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Ploetz EA, Smith PE. Infinitely dilute partial molar properties of proteins from computer simulation. J Phys Chem B 2014; 118:12844-54. [PMID: 25325571 PMCID: PMC4234426 DOI: 10.1021/jp508632h] [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] [Indexed: 11/30/2022]
Abstract
A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University , 213 CBC Building, Manhattan, Kansas 66506-0401, United States
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Cameron DL, Jakus J, Pauleta SR, Pettigrew GW, Cooper A. Pressure Perturbation Calorimetry and the Thermodynamics of Noncovalent Interactions in Water: Comparison of Protein−Protein, Protein−Ligand, and Cyclodextrin−Adamantane Complexes. J Phys Chem B 2010; 114:16228-35. [DOI: 10.1021/jp107110t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diane L. Cameron
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Joanna Jakus
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Sofia R. Pauleta
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Graham W. Pettigrew
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
| | - Alan Cooper
- WestChem Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K., REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH9 1QH, U.K
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Aichmayer B, Wiedemann-Bidlack FB, Gilow C, Simmer JP, Yamakoshi Y, Emmerling F, Margolis HC, Fratzl P. Amelogenin nanoparticles in suspension: deviations from spherical shape and pH-dependent aggregation. Biomacromolecules 2010; 11:369-76. [PMID: 20038137 PMCID: PMC2817559 DOI: 10.1021/bm900983b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is well-known that amelogenin self-assembles to form nanoparticles, usually referred to as amelogenin nanospheres, despite the fact that not much is known about their actual shape in solution. In the current paper, we combine SAXS and DLS to study the three-dimensional shape of the recombinant amelogenins rP172 and rM179. Our results show for the first time that amelogenins build oblate nanoparticles in suspension using experimental approaches that do not require the proteins to be in contact with a support material surface. The SAXS studies give evidence for the existence of isolated amelogenin nano-oblates with aspect ratios in the range of 0.45-0.5 at pH values higher than pH 7.2 and show an aggregation of these nano-oblates at lower pH values. The role of the observed oblate shape in the formation of chain-like structures at physiological conditions is discussed as a key factor in the biomineralization of dental enamel.
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Affiliation(s)
- Barbara Aichmayer
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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Brovchenko I, Andrews MN, Oleinikova A. Volumetric properties of human islet amyloid polypeptide in liquid water. Phys Chem Chem Phys 2010; 12:4233-8. [DOI: 10.1039/b918706e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Singh G, Brovchenko I, Oleinikova A, Winter R. Demixing transition of the aqueous solution of amyloidogenic peptides: a REMD simulation study. J Phys Chem B 2009; 113:9863-70. [PMID: 19569617 DOI: 10.1021/jp901144v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aggregation of amyloidogenic peptides in liquid water is studied at various temperatures by replica exchange molecular dynamics (REMD) simulations. The formation of a peptide aggregate upon decreasing the temperature reveals features typical for a first-order demixing phase transition, which is smeared out due to the finite size of the simulation box. Various properties of the ensemble of peptides were used to describe the temperature-induced demixing phase transition, which was found to occur at about 375 K. The hydrational and volumetric properties of the peptides and their aggregates are analyzed.
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Affiliation(s)
- Gurpreet Singh
- Physical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, Dortmund, D-44227, Germany
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Brovchenko I, Burri RR, Krukau A, Oleinikova A. Thermal expansivity of amyloid β16–22 peptides and their aggregates in water. Phys Chem Chem Phys 2009; 11:5035-40. [DOI: 10.1039/b820340g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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