401
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Lin S, Zhang J, Strano MS, Blankschtein D. Understanding selective molecular recognition in integrated carbon nanotube-polymer sensors by simulating physical analyte binding on carbon nanotube-polymer scaffolds. SOFT MATTER 2014; 10:5991-6004. [PMID: 24992310 DOI: 10.1039/c4sm00974f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Macromolecular scaffolds made of polymer-wrapped single-walled carbon nanotubes (SWCNTs) have been explored recently (Zhang et al., Nature Nanotechnology, 2013) as a new class of molecular-recognition motifs. However, selective analyte recognition is still challenging and lacks the underlying fundamental understanding needed for its practical implementation in biological sensors. In this report, we combine coarse-grained molecular dynamics (CGMD) simulations, physical adsorption/binding theories, and photoluminescence (PL) experiments to provide molecular insight into the selectivity of such sensors towards a large set of biologically important analytes. We find that the physical binding affinities of the analytes on a bare SWCNT partially correlate with their distribution coefficients in a bulk water/octanol system, suggesting that the analyte hydrophobicity plays a key role in determining the binding affinities of the analytes considered, along with the various specific interactions between the analytes and the polymer anchor groups. Two distinct categories of analytes are identified to demonstrate a complex picture for the correlation between optical sensor signals and the simulated binding affinities. Specifically, a good correlation was found between the sensor signals and the physical binding affinities of the three hormones (estradiol, melatonin, and thyroxine), the neurotransmitter (dopamine), and the vitamin (riboflavin) to the SWCNT-polymer scaffold. The four amino acids (aspartate, glycine, histidine, and tryptophan) and the two monosaccharides (fructose and glucose) considered were identified as blank analytes which are unable to induce sensor signals. The results indicate great success of our physical adsorption-based model in explaining the ranking in sensor selectivities. The combined framework presented here can be used to screen and select polymers that can potentially be used for creating synthetic molecular recognition motifs.
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Affiliation(s)
- Shangchao Lin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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402
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Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field. J Comput Aided Mol Des 2014; 28:1093-107. [DOI: 10.1007/s10822-014-9787-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 08/07/2014] [Indexed: 02/01/2023]
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403
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Flinner N, Mirus O, Schleiff E. The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation. Int J Mol Sci 2014; 15:14247-68. [PMID: 25196522 PMCID: PMC4159849 DOI: 10.3390/ijms150814247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/14/2014] [Accepted: 08/06/2014] [Indexed: 11/17/2022] Open
Abstract
The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA.
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Affiliation(s)
- Nadine Flinner
- Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany.
| | - Oliver Mirus
- Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany.
| | - Enrico Schleiff
- Cluster of Excellence Macromolecular Complexes, Center of Membrane Proteomics, Department of Biosciences, Molecular Cell Biology of Plants, GU Frankfurt am Main, 60439 Frankfurt, Germany.
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404
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Negami T, Shimizu K, Terada T. Coarse-grained molecular dynamics simulations of protein-ligand binding. J Comput Chem 2014; 35:1835-45. [PMID: 25043724 DOI: 10.1002/jcc.23693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/06/2014] [Accepted: 07/09/2014] [Indexed: 01/25/2023]
Abstract
Coarse-grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein-ligand binding processes. We chose two protein-ligand systems, the levansucrase-sugar (glucose or sucrose), and LinB-1,2-dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse-grained (CG) ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase-sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand-binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein-ligand binding processes.
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Affiliation(s)
- Tatsuki Negami
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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405
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Structural and functional characterization of DUF1471 domains of Salmonella proteins SrfN, YdgH/SssB, and YahO. PLoS One 2014; 9:e101787. [PMID: 25010333 PMCID: PMC4092069 DOI: 10.1371/journal.pone.0101787] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/07/2014] [Indexed: 11/20/2022] Open
Abstract
Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed α+β fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.
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406
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Molza AE, Férey N, Czjzek M, Le Rumeur E, Hubert JF, Tek A, Laurent B, Baaden M, Delalande O. Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly. Faraday Discuss 2014; 169:45-62. [PMID: 25340652 DOI: 10.1039/c3fd00134b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
At present, our molecular knowledge of dystrophin, the protein encoded by the DMD gene and mutated in myopathy patients, remains limited. To get around the absence of its atomic structure, we have developed an innovative interactive docking method based on the BioSpring software in combination with Small-angle X-ray Scattering (SAXS) data. BioSpring allows interactive handling of biological macromolecules thanks to an augmented Elastic Network Model (aENM) that combines the spring network with non-bonded terms between atoms or pseudo-atoms. This approach can be used for building molecular assemblies even on a desktop or a laptop computer thanks to code optimizations including parallel computing and GPU programming. By combining atomistic and coarse-grained models, the approach significantly simplifies the set-up of multi-scale scenarios. BioSpring is remarkably efficient for the preparation of numeric simulations or for the design of biomolecular models integrating qualitative experimental data restraints. The combination of this program and SAXS allowed us to propose the first high-resolution models of the filamentous central domain of dystrophin, covering repeats 11 to 17. Low-resolution interactive docking experiments driven by a potential grid enabled us to propose how dystrophin may associate with F-actin and nNOS. This information provides an insight into medically relevant discoveries to come.
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Affiliation(s)
- A-E Molza
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Univ. Rennes 1, Campus Santé, 2 av du Pr Léon Bernard, 35043 Rennes Cedex, France.
