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Forder JK, Palakollu V, Adhikari S, Blanco MA, Derebe MG, Ferguson HM, Luthra SA, Munsell EV, Roberts CJ. Electrostatically Mediated Attractive Self-Interactions and Reversible Self-Association of Fc-Fusion Proteins. Mol Pharm 2024; 21:1321-1333. [PMID: 38334418 DOI: 10.1021/acs.molpharmaceut.3c01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Attractive self-interactions and reversible self-association are implicated in many problematic solution behaviors for therapeutic proteins, such as irreversible aggregation, elevated viscosity, phase separation, and opalescence. Protein self-interactions and reversible oligomerization of two Fc-fusion proteins (monovalent and bivalent) and the corresponding fusion partner protein were characterized experimentally with static and dynamic light scattering as a function of pH (5 and 6.5) and ionic strength (10 mM to at least 300 mM). The fusion partner protein and monovalent Fc-fusion each displayed net attractive electrostatic self-interactions at pH 6.5 and net repulsive electrostatic self-interactions at pH 5. Solutions of the bivalent Fc-fusion contained higher molecular weight species that prevented quantification of typical interaction parameters (B22 and kD). All three of the proteins displayed reversible self-association at pH 6.5, where oligomers dissociated with increased ionic strength. Coarse-grained molecular simulations were used to model the self-interactions measured experimentally, assess net self-interactions for the bivalent Fc-fusion, and probe the specific electrostatic interactions between charged amino acids that were involved in attractive electrostatic self-interactions. Mayer-weighted pairwise electrostatic energies from the simulations suggested that attractive electrostatic self-interactions at pH 6.5 for the two Fc-fusion proteins were due to cross-domain interactions between the fusion partner domain(s) and the Fc domain.
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Affiliation(s)
- James K Forder
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19713, United States
| | - Veerabhadraiah Palakollu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19713, United States
| | - Sudeep Adhikari
- Analytical R&D, Digital & NMR Sciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Marco A Blanco
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Mehabaw Getahun Derebe
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Heidi M Ferguson
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Suman A Luthra
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Erik V Munsell
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19713, United States
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Shahfar H, Forder JK, Roberts CJ. Toward a Suite of Coarse-Grained Models for Molecular Simulation of Monoclonal Antibodies and Therapeutic Proteins. J Phys Chem B 2021; 125:3574-3588. [PMID: 33821645 DOI: 10.1021/acs.jpcb.1c01903] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of coarse-grained models for molecular simulation of proteins are considered, with emphasis on the application of predicting protein-protein self-interactions for monoclonal antibodies (MAbs). As an illustrative example and for quantitative comparison, the models are used to predict osmotic virial coefficients over a broad range of attractive and repulsive self-interactions and solution conditions for a series of MAbs where the second osmotic virial coefficient has been experimentally determined in prior work. The models are compared based on how well they can predict experimental behavior, their computational burdens, and scalability. An intermediate-resolution model is also introduced that can capture specific electrostatic interactions with improved efficiency and similar or improved accuracy when compared to the previously published models. Guidance is included for the selection of coarse-grained models more generally for capturing a balance of electrostatic, steric, and short-ranged nonelectrostatic interactions for proteins from low to high concentrations.
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Affiliation(s)
- Hassan Shahfar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - James K Forder
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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Kalyuzhnyi YV, Vlachy V. Explicit-water theory for the salt-specific effects and Hofmeister series in protein solutions. J Chem Phys 2017; 144:215101. [PMID: 27276970 DOI: 10.1063/1.4953067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Effects of addition of salts on stability of aqueous protein solutions are studied theoretically and the results are compared with experimental data. In our approach, all the interacting species, proteins, ions, and water molecules, are accounted for explicitly. Water molecules are modeled as hard spheres with four off-center attractive square-well sites. These sites serve to bind either another water or to solvate the ions or protein charges. The ions are represented as charged hard spheres, and decorated by attractive sites to allow solvation. Spherical proteins simultaneously possess positive and negative groups, represented by charged hard spheres, attached to the surface of the protein. The attractive square-well sites, mimicking the protein-protein van der Waals interaction, are located on the surface of the protein. To obtain numerical results, we utilized the energy route of Wertheim's associative mean spherical approximation. From measurable properties, we choose to calculate the second virial coefficient B2, which is closely related to the tendency of proteins to aggregate and eventually crystalize. Calculations are in agreement with experimental trends: (i) For low concentration of added salt, the alkali halide salts follow the inverse Hofmeister series. (ii) At higher concentration of added salt, the trend is reversed. (iii) When cations are varied, the salts follow the direct Hofmeister series. (iv) In contrast to the colloidal theories, our approach correctly predicts the non-monotonic behavior of B2 upon addition of salts. (v) With respect to anions, the theory predicts for the B2 values to follow different sequences below and above the iso-ionic point, as also confirmed experimentally. (vi) A semi-quantitative agreement between measured and calculated values for the second virial coefficient, as functions of pH of solution and added salt type and concentration, is obtained.
