1
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Interlandi G. Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations. Proteins 2024. [PMID: 38829206 DOI: 10.1002/prot.26706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
The blood protein von Willebrand factor (VWF) is a large multimeric protein that, when activated, binds to blood platelets, tethering them to the site of vascular injury and initiating blood coagulation. This process is critical for the normal hemostatic response, but especially under inflammatory conditions, it is thought to be a major player in pathological thrombus formation. For this reason, VWF has been the target for the development of anti-thrombotic therapeutics. However, it is challenging to prevent pathological thrombus formation while still allowing normal physiological blood coagulation, as currently available anti-thrombotic therapeutics are known to cause unwanted bleeding, in particular intracranial hemorrhage. This work explores the possibility of inhibiting VWF selectively under the inflammatory conditions present during pathological thrombus formation. In particular, the A2 domain of VWF is known to inhibit the neighboring A1 domain from binding to the platelet surface receptor GpIbα, and this auto-inhibitory mechanism has been shown to be removed by oxidizing agents released during inflammation. Hence, finding drug molecules that bind at the interface between A1 and A2 only under oxidizing conditions could restore such an auto-inhibitory mechanism. Here, by using a combination of computational docking, molecular dynamics simulations, and free energy perturbation calculations, a ligand from the ZINC15 database was identified that binds at the A1A2 interface, with the interaction being stronger under oxidizing conditions. The results provide a framework for the discovery of drug molecules that bind to a protein selectively in the presence of inflammatory conditions.
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Affiliation(s)
- Gianluca Interlandi
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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2
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Decherchi S, Cavalli A. Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation. Chem Rev 2020; 120:12788-12833. [PMID: 33006893 PMCID: PMC8011912 DOI: 10.1021/acs.chemrev.0c00534] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds by estimating their binding affinity to proteins. This is challenging due to the complexity of the simulated system. To assess the present and future value of simulation for drug discovery, we review key applications of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions and for estimating the rate coefficients of very slow processes of pharmacological interest. We outline the statistical mechanics and computational background behind this research, including methods such as steered molecular dynamics and metadynamics. We review recent applications to pharmacology and drug discovery and discuss possible guidelines for the practitioner. Recent trends in machine learning are also briefly discussed. Thanks to the rapid development of methods for characterizing and quantifying rare events, simulation's role in drug discovery is likely to expand, making it a valuable complement to experimental and clinical approaches.
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Affiliation(s)
- Sergio Decherchi
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
| | - Andrea Cavalli
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, 40126 Bologna, Italy
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3
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Orndorff PB, Le Phan ST, Li KH, van der Vaart A. Conformational Free-Energy Differences of Large Solvated Systems with the Focused Confinement Method. J Chem Theory Comput 2020; 16:5163-5173. [DOI: 10.1021/acs.jctc.0c00403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul B. Orndorff
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Sang T. Le Phan
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ka Ho Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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4
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Gobbo D, Ballone P, Decherchi S, Cavalli A. Solubility Advantage of Amorphous Ketoprofen. Thermodynamic and Kinetic Aspects by Molecular Dynamics and Free Energy Approaches. J Chem Theory Comput 2020; 16:4126-4140. [PMID: 32463689 DOI: 10.1021/acs.jctc.0c00166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermodynamic and kinetic aspects of crystalline (c-KTP) and amorphous (a-KTP) ketoprofen dissolution in water have been investigated by molecular dynamics simulation focusing on free energy properties. Absolute free energies of all relevant species and phases have been determined by thermodynamic integration on a novel path, first connecting the harmonic to the anharmonic system Hamiltonian at low T and then extending the result to the temperature of interest. The free energy required to transfer one ketoprofen molecule from the crystal to the solution is in fair agreement with the experimental value. The absolute free energy of the amorphous form is 19.58 kJ/mol higher than for the crystal, greatly enhancing the ketoprofen concentration in water, although as a metastable species in supersaturated solution. The kinetics of the dissolution process has been analyzed by computing the free energy profile along a reaction coordinate bringing one ketoprofen molecule from the crystal or amorphous phase to the solvated state. This computation confirms that, compared to the crystal form, the dissolution rate is nearly 7 orders of magnitude faster for the amorphous form, providing one further advantage to the latter in terms of bioavailability. The problem of drug solubility, of great practical importance, is used here as a test bed for a refined method to compute absolute free energies, which could be of great interest in biophysics and drug discovery in particular.