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407
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Guixà-González R, Ramírez-Anguita JM, Kaczor AA, Selent J. Simulating G protein-coupled receptors in native-like membranes: from monomers to oligomers. Methods Cell Biol 2014; 117:63-90. [PMID: 24143972 DOI: 10.1016/b978-0-12-408143-7.00004-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
G protein-coupled receptors (GPCRs) are one of the most relevant superfamilies of transmembrane proteins as they participate in an important variety of biological events. Recently, the scientific community is witnessing an advent of a GPCR crystallization age along with impressive improvements achieved in the field of computer simulations during the last two decades. Computer simulation techniques such as molecular dynamics (MD) simulations are now frequent tools to study the dynamic behavior of GPCRs and, more importantly, to model the complex membrane environment where these proteins spend their lifetime. Thanks to these tools, GPCRs can be simulated not only longer but also in a more "physiological" fashion. In this scenario, scientists are taking advantage of such advances to approach certain phenomena such as GPCR oligomerization occurring only at timescales not reachable until now. Thus, despite current MD simulations having important limitations today, they have become an essential tool to study key biophysical properties of GPCRs and GPCR oligomers.
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Affiliation(s)
- Ramon Guixà-González
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra/IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, Barcelona, Spain
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408
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Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:225-248. [PMID: 25309628 PMCID: PMC4171755 DOI: 10.1002/wcms.1169] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
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Affiliation(s)
- Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Cesar A Lopez
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Srinivasa M Gopal
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
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409
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LeBard DN. Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.899700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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410
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Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA. Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers. J Chem Theory Comput 2014; 10:2137-2150. [PMID: 24910542 PMCID: PMC4044725 DOI: 10.1021/ct401028g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond timescales, it is essential to develop accurate coarse-grained simulation models that can reach these timescales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0-40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudo-bond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the "angle-corrected model") slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other CG models in a DOPC/cholesterol simulation series, which further argues for its efficacy and generalizability. These results argue for the importance of systematic optimization for coarse-graining biologically important molecules like cholesterol with complicated molecular structure.
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Affiliation(s)
- Michael D Daily
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Brett N Olsen
- Department of Medicine, Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri
| | - Paul H Schlesinger
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel S Ory
- Department of Medicine, Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri
| | - Nathan A Baker
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington
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411
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Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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412
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Ávila CL, Torres-Bugeau CM, Barbosa LRS, Sales EM, Ouidja MO, Socías SB, Celej MS, Raisman-Vozari R, Papy-Garcia D, Itri R, Chehín RN. Structural characterization of heparin-induced glyceraldehyde-3-phosphate dehydrogenase protofibrils preventing α-synuclein oligomeric species toxicity. J Biol Chem 2014; 289:13838-50. [PMID: 24671416 DOI: 10.1074/jbc.m113.544288] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that has been associated with neurodegenerative diseases. GAPDH colocalizes with α-synuclein in amyloid aggregates in post-mortem tissue of patients with sporadic Parkinson disease and promotes the formation of Lewy body-like inclusions in cell culture. In a previous work, we showed that glycosaminoglycan-induced GAPDH prefibrillar species accelerate the conversion of α-synuclein to fibrils. However, it remains to be determined whether the interplay among glycosaminoglycans, GAPDH, and α-synuclein has a role in pathological states. Here, we demonstrate that the toxic effect exerted by α-synuclein oligomers in dopaminergic cell culture is abolished in the presence of GAPDH prefibrillar species. Structural analysis of prefibrillar GAPDH performed by small angle x-ray scattering showed a particle compatible with a protofibril. This protofibril is shaped as a cylinder 22 nm long and a cross-section diameter of 12 nm. Using biocomputational techniques, we obtained the first all-atom model of the GAPDH protofibril, which was validated by cross-linking coupled to mass spectrometry experiments. Because GAPDH can be secreted outside the cell where glycosaminoglycans are present, it seems plausible that GAPDH protofibrils could be assembled in the extracellular space kidnapping α-synuclein toxic oligomers. Thus, the role of GAPDH protofibrils in neuronal proteostasis must be considered. The data reported here could open alternative ways in the development of therapeutic strategies against synucleinopathies like Parkinson disease.
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Affiliation(s)
- César L Ávila
- From the Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj," FBQF-UNT, Chacabuco 461, T4000ILI Tucumán, Argentina
| | - Clarisa M Torres-Bugeau
- From the Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj," FBQF-UNT, Chacabuco 461, T4000ILI Tucumán, Argentina
| | - Leandro R S Barbosa
- the Instituto de Física da Universidade de São Paulo, Rua do Matão, Travessa R, 187, São Paulo, Brazil
| | - Elisa Morandé Sales
- the Instituto de Física da Universidade de São Paulo, Rua do Matão, Travessa R, 187, São Paulo, Brazil
| | - Mohand O Ouidja
- INSERM U1127, CNRS UMR 7225, Institut de Cerveau et de la Moelle Epinière, Paris, France, the Laboratoire Croissance, Réparation et Régénération Tissulaires, CNRS EAC 7149, Université Paris Est Créteil, Université Paris Est, F-94000, Créteil, France, and
| | - Sergio B Socías
- INSERM U1127, CNRS UMR 7225, Institut de Cerveau et de la Moelle Epinière, Paris, France
| | - M Soledad Celej
- the Departamento de Química Biológica, Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Rita Raisman-Vozari
- INSERM U1127, CNRS UMR 7225, Institut de Cerveau et de la Moelle Epinière, Paris, France
| | - Dulce Papy-Garcia
- the Laboratoire Croissance, Réparation et Régénération Tissulaires, CNRS EAC 7149, Université Paris Est Créteil, Université Paris Est, F-94000, Créteil, France, and
| | - Rosangela Itri
- the Instituto de Física da Universidade de São Paulo, Rua do Matão, Travessa R, 187, São Paulo, Brazil
| | - Rosana N Chehín
- From the Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj," FBQF-UNT, Chacabuco 461, T4000ILI Tucumán, Argentina,
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413
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Bereau T, Wang ZJ, Deserno M. More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization. J Chem Phys 2014; 140:115101. [PMID: 24655203 PMCID: PMC3977883 DOI: 10.1063/1.4867465] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/04/2014] [Indexed: 11/14/2022] Open
Abstract
Interfacial systems are at the core of fascinating phenomena in many disciplines, such as biochemistry, soft-matter physics, and food science. However, the parametrization of accurate, reliable, and consistent coarse-grained (CG) models for systems at interfaces remains a challenging endeavor. In the present work, we explore to what extent two independently developed solvent-free CG models of peptides and lipids--of different mapping schemes, parametrization methods, target functions, and validation criteria--can be combined by only tuning the cross-interactions. Our results show that the cross-parametrization can reproduce a number of structural properties of membrane peptides (for example, tilt and hydrophobic mismatch), in agreement with existing peptide-lipid CG force fields. We find encouraging results for two challenging biophysical problems: (i) membrane pore formation mediated by the cooperative action of several antimicrobial peptides, and (ii) the insertion and folding of the helix-forming peptide WALP23 in the membrane.