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Affiliation(s)
- Yuriy V Kalyuzhnyi
- Institute for Condensed Matter Physics, NASU, Svientsitskoho 1, 79011 Lviv, Ukraine
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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Yigit C, Heyda J, Dzubiella J. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions. J Chem Phys 2015; 143:064904. [DOI: 10.1063/1.4928077] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Cemil Yigit
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany
- Helmholtz Virtual Institute “Multifunctional Biomaterials for Medicine,” 14513 Teltow, Germany
- Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, 166 28 Praha 6, Czech Republic
| | - Joachim Dzubiella
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany
- Helmholtz Virtual Institute “Multifunctional Biomaterials for Medicine,” 14513 Teltow, Germany
- Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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Platten F, Valadez-Pérez NE, Castañeda-Priego R, Egelhaaf SU. Extended law of corresponding states for protein solutions. J Chem Phys 2015; 142:174905. [DOI: 10.1063/1.4919127] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | | | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
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6
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Pethica BA. Misuse of thermodynamics in the interpretation of isothermal titration calorimetry data for ligand binding to proteins. Anal Biochem 2015; 472:21-9. [DOI: 10.1016/j.ab.2014.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 10/24/2022]
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Heinen M, Palberg T, Löwen H. Coupling between bulk- and surface chemistry in suspensions of charged colloids. J Chem Phys 2014; 140:124904. [DOI: 10.1063/1.4869338] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abramo MC, Caccamo C, Cavero M, Costa D, Pellicane G, Ruberto R, Wanderlingh U. Effective protein-protein interaction from structure factor data of a lysozyme solution. J Chem Phys 2013; 139:054904. [DOI: 10.1063/1.4817191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chan HY, Lankevich V, Vekilov PG, Lubchenko V. Anisotropy of the Coulomb interaction between folded proteins: consequences for mesoscopic aggregation of lysozyme. Biophys J 2012; 102:1934-43. [PMID: 22768950 DOI: 10.1016/j.bpj.2012.03.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 02/16/2012] [Accepted: 03/02/2012] [Indexed: 10/28/2022] Open
Abstract
Toward quantitative description of protein aggregation, we develop a computationally efficient method to evaluate the potential of mean force between two folded protein molecules that allows for complete sampling of their mutual orientation. Our model is valid at moderate ionic strengths and accounts for the actual charge distribution on the surface of the molecules, the dielectric discontinuity at the protein-solvent interface, and the possibility of protonation or deprotonation of surface residues induced by the electric field due to the other protein molecule. We apply the model to the protein lysozyme, whose solutions exhibit both mesoscopic clusters of protein-rich liquid and liquid-liquid separation; the former requires that protein form complexes with typical lifetimes of approximately milliseconds. We find the electrostatic repulsion is typically lower than the prediction of the Derjaguin-Landau-Verwey-Overbeek theory. The Coulomb interaction in the lowest-energy docking configuration is nonrepulsive, despite the high positive charge on the molecules. Typical docking configurations barely involve protonation or deprotonation of surface residues. The obtained potential of mean force between folded lysozyme molecules is consistent with the location of the liquid-liquid coexistence, but produces dimers that are too short-lived for clusters to exist, suggesting lysozyme undergoes conformational changes during cluster formation.
