [PMID: 32297102 PMCID: PMC7203591 DOI: 10.1007/s11120-020-00741-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
Collapse
Affiliation(s)
- Nicoletta Liguori
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
46
|
Sun F, Schroer CFE, Palacios CR, Xu L, Luo SZ, Marrink SJ. Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2. PLoS Comput Biol 2020; 16:e1007777. [PMID: 32271757 PMCID: PMC7173942 DOI: 10.1371/journal.pcbi.1007777] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/21/2020] [Accepted: 03/06/2020] [Indexed: 12/22/2022] Open
Abstract
The co-localization of Cluster-of-Differentiation-44 protein (CD44) and cytoplasmic adaptors in specific membrane environments is crucial for cell adhesion and migration. The process is controlled by two different pathways: On the one hand palmitoylation keeps CD44 in lipid raft domains and disables the linking to the cytoplasmic adaptor, whereas on the other hand, the presence of phosphatidylinositol-4,5-biphosphate (PIP2) lipids accelerates the formation of the CD44-adaptor complex. The molecular mechanism explaining how CD44 is migrating into and out of the lipid raft domains and its dependence on both palmitoylations and the presence of PIP2 remains, however, elusive. In this study, we performed extensive molecular dynamics simulations to study the raft affinity and translocation of CD44 in phase separated model membranes as well as more realistic plasma membrane environments. We observe a delicate balance between the influence of the palmitoylations and the presence of PIP2 lipids: whereas the palmitoylations of CD44 increases the affinity for raft domains, PIP2 lipids have the opposite effect. Additionally, we studied the association between CD44 and the membrane adaptor FERM in dependence of these factors. We find that the presence of PIP2 lipids allows CD44 and FERM to associate in an experimentally observed binding mode whereas the highly palmitoylated species shows no binding affinity. Together, our results shed light on the sophisticated mechanism on how membrane translocation and peripheral protein association can be controlled by both protein modifications and membrane composition. Cytoskeleton protein complex involving with association of CD44 and ERMs is critical for cancer-related cellular adhesion and migration. The protein interactions are found to be modulated by chemical modification and membrane microenvironments, but the inherent mechanism is unclear. We obtained molecular dynamic details of CD44 localization switching between raft/non-raft subdomains regulated by palmitoylations and PIP2 molecules. Binding of PIP2 on the palmitoylated CD44 enables it to release from lipid raft, revealing an exceptional role of PIP2 in mediating protein translocation. PIP2 is beneficial for CD44 to associate with the active domain of ERM, in a nearly crystal structure mode. The molecular information will enhance our understanding for PIP2 regulation to protein translocation and membrane association.
Collapse
Affiliation(s)
- Fude Sun
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Science, Hebei University of Technology, Tianjin, China
| | - Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Carlos R Palacios
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Lida Xu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, The Netherlands
| |
Collapse
|
47
|
Gupta R, Badhe Y, Mitragotri S, Rai B. Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations. NANOSCALE 2020; 12:6318-6333. [PMID: 32133467 DOI: 10.1039/c9nr09947f] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nanoparticles are being explored for topical and oral drug delivery applications as they can cross various biological barriers, for example, the intestinal epithelium. The ability of nanoparticles to cross barriers depends on their morphological and surface properties such as size, surface chemistry and shape, among others. The effect of nanoparticle size on their membrane permeability has been well studied both experimentally and theoretically. However, less attention has been given to understand the role of nanoparticle shape in their translocation across biological barrier membranes. Here, we report on the influence of the nanoparticle's shape, surface chemistry and concentration on their permeation across a human intestinal apical cell membrane model. A representative multicomponent lipid bilayer model of the human intestinal apical membrane was built. The free energy of permeation of nanoparticles across the model lipid bilayer was calculated using multiple umbrella sampling simulations. The interaction of these nanoparticles with the model lipid bilayer was captured using extensive microsecond unrestrained molecular dynamics simulations. We observed that: (a) irrespective of the surface chemistry, the efficacy of nanoparticle penetration across the lipid layer was in the order of rod > disc > sphere; (b) irrespective of the shape, apolar and nonpolar nanoparticles were found to locate in the interior of the lipid bilayer, whereas charged and polar nanoparticles were either adsorbed on the lipid headgroups or remained in the water layer; (c) apolar and nonpolar disc shaped nanoparticles had higher efficacy in permeation across the lipid bilayer as compared to disc and sphere shaped nanoparticles; and (d) at a higher concentration of nanoparticles, sphere and disc shaped nanoparticles exhibited more agglomeration as compared to rod shaped nanoparticles. Based on these outcomes, a few nanoparticles were designed which penetrated readily into the lipid layer and these nanoparticles were also able to co-deliver a therapeutic protein inside the lipid layer. The apical model lipid membrane and protocols used in this study can thus be utilized for the in silico design of nanoparticles for the oral delivery of therapeutics.
