1
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Hegde O, Li T, Sharma A, Borja M, Jacobs WM, Rogers WB. Competition between Self-Assembly and Phase Separation Governs High-Temperature Condensation of a DNA Liquid. PHYSICAL REVIEW LETTERS 2024; 132:208401. [PMID: 38829088 DOI: 10.1103/physrevlett.132.208401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2024] [Accepted: 04/19/2024] [Indexed: 06/05/2024]
Abstract
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite behavior, whereby self-assembly of DNA oligonucleotides into finite-sized, stoichiometric clusters tends to inhibit phase separation. We first use microfluidics-based experiments to map a novel phase transition in which the oligonucleotides condense as the temperature increases at high concentrations of divalent cations. We then show that a theoretical model of competition between self-assembly and phase separation quantitatively predicts changes in experimental phase diagrams arising from DNA sequence perturbations. Our results point to a general mechanism by which self-assembly shapes phase boundaries in complex biopolymer solutions.
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Affiliation(s)
- Omkar Hegde
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Tianhao Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Anjali Sharma
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Marco Borja
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - W Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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2
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Kim J, Qin S, Zhou HX, Rosen MK. Surface Charge Can Modulate Phase Separation of Multidomain Proteins. J Am Chem Soc 2024; 146:3383-3395. [PMID: 38262618 PMCID: PMC10859935 DOI: 10.1021/jacs.3c12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Phase separation has emerged as an important mechanism explaining the formation of certain biomolecular condensates. Biological phase separation is often driven by the multivalent interactions of modular protein domains. Beyond valency, the physical features of folded domains that promote phase separation are poorly understood. We used a model system─the small ubiquitin modifier (SUMO) and its peptide ligand, the SUMO interaction motif (SIM)─to examine how domain surface charge influences multivalency-driven phase separation. Phase separation of polySUMO and polySIM was altered by pH via a change in the protonation state of SUMO surface histidines. These effects were recapitulated by histidine mutations, which modulated SUMO solubility and polySUMO-polySIM phase separation in parallel and were quantitatively explained by atomistic modeling of weak interactions among proteins in the system. Thus, surface charge can tune the phase separation of multivalent proteins, suggesting a means of controlling phase separation biologically, evolutionarily, and therapeutically.
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Affiliation(s)
- Jonggul Kim
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
| | - Sanbo Qin
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Huan-Xiang Zhou
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Department
of Physics, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Michael K. Rosen
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
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3
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Makowski EK, Wang T, Zupancic JM, Huang J, Wu L, Schardt JS, De Groot AS, Elkins SL, Martin WD, Tessier PM. Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning. Nat Biomed Eng 2024; 8:45-56. [PMID: 37666923 PMCID: PMC10842909 DOI: 10.1038/s41551-023-01074-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/29/2023] [Indexed: 09/06/2023]
Abstract
Antibody development, delivery, and efficacy are influenced by antibody-antigen affinity interactions, off-target interactions that reduce antibody bioavailability and pharmacokinetics, and repulsive self-interactions that increase the stability of concentrated antibody formulations and reduce their corresponding viscosity. Yet identifying antibody variants with optimal combinations of these three types of interactions is challenging. Here we show that interpretable machine-learning classifiers, leveraging antibody structural features descriptive of their variable regions and trained on experimental data for a panel of 80 clinical-stage monoclonal antibodies, can identify antibodies with optimal combinations of low off-target binding in a common physiological-solution condition and low self-association in a common antibody-formulation condition. For three clinical-stage antibodies with suboptimal combinations of off-target binding and self-association, the classifiers predicted variable-region mutations that optimized non-affinity interactions while maintaining high-affinity antibody-antigen interactions. Interpretable machine-learning models may facilitate the optimization of antibody candidates for therapeutic applications.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Zupancic
