1
|
Do HN, Zhao M, Alam SM, Gnanakaran S. Dynamics and Activation of Membrane-Bound B Cell Receptor Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602784. [PMID: 39026873 PMCID: PMC11257630 DOI: 10.1101/2024.07.10.602784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
B-cell receptor complexes (BCR) are expressed on the surface of a B-cell and are the critical regulators of adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation of antibody-producing B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structure of the human B-cell antigen receptor of the IgM isotype was published. Given the new asymmetric BCR complex, we have carried out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane. We identified two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding caused increased flexibility in regions distal to the antigen binding site. Second, this increased flexibility led to the rearrangement of helices in transmembrane helices, including the relative interaction of Igα/Igβ, which has been responsible for intracellular signaling. Further, these transmembrane rearrangements led to changes in localized lipid composition. Even though the simulations considered only a single BCR complex, our work indirectly supports the dissociation activation model.
Collapse
Affiliation(s)
- Hung N. Do
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Mingfei Zhao
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke School of Medicine
- Department of Medicine, Duke School of Medicine, Durham, North Carolina 27710, USA
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| |
Collapse
|
2
|
Borges-Araújo L, Pereira GP, Valério M, Souza PCT. Assessing the Martini 3 protein model: A review of its path and potential. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141014. [PMID: 38670324 DOI: 10.1016/j.bbapap.2024.141014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field - Martini 3 - a new iteration of its protein model was also made available. The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short time since its release, many of which would not have been possible before. Furthermore, we discuss reported limitations, potential directions for model improvement and comment on what the likely future development and application avenues are.
Collapse
Affiliation(s)
- Luís Borges-Araújo
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Gilberto P Pereira
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Mariana Valério
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Paulo C T Souza
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France.
| |
Collapse
|
3
|
Smardz P, Anila MM, Rogowski P, Li MS, Różycki B, Krupa P. A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta. Int J Mol Sci 2024; 25:6698. [PMID: 38928405 PMCID: PMC11204378 DOI: 10.3390/ijms25126698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and transient structural elements. This work presents computational methods for studying IDPs at various resolutions using the Amber and Gromacs packages with both all-atom (Amber ff19SB with the OPC water model) and coarse-grained (Martini 3 and SIRAH) approaches. The effectiveness of these methodologies is demonstrated by examining the monomeric form of amyloid-β (Aβ42), an IDP, with and without disulfide bonds at different resolutions. Our results clearly show that the addition of a disulfide bond decreases the β-content of Aβ42; however, it increases the tendency of the monomeric Aβ42 to form fibril-like conformations, explaining the various aggregation rates observed in experiments. Moreover, analysis of the monomeric Aβ42 compactness, secondary structure content, and comparison between calculated and experimental chemical shifts demonstrates that all three methods provide a reasonable choice to study IDPs; however, coarse-grained approaches may lack some atomistic details, such as secondary structure recognition, due to the simplifications used. In general, this study not only explains the role of disulfide bonds in Aβ42 but also provides a step-by-step protocol for setting up, conducting, and analyzing molecular dynamics (MD) simulations, which is adaptable for studying other biomacromolecules, including folded and disordered proteins and peptides.
Collapse
Affiliation(s)
| | | | | | | | | | - Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland; (P.S.); (M.M.A.); (P.R.); (M.S.L.); (B.R.)
| |
Collapse
|
4
|
Anila MM, Rogowski P, Różycki B. Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3. Molecules 2024; 29:2768. [PMID: 38930833 PMCID: PMC11207097 DOI: 10.3390/molecules29122768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Galectin-3 is a protein involved in many intra- and extra-cellular processes. It has been identified as a diagnostic or prognostic biomarker for certain types of heart disease, kidney disease and cancer. Galectin-3 comprises a carbohydrate recognition domain (CRD) and an N-terminal domain (NTD), which is unstructured and contains eight collagen-like Pro-Gly-rich tandem repeats. While the structure of the CRD has been solved using protein crystallography, current knowledge about conformations of full-length galectin-3 is limited. To fill in this knowledge gap, we performed molecular dynamics (MD) simulations of full-length galectin-3. We systematically re-scaled the solute-solvent interactions in the Martini 3 force field to obtain the best possible agreement between available data from SAXS experiments and the ensemble of conformations generated in the MD simulations. The simulation conformations were found to be very diverse, as reflected, e.g., by (i) large fluctuations in the radius of gyration, ranging from about 2 to 5 nm, and (ii) multiple transient contacts made by amino acid residues in the NTD. Consistent with evidence from NMR experiments, contacts between the CRD and NTD were observed to not involve the carbohydrate-binding site on the CRD surface. Contacts within the NTD were found to be made most frequently by aromatic residues. Formation of fuzzy complexes with unspecific stoichiometry was observed to be mediated mostly by the NTD. Taken together, we offer a detailed picture of the conformational ensemble of full-length galectin-3, which will be important for explaining the biological functions of this protein at the molecular level.