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Affiliation(s)
- Ho Yin Chan
- Department of Physics, University of Houston, Houston, Texas, USA
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Valadez-Pérez NE, Benavides AL, Schöll-Paschinger E, Castañeda-Priego R. Phase behavior of colloids and proteins in aqueous suspensions: Theory and computer simulations. J Chem Phys 2012; 137:084905. [PMID: 22938263 DOI: 10.1063/1.4747193] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Néstor E Valadez-Pérez
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico
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11
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Pellicane G. Colloidal Model of Lysozyme Aqueous Solutions: A Computer Simulation and Theoretical Study. J Phys Chem B 2012; 116:2114-20. [DOI: 10.1021/jp212048j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giuseppe Pellicane
- School of Chemistry
and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209,
Pietermaritzburg, South Africa
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12
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Buck PM, Kumar S, Wang X, Agrawal NJ, Trout BL, Singh SK. Computational methods to predict therapeutic protein aggregation. Methods Mol Biol 2012; 899:425-451. [PMID: 22735968 DOI: 10.1007/978-1-61779-921-1_26] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein based biotherapeutics have emerged as a successful class of pharmaceuticals. However, these macromolecules endure a variety of physicochemical degradations during manufacturing, shipping, and storage, which may adversely impact the drug product quality. Of these degradations, the irreversible self-association of therapeutic proteins to form aggregates is a major challenge in the formulation of these molecules. Tools to predict and mitigate protein aggregation are, therefore, of great interest to biopharmaceutical research and development. In this chapter, a number of such computational tools developed to understand and predict the various steps involved in protein aggregation are described. These tools can be grouped into three general classes: unfolding kinetics and native state thermal stability, colloidal stability, and sequence/structure based aggregation liabilities. Chapter sections introduce each class by discussing how these predictive tools provide insight into the molecular events leading to protein aggregation. The computational methods are then explained in detail along with their advantages and limitations.
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Affiliation(s)
- Patrick M Buck
- Biotherapeutics Pharmaceutical Research and Development, Pfizer, Inc, St. Louis, MO, USA
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14
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Choudhary MA, Li D, Emmerich H, Löwen H. DDFT calibration and investigation of an anisotropic phase-field crystal model. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:265005. [PMID: 21666297 DOI: 10.1088/0953-8984/23/26/265005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The anisotropic phase-field crystal model recently proposed and used by Prieler et al (2009 J. Phys.: Condens. Matter 21 464110) is derived from microscopic density functional theory for anisotropic particles with fixed orientation. Its morphology diagram is also explored. In particular we have investigated the influence of anisotropy and undercooling on the process of nucleation and microstructure formation from the atomic to the microscale. To that end numerical simulations were performed varying those dimensionless parameters which represent anisotropy and undercooling in our anisotropic phase-field crystal model. The results from these numerical simulations are summarized in terms of a morphology diagram of the stable state phases. These stable phases are also investigated with respect to their kinetics and characteristic morphological features.
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15
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Colla TE, Levin Y. The renormalized Jellium model of colloidal suspensions with multivalent counterions. J Chem Phys 2010; 133:234105. [DOI: 10.1063/1.3523349] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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16
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Effective interactions between charged nanoparticles in water: What is left from the DLVO theory? Curr Opin Colloid Interface Sci 2010. [DOI: 10.1016/j.cocis.2009.05.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Allahyarov E, Löwen H. Nonadditivity in the effective interactions of binary charged colloidal suspensions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:424117. [PMID: 21715852 DOI: 10.1088/0953-8984/21/42/424117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Based on primitive model computer simulations with explicit microions, we calculate the effective interactions in a binary mixture of charged colloids with species A and B for different size and charge ratios. An optimal pairwise interaction is obtained by fitting the many-body effective forces. This interaction is close to a Yukawa (or Derjaguin-Landau-Verwey-Overbeek (DLVO)) pair potential but the AB cross-interaction is different from the geometric mean of the two direct AA and BB interactions. As a function of charge asymmetry, the corresponding nonadditivity parameter is first positive, then significantly negative and is then positive again. We finally show that an inclusion of nonadditivity within an optimal effective Yukawa model gives better predictions for the fluid pair structure than DLVO theory.