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Affiliation(s)
- Tristan Bereau
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Zun-Jing Wang
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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414
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Johnston JM, Filizola M. Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors. PLoS One 2014; 9:e90694. [PMID: 24651466 PMCID: PMC3944890 DOI: 10.1371/journal.pone.0090694] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/05/2014] [Indexed: 11/23/2022] Open
Abstract
The recent mu-opioid receptor (MOPr) and kappa-opioid receptor (KOPr) crystal structures have inspired hypotheses of physiologically relevant dimerization contacts, specifically: a closely packed interface involving transmembrane (TM) helices TM5 and TM6, and a less compact interface, involving TM1, TM2, and helix 8 (H8). While the former was only found in MOPr crystals, similar arrangements of the latter were identified for both KOPr and MOPr. The relevance of these interfaces outside of a crystal lattice is called into question by the possibility that they might be influenced by the specific crystallization conditions. In this study, we have employed umbrella sampling molecular dynamics simulations of coarse-grained representations of the interacting MOPr or KOPr crystallographic structures, in the absence of the T4 lysozyme, and in an explicit lipid-water environment, to determine the strength of receptor dimerization at the different crystallographic interfaces. We note that the shape of the interface plays a dominant role in the strength of the interaction, and the pattern of contacting residues defines the shape of the potential of mean force. This information can be used to guide experiments aimed at exploring the role of dimerization in opioid receptor function.
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MESH Headings
- Animals
- Computer Simulation
- Crystallography, X-Ray
- Humans
- Mice
- Models, Molecular
- Protein Binding
- Protein Multimerization
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, Opioid, kappa/chemistry
- Receptors, Opioid, kappa/metabolism
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/metabolism
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Affiliation(s)
- Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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415
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Johner N, Mondal S, Morra G, Caffrey M, Weinstein H, Khelashvili G. Protein and lipid interactions driving molecular mechanisms of in meso crystallization. J Am Chem Soc 2014; 136:3271-84. [PMID: 24494670 PMCID: PMC3985912 DOI: 10.1021/ja4129839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recent advances in the in meso crystallization technique for the structural characterization of G-protein coupled receptor (GPCR) proteins have established the usefulness of the lipidic-cubic phases (LCPs) in the field of crystallography of membrane proteins. It is surprising that despite the success of the approach, the molecular mechanisms of the in meso method are still not well understood. Therefore, the approach must rely on extensive screening for a suitable protein construct, for host and additive lipids, and for the appropriate precipitants and temperature. To shed light on the in meso crystallization mechanisms, we used extensive coarse-grained molecular dynamics simulations to study, in molecular detail, LCPs under different conditions (compositions and temperatures relevant to crystallogenesis) and their interactions with different types of GPCR constructs. The results presented show how the modulation of the lattice constant of the LCP (triggered by the addition of precipitant during the in meso assay), or of the host lipid type, can destabilize monomeric proteins in the bilayer of the LCP and thus drive their aggregation into the stacked lamellae, where the residual hydrophobic mismatch between the protein and the membrane can drive the formation of lateral contacts leading to nucleation and crystal growth. Moreover, we demonstrate how particular protein designs (such as transmembrane proteins engineered to contain large polar regions) can promote protein stacking interactions in the third, out-of-plane, dimension. The insights provided by the new aspects of the specific molecular mechanisms responsible for protein-protein interactions inside the cubic phase presented here should be helpful in guiding the rational design of future in meso trials with successful outcomes.
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Affiliation(s)
- Niklaus Johner
- Weill Cornell Medical College of Cornell University , New York, New York, 10065, United States
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416
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Shen H, Li Y, Ren P, Zhang D, Li G. An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials. J Chem Theory Comput 2014; 10:731-750. [PMID: 24659927 PMCID: PMC3958967 DOI: 10.1021/ct400974z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Gay–Berne
anisotropic potential has been widely used to
evaluate the nonbonded interactions between coarse-grained particles
being described as elliptical rigid bodies. In this paper, we are
presenting a coarse-grained model for twenty kinds of amino acids
and proteins, based on the anisotropic Gay–Berne and point
electric multipole (EMP) potentials. We demonstrate that the anisotropic
coarse-grained model, namely GBEMP model, is able to reproduce many
key features observed from experimental protein structures (Dunbrack
Library), as well as from atomistic force field simulations (using
AMOEBA, AMBER, and CHARMM force fields), while saving the computational
cost by a factor of about 10–200 depending on specific cases
and atomistic models. More importantly, unlike other coarse-grained
approaches, our framework is based on the fundamental intermolecular
forces with explicit treatment of electrostatic and repulsion-dispersion
forces. As a result, the coarse-grained protein model presented an
accurate description of nonbonded interactions (particularly electrostatic
component) between hetero/homodimers (such as peptide–peptide,
peptide–water). In addition, the encouraging performance of
the model was reflected by the excellent correlation between GBEMP
and AMOEBA models in the calculations of the dipole moment of peptides.