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Affiliation(s)
- D Gobbo
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - P Ballone
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy.,School of Physics, University College Dublin, Dublin, Ireland.,Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - S Decherchi
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - A Cavalli
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy.,University of Bologna, Bologna 40126, Italy
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5
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van der Vaart A, Orndorff PB, Le Phan ST. Calculation of Conformational Free Energies with the Focused Confinement Method. J Chem Theory Comput 2019; 15:6760-6768. [DOI: 10.1021/acs.jctc.9b00590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Paul B. Orndorff
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Sang T. Le Phan
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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6
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Shrivastav G, Vanden-Eijnden E, Abrams CF. Mapping saddles and minima on free energy surfaces using multiple climbing strings. J Chem Phys 2019; 151:124112. [PMID: 31575198 DOI: 10.1063/1.5120372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Locating saddle points on free energy surfaces is key in characterizing multistate transition events in complicated molecular-scale systems. Because these saddle points represent transition states, determining minimum free energy pathways to these saddles and measuring their free energies relative to their connected minima are further necessary, for instance, to estimate transition rates. In this work, we propose a new multistring version of the climbing string method in collective variables to locate all saddles and corresponding pathways on free energy surfaces. The method uses dynamic strings to locate saddles and static strings to keep a history of prior strings converged to saddles. Interaction of the dynamic strings with the static strings is used to avoid the convergence to already-identified saddles. Additionally, because the strings approximate curves in collective-variable space, and we can measure free energy along each curve, identification of any saddle's two connected minima is guaranteed. We demonstrate this method to map the network of stationary points in the 2D and 4D free energy surfaces of alanine dipeptide and alanine tripeptide, respectively.
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Affiliation(s)
- Gourav Shrivastav
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Eric Vanden-Eijnden
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
| | - Cameron F Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
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7
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Knoch F, Speck T. Non-equilibrium Markov state modeling of periodically driven biomolecules. J Chem Phys 2019; 150:054103. [DOI: 10.1063/1.5055818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Fabian Knoch
- Institut für Physik, Johannes Gutenberg-Universität Mainz,
Staudingerweg 7-9, 55128 Mainz, Germany
| | - Thomas Speck
- Institut für Physik, Johannes Gutenberg-Universität Mainz,
Staudingerweg 7-9, 55128 Mainz, Germany
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8
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Zeng X, Zhu L, Zheng X, Cecchini M, Huang X. Harnessing complexity in molecular self-assembly using computer simulations. Phys Chem Chem Phys 2018; 20:6767-6776. [PMID: 29479585 DOI: 10.1039/c7cp06181a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In molecular self-assembly, hundreds of thousands of freely-diffusing molecules associate to form ordered and functional architectures in the absence of an actuator. This intriguing phenomenon plays a critical role in biology and has become a powerful tool for the fabrication of advanced nanomaterials. Due to the limited spatial and temporal resolutions of current experimental techniques, computer simulations offer a complementary strategy to explore self-assembly with atomic resolution. Here, we review recent computational studies focusing on both thermodynamic and kinetic aspects. As we shall see, thermodynamic approaches based on modeling and statistical mechanics offer initial guidelines to design nanostructures with modest computational effort. Computationally more intensive analyses based on molecular dynamics simulations and kinetic network models (KNMs) reach beyond it, opening the door to the rational design of self-assembly pathways. Current limitations of these methodologies are discussed. We anticipate that the synergistic use of thermodynamic and kinetic analyses based on computer simulations will provide an important contribution to the de novo design of self-assembly.