Collapse
Affiliation(s)
| | | | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland; (M.M.A.); (P.R.)
| |
Collapse
|
5
|
Ozturk TN, König M, Carpenter TS, Pedersen KB, Wassenaar TA, Ingólfsson HI, Marrink SJ. Building complex membranes with Martini 3. Methods Enzymol 2024; 701:237-285. [PMID: 39025573 DOI: 10.1016/bs.mie.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.
Collapse
Affiliation(s)
- Tugba Nur Ozturk
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Helgi I Ingólfsson
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
6
|
Ingólfsson HI, Rizuan A, Liu X, Mohanty P, Souza PCT, Marrink SJ, Bowers MT, Mittal J, Berry J. Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation. Biophys J 2023; 122:4370-4381. [PMID: 37853696 PMCID: PMC10720261 DOI: 10.1016/j.bpj.2023.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/27/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023] Open
Abstract
The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent C⍺ model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.
Collapse
Affiliation(s)
- Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas
| | - Xikun Liu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, Lyon, France; Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas; Department of Chemistry, Texas A&M University, College Station, Texas; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas
| | - Joel Berry
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| |
Collapse
|
7
|
Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. J Chem Theory Comput 2023; 19:7387-7404. [PMID: 37796943 DOI: 10.1021/acs.jctc.3c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
Collapse
Affiliation(s)
- Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Ana C Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tugba Nur Ozturk
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Rúa de Jenaro de la Fuente, 15705 Santiago de Compostela, Spain
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| |
Collapse
|
8
|
Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nat Commun 2023; 14:4484. [PMID: 37491368 PMCID: PMC10368641 DOI: 10.1038/s41467-023-40266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.
Collapse
Affiliation(s)
- Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Mark Nijland
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Aike Jeucken
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Rheinberger
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Siewert J Marrink
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Molecular Dynamics Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Cristina Paulino
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
9
|
Ren M, Ma Z, Zhao L, Wang Y, An H, Sun F. Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection. J Chem Inf Model 2023; 63:4423-4432. [PMID: 37382878 DOI: 10.1021/acs.jcim.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Transmissibility of SARS-CoV-2 initially relies on its trimeric Spike-RBDs to tether the ACE-2 on host cells, and enhanced self-association of ACE-2 engaged with Spike facilitates the viral infection. Two primary packing modes of Spike-ACE2 heteroproteins exist potentially due to discrepant amounts of RBDs loading on ACE-2, but the resultant self-association difference is inherently unclear. We used extensive coarse-grained dynamic simulations to characterize the self-association efficiency, the conformation relevance, and the molecular mechanism of ACE-2 with different RBD amounts. It was revealed that the ACE-2 hanging two/full RBDs (Mode-A) rapidly dimerized into the heteroprotein complex in a compact "linear" conformation, while the bare ACE-2 showed weakened self-association and a protein complex. The RBD-tethered ectodomains of ACE-2 presented a more upright conformation relative to the membrane, and the intermolecular ectodomains were predominantly packed by the neck domains, which was obligated to the rapid protein self-association in a compact pattern. Noted is the fact that the ACE-2 tethered by a single RBD (Mode-B) retained considerable self-association efficiency and clustering capability, which unravels the interrelation of ACE-2 colocalization and protein cross-linkage. The molecular perspectives in this study expound the self-association potency of ACE-2 with different RBD amounts and the viral activity implications, which can greatly enhance our comprehension of SARS-CoV-2 infection details.
Collapse
Affiliation(s)
- Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Lina Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yanjiao Wang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| |
Collapse
|
10
|
Spinti JK, Neiva Nunes F, Melo MN. Room for improvement in the initial martini 3 parameterization of peptide interactions. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
|
11
|
Franco-Ulloa S, Riccardi L, Rimembrana F, Grottin E, Pini M, De Vivo M. NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution. J Chem Theory Comput 2023; 19:1582-1591. [PMID: 36795071 PMCID: PMC10018737 DOI: 10.1021/acs.jctc.2c01029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Functionalized metal nanoparticles (NPs) are macromolecular assemblies with a tunable physicochemical profile that makes them interesting for biotechnology, materials science, and energy conversion. In this regard, molecular simulations offer a way to scrutinize the structural and dynamical features of monolayer-protected NPs and their interactions with relevant matrices. Previously, we developed NanoModeler, a webserver that automates the preparation of functionalized gold NPs for atomistic molecular dynamics (MD) simulations. Here, we present NanoModeler CG (www.nanomodeler.it), a new release of NanoModeler that now also allows the building and parametrizing of monolayer-protected metal NPs at a coarse-grained (CG) resolution. This new version extends our original methodology to NPs of eight different core shapes, conformed by up to 800,000 beads and coated by eight different monolayer morphologies. The resulting topologies are compatible with the Martini force field but are easily extendable to any other set of parameters parsed by the user. Finally, we demonstrate NanoModeler CG's capabilities by reproducing experimental structural features of alkylthiolated NPs and rationalizing the brush-to-mushroom phase transition of PEGylated anionic NPs. By automating the construction and parametrization of functionalized NPs, the NanoModeler series offers a standardized way to computationally model monolayer-protected nanosized systems.
