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Yang S, Song C. Switching Go̅ -Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions. J Chem Theory Comput 2024; 20:2618-2629. [PMID: 38447049 DOI: 10.1021/acs.jctc.3c01222] [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: 03/08/2024]
Abstract
Proteins are dynamic biomolecules that can transform between different conformational states when exerting physiological functions, which is difficult to simulate using all-atom methods. Coarse-grained (CG) Go̅-like models are widely used to investigate large-scale conformational transitions, which usually adopt implicit solvent models and therefore cannot explicitly capture the interaction between proteins and surrounding molecules, such as water and lipid molecules. Here, we present a new method, named Switching Go̅-Martini, to simulate large-scale protein conformational transitions between different states, based on the switching Go̅ method and the CG Martini 3 force field. The method is straightforward and efficient, as demonstrated by the benchmarking applications for multiple protein systems, including glutamine binding protein (GlnBP), adenylate kinase (AdK), and β2-adrenergic receptor (β2AR). Moreover, by employing the Switching Go̅-Martini method, we can not only unveil the conformational transition from the E2Pi-PL state to E1 state of the type 4 P-type ATPase (P4-ATPase) flippase ATP8A1-CDC50 but also provide insights into the intricate details of lipid transport.
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Affiliation(s)
- Song Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chen Song
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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2
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Zhou H, Shiel E, Bell T, Lin S, Lenhert S. Kinetic Mechanism of Surfactant-Based Molecular Recognition: Selective Permeability across an Oil-Water Interface Regulated by Supramolecular Aggregates. J Phys Chem B 2023; 127:10201-10214. [PMID: 37972386 DOI: 10.1021/acs.jpcb.3c05017] [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: 11/19/2023]
Abstract
Lipids are known to play a vital role in the molecular organization of all cellular life. Molecular recognition is another fundamental biological process that is generally attributed to biological polymers, such as proteins and nucleic acids. However, there is evidence that aggregates of lipids and lipid-like molecules are also capable of selectively binding to or regulating the partitioning of other molecules. We previously demonstrated that a model two-phase octanol/water system can selectively partition Red 40 and Blue 1 dyes added to an aqueous phase, with the selectivity depending on the surfactant (e.g., cetyltrimethylammonium bromide) dissolved in the organic phase. Here, we elucidate the mechanism of molecular recognition in this system by using quantitative partitioning experiments and molecular dynamics (MD) simulations. Our results indicate that the selectivity for the red dye is thermodynamically favored at all surfactant concentrations, while selectivity for the blue dye is kinetically favored at high surfactant concentrations. The kinetic selectivity for the blue dye correlates with the presence of molecular aggregation at the oil-water interface. Coarse-grained MD simulations elucidate nanoscale supramolecular structures that can preferentially bind one small molecule rather than another at an interface, providing a selectively permeable barrier in the absence of proteins. The results suggest a new supramolecular mechanism for molecular recognition with potential applications in drug delivery, drug discovery, and biosensing.
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Affiliation(s)
- Huanhuan Zhou
- Department of Biological Science and Integrative Nanoscience Institute, Florida State University, Tallahassee, Florida 32306, United States
| | - Emily Shiel
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Tracey Bell
- Department of Biological Science and Integrative Nanoscience Institute, Florida State University, Tallahassee, Florida 32306, United States
| | - Shangchao Lin
- Institute of Engineering Thermophysics, School of Mechanical and Power Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Steven Lenhert
- Department of Biological Science and Integrative Nanoscience Institute, Florida State University, Tallahassee, Florida 32306, United States
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Conflitti P, Raniolo S, Limongelli V. Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness. J Chem Theory Comput 2023; 19:6047-6061. [PMID: 37656199 PMCID: PMC10536999 DOI: 10.1021/acs.jctc.3c00641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 09/02/2023]
Abstract
Computational techniques applied to drug discovery have gained considerable popularity for their ability to filter potentially active drugs from inactive ones, reducing the time scale and costs of preclinical investigations. The main focus of these studies has historically been the search for compounds endowed with high affinity for a specific molecular target to ensure the formation of stable and long-lasting complexes. Recent evidence has also correlated the in vivo drug efficacy with its binding kinetics, thus opening new fascinating scenarios for ligand/protein binding kinetic simulations in drug discovery. The present article examines the state of the art in the field, providing a brief summary of the most popular and advanced ligand/protein binding kinetics techniques and evaluating their current limitations and the potential solutions to reach more accurate kinetic models. Particular emphasis is put on the need for a paradigm change in the present methodologies toward ligand and protein parametrization, the force field problem, characterization of the transition states, the sampling issue, and algorithms' performance, user-friendliness, and data openness.
