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Mazurek AH, Szeleszczuk Ł, Gubica T. Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes. Int J Mol Sci 2021; 22:9422. [PMID: 34502331 PMCID: PMC8431145 DOI: 10.3390/ijms22179422] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022] Open
Abstract
Cyclodextrins (CDs) are highly respected for their ability to form inclusion complexes via host-guest noncovalent interactions and, thus, ensofance other molecular properties. Various molecular modeling methods have found their applications in the analysis of those complexes. However, as showed in this review, molecular dynamics (MD) simulations could provide the information unobtainable by any other means. It is therefore not surprising that published works on MD simulations used in this field have rapidly increased since the early 2010s. This review provides an overview of the successful applications of MD simulations in the studies on CD complexes. Information that is crucial for MD simulations, such as application of force fields, the length of the simulation, or solvent treatment method, are thoroughly discussed. Therefore, this work can serve as a guide to properly set up such calculations and analyze their results.
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Affiliation(s)
- Anna Helena Mazurek
- Department of Physical Chemistry, Chair of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Doctoral School, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland;
| | - Łukasz Szeleszczuk
- Department of Physical Chemistry, Chair of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland;
| | - Tomasz Gubica
- Department of Physical Chemistry, Chair of Physical Pharmacy and Bioanalysis, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland;
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Marchetto A, Si Chaib Z, Rossi CA, Ribeiro R, Pantano S, Rossetti G, Giorgetti A. CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations. Molecules 2020; 25:E5934. [PMID: 33333836 PMCID: PMC7765266 DOI: 10.3390/molecules25245934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/28/2020] [Indexed: 12/17/2022] Open
Abstract
Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.
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Affiliation(s)
- Alessandro Marchetto
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Carlo Alberto Rossi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
| | - Rui Ribeiro
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay;
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
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Damre M, Marchetto A, Giorgetti A. MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. Nucleic Acids Res 2020; 47:W456-W461. [PMID: 31106328 PMCID: PMC6602572 DOI: 10.1093/nar/gkz416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 01/06/2023] Open
Abstract
Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories.
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Affiliation(s)
- Mangesh Damre
- Neurobiology, International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy.,Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy
| | - Alessandro Marchetto
- Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy.,Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany
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Ergin G, Lbadaoui-Darvas M, Takahama S. Molecular Structure Inhibiting Synergism in Charged Surfactant Mixtures: An Atomistic Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14093-14104. [PMID: 29160707 DOI: 10.1021/acs.langmuir.7b03346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synergistic and nonsynergistic surfactant-water mixtures of sodium dodecyl sulfate (SDS), lauryl betaine (C12B), and cocoamidopropyl betaine (CAPB) systems are studied using molecular simulation to understand the role of interactions among headgroups, tailgroups, and water on structural and thermodynamic properties at the air-water interface. SDS is an anionic surfactant, while C12B and CAPB are zwitterionic; CAPB differs from C12B by an amide group in the tail. While the lowest surface tensions at high surface concentrations in the SDS-C12B synergistic system could not be reproduced by simulation, estimated partitioning between surface and bulk shows trends consistent with synergism. Structural analysis shows the influence of the SDS headgroup pulling C12B to the surface, resulting in closely packed structures compared to their respective homomolecular-surfactant systems. The SDS-CAPB system, on the other hand, is nonsynergistic when the surfactants are mixed on account of the tilted structure of the CAPB tail. The translational excess entropy due to the tailgroup interactions discriminates between the synergistic and nonsynergistic systems. The implications of such interactions on surfactant effects in complex, multicomponent atmospheric aerosols are discussed.
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Affiliation(s)
- Gözde Ergin
- Atmospheric Particle and Research Laboratory, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Mária Lbadaoui-Darvas
- Atmospheric Particle and Research Laboratory, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Satoshi Takahama
- Atmospheric Particle and Research Laboratory, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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Bhadra P, Pal D. Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield. Comput Biol Med 2017; 83:134-142. [PMID: 28279862 DOI: 10.1016/j.compbiomed.2017.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/18/2017] [Accepted: 02/22/2017] [Indexed: 11/28/2022]
Abstract
Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions.
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Affiliation(s)
- Pratiti Bhadra
- Institute Mathematics Initiative, Indian Institute of Science, Bengaluru 560012, India
| | - Debnath Pal
- Institute Mathematics Initiative, Indian Institute of Science, Bengaluru 560012, India; Computational and Data Sciences, Indian Institute of Science, Bengaluru 560012, India.
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Dehnavi E, Fathi-Roudsari M, Mirzaie S, Arab SS, Ranaei Siadat SO, Khajeh K. Engineering disulfide bonds in Selenomonas ruminantium β-xylosidase by experimental and computational methods. Int J Biol Macromol 2016; 95:248-255. [PMID: 27818293 DOI: 10.1016/j.ijbiomac.2016.10.104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/22/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
Homotetrameric β-xylosidase from Selenomonas ruminantium (SXA) is one of the most efficient enzymes known for the hydrolysis of cell wall hemicellulose. SXA shows a rapid rate of activity loss at temperatures above 50°C. In this study, we have introduced two inter-subunit disulfide bridges with one point mutation. Lys237 was chosen to be replaced with cysteine since it interacts with the same residue in the opposite subunit. While pH optimum, temperature profile and catalytic efficiency of the mutated variant were similar to the native enzyme, the mutated enzyme showed about 40% increase in thermal stability at 55°C. Our results showed that introduction of a single residue mutation in structure of SXA results in appearance of two disulfide bonds at dimer-dimer interface of the enzyme. Coarse-grained molecular dynamics (CG-MD) simulations also proved lower amounts of root mean square fluctuation (RMSF) for position 237 and potential energy for mutated SXA. Based these results, we suggest that choosing a correct residue for mutation in multi subunit proteins results in multiple site conversions which equals to several simultaneous mutations. Furthermore, CG-MD simulation in agreement with experimental methods showed higher thermostability of mutated SXA which proved applicability of this simulation for thermostability analysis.
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Affiliation(s)
- Ehsan Dehnavi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | | | - Sako Mirzaie
- Department of Biochemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Seyed Omid Ranaei Siadat
- Protein Engineering Laboratory, Protein Research Center (PRC), Shahid Beheshti University, GC, Tehran, Iran; Nanobiotechnology Engineering Laboratory, Faculty of Engineering and New Technologies, Shahid Beheshti University, GC, Tehran, Iran.
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
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