Collapse
Affiliation(s)
- Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy.,Expert Analytics, Møllergata 8, Oslo 0179, Norway
| | - Laura Riccardi
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Federico Rimembrana
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Edwin Grottin
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Mattia Pini
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| |
Collapse
|
12
|
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
|
13
|
Nagaraju M, Liu H. A scoring function for the prediction of protein complex interfaces based on the neighborhood preferences of amino acids. Acta Crystallogr D Struct Biol 2023; 79:31-39. [PMID: 36601805 DOI: 10.1107/s2059798322011858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Proteins often assemble into functional complexes, the structures of which are more difficult to obtain than those of the individual protein molecules. Given the structures of the subunits, it is possible to predict plausible complex models via computational methods such as molecular docking. Assessing the quality of the predicted models is crucial to obtain correct complex structures. Here, an energy-scoring function was developed based on the interfacial residues of structures in the Protein Data Bank. The statistically derived energy function (Nepre) imitates the neighborhood preferences of amino acids, including the types and relative positions of neighboring residues. Based on the preference statistics, a program iNepre was implemented and its performance was evaluated with several benchmarking decoy data sets. The results show that iNepre scores are powerful in model ranking to select the best protein complex structures.
Collapse
Affiliation(s)
- Mulpuri Nagaraju
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, People's Republic of China
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, People's Republic of China
| |
Collapse
|
14
|
Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys J 2022; 121:3630-3650. [PMID: 35778842 PMCID: PMC9617161 DOI: 10.1016/j.bpj.2022.06.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.
Collapse
Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Francesco Di Natale
- Applications, Simulations, and Quality, Lawrence Livermore National Laboratory, Livermore, California
| | | | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Albert H Chan
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Harsh Bhatia
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Gulcin Gulten
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tyler Reddy
- CCS-7, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Violetta Burns
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Nick Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Peer-Timo Bremer
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - De Chen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Rebika Shrestha
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thomas Turbyville
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
| |
Collapse
|
15
|
Thallmair V, Schultz L, Zhao W, Marrink SJ, Oliver D, Thallmair S. Two cooperative binding sites sensitize PI(4,5)P 2 recognition by the tubby domain. SCIENCE ADVANCES 2022; 8:eabp9471. [PMID: 36070381 PMCID: PMC9451155 DOI: 10.1126/sciadv.abp9471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 05/22/2023]
Abstract
Phosphoinositides (PIs) are lipid signaling molecules that operate by recruiting proteins to cellular membranes via PI recognition domains. The dominant PI of the plasma membrane is phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. One of only two PI(4,5)P2 recognition domains characterized in detail is the tubby domain. It is essential for targeting proteins into cilia involving reversible membrane association. However, the PI(4,5)P2 binding properties of tubby domains have remained enigmatic. Here, we used coarse-grained molecular dynamics simulations to explore PI(4,5)P2 binding by the prototypic tubby domain. The comparatively low PI(4,5)P2 affinity of the previously described canonical binding site is underpinned in a cooperative manner by a previously unknown, adjacent second binding site. Mutations in the previously unknown site impaired PI(4,5)P2-dependent plasma membrane localization in living cells and PI(4,5)P2 interaction in silico, emphasizing its importance for PI(4,5)P2 affinity. The two-ligand binding mode may serve to sharpen the membrane association-dissociation cycle of tubby-like proteins that underlies delivery of ciliary cargo.
Collapse
Affiliation(s)
- Veronika Thallmair
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
| | - Lea Schultz
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
| | - Wencai Zhao
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Dominik Oliver
- Institute for Physiology and Pathophysiology, Philipps University Marburg, Deutschhausstr. 1-2, 35037 Marburg, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps University Marburg, Marburg, Germany
- Corresponding author. (S.T.); (D.O.)
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
- Corresponding author. (S.T.); (D.O.)