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Affiliation(s)
- Paolo Conflitti
- Faculty
of Biomedical Sciences, Euler Institute, Universitá della Svizzera italiana (USI), 6900 Lugano, Switzerland
| | - Stefano Raniolo
- Faculty
of Biomedical Sciences, Euler Institute, Universitá della Svizzera italiana (USI), 6900 Lugano, Switzerland
| | - Vittorio Limongelli
- Faculty
of Biomedical Sciences, Euler Institute, Universitá della Svizzera italiana (USI), 6900 Lugano, Switzerland
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
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Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
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Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
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Pino JA, Nuñez-Vivanco G, Hidalgo G, Reyes Parada M, Khoshbouei H, Torres GE. Identification of Critical Residues in the Carboxy Terminus of the Dopamine Transporter Involved in the G Protein βγ-Induced Dopamine Efflux. Front Pharmacol 2021; 12:642881. [PMID: 33841159 PMCID: PMC8025876 DOI: 10.3389/fphar.2021.642881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
The dopamine transporter (DAT) plays a crucial role in the regulation of brain dopamine (DA) homeostasis through the re-uptake of DA back into the presynaptic terminal. In addition to re-uptake, DAT is also able to release DA through a process referred to as DAT-mediated DA efflux. This is the mechanism by which potent and highly addictive psychostimulants, such as amphetamine (AMPH) and its analogues, increase extracellular DA levels in motivational and reward areas of the brain. Recently, we discovered that G protein βγ subunits (Gβγ) binds to the DAT, and that activation of Gβγ results in DAT-mediated efflux - a similar mechanism as AMPH. Previously, we have shown that Gβγ binds directly to a stretch of 15 residues within the intracellular carboxy terminus of DAT (residues 582-596). Additionally, a TAT peptide containing residues 582 to 596 of DAT was able to block the Gβγ-induced DA efflux through DAT. Here, we use a combination of computational biology, mutagenesis, biochemical, and functional assays to identify the amino acid residues within the 582-596 sequence of the DAT carboxy terminus involved in the DAT-Gβγ interaction and Gβγ-induced DA efflux. Our in-silico protein-protein docking analysis predicted the importance of F587 and R588 residues in a network of interactions with residues in Gβγ. In addition, we observed that mutating R588 to alanine residue resulted in a mutant DAT which exhibited attenuated DA efflux induced by Gβγ activation. We demonstrate that R588, and to a lesser extent F5837, located within the carboxy terminus of DAT play a critical role in the DAT-Gβγ physical interaction and promotion of DA efflux. These results identify a potential new pharmacological target for the treatment of neuropsychiatric conditions in which DAT functionality is implicated including ADHD and substance use disorder.
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Affiliation(s)
- José A Pino
- Departamento de Medicina, Facultad de Medicina, Universidad de Atacama, Copiapó, Chile
| | - Gabriel Nuñez-Vivanco
- Centro de Bioinformática, Simulación y Modelado, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Gabriela Hidalgo
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, United States
| | - Miguel Reyes Parada
- Centro de Investigación Biomédica y Aplicada (CIBAP), Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile.,Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Habibeh Khoshbouei
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, FL, United States
| | - Gonzalo E Torres
- Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, New York, NY, United States
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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.
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