In brief, the GBEMP model given here is general and transferable,
suitable for simulating complex biomolecular systems.
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Affiliation(s)
- Hujun Shen
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China
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417
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Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. J Chem Theory Comput 2014; 10:676-90. [PMID: 26580045 DOI: 10.1021/ct400617g] [Citation(s) in RCA: 454] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations. For this process, called backmapping or reverse transformation, several tools are available, but these commonly require libraries of molecule fragments or they are linked to a specific software package. In addition, the methods are usually restricted to specific molecules and to a specific force field. Here, we present an alternative method, consisting of geometric projection and subsequent force-field based relaxation. This method is designed to be simple and flexible, and offers a generic solution for resolution transformation. For simple systems, the conversion only requires a list of particle correspondences on the two levels of resolution. For special cases, such as nondefault protonation states of amino acids and virtual sites, a target particle list can be specified. The mapping uses simple building blocks, which list the particles on the different levels of resolution. For conversion to higher resolution, the initial model is relaxed with several short cycles of energy minimization and position-restrained MD. The reconstruction of an atomistic backbone from a coarse-grained model is done using a new dedicated algorithm. The method is generic and can be used to map between any two particle based representations, provided that a mapping can be written. The focus of this work is on the coarse-grained MARTINI force field, for which mapping definitions are written to allow conversion to and from the higher-resolution force fields GROMOS, CHARMM, and AMBER, and to and from a simplified three-bead lipid model. Together, these offer the possibility to simulate mesoscopic membrane structures, to be transformed to MARTINI and subsequently to an atomistic model for investigation of detailed interactions. The method was tested on a set of systems ranging from a simple, single-component bilayer to a large protein-membrane-solvent complex. The results demonstrate the efficiency and the efficacy of the new approach.
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Affiliation(s)
- Tsjerk A Wassenaar
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW , Calgary, Alberta, Canada T2N 1N4.,Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Computational Biology, Department of Biology, University of Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW , Calgary, Alberta, Canada T2N 1N4
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418
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Horn JN, Kao TC, Grossfield A. Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:75-94. [PMID: 24158802 DOI: 10.1007/978-94-007-7423-0_5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein function is a complicated interplay between structure and dynamics, which can be heavily influenced by environmental factors and conditions. This is particularly true in the case of membrane proteins, such as the visual receptor rhodopsin. It has been well documented that lipid headgroups, polyunsaturated tails, and the concentration of cholesterol in membranes all play a role in the function of rhodopsin. Recently, we used all-atom simulations to demonstrate that different lipid species have preferential interactions and possible binding sites on rhodopsin's surface, consistent with experiment. However, the limited timescales of the simulations meant that the statistical uncertainty of these results was substantial. Accordingly, we present here 32 independent 1.6 μs coarse-grained simulations exploring lipids and cholesterols surrounding rhodopsin and opsin, in lipid bilayers mimicking those found naturally. Our results agree with those found experimentally and in previous simulations, but with far better statistical certainty. The results demonstrate the value of combining all-atom and coarse-grained models with experiment to provide a well-rounded view of lipid-protein interactions.
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Affiliation(s)
- Joshua N Horn
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, 712, Rochester, NY, 14642, USA
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419
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Johnston JM, Filizola M. Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:95-125. [PMID: 24158803 PMCID: PMC4074508 DOI: 10.1007/978-94-007-7423-0_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field.
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Affiliation(s)
- Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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420
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Hills RD. Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics. Methods Mol Biol 2014; 1084:123-140. [PMID: 24061919 DOI: 10.1007/978-1-62703-658-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Characterization of the protein conformational landscape remains a challenging problem, whether it concerns elucidating folding mechanisms, predicting native structures or modeling functional transitions. Coarse-grained molecular dynamics simulation methods enable exhaustive sampling of the energetic landscape at resolutions of biological interest. The general utility of structure-based models is reviewed along with their differing levels of approximation. Simple Gō models incorporate attractive native interactions and repulsive nonnative contacts, resulting in an ideal smooth landscape. Non-Gō coarse-grained models reduce the parameter set as needed but do not include bias to any desired native structure. While non-Gō models have achieved limited success in protein coarse-graining, they can be combined with native structured-based potentials to create a balanced and powerful force field. Recent applications of such Gō-like models have yielded insight into complex folding mechanisms and conformational transitions in large macromolecules. The accuracy and usefulness of reduced representations are also revealed to be a function of the mathematical treatment of the intrinsic bonded topology.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, University of New England, Portland, ME, USA
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421
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Loison C, Nasir MN, Benichou E, Besson F, Brevet PF. Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation. Phys Chem Chem Phys 2014; 16:2136-48. [DOI: 10.1039/c3cp53101e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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422
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Bacteriocin AS-48 binding to model membranes and pore formation as revealed by coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2524-31. [DOI: 10.1016/j.bbamem.2013.05.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 05/24/2013] [Accepted: 05/31/2013] [Indexed: 02/05/2023]
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423
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Siuda I, Thøgersen L. Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. J Mol Model 2013; 19:4931-45. [DOI: 10.1007/s00894-013-1991-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/29/2013] [Indexed: 11/24/2022]
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424
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Chen WW, Yoon YJ, Leong SSJ, Kwak SK. Dimers of human β-defensins and their interactions with the POPG membrane. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.773433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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425
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Stark AC, Andrews CT, Elcock AH. Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field. J Chem Theory Comput 2013; 9. [PMID: 24223529 DOI: 10.1021/ct400008p] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.