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jie Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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4
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Li L, Gui C, Hu J, Różycki B. Membrane-Mediated Cooperative Interactions of CD47 and SIRP α. MEMBRANES 2023; 13:871. [PMID: 37999357 PMCID: PMC10673186 DOI: 10.3390/membranes13110871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
The specific binding of the ubiquitous 'marker of self' protein CD47 to the SIRPα protein anchored in the macrophage plasma membrane results in the inhibition of the engulfment of 'self' cells by macrophages and thus constitutes a key checkpoint of our innate immune system. Consequently, the CD47-SIRPα protein complex has been recognized as a potential therapeutic target in cancer and inflammation. Here, we introduce a lattice-based mesoscale model for the biomimetic system studied recently in fluorescence microscopy experiments where GFP-tagged CD47 proteins on giant plasma membrane vesicles bind to SIRPα proteins immobilized on a surface. Computer simulations of the lattice-based mesoscale model allow us to study the biomimetic system on multiple length scales, ranging from single nanometers to several micrometers and simultaneously keep track of single CD47-SIRPα binding and unbinding events. Our simulations not only reproduce data from the fluorescence microscopy experiments but also are consistent with results of several other experiments, which validates our numerical approach. In addition, our simulations yield quantitative predictions on the magnitude and range of effective, membrane-mediated attraction between CD47-SIRPα complexes. Such detailed information on CD47-SIRPα interactions cannot be obtained currently from experiments alone. Our simulation results thus extend the present understanding of cooperative effects in CD47-SIRPα interactions and may have an influence on the advancement of new cancer treatments.
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Affiliation(s)
- Long Li
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China; (L.L.); (C.G.); (J.H.)
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Chen Gui
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China; (L.L.); (C.G.); (J.H.)
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China; (L.L.); (C.G.); (J.H.)
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland
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5
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Manning GS, Kay AR. The physical basis of osmosis. J Gen Physiol 2023; 155:e202313332. [PMID: 37624228 PMCID: PMC10457415 DOI: 10.1085/jgp.202313332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/12/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Osmosis is an important force in all living organisms, yet the molecular basis of osmosis is widely misunderstood as arising from diffusion of water across a membrane separating solutions of differing osmolarities, and hence different water concentrations. In 1923, Peter Debye proposed a physical model for a semipermeable membrane emphasizing the repulsive forces between solute molecules and membrane that prevent the solute from entering the membrane. His work was hardly noticed at the time and slipped out of view. We show that Debye's analysis of van 't Hoff's law for osmotic equilibrium also provides a consistent and plausible mechanism for osmotic flow. A difference in osmolyte concentrations in solutions separated by a semipermeable membrane leads to different pressures at the two water-membrane interfaces because the total repulsive force between solute molecules and the membrane is different at the two interfaces. Water is therefore driven through the membrane for exactly the same reason that pure water flows in response to an imposed hydrostatic pressure difference. In this paper, we present the Debye model in both equilibrium and flow conditions. We point out its applicability regardless of the nature of the membrane with examples ranging from the predominantly convective flow of water through synthetic membranes and capillary walls to the purely diffusive flow of independent water molecules through a lipid bilayer and the flow of a single-file column of water molecules in narrow protein channels.
