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Poruthoor AJ, Sharma A, Grossfield A. Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics. Biophys J 2023; 122:4144-4159. [PMID: 37742069 PMCID: PMC10645549 DOI: 10.1016/j.bpj.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023] Open
Abstract
Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.
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Affiliation(s)
- Ashlin J Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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2
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Poruthoor AJ, Sharma A, Grossfield A. Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526537. [PMID: 36778479 PMCID: PMC9915641 DOI: 10.1101/2023.01.31.526537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid-liquid phase separation (LLPS) inside the cell often results in biological condensates that can critically impact cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the so-called "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For this reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation - essentially measuring the sign (but not the amplitude) of the free energy change upon separation - rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from molecular dynamics simulations. SIGNIFICANCE Standard molecular dynamics simulations can determine the sign the free energy change upon phase separation, but not the amplitude. We present a new method to determine the phase separation free energy for lipid membranes, based on a enhanced sampling using the weighted ensemble method combined with a novel collective variable, validated using coarse-grained simulations applied to several simple systems. The new method will be valuable as a way to develop models that connect molecular-level structural features to the thermodynamics of phase separation.
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Affiliation(s)
- Ashlin J. Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642
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3
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Firouzi R, Sowlati-Hashjin S, Chávez-García C, Ashouri M, Karimi-Jafari MH, Karttunen M. Identification of Catechins' Binding Sites in Monomeric A β42 through Ensemble Docking and MD Simulations. Int J Mol Sci 2023; 24:ijms24098161. [PMID: 37175868 PMCID: PMC10179585 DOI: 10.3390/ijms24098161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
The assembly of the amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline-in the framework of the ensemble docking strategy-to identify catechins' binding sites in monomeric Aβ42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ42. Additionally, it has been found that all the studied ligands, especially EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.
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Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran 1496813151, Iran
| | | | - Cecilia Chávez-García
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Mitra Ashouri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran P.O. Box 14155-6619, Iran
| | - Mohammad Hossein Karimi-Jafari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran P.O. Box 14155-6619, Iran
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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4
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Li L, Liu J, Li X, Tang Y, Shi C, Zhang X, Cui Y, Wang L, Xu W. Influencing factors and characterization methods of nanoparticles regulating amyloid aggregation. SOFT MATTER 2022; 18:3278-3290. [PMID: 35437550 DOI: 10.1039/d1sm01704g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human disorders associated with amyloid aggregation, such as Alzheimer's disease and Parkinson's disease, afflict the lives of millions worldwide. When peptides and proteins in the body are converted to amyloids, which have a tendency to aggregate, the toxic oligomers produced during the aggregation process can trigger a range of diseases. Nanoparticles (NPs) have been found to possess surface effects that can modulate the amyloid aggregation process and they have potential application value in the treatment of diseases related to amyloid aggregation and fibrillary tangles. In this review, we discuss recent progress relating to studies of nanoparticles that regulate amyloid aggregation. The review focuses on the factors influencing this regulation, which are important as guidelines for the future design of NPs for the treatment of amyloid aggregation. We describe the characterization methods that have been utilized so far in such studies. This review provides research information and characterization methods for the rational design of NPs, which should result in therapeutic strategies for amyloid diseases.
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Affiliation(s)
- Lingyi Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Jianhui Liu
- Yantai Center of Ecology and Environment Monitoring of Shandong Province, Yantai 264025, China
| | - Xinyue Li
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Yuanhan Tang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Changxin Shi
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Xin Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Yuming Cui
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
| | - Linlin Wang
- State Key Laboratory of Long-Acting and Targeting Drug Delivery System, Shandong Luye Pharmaceutical Co., Ltd, Yantai 264000, China.
| | - Wenlong Xu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China.
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5
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Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021; 11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Agnieszka G. Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India;
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6
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Casalini T. Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations. J Control Release 2021; 332:390-417. [PMID: 33675875 DOI: 10.1016/j.jconrel.2021.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.