| |
Collapse
|
16
|
López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
Collapse
Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| |
Collapse
|
17
|
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
|
18
|
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
|
19
|
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: 19] [Impact Index Per Article: 6.3] [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
|
20
|
Braun L, Schoen I, Vogel V. PIP 2-induced membrane binding of the vinculin tail competes with its other binding partners. Biophys J 2021; 120:4608-4622. [PMID: 34411575 DOI: 10.1016/j.bpj.2021.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 01/09/2023] Open
Abstract
Vinculin plays a key role during the first phase of focal adhesion formation and interacts with the plasma membrane through specific binding of its tail domain to the lipid phosphatidylinositol 4,5-bisphosphate (PIP2). Our understanding of the PIP2-vinculin interaction has been hampered by contradictory biochemical and structural data. Here, we used a multiscale molecular dynamics simulation approach, in which unbiased coarse-grained molecular dynamics were used to generate starting structures for subsequent microsecond-long all-atom simulations. This allowed us to map the interaction of the vinculin tail with PIP2-enriched membranes in atomistic detail. In agreement with experimental data, we have shown that membrane binding is sterically incompatible with the intramolecular interaction between vinculin's head and tail domain. Our simulations further confirmed biochemical and structural results, which identified two positively charged surfaces, the basic collar and the basic ladder, as the main PIP2 interaction sites. By introducing a valency-disaggregated binding network analysis, we were able to map the protein-lipid interactions in unprecedented detail. In contrast to the basic collar, in which PIP2 is specifically recognized by an up to hexavalent binding pocket, the basic ladder forms a series of low-valency binding sites. Importantly, many of these PIP2 binding residues are also involved in maintaining vinculin in a closed, autoinhibited conformation. These findings led us to propose a molecular mechanism for the coupling between vinculin activation and membrane binding. Finally, our refined binding site suggests an allosteric relationship between PIP2 and F-actin binding that disfavors simultaneous interaction with both ligands, despite nonoverlapping binding sites.
Collapse
Affiliation(s)
- Lukas Braun
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
| | - Ingmar Schoen
- School of Pharmacy and Biomolecular Sciences, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
21
|
Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations. Biosystems 2021; 209:104505. [PMID: 34403719 DOI: 10.1016/j.biosystems.2021.104505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/30/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022]
Abstract
The tetraspanin family plays key roles in many physiological processes, such as, tumour invasion, cell motility, virus infection, cell attachment and entry. Tetraspanins function as molecular scaffolds organized in microdomains with interesting downstream cellular consequences. However, despite their relevance in human physiology, the precise mechanisms of their various functions remain elusive. In particular, the full-length CD81 tetraspanin has interesting cholesterol-related properties that modulate its activity in cells. In this work, we study the opening transition of CD81 under different conditions. We propose that such conformational change is a collaborative process enhanced by simultaneous interactions between multiple identical CD81 tetraspanins. With molecular dynamics simulations we describe the crucial role of a ternary lipid bilayer with cholesterol in CD81 conformational dynamics, observing two emergent properties: first, clusters of CD81 collectively segregate one tetraspanin while favouring one opening transition, second, cumulative cholesterol sequestering by CD81 tetraspanins inhibits large membrane deformations due to local density variations.
Collapse
|
22
|
Liaci AM, Steigenberger B, Telles de Souza PC, Tamara S, Gröllers-Mulderij M, Ogrissek P, Marrink SJ, Scheltema RA, Förster F. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Mol Cell 2021; 81:3934-3948.e11. [PMID: 34388369 DOI: 10.1016/j.molcel.2021.07.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre-proteins with exquisite specificity. Although the determinants of this process have been established empirically, the molecular details of SP recognition and removal remain elusive. Here, we show that the human SPC exists in two functional paralogs with distinct proteolytic subunits. We determined the atomic structures of both paralogs using electron cryo-microscopy and structural proteomics. The active site is formed by a catalytic triad and abuts the ER membrane, where a transmembrane window collectively formed by all subunits locally thins the bilayer. Molecular dynamics simulations indicate that this unique architecture generates specificity for SPs based on the length of their hydrophobic segments.
Collapse
Affiliation(s)
- A Manuel Liaci
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Paulo Cesar Telles de Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands; Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS and University of Lyon, Lyon, France
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Mariska Gröllers-Mulderij
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Patrick Ogrissek
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands; Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands.
| |
Collapse
|
23
|
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
|
24
|
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: 435] [Impact Index Per Article: 145.0] [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
|
25
|
Grünewald F, Kroon PC, Souza PCT, Marrink SJ. Protocol for Simulations of PEGylated Proteins with Martini 3. Methods Mol Biol 2021; 2199:315-335. [PMID: 33125658 DOI: 10.1007/978-1-0716-0892-0_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (MD) simulations can be applied to study specific protein-polymer systems at molecular level detail. Here we present instructions on how to simulate PEGylated proteins using the latest iteration of the Martini coarse-grained (CG) force-field. CG MD simulations offer near atomistic information and at the same time allow to study complex biological systems over longer time and length scales than fully atomistic-level simulations.
Collapse
Affiliation(s)
- Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Peter C Kroon
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands. .,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
26
|
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
|
27
|
Hitzenberger M, Götz A, Menig S, Brunschweiger B, Zacharias M, Scharnagl C. The dynamics of γ-secretase and its substrates. Semin Cell Dev Biol 2020; 105:86-101. [DOI: 10.1016/j.semcdb.2020.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/18/2022]
|
28
|
Protein-ligand binding with the coarse-grained Martini model. Nat Commun 2020; 11:3714. [PMID: 32709852 PMCID: PMC7382508 DOI: 10.1038/s41467-020-17437-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of substrates by enzymes. Nowadays, computer-aided design of protein–ligand binding is an important tool to accomplish this task. Current approaches typically rely on high-throughput docking essays or computationally expensive atomistic molecular dynamics simulations. Here, we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein–ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways. Our approach is applied to a range of systems from the well-characterized T4 lysozyme over members of the GPCR family and nuclear receptors to a variety of enzymes. The presented results open the way to high-throughput screening of ligand libraries or protein mutations using the coarse-grained Martini model. Computer-aided design of protein-ligand binding is important for the development of novel drugs. Here authors present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand binding interactions of small drug-like molecules.