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Affiliation(s)
- Gerald S. Manning
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Alan R. Kay
- Department of Biology, University of Iowa, Iowa City, IA, USA
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6
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Rajoub N, Gerard CJJ, Pantuso E, Fontananova E, Caliandro R, Belviso BD, Curcio E, Nicoletta FP, Pullen J, Chen W, Heng JYY, Ruane S, Liddell J, Alvey N, Ter Horst JH, Di Profio G. A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification. Nat Protoc 2023; 18:2998-3049. [PMID: 37697106 DOI: 10.1038/s41596-023-00869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/06/2023] [Indexed: 09/13/2023]
Abstract
Monoclonal antibodies (mAbs) are commonly used biologic drugs for the treatment of diseases such as rheumatoid arthritis, multiple sclerosis, COVID-19 and various cancers. They are produced in Chinese hamster ovary cell lines and are purified via a number of complex and expensive chromatography-based steps, operated in batch mode, that rely heavily on protein A resin. The major drawback of conventional procedures is the high cost of the adsorption media and the extensive use of chemicals for the regeneration of the chromatographic columns, with an environmental cost. We have shown that conventional protein A chromatography can be replaced with a single crystallization step and gram-scale production can be achieved in continuous flow using the template-assisted membrane crystallization process. The templates are embedded in a membrane (e.g., porous polyvinylidene fluoride with a layer of polymerized polyvinyl alcohol) and serve as nucleants for crystallization. mAbs are flexible proteins that are difficult to crystallize, so it can be challenging to determine the optimal conditions for crystallization. The objective of this protocol is to establish a systematic and flexible approach for the design of a robust, economic and sustainable mAb purification platform to replace at least the protein A affinity stage in traditional chromatography-based purification platforms. The procedure provides details on how to establish the optimal parameters for separation (crystallization conditions, choice of templates, choice of membrane) and advice on analytical and characterization methods.
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Affiliation(s)
- Nazer Rajoub
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Charline J J Gerard
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Elvira Pantuso
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy
| | - Enrica Fontananova
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy
| | - Rocco Caliandro
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Cristallografia (IC), Bari, Italy
| | - Benny D Belviso
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Cristallografia (IC), Bari, Italy
| | - Efrem Curcio
- Department of Environmental Engineering, University of Calabria, Rende, Italy
| | - Fiore P Nicoletta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Edificio Polifunzionale, Rende, Italy
| | - James Pullen
- FUJIFILM Diosynth Biotechnologies, Billingham, UK
| | - Wenqian Chen
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Jerry Y Y Heng
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Sean Ruane
- Center for Process Innovation (CPI), Darlington, UK
| | - John Liddell
- Center for Process Innovation (CPI), Darlington, UK
| | | | - Joop H Ter Horst
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Gianluca Di Profio
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy.
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7
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Yuan F, Lee CT, Sangani A, Houser JR, Wang L, Lafer EM, Rangamani P, Stachowiak JC. The ins and outs of membrane bending by intrinsically disordered proteins. SCIENCE ADVANCES 2023; 9:eadg3485. [PMID: 37418523 PMCID: PMC10328403 DOI: 10.1126/sciadv.adg3485] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Membrane curvature is essential to diverse cellular functions. While classically attributed to structured domains, recent work illustrates that intrinsically disordered proteins are also potent drivers of membrane bending. Specifically, repulsive interactions among disordered domains drive convex bending, while attractive interactions drive concave bending, creating membrane-bound, liquid-like condensates. How might disordered domains that contain both repulsive and attractive domains affect curvature? Here, we examined chimeras that combined attractive and repulsive interactions. When the attractive domain was closer to the membrane, its condensation amplified steric pressure among repulsive domains, leading to convex curvature. In contrast, when the repulsive domain was closer to the membrane, attractive interactions dominated, resulting in concave curvature. Further, a transition from convex to concave curvature occurred with increasing ionic strength, which reduced repulsion while enhancing condensation. In agreement with a simple mechanical model, these results illustrate a set of design rules for membrane bending by disordered proteins.