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Affiliation(s)
- Austin C Stark
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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426
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Lloris-Garcerá P, Slusky JSG, Seppälä S, Prieß M, Schäfer LV, von Heijne G. In vivo trp scanning of the small multidrug resistance protein EmrE confirms 3D structure models'. J Mol Biol 2013; 425:4642-51. [PMID: 23920359 DOI: 10.1016/j.jmb.2013.07.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/10/2013] [Accepted: 07/28/2013] [Indexed: 11/28/2022]
Abstract
The quaternary structure of the homodimeric small multidrug resistance protein EmrE has been studied intensely over the past decade. Structural models derived from both two- and three-dimensional crystals show EmrE as an anti-parallel homodimer. However, the resolution of the structures is rather low and their relevance for the in vivo situation has been questioned. Here, we have challenged the available structural models by a comprehensive in vivo Trp scanning of all four transmembrane helices in EmrE. The results are in close agreement with the degree of lipid exposure of individual residues predicted from coarse-grained molecular dynamics simulations of the anti-parallel dimeric structure obtained by X-ray crystallography, strongly suggesting that the X-ray structure provides a good representation of the active in vivo form of EmrE.
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Affiliation(s)
- Pilar Lloris-Garcerá
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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427
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Li H, Gorfe AA. Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field. PLoS One 2013; 8:e71018. [PMID: 23923044 PMCID: PMC3724741 DOI: 10.1371/journal.pone.0071018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/28/2013] [Indexed: 11/25/2022] Open
Abstract
Lipid-anchored Ras oncoproteins assemble into transient, nano-sized substructures on the plasma membrane. These substructures, called nanoclusters, were proposed to be crucial for high-fidelity signal transmission in cells. However, the molecular basis of Ras nanoclustering is poorly understood. In this work, we used coarse-grained (CG) molecular dynamics simulations to investigate the molecular mechanism by which full-length H-ras proteins form nanoclusters in a model membrane. We chose two different conformations of H-ras that were proposed to represent the active and inactive state of the protein, and a domain-forming model bilayer made up of di16:0-PC (DPPC), di18:2-PC (DLiPC) and cholesterol. We found that, irrespective of the initial conformation, Ras molecules assembled into a single large aggregate. However, the two binding modes, which are characterized by the different orientation of the G-domain with respect to the membrane, differ in dynamics and organization during and after aggregation. Some of these differences involve regions of Ras that are important for effector/modulator binding, which may partly explain observed differences in the ability of active and inactive H-ras nanoclusters to recruit effectors. The simulations also revealed some limitations in the CG force field to study protein assembly in solution, which we discuss in the context of proposed potential avenues of improvement.
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Affiliation(s)
- Hualin Li
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, United States of America
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, United States of America
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428
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Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA. Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. PLoS Comput Biol 2013; 9:e1003156. [PMID: 23935474 PMCID: PMC3723492 DOI: 10.1371/journal.pcbi.1003156] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 06/11/2013] [Indexed: 01/19/2023] Open
Abstract
Group VI Ca²⁺-independent phospholipase A₂ (iPLA₂) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear pharmaceutical relevance, no X-ray or NMR structural information is currently available for the iPLA₂ or its membrane complex. In this paper, we combine homology modeling with coarse-grained (CG) and all-atom (AA) molecular dynamics (MD) simulations to build structural models of iPLA₂ in association with a phospholipid bilayer. CG-MD simulations of the membrane insertion process were employed to provide a starting point for an atomistic description. Six AA-MD simulations were then conducted for 60 ns, starting from different initial CG structures, to refine the membrane complex. The resulting structures are shown to be consistent with each other and with deuterium exchange mass spectrometry (DXMS) experiments, suggesting that our approach is suitable for the modeling of iPLA₂ at the membrane surface. The models show that an anchoring region (residues 710-724) forms an amphipathic helix that is stabilized by the membrane. In future studies, the proposed iPLA₂ models should provide a structural basis for understanding the mechanisms of lipid extraction and drug-inhibition. In addition, the dual-resolution approach discussed here should provide the means for the future exploration of the impact of lipid diversity and sequence mutations on the activity of iPLA₂ and related enzymes.
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Affiliation(s)
- Denis Bucher
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America.
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429
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Bulacu M, Goga N, Zhao W, Rossi G, Monticelli L, Periole X, Tieleman DP, Marrink SJ. Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations. J Chem Theory Comput 2013; 9:3282-92. [DOI: 10.1021/ct400219n] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monica Bulacu
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Nicolae Goga
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
- FILS, Politechnica University of Bucharest, Splaiul Independentei 313,
Bucharest, Romania
| | - Wei Zhao
- Department
of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
T2N 1N4
| | | | - Luca Monticelli
- INSERM, UMR-S665, Paris, F-75015, France, and
- INTS, Paris, France
| | - Xavier Periole
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
- Department
of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
T2N 1N4
| | - D. Peter Tieleman
- Department
of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
T2N 1N4
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
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430
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Abstract
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.
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Affiliation(s)
- Ryan Bradley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-215-898-0487; Fax: +1-215-573-2071
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431
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Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex. PLoS One 2013; 8:e66935. [PMID: 23776704 PMCID: PMC3680412 DOI: 10.1371/journal.pone.0066935] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/13/2013] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1) in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154) of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137) in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.