Collapse
|
29
|
Biophysical characterization of p53 core domain aggregates. Biochem J 2020; 477:111-120. [PMID: 31841126 DOI: 10.1042/bcj20190778] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/16/2022]
Abstract
Aggregation is the cause of numerous protein conformation diseases. A common facet of these maladies is the transition of a protein from its functional native state into higher order forms, such as oligomers and amyloid fibrils. p53 is an essential tumor suppressor that is prone to such conformational transitions, resulting in its compromised ability to avert cancer. This work explores the biophysical properties of early-, mid-, and late-stage p53 core domain (p53C) aggregates. Atomistic and coarse-grained molecular dynamics (MD) simulations suggest that early- and mid-stage p53C aggregates have a polymorphic topology of antiparallel and parallel β-sheets that localize to the core amyloidogenic sequence. Both topologies involve similar extents of interstrand mainchain hydrogen bonding, while sidechain interactions could play a role in regulating strand orientation. The free energy difference between the antiparallel and parallel states was within statistical uncertainty. Negative stain electron microscopy of mature fibrils shows a wide distribution of fiber widths, indicating that polymorphism may extend to the quaternary structure level. Circular dichroism of the fibrils was indicative of β-sheet rich structures in atypical conformations. The Raman spectrum of aggregated p53C was consistent with a mixture of arranged β-sheets and heterogeneous structural elements, which is compatible with the MD findings of an ordered β-sheet nucleus flanked by disordered structure. Structural polymorphism is a common property of amyloids; however, because certain polymorphs of the same protein can be more harmful than others, going forward it will be pertinent to establish correlations between p53C aggregate structure and pathology.
Collapse
|
30
|
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
|
31
|
Khan HM, Souza PCT, Thallmair S, Barnoud J, de Vries AH, Marrink SJ, Reuter N. Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field. J Chem Theory Comput 2020; 16:2550-2560. [PMID: 32096995 PMCID: PMC7175457 DOI: 10.1021/acs.jctc.9b01194] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Cation−π
interactions play an important
role in biomolecular recognition, including interactions between membrane
phosphatidylcholine lipids and aromatic amino acids of peripheral
proteins. While molecular mechanics coarse grain (CG) force fields
are particularly well suited to simulate membrane proteins in general,
they are not parameterized to explicitly reproduce cation−π
interactions. We here propose a modification of the polarizable MARTINI
coarse grain (CG) model enabling it to model membrane binding events
of peripheral proteins whose aromatic amino acid interactions with
choline headgroups are crucial for their membrane binding. For this
purpose, we first collected and curated a dataset of eight peripheral
proteins from different families. We find that the MARTINI CG model
expectedly underestimates aromatics–choline interactions and
is unable to reproduce membrane binding of the peripheral proteins
in our dataset. Adjustments of the relevant interactions in the polarizable
MARTINI force field yield significant improvements in the observed
binding events. The orientation of each membrane-bound protein is
comparable to reference data from all-atom simulations and experimental
binding data. We also use negative controls to ensure that choline–aromatics
interactions are not overestimated. We finally check that membrane
properties, transmembrane proteins, and membrane translocation potential
of mean force (PMF) of aromatic amino acid side-chain analogues are
not affected by the new parameter set. This new version “MARTINI
2.3P” is a significant improvement over its predecessors and
is suitable for modeling membrane proteins including peripheral membrane
binding of peptides and proteins.
Collapse
Affiliation(s)
- Hanif M Khan
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway.,Department of Chemistry, University of Bergen, N-5020 Bergen, Norway
| |
Collapse
|
32
|
Corey RA, Stansfeld PJ, Sansom MS. The energetics of protein-lipid interactions as viewed by molecular simulations. Biochem Soc Trans 2020; 48:25-37. [PMID: 31872229 PMCID: PMC7054751 DOI: 10.1042/bst20190149] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
Abstract
Membranes are formed from a bilayer containing diverse lipid species with which membrane proteins interact. Integral, membrane proteins are embedded in this bilayer, where they interact with lipids from their surroundings, whilst peripheral membrane proteins bind to lipids at the surface of membranes. Lipid interactions can influence the function of membrane proteins, either directly or allosterically. Both experimental (structural) and computational approaches can reveal lipid binding sites on membrane proteins. It is, therefore, important to understand the free energies of these interactions. This affords a more complete view of the engagement of a particular protein with the biological membrane surrounding it. Here, we describe many computational approaches currently in use for this purpose, including recent advances using both free energy and unbiased simulation methods. In particular, we focus on interactions of integral membrane proteins with cholesterol, and with anionic lipids such as phosphatidylinositol 4,5-bis-phosphate and cardiolipin. Peripheral membrane proteins are exemplified via interactions of PH domains with phosphoinositide-containing membranes. We summarise the current state of the field and provide an outlook on likely future directions of investigation.