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Affiliation(s)
- Feng Yuan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Arjun Sangani
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Justin R. Houser
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eileen M. Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jeanne C. Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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8
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States.,Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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9
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Hansen J, Moll CJ, López Flores L, Castañeda-Priego R, Medina-Noyola M, Egelhaaf SU, Platten F. Phase separation and dynamical arrest of protein solutions dominated by short-range attractions. J Chem Phys 2023; 158:024904. [PMID: 36641409 DOI: 10.1063/5.0128643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The interplay of liquid-liquid phase separation (LLPS) and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as condensed matter physics, materials science, food engineering, and the pharmaceutical industry. In this context, protein solutions exhibit remarkable equilibrium and non-equilibrium behaviors. In the regime where attractive and repulsive forces compete, it has been demonstrated, for example, that the location of the dynamical arrest line seems to be independent of ionic strength, so that the arrest lines at different ionic screening lengths overlap, in contrast to the LLPS coexistence curves, which strongly depend on the salt concentration. In this work, we show that the same phenomenology can also be observed when the electrostatic repulsions are largely screened, and the range and strength of the attractions are varied. In particular, using lysozyme in brine as a model system, the metastable gas-liquid binodal and the dynamical arrest line as well as the second virial coefficient have been determined for various solution conditions by cloud-point measurements, optical microscopy, centrifugation experiments, and light scattering. With the aim of understanding this new experimental phenomenology, we apply the non-equilibrium self-consistent generalized Langevin equation theory to a simple model system with only excluded volume plus short-range attractions, to study the dependence of the predicted arrest lines on the range of the attractive interaction. The theoretical predictions find a good qualitative agreement with experiments when the range of the attraction is not too small compared with the size of the protein.
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Affiliation(s)
- Jan Hansen
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Carolyn J Moll
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Leticia López Flores
- Instituto de Física "Manuel Sandoval Vallarta," Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, Mexico
| | | | - Magdaleno Medina-Noyola
- Instituto de Física "Manuel Sandoval Vallarta," Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, Mexico
| | - Stefan U Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
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10
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Shahfar H, O'Brien CJ, Budyak IL, Roberts CJ. Predicting Experimental B22 Values and the Effects of Histidine Charge States for Monoclonal Antibodies Using Coarse-Grained Molecular Simulations. Mol Pharm 2022; 19:3820-3830. [PMID: 36194430 DOI: 10.1021/acs.molpharmaceut.2c00337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Static light scattering (SLS) was used to characterize five monoclonal antibodies (MAbs) as a function of total ionic strength (TIS) at pH values between 5.5 and 7.0. Second osmotic virial coefficient (B22) values were determined experimentally for each MAb as a function of TIS using low protein concentration SLS data. Coarse-grained molecular simulations were performed to predict the B22 values for each MAb at a given pH and TIS. To include the effect of charge fluctuations of titratable residues in the B22 calculations, a statistical approach was introduced in the Monte Carlo algorithm based on the protonation probability based on a given pH value and the Henderson-Hasselbalch equation. The charged residues were allowed to fluctuate individually, based on the sampled microstates and the influence of electrostatic interactions on net protein-protein interactions during the simulations. Compared to static charge simulations, the new approach provided improved results compared to experimental B22 values at pH conditions near the pKa of titratable residues.
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Affiliation(s)
- Hassan Shahfar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
| | - Christopher J O'Brien
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
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11
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Uttinger MJ, Hundschell CS, Lautenbach V, Pusara S, Bäther S, Heyn TR, Keppler JK, Wenzel W, Walter J, Kozlowska M, Wagemans AM, Peukert W. Determination of specific and non-specific protein-protein interactions for beta-lactoglobulin by analytical ultracentrifugation and membrane osmometry experiments. SOFT MATTER 2022; 18:6739-6756. [PMID: 36040122 DOI: 10.1039/d2sm00908k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Protein-protein interactions are essential for the understanding of biological processes. Specific protein aggregation is an important aspect for many biological systems. In particular, electrostatic interactions play the key role for protein-protein interactions, as many amino acids have pH-dependent charge states. Moreover, protein dissociation is directly related to the solution pH, ionic strength, temperature and protein concentration. The subtle interplay between different specific and non-specific interactions is demonstrated for beta-lactoglobulin (BLG) with a focus on low salt concentrations, thus mimicking technically relevant processing conditions. BLG is a well-characterized model system, proven to attain its monomer-dimer equilibrium strongly dependent upon the pH of the solution. In this manuscript, we present a unique combination of analytical ultracentrifugation and membrane osmometry experiments, which quantifies specific and non-specific interactions, i.e. in terms of the dimer dissociation constants and the second osmotic virial coefficient, at pH 3 and 7 and sodium chloride concentrations of 10 mM and 100 mM. This provides direct insight to protein-protein interactions for a system with a concentration-dependent monomer-dimer equilibrium. Moreover, using a coarse-grained extended DLVO model in combination with molecular dynamics simulations, we quantify non-specific monomer-monomer, monomer-dimer and dimer-dimer interactions as well as the binding free energy of BLG dimerization from theoretical calculations. The experimentally determined interactions are shown to be mainly governed by electrostatic interactions and further agree with free energy calculations. Our experimental protocol aims to determine non-specific and specific interactions for a dynamically interacting system and provides an understanding of protein-protein interactions for BLG at low salt concentrations.