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Affiliation(s)
- E Allahyarov
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany. Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA. Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, Russia
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18
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Le Brun V, Friess W, Schultz-Fademrecht T, Muehlau S, Garidel P. Lysozyme-lysozyme self-interactions as assessed by the osmotic second virial coefficient: Impact for physical protein stabilization. Biotechnol J 2009; 4:1305-19. [DOI: 10.1002/biot.200800274] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Messina R. Electrostatics in soft matter. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:113102. [PMID: 21693906 DOI: 10.1088/0953-8984/21/11/113102] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Recent progress in understanding the effect of electrostatics in soft matter is presented. A vast number of materials contain ions, ranging from the molecular scale (e.g. electrolyte) to the meso/macroscopic one (e.g. charged colloidal particles or polyelectrolytes). Their (micro)structure and physico-chemical properties are especially dictated by the famous and redoubtable long-ranged Coulomb interaction. In particular, theoretical and simulational aspects, including the experimental motivations, will be discussed.
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Affiliation(s)
- René Messina
- Institut für Theoretische Physik II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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20
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Pellicane G, Smith G, Sarkisov L. Molecular dynamics characterization of protein crystal contacts in aqueous solutions. PHYSICAL REVIEW LETTERS 2008; 101:248102. [PMID: 19113673 DOI: 10.1103/physrevlett.101.248102] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Indexed: 05/27/2023]
Abstract
We employ nonequilibrium molecular dynamics simulation to characterize the effective interactions between lysozyme molecules involved in the formation of two hydrophobic crystal contacts. We show that the effective interactions between crystal contacts do not exceed a few kT, the range of the attractive part of the potential is less than 4 angstroms, and, within this range, there is a significant depletion of water density between two protein contacts. Our findings highlight the different natures of protein crystallization and protein recognition processes.
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Affiliation(s)
- Giuseppe Pellicane
- Dipartimento di Fisica, Università degli Studi di Messina, Contrada Papardo, 98166 Messina, Italy
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21
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Gögelein C, Nägele G, Tuinier R, Gibaud T, Stradner A, Schurtenberger P. A simple patchy colloid model for the phase behavior of lysozyme dispersions. J Chem Phys 2008; 129:085102. [DOI: 10.1063/1.2951987] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Giger K, Vanam RP, Seyrek E, Dubin PL. Suppression of Insulin Aggregation by Heparin. Biomacromolecules 2008; 9:2338-44. [DOI: 10.1021/bm8002557] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katie Giger
- Department of Chemistry, Indiana University-Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202
| | - Ram P. Vanam
- Department of Chemistry, Indiana University-Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202
| | - Emek Seyrek
- Department of Chemistry, Indiana University-Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202
| | - Paul L. Dubin
- Department of Chemistry, Indiana University-Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202
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Karanikas S, Dzubiella J, Moncho-Jordá A, Louis AA. Density profiles and solvation forces for a Yukawa fluid in a slit pore. J Chem Phys 2008; 128:204704. [DOI: 10.1063/1.2921134] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Klupsch T, Walter A, Mühlig P, Hilgenfeld R. Combined kinetic osmometry and pyrometric microcalorimetry: Direct measurement of the protein–precipitant (salt) interaction. Colloids Surf A Physicochem Eng Asp 2008. [DOI: 10.1016/j.colsurfa.2007.11.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Dahirel V, Jardat M, Dufrêche JF, Turq P. Toward the description of electrostatic interactions between globular proteins: Potential of mean force in the primitive model. J Chem Phys 2007; 127:095101. [PMID: 17824765 DOI: 10.1063/1.2767626] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern. Contrarily to Poisson-Boltzmann predictions, attractive, and repulsive direct forces between proteins are not screened similarly. Moreover, it has been shown that the relative orientations of the charge patterns strongly influence salt-mediated interactions. More precisely, for short distances between the proteins, ions enhance the difference of the effective forces between (i) like-charged and oppositely charged proteins, (ii) attractive and repulsive relative orientations of the proteins, which may affect the selectivity of protein/protein recognition. Finally, such results observed with the simplest models are applied to a more elaborate one to demonstrate their generality.