Collapse
Affiliation(s)
- Robin A. Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| |
Collapse
|
33
|
Caparotta M, Bustos DM, Masone D. Order–disorder skewness in alpha-synuclein: a key mechanism to recognize membrane curvature. Phys Chem Chem Phys 2020; 22:5255-5263. [DOI: 10.1039/c9cp04951g] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently, membrane curvature is understood as an active mechanism to control cells spatial organization and activity.
Collapse
Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
| | - Diego M. Bustos
- Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ingeniería
| |
Collapse
|
34
|
Ghermezcheshme H, Makki H, Mohseni M, Ebrahimi M, de With G. MARTINI-based simulation method for step-growth polymerization and its analysis by size exclusion characterization: a case study of cross-linked polyurethane. Phys Chem Chem Phys 2019; 21:21603-21614. [PMID: 31544200 DOI: 10.1039/c9cp03407b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simulation studies of step-growth polymerization, e.g., polymerization of polyurethane systems, hold great promise due to having complete control over the reaction conditions and being able to perform an in-depth analysis of network structures. In this work, we developed a (completely automated) simulation method based on a coarse-grained (CG) methodology, i.e., the MARTINI model, to study the cross-linking reaction of a diol, a tri-isocyanate molecule and one-hydroxyl functional molecule to form a polyurethane network without and with dangling chains. This method is capable of simulating the cross-linking reactions not only up to very high conversions, but also under rather complicated reaction conditions, i.e., a non-stoichiometric ratio of the reactants, solvent evaporation and multi-step addition of the reactants. We introduced a novel network analysis, similar to size-exclusion chromatography based on graph theory, to study the growth of the network during the polymerization process. By combining the reaction simulations with these analysis methods, a set of correlations between the reaction conditions, reaction mechanisms and final network structure and properties is revealed. For instance, a two-step addition of materials for the reaction, i.e., first the dangling chain to the tri-isocyanate and then the diol, leads to the highest integrated network structure. We observed that different reaction conditions lead to different glass transition temperatures (Tg) of the network due to the distinct differences in the final network structures obtained. For example, by addition of dangling chains to the network, the Tg decreases as compared to the network without dangling chains, as also is commonly observed experimentally.
Collapse
Affiliation(s)
- Hassan Ghermezcheshme
- Department of Polymer and Color Engineering, Amirkabir University of Technology, 424 Hafez Ave., Tehran, Iran.
| | - Hesam Makki
- Department of Polymer and Color Engineering, Amirkabir University of Technology, 424 Hafez Ave., Tehran, Iran.
| | - Mohsen Mohseni
- Department of Polymer and Color Engineering, Amirkabir University of Technology, 424 Hafez Ave., Tehran, Iran.
| | - Morteza Ebrahimi
- Department of Polymer and Color Engineering, Amirkabir University of Technology, 424 Hafez Ave., Tehran, Iran.
| | - Gijsbertus de With
- Laboratory of Physical Chemistry, Department of Chemical Engineering & Chemistry, Eindhoven University of Technology, POB 513, NL-5600 MB Eindhoven, The Netherlands
| |
Collapse
|
35
|
Rajagopal N, Nangia S. Obtaining Protein Association Energy Landscape for Integral Membrane Proteins. J Chem Theory Comput 2019; 15:6444-6455. [DOI: 10.1021/acs.jctc.9b00626] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, New York 13244, United States
| |
Collapse
|
36
|
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
Collapse
Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
37
|
Rajagopal N, Irudayanathan FJ, Nangia S. Palmitoylation of Claudin-5 Proteins Influences Their Lipid Domain Affinity and Tight Junction Assembly at the Blood–Brain Barrier Interface. J Phys Chem B 2019; 123:983-993. [DOI: 10.1021/acs.jpcb.8b09535] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse 13244, United States
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse 13244, United States
| |
Collapse
|
38
|
Masone D, Bustos DM. Transmembrane domain dimerization induces cholesterol rafts in curved lipid bilayers. Phys Chem Chem Phys 2019; 21:268-274. [DOI: 10.1039/c8cp06783j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Are the dimerization of transmembrane (TM) domains and the reorganization of the lipid bilayer two independent events?
Collapse
Affiliation(s)
- Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ingeniería
| | - Diego M. Bustos
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ciencias Exactas y Naturales
| |
Collapse
|
39
|
Abstract
Martini is a coarse-grained (CG) force field suitable for molecular dynamics (MD) simulations of (bio)molecular systems. It is based on mapping of two to four heavy atoms to one CG particle. The effective interactions between the CG particles are parametrized to reproduce partitioning free energies of small chemical compounds between polar and apolar phases. In this chapter, a summary of the key elements of this CG force field is presented, followed by an example of practical application: a lipoplex-membrane fusion experiment. Formulated as hands-on practice, this chapter contains guidelines to build CG models of important biological systems, such as asymmetric bilayers and double-stranded DNA. Finally, a series of notes containing useful information, limitations, and tips are described in the last section.