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Affiliation(s)
- Xiangze Zeng
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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9
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Remsing RC, Xi E, Patel AJ. Protein Hydration Thermodynamics: The Influence of Flexibility and Salt on Hydrophobin II Hydration. J Phys Chem B 2018; 122:3635-3646. [DOI: 10.1021/acs.jpcb.7b12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard C. Remsing
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Erte Xi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J. Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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10
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Boonstra S, Onck PR, van der Giessen E. Computation of Hemagglutinin Free Energy Difference by the Confinement Method. J Phys Chem B 2017; 121:11292-11303. [PMID: 29151344 PMCID: PMC5742479 DOI: 10.1021/acs.jpcb.7b09699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/15/2017] [Indexed: 11/28/2022]
Abstract
Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs.
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Affiliation(s)
- Sander Boonstra
- Micromechanics of Materials,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Patrick R. Onck
- Micromechanics of Materials,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Erik van der Giessen
- Micromechanics of Materials,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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11
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Villemot F, Peguero-Tejada A, van der Vaart A. Calculation of conformational free energies by confinement simulations in explicit water with implicit desolvation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1391386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- François Villemot
- Department of Chemistry, University of South Florida , Tampa, FL, USA
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12
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Co-operative intra-protein structural response due to protein–protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding. J Comput Aided Mol Des 2017; 31:891-903. [DOI: 10.1007/s10822-017-0057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/30/2017] [Indexed: 12/29/2022]
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13
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Samanta S, Mukherjee S. Microscopic insight into thermodynamics of conformational changes of SAP-SLAM complex in signal transduction cascade. J Chem Phys 2017; 146:165103. [DOI: 10.1063/1.4981259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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14
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Poblete H, Miranda-Carvajal I, Comer J. Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives. J Phys Chem B 2017; 121:3895-3907. [PMID: 28291356 DOI: 10.1021/acs.jpcb.7b01130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding the interaction of carbon nanomaterials with proteins is essential for determining the potential effects of these materials on health and in the design of biotechnology based on them. Here we leverage explicit-solvent molecular simulation and multidimensional free-energy calculations to investigate how adsorption to carbon nanomaterial surfaces affects the conformational equilibrium of alanine dipeptide, a widely used model of protein backbone structure. We find that the two most favorable structures of alanine dipeptide on graphene (or large carbon nanotubes) correspond to the two amide linkages lying in the same plane, flat against the surface, rather than the nonplanar α-helix-like and β-sheet-like conformations that predominate in aqueous solution. On graphenic surfaces, the latter conformations are metastable and most often correspond to amide-π stacking of the N-terminal amide. The calculations highlight the key role of amide-π interactions in determining the conformational equilibrium. Lesser but significant contributions from hydrogen bonding to the high density interfacial water layer or to the hydroxy groups of hydroxylated graphene also define the most favorable conformations. This work should yield insight on the influence of carbon nanotubes, graphene, and their functionalized derivatives on protein structure.
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Affiliation(s)
- Horacio Poblete
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University , Manhattan, Kansas 66506-5802, United States
| | - Ingrid Miranda-Carvajal
- Universidad Nacional de Colombia , sede Bogotá, Facultad de Ciencias, Departamento de Química, Carrera 30 No. 45-03, Bogotá, 111321, Colombia
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University , Manhattan, Kansas 66506-5802, United States
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15
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Montalvo-Acosta JJ, Cecchini M. Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding. Mol Inform 2016; 35:555-567. [PMID: 27554325 DOI: 10.1002/minf.201600052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/01/2016] [Indexed: 11/08/2022]
Abstract
The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline.
