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Visscher KM, Vosmeer CR, Luirink RA, Geerke DP. A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols. J Comput Chem 2018; 38:508-517. [PMID: 28133840 DOI: 10.1002/jcc.24702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/24/2016] [Accepted: 11/14/2016] [Indexed: 11/05/2022]
Abstract
In this work, parameters are optimized for a charge-on-spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico-chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed-phase polarizabilities, and starting from the non-polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure-liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure-liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen-bonding and non-hydrogen-bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Koen M Visscher
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
| | - C Ruben Vosmeer
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
| | - Rosa A Luirink
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, HZ, Amsterdam, the Netherlands
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Vosmeer CR, Kooi DP, Capoferri L, Terpstra MM, Vermeulen NPE, Geerke DP. Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions. J Mol Model 2016; 22:31. [PMID: 26757914 PMCID: PMC4710667 DOI: 10.1007/s00894-015-2883-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/29/2015] [Indexed: 11/24/2022]
Abstract
Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly.
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Affiliation(s)
- C Ruben Vosmeer
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Derk P Kooi
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Luigi Capoferri
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Margreet M Terpstra
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Nico P E Vermeulen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands.
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Vosmeer CR, Kiewisch K, Keijzer K, Visscher L, Geerke DP. A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities. Phys Chem Chem Phys 2015; 16:17857-62. [PMID: 25042275 DOI: 10.1039/c4cp02401j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the solvent molecules when evaluating atomic polarizabilities of a methanol solute. In a first step, we show that solute polarizabilities are not significantly affected upon substantially increasing the MM dipole moments towards values that are typically reported in literature for water solvent molecules. Subsequently, solute polarization is evaluated in the presence of a QM described solvent (using the frozen-density embedding method). In the latter case, lower oxygen polarizabilities were obtained than when using MM point charges to describe the solvent, due to introduction of Pauli-repulsion effects.
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Affiliation(s)
- C Ruben Vosmeer
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands.
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Maiwald S, Sivapalaratnam S, Motazacker MM, van Capelleveen JC, Bot I, de Jager SC, van Eck M, Jolley J, Kuiper J, Stephens J, Albers CA, Vosmeer CR, Kruize H, Geerke DP, van der Wal AC, van der Loos CM, Kastelein JJP, Trip MD, Ouwehand WH, Dallinga-Thie GM, Hovingh GK. Mutation in KERA identified by linkage analysis and targeted resequencing in a pedigree with premature atherosclerosis. PLoS One 2014; 9:e98289. [PMID: 24879339 PMCID: PMC4039470 DOI: 10.1371/journal.pone.0098289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/30/2014] [Indexed: 01/29/2023] Open
Abstract
AIMS Genetic factors explain a proportion of the inter-individual variation in the risk for atherosclerotic events, but the genetic basis of atherosclerosis and atherothrombosis in families with Mendelian forms of premature atherosclerosis is incompletely understood. We set out to unravel the molecular pathology in a large kindred with an autosomal dominant inherited form of premature atherosclerosis. METHODS AND RESULTS Parametric linkage analysis was performed in a pedigree comprising 4 generations, of which a total of 11 members suffered from premature vascular events. A parametric LOD-score of 3.31 was observed for a 4.4 Mb interval on chromosome 12. Upon sequencing, a non-synonymous variant in KERA (c.920C>G; p.Ser307Cys) was identified. The variant was absent from nearly 28,000 individuals, including 2,571 patients with premature atherosclerosis. KERA, a proteoglycan protein, was expressed in lipid-rich areas of human atherosclerotic lesions, but not in healthy arterial specimens. Moreover, KERA expression in plaques was significantly associated with plaque size in a carotid-collar Apoe-/- mice (r2 = 0.69; p<0.0001). CONCLUSION A rare variant in KERA was identified in a large kindred with premature atherosclerosis. The identification of KERA in atherosclerotic plaque specimen in humans and mice lends support to its potential role in atherosclerosis.
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Affiliation(s)
- Stephanie Maiwald
- Department of Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
| | | | - Mahdi M. Motazacker
- Department of Experimental Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
| | | | - Ilze Bot
- Division of Biopharmaceutics, Leiden/Amsterdam Centre for Drug Research, Leiden, the Netherlands
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Saskia C. de Jager
- Division of Biopharmaceutics, Leiden/Amsterdam Centre for Drug Research, Leiden, the Netherlands
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Miranda van Eck
- Division of Biopharmaceutics, Leiden/Amsterdam Centre for Drug Research, Leiden, the Netherlands
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Jennifer Jolley
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Johan Kuiper
- Division of Biopharmaceutics, Leiden/Amsterdam Centre for Drug Research, Leiden, the Netherlands
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Jonathon Stephens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Cornelius A. Albers
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - C. Ruben Vosmeer
- Amsterdam Institute of Molecules, Medicines and Systems, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, Amsterdam, the Netherlands
| | - Heleen Kruize
- Amsterdam Institute of Molecules, Medicines and Systems, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, Amsterdam, the Netherlands
| | - Daan P. Geerke
- Amsterdam Institute of Molecules, Medicines and Systems, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, Amsterdam, the Netherlands
| | | | | | - John J. P. Kastelein
- Department of Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
| | - Mieke D. Trip
- Department of Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Geesje M. Dallinga-Thie
- Department of Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
| | - G. Kees Hovingh
- Department of Vascular Medicine, Academic Medical Centre, Amsterdam, the Netherlands
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Vosmeer CR, Rustenburg AS, Rice JE, Horn HW, Swope WC, Geerke DP. QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation. J Chem Theory Comput 2012; 8:3839-53. [PMID: 26593025 DOI: 10.1021/ct300085z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Accounting for electronic polarization effects in biomolecular simulation (by using a polarizable force field) can increase the accuracy of simulation results. However, the use of gas-phase estimates of atomic polarizabilities αi usually leads to overpolarization in condensed-phase systems. In the current work, a combined QM/MM approach has been employed to obtain condensed-phase estimates of atomic polarizabilities for water and methanol (QM) solutes in the presence of (MM) solvents of different polarity. In a next step, the validity of the linear response and isotropy assumptions were evaluated based on the observed condensed-phase distributions of αi values. The observed anisotropy and low average values for the polarizability of methanol's carbon atom in polar solvents was explained in terms of strong solute-solvent interactions involving its adjacent hydroxyl group. Our QM/MM estimates for atomic polarizabilities were found to be close to values used in previously reported polarizable water and methanol models. Using our estimate for αO of methanol, a single set of polarizable force field parameters was obtained that is directly transferable between environments of different polarity.
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Affiliation(s)
- C Ruben Vosmeer
- Leiden/Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ariën S Rustenburg
- Leiden/Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Julia E Rice
- IBM Almaden Research Center , 650 Harry Road, San Jose, California 95120, United States
| | - Hans W Horn
- IBM Almaden Research Center , 650 Harry Road, San Jose, California 95120, United States
| | - William C Swope
- IBM Almaden Research Center , 650 Harry Road, San Jose, California 95120, United States
| | - Daan P Geerke
- Leiden/Amsterdam Center for Drug Research, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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