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Affiliation(s)
- Tommaso Casalini
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich 8093, Switzerland; Polymer Engineering Laboratory, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via la Santa 1, Lugano 6962, Switzerland.
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7
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Metadynamics to Enhance Sampling in Biomolecular Simulations. Methods Mol Biol 2019. [PMID: 31396904 DOI: 10.1007/978-1-4939-9608-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.
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8
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Du P, Rick SW, Kumar R. Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide. Phys Chem Chem Phys 2018; 20:23386-23396. [DOI: 10.1039/c8cp03283a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained model of DMA, containing the basic motif of the peptoid backbone, based on short ranged many-body ranged interactions.
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Affiliation(s)
- Pu Du
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | - Steven W. Rick
- Department of Chemistry
- University of New Orleans
- New Orleans
- USA
| | - Revati Kumar
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
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9
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Qi R, Wei G, Ma B, Nussinov R. Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example. Methods Mol Biol 2018; 1777:101-119. [PMID: 29744830 PMCID: PMC6484850 DOI: 10.1007/978-1-4939-7811-3_5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein aggregation is associated with many human diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and type II diabetes (T2D). Understanding the molecular mechanism of protein aggregation is essential for therapy development. Molecular dynamics (MD) simulations have been shown as powerful tools to study protein aggregation. However, conventional MD simulations can hardly sample the whole conformational space of complex protein systems within acceptable simulation time as it can be easily trapped in local minimum-energy states. Many enhanced sampling methods have been developed. Among these, the replica exchange molecular dynamics (REMD) method has gained great popularity. By combining MD simulation with the Monte Carlo algorithm, the REMD method is capable of overcoming high energy-barriers easily and of sampling sufficiently the conformational space of proteins. In this chapter, we present a brief introduction to REMD method and a practical application protocol with a case study of the dimerization of the 11-25 fragment of human islet amyloid polypeptide (hIAPP(11-25)), using the GROMACS software. We also provide solutions to problems that are often encountered in practical use, and provide some useful scripts/commands from our research that can be easily adapted to other systems.
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Affiliation(s)
- Ruxi Qi
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, P.R. China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, P.R. China.
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA.
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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10
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Hosseinzadeh G, Maghari A, Farnia SMF, Moosavi-Movahedi AA. Interaction mechanism of insulin with ZnO nanoparticles by replica exchange molecular dynamics simulation. J Biomol Struct Dyn 2017; 36:3623-3635. [DOI: 10.1080/07391102.2017.1396254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ghader Hosseinzadeh
- School of Chemistry, University of Tehran, Tehran, Iran
- Department of Polymer Science and Engineering, University of Bonab, Bonab, Iran
| | - Ali Maghari
- School of Chemistry, University of Tehran, Tehran, Iran
| | | | - Ali A. Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
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11
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Affiliation(s)
- Marco Nava
- Department of Chemistry and
Applied Biosciences, ETH Zurich, and Facoltà di Informatica,
Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
| | - Ferruccio Palazzesi
- Department of Chemistry and
Applied Biosciences, ETH Zurich, and Facoltà di Informatica,
Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
| | - Claudio Perego
- Department of Chemistry and
Applied Biosciences, ETH Zurich, and Facoltà di Informatica,
Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
| | - Michele Parrinello
- Department of Chemistry and
Applied Biosciences, ETH Zurich, and Facoltà di Informatica,
Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
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12
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Wang Y, Papaleo E, Lindorff-Larsen K. Mapping transiently formed and sparsely populated conformations on a complex energy landscape. eLife 2016; 5. [PMID: 27552057 PMCID: PMC5050026 DOI: 10.7554/elife.17505] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally. DOI:http://dx.doi.org/10.7554/eLife.17505.001 Proteins are the workhorses of cells, where they perform a wide range of roles. To do so, they adopt specific three-dimensional structures that enable them to interact with other molecules as necessary. Often a protein needs to be able to shift between different states with distinct structures as it goes about its job. To fully understand how a protein works, it is important to be able to characterize these different structures and how the protein changes between them. Many of the experimental