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Hernández-Cifre JG, Rodríguez-Schmidt R, Almagro-Gómez CM, García de la Torre J. Calculation of the friction, diffusion and sedimentation coefficients of nanoplatelets of arbitrary shape. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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2
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Zhu K, Pamies R, Al‐Manasir N, Ginés Hernández Cifre J, García de la Torre J, Nyström B, Kjøniksen A. The Effect of Number of Arms on the Aggregation Behavior of Thermoresponsive Poly(N-isopropylacrylamide) Star Polymers. Chemphyschem 2020; 21:1258-1271. [PMID: 32352214 PMCID: PMC7317447 DOI: 10.1002/cphc.202000273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/29/2020] [Indexed: 12/02/2022]
Abstract
The thermoresponsive nature of aqueous solutions of poly(N-isopropylacrylamide) (PNIPAAM) star polymers containing 2, 3, 4, and 6 arms has been investigated by turbidity, dynamic light scattering, rheology, and rheo-SALS. Simulations of the thermosensitive nature of the single star polymers have also been conducted. Some of the samples form aggregates even at temperatures significantly below the lower critical solution temperature (LCST) of PNIPAAM. Increasing concentration and number of arms promotes associations at low temperatures. When the temperature is raised, there is a competition between size increase due to enhanced aggregation and a size reduction caused by contraction. Monte Carlo simulations show that the single stars contract with increasing temperature, and that this contraction is more pronounced when the number of arms is increased. Some samples exhibit a minimum in the turbidity data after the initial increase at the cloud point. The combined rheology and rheo-SALS data suggest that this is due to a fragmentation of the aggregates followed by re-aggregation at even higher temperatures. Although the 6-arm star polymer aggregates more than the other stars at low temperatures, the more compact structure renders it less prone to aggregation at temperatures above the cloud point.
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Affiliation(s)
- Kaizheng Zhu
- Faculty of EngineeringØstfold University CollegeP.O. Box 7001757HaldenNorway
| | - Ramón Pamies
- Department of Material Engineering and ManufacturingTechnical University of Cartagena CartagenaMurcia30202Spain
| | | | | | | | - Bo Nyström
- Department of ChemistryUniversity of OsloP.O. Box 1033, Blindern0315OsloNorway
| | - Anna‐Lena Kjøniksen
- Faculty of EngineeringØstfold University CollegeP.O. Box 7001757HaldenNorway
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García de la Torre J, Hernández Cifre J. Hydrodynamic Properties of Biomacromolecules and Macromolecular Complexes: Concepts and Methods. A Tutorial Mini-review. J Mol Biol 2020; 432:2930-2948. [DOI: 10.1016/j.jmb.2019.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 01/08/2023]
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Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1. J Mol Biol 2018; 430:2164-2180. [PMID: 29775635 DOI: 10.1016/j.jmb.2018.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 11/20/2022]
Abstract
Many signaling proteins consist of globular domains connected by flexible linkers that allow for substantial domain motion. Because these domains often serve as complementary functional modules, the possibility of functionally important domain motions arises. To explore this possibility, we require knowledge of the ensemble of protein conformations sampled by interdomain motion. Measurements of NMR residual dipolar couplings (RDCs) of backbone HN bonds offer a per-residue characterization of interdomain dynamics, as the couplings are sensitive to domain orientation. A challenge in reaching this potential is the need to interpret the RDCs as averages over dynamic ensembles of domain conformations. Here, we address this challenge by introducing an efficient protocol for generating conformational ensembles appropriate for flexible, multi-domain proteins. The protocol uses map-restrained self-guided Langevin dynamics simulations to promote collective, interdomain motion while restraining the internal domain motion to near rigidity. Critically, the simulations retain an all-atom description for facile inclusion of site-specific NMR RDC restraints. The result is the rapid generation of conformational ensembles consistent with the RDC data. We illustrate this protocol on human Pin1, a two-domain peptidyl-prolyl isomerase relevant for cancer and Alzheimer's disease. The results include the ensemble of domain orientations sampled by Pin1, as well as those of a dysfunctional variant, I28A-Pin1. The differences between the ensembles corroborate our previous spin relaxation results that showed weakened interdomain contact in the I28A variant relative to wild type. Our protocol extends our abilities to explore the functional significance of protein domain motions.