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Affiliation(s)
- Vincent Dahirel
- Université Pierre et Marie Curie-Paris 6, Laboratoire Liquides Ioniques et Interfaces Chargées, UMR CNRS 7612, Case Courrier 51, 4 Place Jussieu 75005 Paris, France.
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26
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Podgornik R, Ličer M. Polyelectrolyte bridging interactions between charged macromolecules. Curr Opin Colloid Interface Sci 2006. [DOI: 10.1016/j.cocis.2006.08.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Mühlbacher F, Schiessel H, Holm C. Tail-induced attraction between nucleosome core particles. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:031919. [PMID: 17025679 DOI: 10.1103/physreve.74.031919] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Indexed: 05/12/2023]
Abstract
We study a possible electrostatic mechanism underlying the compaction of DNA inside the nuclei of eucaryotes: the tail-bridging effect between nucleosomes, the fundamental DNA packaging units of the chromatin complex. As a simple model of the nucleosome we introduce the eight-tail colloid, a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We show that our complexes attract each other via the formation of chain bridges and contrast this to the effect of attraction via charge patches. We demonstrate that the attraction between eight-tail colloids can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation is controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.
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Affiliation(s)
- F Mühlbacher
- Max-Planck-Institut für Polymerforschung, Theory Group, PO Box 3147, D-55021, Mainz, Germany
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28
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Schiessel H. The nucleosome: a transparent, slippery, sticky and yet stable DNA-protein complex. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2006; 19:251-62. [PMID: 16453064 DOI: 10.1140/epje/i2005-10049-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Accepted: 01/19/2006] [Indexed: 05/06/2023]
Abstract
Roughly three quarters of eucaryotic DNA are tightly wrapped onto protein cylinders organized in so-called nucleosomes. Despite this fact, the wrapped DNA cannot be inert since DNA is at the heart of many crucial life processes. We focus here on physical mechanisms that might allow nucleosomes to perform a great deal of such processes, specifically 1) on unwrapping fluctuations that give DNA-binding proteins access to the wrapped DNA portions without disrupting the nucleosome as a whole, 2) on corkscrew sliding along DNA and some implications and on 3) tail-bridging-induced attraction between nucleosomes as a means of controlling higher-order folding.
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Affiliation(s)
- H Schiessel
- Instituut-Lorentz, Universiteit Leiden, Postbus 9506, 2300 RA, Leiden, The Netherlands.
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29
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Nonlinear screening on the charged surfaces with trivalent and tetravalent salt ions: Monte Carlo simulations. Colloids Surf A Physicochem Eng Asp 2006. [DOI: 10.1016/j.colsurfa.2005.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Payne RW, Nayar R, Tarantino R, Del Terzo S, Moschera J, Di J, Heilman D, Bray B, Manning MC, Henry CS. Second virial coefficient determination of a therapeutic peptide by self-interaction chromatography. Biopolymers 2006; 84:527-33. [PMID: 16767741 DOI: 10.1002/bip.20554] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Self-interaction of macromolecules has been shown to play an important role in a number of physical processes, including crystallization, solubility, viscosity, and aggregation. Peptide self-interaction is not as well studied as for larger proteins, but should play an equally important role. The osmotic second virial coefficient, B, can be used to quantify peptide and protein self-interaction. B values are typically measured using static light scattering (SLS). Peptides, however, do not scatter enough light to allow such measurements. This study describes the first use of self-interaction chromatography (SIC) for the measurement of peptide B values because SIC does not have the molecular size limitations of SLS. In the present work, SIC was used to measure B for enfuvirtide, a 36-amino acid therapeutic peptide, as a function of salt concentration, salt type, and pH. B was found to correlate strongly with solubility and apparent molecular weight. In general, the solubility of enfuvirtide increases with pH from 6 to 10 and decreases as the salt concentration increases from 0 to 0.5M for three different salts. The effect of peptide concentration on B was also investigated and shown to have a significant effect, but only at high concentrations (>80 mg/mL).