techniques used to study protein structure rely on isolating the individual structural forms of a protein. Since many structures only exist briefly, this can be very difficult. To complement experimental results, computer simulations allow researchers to model how atoms behave within a molecule. However, a number of factors limit how well these models represent what happens experimentally, such as the accuracy of the physical description used for the modeling. Wang et al. set out to test and benchmark how well computer simulations could model changes in structure for a protein called T4 lysozyme, which has been studied extensively using experimental techniques. T4 lysozyme exists in two different states that have distinct structures. By comparing existing detailed experimental measurements with the results of their simulations, Wang et al. found that the simulations could capture key aspects of how T4 lysozyme changes its shape. The simulations described the structure of the protein in both states and accurately determined the relative proportion of molecules that are found in each state. They could also determine how long it takes for a molecule to change its shape from one state to the other. The findings allowed Wang et al. to describe in fine detail – down to the level of individual atoms – how the protein changes its shape and how mutations in the protein affect its ability to do so. A key question for future studies is whether these insights can be extended to other proteins that are less well characterized experimentally than T4 lysozyme. DOI:http://dx.doi.org/10.7554/eLife.17505.002
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Affiliation(s)
- Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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13
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Sprenger KG, He Y, Pfaendtner J. Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation. FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION 2016. [DOI: 10.1007/978-981-10-1128-3_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Grazioso G, Sgrignani J, Capelli R, Matera C, Dallanoce C, De Amici M, Cavalli A. Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics. J Chem Inf Model 2015; 55:2528-39. [PMID: 26569022 DOI: 10.1021/acs.jcim.5b00459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing attention has recently been devoted to allosteric modulators, as they can provide inherent advantages over classic receptor agonists. In the field of nicotinic receptors (nAChRs), the main advantage is that allosteric modulators can trigger pharmacological responses, limiting receptor desensitization. Most of the known allosteric ligands are "positive allosteric modulators" (PAMs), which increase both sensitivity to receptor agonists and current amplitude. Intriguingly, some allosteric modulators are also able to activate the α7 receptor (α7-nAChR) even in the absence of orthosteric agonists. These compounds have been named "ago-allosteric modulators" and GAT107 has been studied in depth because of its unique mechanism of action. We here investigate by molecular dynamics simulations, metadynamics, and essential dynamics the activation mechanism of α7-nAChR, in the presence of different nicotinic modulators. We determine the free energy profiles associated with the closed-to-open motion of the loop C, and we highlight mechanistic differences observed in the presence of different modulators. In particular, we demonstrate that GAT107 triggers conformational motions and cross-talk similar to those observed when the α7-nACh receptor is in complex with both an agonist and an allosteric modulator.
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Affiliation(s)
- Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Jacopo Sgrignani
- Institute of Research in Biomedicine (IRB) , Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Romina Capelli
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Carlo Matera
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Clelia Dallanoce
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco De Amici
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica "Pietro Pratesi", Università degli Studi di Milano , Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Andrea Cavalli
- Drug Discovery and Development-Computation, Istituto Italiano di Tecnologia , Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotecnology, University of Bologna , Via Belmeloro 6, 40126 Bologna, Italy
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15
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Pfaendtner J, Bonomi M. Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics. J Chem Theory Comput 2015; 11:5062-7. [DOI: 10.1021/acs.jctc.5b00846] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Massimiliano Bonomi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Papaleo E. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. Front Mol Biosci 2015; 2:28. [PMID: 26075210 PMCID: PMC4445042 DOI: 10.3389/fmolb.2015.00028] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/08/2015] [Indexed: 12/11/2022] Open
Abstract
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
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Affiliation(s)
- Elena Papaleo
- Structural Biology and Nuclear Magnetic Resonance Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
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Baker CM. Polarizable force fields for molecular dynamics simulations of biomolecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1215] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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