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Erwin N, Patra S, Dwivedi M, Weise K, Winter R. Influence of isoform-specific Ras lipidation motifs on protein partitioning and dynamics in model membrane systems of various complexity. Biol Chem 2017; 398:547-563. [PMID: 27977396 DOI: 10.1515/hsz-2016-0289] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/07/2016] [Indexed: 12/17/2022]
Abstract
The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid mixtures, heterogeneous raft model membranes up to complex native-like lipid mixtures (GPMVs) in the absence and presence of integral membrane proteins have been explored in the last decade in a combined chemical-biological and biophysical approach. These studies have revealed pronounced isoform-specific differences regarding the lateral distribution in membranes and formation of protein-rich membrane domains. In this context, we will also discuss the effects of lipid head group structure and charge density on the partitioning behavior of the lipoproteins. Moreover, the dynamic properties of N-Ras and K-Ras4B have been studied in different model membrane systems and native-like crowded milieus. Addition of crowding agents such as Ficoll and its monomeric unit, sucrose, gradually favors clustering of Ras proteins in forming small oligomers in the bulk; only at very high crowder concentrations association is disfavored.
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Affiliation(s)
- Nelli Erwin
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Satyajit Patra
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Mridula Dwivedi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Katrin Weise
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Dortmund Technical University, Otto-Hahn-Strasse 4a, D-44227 Dortmund
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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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Urban MJ, Holder IT, Schmid M, Fernandez Espin V, Garcia de la Torre J, Hartig JS, Cölfen H. Shape Analysis of DNA-Au Hybrid Particles by Analytical Ultracentrifugation. ACS NANO 2016; 10:7418-7427. [PMID: 27459174 DOI: 10.1021/acsnano.6b01377] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Current developments in nanotechnology have increased the demand for nanocrystal assemblies with well-defined shapes and tunable sizes. DNA is a particularly well-suited building block in nanoscale assemblies because of its scalable sizes, conformational variability, and convenient self-assembly capabilities via base pairing. In hybrid materials, gold nanoparticles (AuNPs) can be assembled into nanoparticle structures with programmable interparticle distances by applying appropriate DNA sequences. However, the development of stoichiometrically defined DNA/NP structures is still challenging since product mixtures are frequently obtained and their purification and characterization is the rate-limiting step in the development of DNA-NP hybrid assemblies. Improvements in nanostructure fractionation and characterization techniques offer great potential for nanotechnology applications in general. This study reports the application of analytical ultracentrifugation (AUC) for the characterization of anisotropic DNA-linked metal-crystal assemblies. On the basis of transmission electron microscopy data and the DNA primary sequence, hydrodynamic bead models are set up for the interpretation of the measured frictional ratios and sedimentation coefficients. We demonstrate that the presence of single DNA strands on particle surfaces as well as the shape factors of multiparticle structures in mixtures can be quantitatively described by AUC. This study will significantly broaden the possibilities to analyze mixtures of shape-anisotropic nanoparticle assemblies. By establishing insights into the analysis of nanostructure mixtures based on fundamental principles of sedimentation, a wide range of potential applications in basic research and industry become accessible.
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Affiliation(s)
- Maximilan J Urban
- Department of Chemistry, University of Konstanz , Universitätsstr. 10, 78457 Konstanz, Germany
| | - Isabelle T Holder
- Department of Chemistry, University of Konstanz , Universitätsstr. 10, 78457 Konstanz, Germany
| | - Marius Schmid
- Department of Chemistry, University of Konstanz , Universitätsstr. 10, 78457 Konstanz, Germany
| | | | | | - Jörg S Hartig
- Department of Chemistry, University of Konstanz , Universitätsstr. 10, 78457 Konstanz, Germany
| | - Helmut Cölfen
- Department of Chemistry, University of Konstanz , Universitätsstr. 10, 78457 Konstanz, Germany
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Benítez AA, Hernández Cifre JG, Díaz Baños FG, de la Torre JG. Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA. BMC BIOPHYSICS 2015; 8:11. [PMID: 26629336 PMCID: PMC4666080 DOI: 10.1186/s13628-015-0025-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 11/18/2015] [Indexed: 12/02/2022]
Abstract
Background The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations. Results That scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed. Conclusions The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics. Electronic supplementary material The online version of this article (doi:10.1186/s13628-015-0025-7) contains supplementary material, which is available to authorized users.
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Abstract
The hydrodynamic parameters measured in an AUC experiment, s(20,w) and D(t)(20,w)(0), can be used to gain information on the solution structure of (bio)macromolecules and their assemblies. This entails comparing the measured parameters with those that can be computed from usually "dry" structures by "hydrodynamic modeling." In this chapter, we will first briefly put hydrodynamic modeling in perspective and present the basic physics behind it as implemented in the most commonly used methods. The important "hydration" issue is also touched upon, and the distinction between rigid bodies versus those for which flexibility must be considered in the modeling process is then made. The available hydrodynamic modeling/computation programs, HYDROPRO, BEST, SoMo, AtoB, and Zeno, the latter four all implemented within the US-SOMO suite, are described and their performance evaluated. Finally, some literature examples are presented to illustrate the potential applications of hydrodynamics in the expanding field of multiresolution modeling.