Collapse
Affiliation(s)
- Bart M H Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
40
|
Chavent M, Karia D, Kalli AC, Domański J, Duncan AL, Hedger G, Stansfeld PJ, Seiradake E, Jones EY, Sansom MSP. Interactions of the EphA2 Kinase Domain with PIPs in Membranes: Implications for Receptor Function. Structure 2018; 26:1025-1034.e2. [PMID: 29887500 PMCID: PMC6039763 DOI: 10.1016/j.str.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/15/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022]
Abstract
EphA2 is a member of the receptor tyrosine kinase family. Interactions of the cytoplasmic region of EphA2 with the cell membrane are functionally important and yet remain incompletely characterized. Molecular dynamics simulations combined with biochemical studies reveal the interactions of the transmembrane, juxtamembrane (JM), and kinase domains with the membrane. We describe how the kinase domain is oriented relative to the membrane and how the JM region can modulate this interaction. We highlight the role of phosphatidylinositol phosphates (PIPs) in mediating the interaction of the kinase domain with the membrane and, conversely, how positively charged patches at the kinase surface and in the JM region induce the formation of nanoclusters of PIP molecules in the membrane. Integration of these results with those from previous studies enable computational reconstitution of a near complete EphA2 receptor within a membrane, suggesting a role for receptor-lipid interactions in modulation of EphA2.
Collapse
Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Institut de Pharmacologie et de Biologie Structurale IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Dimple Karia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antreas C Kalli
- Leeds Institute of Cancer and Pathology, St James's University Hospital, University of Leeds, Leeds, UK
| | - Jan Domański
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - George Hedger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
41
|
Masone D, Uhart M, Bustos DM. Bending Lipid Bilayers: A Closed-Form Collective Variable for Effective Free-Energy Landscapes in Quantitative Biology. J Chem Theory Comput 2018; 14:2240-2245. [PMID: 29506389 DOI: 10.1021/acs.jctc.8b00012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Curvature-related processes are of major importance during protein-membrane interactions. The illusive simplicity of membrane reshaping masks a complex molecular process crucial for a wide range of biological functions like fusion, endo- and exocytosis, cell division, cytokinesis, and autophagy. To date, no functional expression of a reaction coordinate capable of biasing molecular dynamics simulations to produce membrane curvature has been reported. This represents a major drawback given that the adequate identification of proper collective variables to enhance sampling is fundamental for restrained dynamics techniques. In this work, we present a closed-form equation of a collective variable that induces bending in lipid bilayers in a controlled manner, allowing for straightforward calculation of free energy landscapes of important curvature-related events, using standard methods such as umbrella sampling and metadynamics. As a direct application of the collective variable, we calculate the bending free energies of a ternary lipid bilayer in the presence and the absence of a Bin/Amphiphysin/Rvs domain with an N-terminal amphipathic helix (N-BAR), a well-known peripheral membrane protein that induces curvature.
Collapse
|
42
|
Naughton FB, Kalli AC, Sansom MS. Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition. J Mol Biol 2018; 430:372-388. [DOI: 10.1016/j.jmb.2017.12.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 11/30/2022]
|
43
|
Abellón-Ruiz J, Kaptan SS, Baslé A, Claudi B, Bumann D, Kleinekathöfer U, van den Berg B. Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Nat Microbiol 2017; 2:1616-1623. [PMID: 29038444 DOI: 10.1038/s41564-017-0046-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/21/2017] [Indexed: 11/09/2022]
Abstract
The Gram-negative bacterial outer membrane (OM) is a unique bilayer that forms an efficient permeation barrier to protect the cell from noxious compounds 1,2 . The defining characteristic of the OM is lipid asymmetry, with phospholipids comprising the inner leaflet and lipopolysaccharides comprising the outer leaflet 1-3 . This asymmetry is maintained by the Mla pathway, a six-component system that is widespread in Gram-negative bacteria and is thought to mediate retrograde transport of misplaced phospholipids from the outer leaflet of the OM to the cytoplasmic membrane 4 . The OM lipoprotein MlaA performs the first step in this process via an unknown mechanism that does not require external energy input. Here we show, using X-ray crystallography, molecular dynamics simulations and in vitro and in vivo functional assays, that MlaA is a monomeric α-helical OM protein that functions as a phospholipid translocation channel, forming a ~20-Å-thick doughnut embedded in the inner leaflet of the OM with a central, amphipathic pore. This architecture prevents access of inner leaflet phospholipids to the pore, but allows outer leaflet phospholipids to bind to a pronounced ridge surrounding the channel, followed by diffusion towards the periplasmic space. Enterobacterial MlaA proteins form stable complexes with OmpF/C 5,6 , but the porins do not appear to play an active role in phospholipid transport. MlaA represents a lipid transport protein that selectively removes outer leaflet phospholipids to help maintain the essential barrier function of the bacterial OM.