Collapse
Affiliation(s)
- Rakesh Gupta
- Physical Science Research Area, Tata Research Development and Design Centre, TCS Research, Tata Consultancy Services, 54B, Hadapsar Industrial Estate, Pune 411013, India.
| | | | | | | |
Collapse
|
48
|
Molecular characterization of the outer membrane of Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183151. [DOI: 10.1016/j.bbamem.2019.183151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/28/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
|
49
|
Wan M, Song J, Li W, Gao L, Fang W. Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm. J Comput Chem 2019; 41:814-829. [DOI: 10.1002/jcc.26131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/07/2019] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mingwei Wan
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
- Institution of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Junjie Song
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
| | - Wenli Li
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational PhotochemistryMinistry of Education, College of Chemistry, Beijing Normal University 19 Xin‐Jie‐Kou‐Wai Street Beijing 100875 China
- Institution of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| |
Collapse
|
50
|
Newe A, Rzeniewicz K, König M, Schroer CFE, Joachim J, Rey-Gallardo A, Marrink SJ, Deka J, Parsons M, Ivetic A. Serine Phosphorylation of L-Selectin Regulates ERM Binding, Clustering, and Monocyte Protrusion in Transendothelial Migration. Front Immunol 2019; 10:2227. [PMID: 31608057 PMCID: PMC6774396 DOI: 10.3389/fimmu.2019.02227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
The migration of circulating leukocytes toward damaged tissue is absolutely fundamental to the inflammatory response, and transendothelial migration (TEM) describes the first cellular barrier that is breached in this process. Human CD14+ inflammatory monocytes express L-selectin, bestowing a non-canonical role in invasion during TEM. In vivo evidence supports a role for L-selectin in regulating TEM and chemotaxis, but the intracellular mechanism is poorly understood. The ezrin-radixin-moesin (ERM) proteins anchor transmembrane proteins to the cortical actin-based cytoskeleton and additionally act as signaling adaptors. During TEM, the L-selectin tail within transmigrating pseudopods interacts first with ezrin to transduce signals for protrusion, followed by moesin to drive ectodomain shedding of L-selectin to limit protrusion. Collectively, interaction of L-selectin with ezrin and moesin fine-tunes monocyte protrusive behavior in TEM. Using FLIM/FRET approaches, we show that ERM binding is absolutely required for outside-in L-selectin clustering. The cytoplasmic tail of human L-selectin contains two serine (S) residues at positions 364 and 367, and here we show that they play divergent roles in regulating ERM binding. Phospho-S364 blocks direct interaction with ERM, whereas molecular modeling suggests phospho-S367 likely drives desorption of the L-selectin tail from the inner leaflet of the plasma membrane to potentiate ERM binding. Serine-to-alanine mutagenesis of S367, but not S364, significantly reduced monocyte protrusive behavior in TEM under flow conditions. Our data propose a model whereby L-selectin tail desorption from the inner leaflet of the plasma membrane and ERM binding are two separable steps that collectively regulate protrusive behavior in TEM.
Collapse
Affiliation(s)
- Abigail Newe
- BHF Centre of Research Excellence, James Black Centre, King's College London, London, United Kingdom
| | - Karolina Rzeniewicz
- BHF Centre of Research Excellence, James Black Centre, King's College London, London, United Kingdom
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| | - Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| | - Justin Joachim
- BHF Centre of Research Excellence, James Black Centre, King's College London, London, United Kingdom
| | - Angela Rey-Gallardo
- BHF Centre of Research Excellence, James Black Centre, King's College London, London, United Kingdom
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, Netherlands
| | - Jürgen Deka
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Aleksandar Ivetic
- BHF Centre of Research Excellence, James Black Centre, King's College London, London, United Kingdom
| |
Collapse
|