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Affiliation(s)
- Mattia Rocco
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy.
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom.
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Ionic strength effect in polyelectrolyte dilute solutions within the Debye–Hückel approximation: Monte Carlo and Brownian dynamics simulations. Polym Bull (Berl) 2014. [DOI: 10.1007/s00289-014-1186-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Amorós D, Ortega A, García de la Torre J. Prediction of Hydrodynamic and Other Solution Properties of Partially Disordered Proteins with a Simple, Coarse-Grained Model. J Chem Theory Comput 2013; 9:1678-85. [DOI: 10.1021/ct300948u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Amorós
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
| | - A. Ortega
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
| | - J. García de la Torre
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
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Characterization of polyelectrolyte features in polysaccharide systems and mucin. Adv Colloid Interface Sci 2010; 158:108-18. [PMID: 19482258 DOI: 10.1016/j.cis.2009.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 04/23/2009] [Accepted: 05/11/2009] [Indexed: 11/22/2022]
Abstract
This review elucidates several aspects on the behavior of charged polysaccharides and mucin. Viscosification of dilute aqueous solutions of hyaluronan (HA) occurs in the course of time at low shear flow, whereas shear thinning as time evolves is found at moderate shear rates. Hydrogen bonds and electrostatic interaction play an important role for the emergence of these features. No time effect of the viscosity is observed for semidilute HA solutions. A degradation of HA is observed at low and high pH and this effect continues over long times, and it is only in the approximate interval 5<pH<10 that HA is stable. Small angle neutron scattering (SANS) measurements on semidilute aqueous solutions of mucin at pH=7 reveal a fractal dimension of 1.4, and the effect of temperature is insignificant on the fractal structure. This suggests that the mucin chains on a semi-local dimensional scale are rod-like. From various experimental methods on solutions of mucin it was found that at pH values around 2 (uncharged polymer), the intensive hydrophobic interactions lead to large association complexes, whereas at pH>>2 the negative charges suppress the tendency of forming associations. At pH<2, the mucin chains are compressed and they are decorated by some positive charges. In the semidilute regime, a fragmented network is developed. The intense association in semidilute solutions of mucin at pH=2 is further supported by the results from rheo-small angle light scattering measurements. Effects of ionic strength on the radius of gyration (R(g)) for dilute solutions of HA (pH=7) and positively charged hydroxyethylcellulose (HEC(+)) are studied with the aid of Monte Carlo simulations, and essential features of the polyelectrolyte effect on R(g) are captured in the computer simulation. Strong interactions are observed in aqueous mixtures of an anionic polysaccharide (HEC(-)) and an oppositely charged surfactant (cetyltrimethylammonium bromide; CTAB); this gives rise to extensive associations and macroscopic phase separation is approached. The massive association complexes are disclosed in the SANS experiments by a pronounced upturn in the scattered intensity at low values of the wave vector.
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Rodríguez Schmidt R, Pamies R, Kjøniksen AL, Zhu K, Hernández Cifre JG, Nyström B, García de la Torre J. Single-Molecule Behavior of Asymmetric Thermoresponsive Amphiphilic Copolymers in Dilute Solution. J Phys Chem B 2010; 114:8887-93. [DOI: 10.1021/jp102442q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ricardo Rodríguez Schmidt
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
| | - Ramón Pamies
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
| | - Anna-Lena Kjøniksen
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
| | - Kaizheng Zhu
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
| | - José G. Hernández Cifre
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
| | - Bo Nyström
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
| | - José García de la Torre
- Departamento de Química Física, Facultad de Química, University of Murcia, Murcia, Spain, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway, and Department of Pharmaceutics, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, N-0316, Oslo, Norway
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de la Torre JG, Ortega Á, Amorós D, Schmidt RR, Cifre JGH. Methods and Tools for the Prediction of Hydrodynamic Coefficients and Other Solution Properties of Flexible Macromolecules in Solution. A Tutorial Minireview. Macromol Biosci 2010; 10:721-30. [DOI: 10.1002/mabi.200900464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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de la Torre JG, Hernández Cifre JG, Ortega Á, Schmidt RR, Fernandes MX, Pérez Sánchez HE, Pamies R. SIMUFLEX: Algorithms and Tools for Simulation of the Conformation and Dynamics of Flexible Molecules and Nanoparticles in Dilute Solution. J Chem Theory Comput 2009; 5:2606-18. [DOI: 10.1021/ct900269n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José García de la Torre
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - José G. Hernández Cifre
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Álvaro Ortega
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Ricardo Rodríguez Schmidt
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Miguel X. Fernandes
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Horacio E. Pérez Sánchez
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - R. Pamies
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