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Affiliation(s)
- Joel José Montalvo-Acosta
- Laboratoire d'Ingénierie des Fonctions Moléculaires ISIS, UMR 7006 CNRS, Université de Strasbourg, F-67083, Strasbourg Cedex, France
| | - Marco Cecchini
- Laboratoire d'Ingénierie des Fonctions Moléculaires ISIS, UMR 7006 CNRS, Université de Strasbourg, F-67083, Strasbourg Cedex, France
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16
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Villemot F, Capelli R, Colombo G, van der Vaart A. Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies. J Chem Theory Comput 2016; 12:2779-89. [PMID: 27120438 DOI: 10.1021/acs.jctc.5b01183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Improvements to the confinement method for the calculation of conformational free energy differences are presented. By taking advantage of phase space overlap between simulations at different frequencies, significant gains in accuracy and speed are reached. The optimal frequency spacing for the simulations is obtained from extrapolations of the confinement energy, and relaxation time analysis is used to determine time steps, simulation lengths, and friction coefficients. At postprocessing, interpolation of confinement energies is used to significantly reduce discretization errors in the calculation of conformational free energies. The efficiency of this protocol is illustrated by applications to alanine n-peptides and lactoferricin. For the alanine-n-peptide, errors were reduced between 2- and 10-fold and sampling times between 8- and 67-fold, while for lactoferricin the long sampling times at low frequencies were reduced 10-100-fold.
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Affiliation(s)
- François Villemot
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
| | - Riccardo Capelli
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , Via Mario Bianco 9, 20131 Milano, Italy.,Dipartimento di Fisica, Università degli Studi di Milano and INFN , Via Celoria 16, 20133 Milano, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , Via Mario Bianco 9, 20131 Milano, Italy
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
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17
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Chen C. Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method. J Phys Chem B 2016; 120:3061-71. [PMID: 26974860 DOI: 10.1021/acs.jpcb.5b11892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.
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Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China
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18
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Capelli R, Villemot F, Moroni E, Tiana G, van der Vaart A, Colombo G. Assessment of Mutational Effects on Peptide Stability through Confinement Simulations. J Phys Chem Lett 2016; 7:126-130. [PMID: 26678679 DOI: 10.1021/acs.jpclett.5b02221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The evaluation of free energy differences between specific states of a system is of fundamental interest in the study of (bio)chemical systems. Herein, we examine the use of the recently introduced confinement method (CM) to evaluate relative free energy changes upon protein/peptide mutations. CM is a path-independent technique that involves the transformation of a configurational state of the system into an ideal crystal permitting the direct computation of free energy differences. We illustrate the method by evaluating the differential stabilities between native and mutant sequences of a model peptide that has been extensively characterized by experimental approaches, the GB1 hairpin. We show a good correlation between calculated and experimental relative stabilities and discuss other possible applications of this method in the context of complex molecular conversions.
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Affiliation(s)
- Riccardo Capelli
- Dipartimento di Fisica, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
| | - François Villemot
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
| | - Guido Tiana
- Dipartimento di Fisica, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN , via Celoria 16, 20133 Milan, Italy
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche , via Mario Bianco 9, 20131 Milan, Italy
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19
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Conti S, Cecchini M. Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach. Phys Chem Chem Phys 2016; 18:31480-31493. [DOI: 10.1039/c6cp05249e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A self-consistent framework based on modeling and statistical mechanics for the theoretical interpretation of self-assembly at surfaces and interfaces is presented.
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Affiliation(s)
- Simone Conti
- Laboratoire d'Ingénierie des Fonctions Moléculaires ISIS
- UMR 7006 CNRS
- Université de Strasbourg
- F-67083 Strasbourg Cedex
- France
| | - Marco Cecchini
- Laboratoire d'Ingénierie des Fonctions Moléculaires ISIS
- UMR 7006 CNRS
- Université de Strasbourg
- F-67083 Strasbourg Cedex
- France
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20
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Cecchini M. Quantum Corrections to the Free Energy Difference between Peptides and Proteins Conformers. J Chem Theory Comput 2015; 11:4011-22. [DOI: 10.1021/acs.jctc.5b00260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Cecchini
- Laboratoire d’Ingénierie
des Fonctions Moléculaires Institut de Science et d’Ingénierie
Supramoléculaires, Université de Strasbourg, 8 allée
Gaspard Monge, F-67083 Strasbourg Cedex, France
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