Collapse
Affiliation(s)
- Javier Abellón-Ruiz
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Shreyas S Kaptan
- Department of Physics & Earth Sciences, Jacobs University Bremen, 28759, Bremen, Germany
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Beatrice Claudi
- Focal Area Infection Biology, University of Basel, CH-4056, Basel, Switzerland
| | - Dirk Bumann
- Focal Area Infection Biology, University of Basel, CH-4056, Basel, Switzerland
| | - Ulrich Kleinekathöfer
- Department of Physics & Earth Sciences, Jacobs University Bremen, 28759, Bremen, Germany
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| |
Collapse
|
44
|
Poma AB, Cieplak M, Theodorakis PE. Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins. J Chem Theory Comput 2017; 13:1366-1374. [PMID: 28195464 DOI: 10.1021/acs.jctc.6b00986] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The application of coarse-grained (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolding and folding processes. To overcome this barrier we have replaced the harmonic bonds with Lennard-Jones interactions based on the contact map of the native protein structure as is done in Go̅-like models. This model exhibits very good agreement with all-atom simulations and the ELNEDIN. Moreover, it can capture the structural motion linked to particular catalytic activity in the Man5B protein, in agreement with all-atom simulations. In addition, our model is based on the van der Waals radii, instead of a cutoff distance, which results in a smaller contact map. In conclusion, we anticipate that our model will provide further possibilities for studying biological systems based on the MARTINI CG force-field by using advanced-sampling methods, such as parallel tempering and metadynamics.
Collapse
Affiliation(s)
- Adolfo B Poma
- Institute of Physics, Polish Academy of Sciences , Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences , Al. Lotników 32/46, 02-668 Warsaw, Poland
| | | |
Collapse
|
45
|
Chen PC, Hologne M, Walker O. Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations. J Phys Chem B 2017; 121:1812-1823. [DOI: 10.1021/acs.jpcb.6b11703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Po-chia Chen
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| |
Collapse
|
46
|
Herzog FA, Braun L, Schoen I, Vogel V. Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes. J Phys Chem B 2017; 121:3523-3535. [DOI: 10.1021/acs.jpcb.6b09349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Florian A. Herzog
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Lukas Braun
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Ingmar Schoen
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Viola Vogel
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
47
|
Fosso-Tande J, Black C, G. Aller S, Lu L, D. Hills Jr R. Simulation of lipid-protein interactions with the CgProt force field. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
48
|
Guo C, Arnon ZA, Qi R, Zhang Q, Adler-Abramovich L, Gazit E, Wei G. Expanding the Nanoarchitectural Diversity Through Aromatic Di- and Tri-Peptide Coassembly: Nanostructures and Molecular Mechanisms. ACS NANO 2016; 10:8316-8324. [PMID: 27548765 DOI: 10.1021/acsnano.6b02739] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular self-assembly is pivotal for the formation of ordered nanostructures, yet the structural diversity obtained by the use of a single type of building block is limited. Multicomponent coassembly, utilized to expand the architectural space, is principally based on empirical observations rather than rational design. Here we report large-scale molecular dynamics simulations of the coassembly of diphenylalanine (FF) and triphenylalanine (FFF) peptides at various mass ratios. Our simulations show that FF and FFF can co-organize into both canonical and noncanonical assemblies. Strikingly, toroid nanostructures, which were rarely observed for the extensively studied FF or FFF, are often seen in the FF-FFF coassembly simulations and later corroborated by scanning electron microscopy. Our simulations demonstrate a wide ratio-dependent variation of nanostructure morphologies including hollow and solid assemblies, much richer than those formed by each individual moiety. The hollow-solid structural transformation displays a discontinuous transition feature, and the toroids appear to be an obligatory intermediate for the structural transition. Interaction analysis reveals that the hollow-solid structural transition is mostly dominated by FF-FFF interactions, while the nanotoroid formation is determined by the competition between FF-water and FFF-water interactions. This study provides both structural and mechanistic insights into the coassembly of FF and FFF peptides, thus offering a molecular basis for the rational design of bionanomaterials utilizing peptide coassembly.
Collapse
Affiliation(s)
- Cong Guo
- Key Laboratory for Computational Physical Sciences (MOE), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University , Shanghai 200433, China
| | | | - Ruxi Qi
- Key Laboratory for Computational Physical Sciences (MOE), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University , Shanghai 200433, China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport , 399 Changhai Road, Shanghai 200438, China
| | | | | | - Guanghong Wei
- Key Laboratory for Computational Physical Sciences (MOE), State Key Laboratory of Surface Physics, and Department of Physics, Fudan University , Shanghai 200433, China
| |
Collapse
|