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432
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Dony N, Crowet JM, Joris B, Brasseur R, Lins L. SAHBNET, an accessible surface-based elastic network: an application to membrane protein. Int J Mol Sci 2013; 14:11510-26. [PMID: 23722660 PMCID: PMC3709745 DOI: 10.3390/ijms140611510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/02/2013] [Accepted: 05/20/2013] [Indexed: 11/06/2022] Open
Abstract
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins.
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Affiliation(s)
- Nicolas Dony
- Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium; E-Mails: (N.D.); (B.J.)
| | - Jean Marc Crowet
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
| | - Bernard Joris
- Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium; E-Mails: (N.D.); (B.J.)
| | - Robert Brasseur
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
| | - Laurence Lins
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +32-81-622-521; Fax: +32-81-622-522
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433
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Affiliation(s)
- Marissa G. Saunders
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637;
| | - Gregory A. Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637;
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434
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Globisch C, Krishnamani V, Deserno M, Peter C. Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation. PLoS One 2013; 8:e60582. [PMID: 23613730 PMCID: PMC3628857 DOI: 10.1371/journal.pone.0060582] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable.
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Affiliation(s)
| | - Venkatramanan Krishnamani
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Christine Peter
- Max Planck Institute for Polymer Research (MPIP), Mainz, Germany
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435
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Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations. PLoS Comput Biol 2013; 9:e1003034. [PMID: 23592976 PMCID: PMC3623702 DOI: 10.1371/journal.pcbi.1003034] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 03/03/2013] [Indexed: 11/19/2022] Open
Abstract
The association of hemagglutinin (HA) with lipid rafts in the plasma membrane is an important feature of the assembly process of influenza virus A. Lipid rafts are thought to be small, fluctuating patches of membrane enriched in saturated phospholipids, sphingolipids, cholesterol and certain types of protein. However, raft-associating transmembrane (TM) proteins generally partition into Ld domains in model membranes, which are enriched in unsaturated lipids and depleted in saturated lipids and cholesterol. The reason for this apparent disparity in behavior is unclear, but model membranes differ from the plasma membrane in a number of ways. In particular, the higher protein concentration in the plasma membrane may influence the partitioning of membrane proteins for rafts. To investigate the effect of high local protein concentration, we have conducted coarse-grained molecular dynamics (CG MD) simulations of HA clusters in domain-forming bilayers. During the simulations, we observed a continuous increase in the proportion of raft-type lipids (saturated phospholipids and cholesterol) within the area of membrane spanned by the protein cluster. Lateral diffusion of unsaturated lipids was significantly attenuated within the cluster, while saturated lipids were relatively unaffected. On this basis, we suggest a possible explanation for the change in lipid distribution, namely that steric crowding by the slow-diffusing proteins increases the chemical potential for unsaturated lipids within the cluster region. We therefore suggest that a local aggregation of HA can be sufficient to drive association of the protein with raft-type lipids. This may also represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes. The cell membrane is composed of a wide variety of lipids and proteins. Until recently, these were thought to be mixed evenly, but we now have evidence of the existence of “lipid rafts” — small, slow-moving areas of membrane in which certain types of lipid and protein accumulate. Rafts have many important biological functions in healthy cells, but also play a role in the assembly of influenza virus. For example, after the viral protein hemagglutinin is made inside the host cell, it accumulates in rafts. Exiting virus particles then take these portions of cell membrane with them as they leave the host cell. However, the mechanism by which proteins associate with lipid rafts is unclear. Here, we have used computers to simulate lipid membranes containing hemagglutinin. The simulations allow us to look in detail at the motions and interactions of individual proteins and lipids. We found that clusters of proteins altered the properties of nearby lipids, leading to accumulation of raft-type lipids. It therefore appears that aggregation of hemagglutinin may be enough to drive its association with rafts. This helps us to better understand both the influenza assembly process and the properties of lipid rafts.
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436
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Arnarez C, Mazat JP, Elezgaray J, Marrink SJ, Periole X. Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1. J Am Chem Soc 2013; 135:3112-20. [PMID: 23363024 DOI: 10.1021/ja310577u] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The respiratory chain is located in the inner membrane of mitochondria and produces the major part of the ATP used by a cell. Cardiolipin (CL), a double charged phospholipid composing ~10-20% of the mitochondrial membrane, plays an important role in the function and supramolecular organization of the respiratory chain complexes. We present an extensive set of coarse-grain molecular dynamics (CGMD) simulations aiming at the determination of the preferential interfaces of CLs on the respiratory chain complex III (cytochrome bc(1), CIII). Six CL binding sites are identified, including the CL binding sites known from earlier structural studies and buried into protein cavities. The simulations revealed the importance of two subunits of CIII (G and K in bovine heart) for the structural integrity of these internal CL binding sites. In addition, new binding sites are found on the membrane-exposed protein surface. The reproducibility of these binding sites over two species (bovine heart and yeast mitochondria) points to an important role for the function of the respiratory chain. Interestingly the membrane-exposed CL binding sites are located on the matrix side of CIII in the inner membrane and thus may provide localized sources of proton ready for uptake by CIII. Furthermore, we found that CLs bound to those membrane-exposed sites bridge the proteins during their assembly into supercomplexes by sharing the binding sites.