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Affiliation(s)
- Robert W Payne
- Department of Chemistry, Colorado State University, Fort Collins, CO
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31
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Gapinski J, Wilk A, Patkowski A, Häussler W, Banchio AJ, Pecora R, Nägele G. Diffusion and microstructural properties of solutions of charged nanosized proteins: Experiment versus theory. J Chem Phys 2005; 123:054708. [PMID: 16108686 DOI: 10.1063/1.1996569] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have reanalyzed our former static small-angle x-ray scattering and photon correlation spectroscopy results on dense solutions of charged spherical apoferritin proteins using theories recently developed for studies of colloids. The static structure factors S(q), and the small-wave-number collective diffusion coefficient D(c) determined from those experiments are interpreted now in terms of a theoretical scheme based on a Derjaguin-Landau-Verwey-Overbeek-type continuum model of charged colloidal spheres. This scheme accounts, in an approximate way, for many-body hydrodynamic interactions. Stokesian dynamics computer simulations of the hydrodynamic function have been performed for the first time for dense charge-stabilized dispersions to assess the accuracy of the theoretical scheme. We show that the continuum model allows for a consistent description of all experimental results, and that the effective particle charge is dependent upon the protein concentration relative to the added salt concentration. In addition, we discuss the consequences of small ions dynamics for the collective protein diffusion within the framework of the coupled-mode theory.
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Affiliation(s)
- J Gapinski
- Institute of Physics, A. Mickiewicz University, 61-614 Poznan, Poland.
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32
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Macroions in Solution. ACTA ACUST UNITED AC 2005. [DOI: 10.1007/1-4020-3659-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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33
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Grandison S, Penfold R, Vanden-Broeck JM. Monte Carlo simulation of an inhomogeneous dielectric continuum model for B-DNA. Phys Chem Chem Phys 2005; 7:3486-95. [PMID: 16273150 DOI: 10.1039/b508393a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thermodynamic and structural properties of the counterion atmosphere surrounding B-DNA are calculated by Monte Carlo simulation in a spatially inhomogeneous, but piecewise uniform, dielectric continuum cell model - the "barbarous" model. A boundary element formulation is implemented to study the sensitivity of these properties with respect to perturbations in the location of discontinuous dielectric boundaries relative to fixed and mobile charges. High concentrations are considered corresponding to the liquid crystalline hexagonally ordered phase of DNA. Primitive model results are verified against other simulation reports and a comparison of barbarous model predictions with experimental data is discussed. The internal energy, osmotic coefficient, radial distributions and the population ratio of counterions in the geometrically resolved major and minor grooves are all found to strongly depend on the dielectric boundary position. This suggests that a self-consistent development of the model should consider a free surface problem where the boundary is not specified a priori.
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Affiliation(s)
- Scott Grandison
- School of Mathematics, University of East Anglia, Norwich, UKNR4 7TJ.
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34
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Morisada S, Muranishi K, Shinto H, Higashitani K. Molecular Dynamics Calculation of Interaction Forces between Colloids in Aqueous Electrolyte Solutions Using an Implicit Solvent Model. KAGAKU KOGAKU RONBUN 2005. [DOI: 10.1252/kakoronbunshu.31.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Morisada S, Muranishi K, Shinto H, Higashitani K. Interactions between colloidal particles in NaCl aqueous solutions: molecular dynamics simulations with an implicit solvent model. ADV POWDER TECHNOL 2005. [DOI: 10.1163/1568552054969951] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Xu B, Huang L, Liang H. Thermodynamic behaviors of polyampholytes at low temperatures. J Chem Phys 2004; 121:7494-500. [PMID: 15473824 DOI: 10.1063/1.1792191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The thermodynamic properties of 6-mer polyampholyte chains were simulated with the multicanonical Monte Carlo method in a three-dimensional off-lattice model. The results demonstrate that the number of the charged monomers on the chain and the sequence significantly affect the transition behaviors of polyampholyte chains. In the case of the random distribution of the charged monomers, two oppositely charged monomers act as two stickers during a collapse process, due to which the movement of monomers is suppressed and the chains can more directly reach their solid state. Interestingly, in a proper arrangement of the charged monomers, the chains may have a proteinlike nondegenerate state, i.e., the chain is designable. The transition of such polyampholyte chains appears to be of a two-state, all-or-none type.