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Echenique GDR, Schmidt RR, Freire JJ, Cifre JGH, Torre JGDL. A Multiscale Scheme for the Simulation of Conformational and Solution Properties of Different Dendrimer Molecules. J Am Chem Soc 2009; 131:8548-56. [DOI: 10.1021/ja901275d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gustavo Del Río Echenique
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
| | - Ricardo Rodríguez Schmidt
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
| | - Juan J. Freire
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
| | - José G. Hernández Cifre
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
| | - José García de la Torre
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
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Abstract
Hydrodynamic bead modeling (HBM) is the representation of a macromolecule by an assembly of spheres (or beads) for which measurable hydrodynamic (and related) parameters are then computed in order to understand better the macromolecular solution conformation. An example-based account is given of the main stages in HBM of rigid macromolecules, namely: model construction, model visualization, accounting for hydration, and hydrodynamic calculations. Different types of models are appropriate for different macromolecules, according to their composition, to what is known about the molecule or according to the types of experimental data that the model should reproduce. Accordingly, the construction of models based on atomic coordinates as well as much lower resolution data (e.g., electron microscopy images) is described. Similarly, several programs for hydrodynamic calculations are summarized, some generating the most basic set of solution parameters (e.g., sedimentation and translational diffusion coefficients, intrinsic viscosity, radius of gyration, and Stokes radius) while others extend to data determined by nuclear magnetic resonance, fluorescence anisotropy, and electric birefringence methods. An insight into the topic of hydrodynamic hydration is given, together with some practical suggestions for its satisfactory treatment in the modeling context. All programs reviewed are freely available.
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Ortega A, García de la Torre J. Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility. Biomacromolecules 2007; 8:2464-75. [PMID: 17645309 DOI: 10.1021/bm700473f] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.
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Affiliation(s)
- A Ortega
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain
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de la Torre JG, Echenique GDR, Ortega A. Improved calculation of rotational diffusion and intrinsic viscosity of bead models for macromolecules and nanoparticles. J Phys Chem B 2007; 111:955-61. [PMID: 17266248 DOI: 10.1021/jp0647941] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conventional Kirkwood-Riseman calculation of the hydrodynamic properties of bead models gives abnormal results for rotational quantities and the intrinsic viscosities for models with a few beads or when one bead is dominant. The reason is that beads are treated as point sources of friction. This can be remedied by introducing terms that are neglected in the conventional treatment of orders 0 and -3 in interbead distances. An alternative strategy is the cubic substitution in which each bead is replaced by a cubic array of minibeads. These procedures require a computational overload that, in the case of the intrinsic viscosity, can be avoided using an estimate of the correction due to the nonzero volume of the beads. We have found how such a correction can be estimated from the geometry of the model, and its application yields results that are within the range of typical experimental errors.
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Affiliation(s)
- J García de la Torre
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain.
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García de la Torre J. Dynamic electro-optic properties of macromolecules and nanoparticles in solution: A review of computational and simulation methodologies. Colloids Surf B Biointerfaces 2007; 56:4-15. [PMID: 17125977 DOI: 10.1016/j.colsurfb.2006.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 09/14/2006] [Accepted: 10/01/2006] [Indexed: 11/20/2022]
Abstract
This paper reviews some theories, and computational and simulation procedures available for the calculation of the time-course of electro-optic properties of particles in solution. For rigid particles, the time evolution of the properties is directly related to their rotational diffusion; therefore, the computational procedures for the calculation of hydrodynamic properties find a direct application in electro-optics. Several of such computational procedures, based on bead models, are reviewed. For flexible particles, the simultaneous effects the external field and the flexibility can be treated with Brownian dynamics simulation. We illustrate the various procedures, with applications to rigid bent rods and flexible, wormlike or hinged rods, trying to show how the absence or presence of flexibility, and its kind, influences the dynamic electro-optic properties, which are therefore valuable sources of information about the conformation of macromolecules and nanoparticles.
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Affiliation(s)
- J García de la Torre
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.
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del Rio Echenique G, Cifre JGH, Rodríguez E, Rubio A, Freire JJ, de la Torre JG. Multi-Scale Simulation of the Conformation and Dynamics of Dendrimeric Macromolecules. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/masy.200651353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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