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Affiliation(s)
- Clement Arnarez
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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437
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Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Sci Rep 2013; 3:1263. [PMID: 23405277 PMCID: PMC3570132 DOI: 10.1038/srep01263] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/07/2013] [Indexed: 01/01/2023] Open
Abstract
The respiratory chain or oxidative phosphorylation system (OxPhos) generates most of the
chemical energy (ATP) used by our cells. The cytochrome c oxidase (CcO) is one of three
protein complexes of OxPhos building up a proton gradient across the inner mitochondrial
membrane, which is ultimately used by the ATP synthase to produce ATP. We present molecular
dynamic simulations of CcO in a mimic of the mitochondrial membrane, and identify precise
binding sites of cardiolipin (CL, signature phospholipid of mitochondria) on the protein
surface. Two of these CL binding sites reveal pathways linking CLs to the entrance of the D
and H proton channels across CcO. CLs being able to carry protons our results strongly
support an involvement of CLs in the proton delivery machinery to CcO. The ubiquitous nature
of CL interactions with the components of the OxPhos suggests that this delivery mechanism
might extend to the other respiratory complexes.
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438
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Abstract
This chapter provides a primer on theories for coarse-grained (CG) modeling and, in particular, reviews several systematic methods for determining effective potentials for CG models. The chapter first reviews a statistical mechanics framework for relating atomistic and CG models. This framework naturally leads to a quantitative criterion for CG models that are "consistent" with a particular atomistic model for the same system. This consistency criterion is equivalent to minimizing the relative entropy between the two models. This criterion implies that a many-body PMF is the appropriate potential for a CG model that is consistent with a particular atomistic model. This chapter then presents a unified exposition of the theory and numerical methods for several approaches for approximating this many-body PMF. Finally, this chapter closes with a brief discussion of a few of the outstanding challenges facing the field of systematic coarse-graining.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
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439
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440
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Abstract
The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. In this chapter the methodology underlying the force field is presented together with details of its parameterization and limitations. Then currently available topologies are described with a short overview of the key elements of their parameterization. These include the new polarizable Martini water model. A set of three selected ongoing studies using the Martini force field is presented. Finally the latest lines of development are discussed.
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441
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de Jong DH, Lopez CA, Marrink SJ. Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Faraday Discuss 2013; 161:347-63; discussion 419-59. [DOI: 10.1039/c2fd20086d] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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442
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Abstract
The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.
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Affiliation(s)
- Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
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443
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Basdevant N, Borgis D, Ha-Duong T. Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION. J Chem Theory Comput 2012; 9:803-13. [PMID: 26589072 DOI: 10.1021/ct300943w] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present here the SCORPION-Solvated COaRse-grained Protein interactION-force field, a physics-based simplified coarse-grained (CG) force field. It combines our previous CG protein model and a novel particle-based water model which makes it suitable for Molecular Dynamics (MD) simulations of protein association processes. The protein model in SCORPION represents each amino acid with one to three beads, for which electrostatic and van der Waals effective interactions are fitted separately to reproduce those of the all-atom AMBER force field. The protein internal flexibility is accounted for by an elastic network model (ENM). We now include in SCORPION a new Polarizable Coarse-Grained Solvent (PCGS) model, which is computationally efficient, consistent with the protein CG representation, and yields accurate electrostatic free energies of proteins. SCORPION is used here for the first time to perform hundreds-of-nanoseconds-long MD simulations of protein/protein recognition in water, here the case of the barnase/barstar complex. These MD simulations showed that, for five of a total of seven simulations starting from several initial conformations, and after a time going from 1 to 500 ns, the proteins bind in a conformation very close to the native bound structure and remain stable in this conformation for the rest of the simulation. An energetic analysis of these MD show that this recognition is driven both by van der Waals and electrostatic interactions between proteins. SCORPION appears therefore as a useful tool to study protein-protein recognition in a solvated environment.
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Affiliation(s)
- Nathalie Basdevant
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS-UEVE-CEA, Université d'Evry-Val-d'Essonne, Bd François Mitterrand, 91025 Evry Cedex, France
| | - Daniel Borgis
- Ecole Normale Supérieure, Département de Chimie, UMR 8640 CNRS-ENS-UPMC, 24 rue Lhomond, 75005 Paris, France
| | - Tap Ha-Duong
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS-UEVE-CEA, Université d'Evry-Val-d'Essonne, Bd François Mitterrand, 91025 Evry Cedex, France
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444
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Sengupta D. Cholesterol Modulates the Structure, Binding Modes, and Energetics of Caveolin–Membrane Interactions. J Phys Chem B 2012. [DOI: 10.1021/jp3077886] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Durba Sengupta
- National Chemical
Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha
Road, Pune 411008, India
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445
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Shen H, Moustafa IM, Cameron CE, Colina CM. Exploring the dynamics of four RNA-dependent RNA polymerases by a coarse-grained model. J Phys Chem B 2012; 116:14515-24. [PMID: 23157550 DOI: 10.1021/jp302709v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this article, we present a hybrid ENM/MARTINI coarse-grained model and examine the impact of reduced chemical detail on both static and dynamic properties by comparing against explicit atomistic simulations. This methodology complements the advanced molecular characterization and dynamics of proteins for medical and bioengineering applications by developing a fundamental understanding of how the motion and molecular characteristics of proteins, viruses, their precursors, and their interactions with the environment govern their behavior in different populations. As an example, we explore the dynamics of RNA-dependent RNA polymerases (RdRPs) from the following viruses: poliovirus, Coxsackie virus B3, human rhinovirus 16, and foot-and-mouth-disease virus. The hybrid coarse-grained model allows the microsecond time scales of interest for biological functions to be explored. Additionally, the ENM/MARTINI model captures the main features obtained from atomistic MD simulations for each of the RdRPs studied herein, including the higher flexibility of the pinky finger and thumb regions, as well as collective motions that might contribute significantly to the conformational transition between the open and closed states.