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Affiliation(s)
- Beisi Xu
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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37
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Tavares FW, Bratko D, Striolo A, Blanch HW, Prausnitz JM. Phase behavior of aqueous solutions containing dipolar proteins from second-order perturbation theory. J Chem Phys 2004; 120:9859-69. [PMID: 15268003 DOI: 10.1063/1.1697387] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Due to the interplay of Coulombic repulsion and attractive dipolar and van der Waals interactions, solutions of globular proteins display a rich variety of phase behavior featuring fluid-fluid and fluid-solid transitions that strongly depend on solution pH and salt concentration. Using a simple model for charge, dispersion and dipole-related contributions to the interprotein potential, we calculate phase diagrams for protein solutions within the framework of second-order perturbation theory. For each phase, we determine the Helmholtz energy as the sum of a hard-sphere reference term and a perturbation term that reflects both the electrostatic and dispersion interactions. Dipolar effects can induce fluid-fluid phase separation or crystallization even in the absence of any significant dispersion attraction. Because dissolved electrolytes screen the charge-charge repulsion more strongly than the dipolar attraction, the ionic strength dependence of the potential of mean force can feature a minimum at intermediate ionic strengths offering an explanation for the observed nonmonotonic dependence of the phase behavior on salt concentration. Inclusion of correlations between charge-dipole and dipole-dipole interactions is essential for a reliable calculation of phase diagrams for systems containing charged dipolar proteins and colloids.
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Affiliation(s)
- F W Tavares
- Department of Chemical Engineering, University of California, Berkeley, California 94720-1462, USA
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38
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Hoffmann N, Likos * CN, Hansen JP. Linear screening of the electrostatic potential around spherical particles with non-spherical charge patterns. Mol Phys 2004. [DOI: 10.1080/00268970410001695688] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Piazza R. Protein interactions and association: an open challenge for colloid science. Curr Opin Colloid Interface Sci 2004. [DOI: 10.1016/j.cocis.2004.01.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Allahyarov E, Gompper G, Löwen H. Attraction between DNA molecules mediated by multivalent ions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 69:041904. [PMID: 15169040 DOI: 10.1103/physreve.69.041904] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Revised: 01/12/2004] [Indexed: 05/23/2023]
Abstract
The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counterion and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modeled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counterions and monovalent salt ions, we find a salt-enhanced repulsion effect: the force is first attractive but gets repulsive with increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging.
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Affiliation(s)
- E Allahyarov
- Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany
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41
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Manno M, Xiao C, Bulone D, Martorana V, San Biagio PL. Thermodynamic instability in supersaturated lysozyme solutions: effect of salt and role of concentration fluctuations. PHYSICAL REVIEW E 2003; 68:011904. [PMID: 12935173 DOI: 10.1103/physreve.68.011904] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2003] [Indexed: 11/07/2022]
Abstract
Experimental and theoretical work has suggested that protein crystal nucleation can be affected by the separation of two metastable liquid phases with different local concentrations, or more specifically by critical density fluctuations. We measure the amplitude and correlation length of local concentration fluctuations by light scattering for supersaturated solutions of hen egg-white lysozyme (at pH 4.5 and at different NaCl concentrations, up to 7% w/v). By extrapolating the critical divergent behavior of concentration fluctuation amplitude versus temperature, we determine the spinodal line, that is the limit of stability. Cloud-point measurements are used to determine liquid-liquid coexistence, consistent with previous work. In the present work, which is an extensive study of off-critical fluctuations in supersaturated protein solution, we observe a nonclassical scaling divergent behavior of the correlation length of concentration fluctuations, thus suggesting that off-critical fluctuations may have a role in crystallization kinetics. To appropriately fit the spinodal data, an entropic term must be added to the van der Waals or to the adhesive hard-sphere model. We interpret this contribution as due to the salt-induced modulation of protein hydration.
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Affiliation(s)
- Mauro Manno
- National Research Council Italy, Institute of Biophysics (Palermo), Via Ugo La Malfa 153, 90146 Palermo, Italy.
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