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Affiliation(s)
- Hujun Shen
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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446
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de Jong DH, Singh G, Bennett WFD, Arnarez C, Wassenaar TA, Schäfer LV, Periole X, Tieleman DP, Marrink SJ. Improved Parameters for the Martini Coarse-Grained Protein Force Field. J Chem Theory Comput 2012; 9:687-97. [DOI: 10.1021/ct300646g] [Citation(s) in RCA: 922] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Djurre H. de Jong
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Gurpreet Singh
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary,
2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4
| | - W. F. Drew Bennett
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary,
2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4
| | - Clement Arnarez
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tsjerk A. Wassenaar
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lars V. Schäfer
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary,
2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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447
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Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B. A tightly regulated molecular toggle controls AAA+ disaggregase. Nat Struct Mol Biol 2012; 19:1338-46. [PMID: 23160353 DOI: 10.1038/nsmb.2441] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/15/2012] [Indexed: 01/22/2023]
Abstract
The ring-forming AAA+ protein ClpB cooperates with the DnaK chaperone system to refold aggregated proteins in Escherichia coli. The M domain, a ClpB-specific coiled-coil structure with two wings, motif 1 and motif 2, is essential to disaggregation, but the positioning and mechanistic role of M domains in ClpB hexamers remain unresolved. We show that M domains nestle at the ClpB ring surface, with both M-domain motifs contacting the first ATPase domain (AAA-1). Both wings contribute to maintaining a repressed ClpB activity state. Motif 2 docks intramolecularly to AAA-1 to regulate ClpB unfolding power, and motif 1 contacts a neighboring AAA-1 domain. Mutations that stabilize motif 2 docking repress ClpB, whereas destabilization leads to derepressed ClpB activity with greater unfolding power that is toxic in vivo. Our results underline the vital nature of tight ClpB activity control and elucidate a regulated M-domain toggle control mechanism.
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Affiliation(s)
- Yuki Oguchi
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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448
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Pleskot R, Pejchar P, Žárský V, Staiger CJ, Potocký M. Structural insights into the inhibition of actin-capping protein by interactions with phosphatidic acid and phosphatidylinositol (4,5)-bisphosphate. PLoS Comput Biol 2012; 8:e1002765. [PMID: 23133367 PMCID: PMC3486809 DOI: 10.1371/journal.pcbi.1002765] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/19/2012] [Indexed: 11/19/2022] Open
Abstract
The actin cytoskeleton is a dynamic structure that coordinates numerous fundamental processes in eukaryotic cells. Dozens of actin-binding proteins are known to be involved in the regulation of actin filament organization or turnover and many of these are stimulus-response regulators of phospholipid signaling. One of these proteins is the heterodimeric actin-capping protein (CP) which binds the barbed end of actin filaments with high affinity and inhibits both addition and loss of actin monomers at this end. The ability of CP to bind filaments is regulated by signaling phospholipids, which inhibit the activity of CP; however, the exact mechanism of this regulation and the residues on CP responsible for lipid interactions is not fully resolved. Here, we focus on the interaction of CP with two signaling phospholipids, phosphatidic acid (PA) and phosphatidylinositol (4,5)-bisphosphate (PIP(2)). Using different methods of computational biology such as homology modeling, molecular docking and coarse-grained molecular dynamics, we uncovered specific modes of high affinity interaction between membranes containing PA/phosphatidylcholine (PC) and plant CP, as well as between PIP(2)/PC and animal CP. In particular, we identified differences in the binding of membrane lipids by animal and plant CP, explaining previously published experimental results. Furthermore, we pinpoint the critical importance of the C-terminal part of plant CPα subunit for CP-membrane interactions. We prepared a GST-fusion protein for the C-terminal domain of plant α subunit and verified this hypothesis with lipid-binding assays in vitro.
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Affiliation(s)
- Roman Pleskot
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Přemysl Pejchar
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Viktor Žárský
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Department of Plant Physiology, Charles University in Prague, Prague, Czech Republic
| | - Christopher J. Staiger
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Martin Potocký
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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449
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Johnston JM, Wang H, Provasi D, Filizola M. Assessing the relative stability of dimer interfaces in g protein-coupled receptors. PLoS Comput Biol 2012; 8:e1002649. [PMID: 22916005 PMCID: PMC3420924 DOI: 10.1371/journal.pcbi.1002649] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors (GPCRs) associate in the plasma membrane to form homo- and/or heteromers. Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debate. Motivated by experimental data suggesting differing stabilities for homomers of the cognate human β1- and β2-adrenergic receptors, we have carried out approximately 160 microseconds of biased molecular dynamics simulations to calculate the dimerization free energy of crystal structure-based models of these receptors, interacting at two interfaces that have often been implicated in GPCR association under physiological conditions. Specifically, results are presented for simulations of coarse-grained (MARTINI-based) and atomistic representations of each receptor, in homodimeric configurations with either transmembrane helices TM1/H8 or TM4/3 at the interface, in an explicit lipid bilayer. Our results support a definite contribution to the relative stability of GPCR dimers from both interface sequence and configuration. We conclude that β1- and β2-adrenergic receptor homodimers with TM1/H8 at the interface are more stable than those involving TM4/3, and that this might be reconciled with experimental studies by considering a model of oligomerization in which more stable TM1 homodimers diffuse through the membrane, transiently interacting with other protomers at interfaces involving other TM helices.
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Affiliation(s)
| | | | | | - Marta Filizola
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail:
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450
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Reddy T, Rainey JK. Multifaceted Substrate Capture Scheme of a Rhomboid Protease. J Phys Chem B 2012; 116:8942-54. [DOI: 10.1021/jp305077k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tyler Reddy
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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