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Affiliation(s)
- M J Uttinger
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
| | - C S Hundschell
- Institute of Food Technology and Food Chemistry, Department of Food Colloids, Technical University Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - V Lautenbach
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
| | - S Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - S Bäther
- Institute of Food Technology and Food Chemistry, Department of Food Colloids, Technical University Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - T R Heyn
- Institute of Human Nutrition and Food Science, Division of Food Technology, Kiel University, 24118 Kiel, Germany
| | - J K Keppler
- Laboratory of Food Process Engineering, Wageningen University, Wageningen, The Netherlands
| | - W Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - J Walter
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
| | - M Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - A M Wagemans
- Institute of Food Technology and Food Chemistry, Department of Food Colloids, Technical University Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - W Peukert
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
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12
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Shimomura T, Sekiguchi M, Honda R, Yamazaki M, Yokoyama M, Uchiyama S. Estimation of the Viscosity of an Antibody Solution from the Diffusion Interaction Parameter. Biol Pharm Bull 2022; 45:1300-1305. [DOI: 10.1248/bpb.b22-00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Reisa Honda
- Department of Pharmaceutical Technology, Astellas Pharma Inc
| | - Miki Yamazaki
- Department of Pharmaceutical Technology, Astellas Pharma Inc
| | - Masami Yokoyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University
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13
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Laber JR, Laue TM, Filoti DI. Use of Debye-Hückel-Henry charge measurements in early antibody development elucidates effects of non-specific association. Antib Ther 2022; 5:211-215. [PMID: 35983303 PMCID: PMC9380711 DOI: 10.1093/abt/tbac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/21/2022] [Accepted: 07/10/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The diffusion interaction parameter (kD) has been demonstrated to be a high-throughput technique for characterizing interactions between proteins in solution. kD reflects both attractive and repulsive interactions, including long-ranged electrostatic repulsions. Here, we plot the mutual diffusion coefficient (Dm) as a function of the experimentally determined Debye-Hückel-Henry surface charge (ZDHH) for seven human monoclonal antibodies (mAbs) in 15 mM histidine, pH 6. We find that graphs of Dm versus ZDHH intersect at ZDHH, ~ 2.6, independent of protein concentration. The same data plotted as kD vs. ZDHH shows a transition from net attractive to net repulsive interactions in the same region of the ZDHH intersection point. These data suggest that there is a minimum surface charge necessary on these mAbs needed to overcome attractive interactions.
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Affiliation(s)
- Joshua R Laber
- Formulation and Biologics Product Development, Nektar Therapeutics , 455 Mission Bay Boulevard South, San Francisco, CA 94158, USA
| | - Thomas M Laue
- Carpenter Professor Emeritus, University of New Hampshire , Durham, NH 03824, USA
| | - Dana I Filoti
- Analytical Research and Development, AbbVie , 100 Research Drive, Worcester, MA 01605, USA
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14
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Mierke CT. Viscoelasticity, Like Forces, Plays a Role in Mechanotransduction. Front Cell Dev Biol 2022; 10:789841. [PMID: 35223831 PMCID: PMC8864183 DOI: 10.3389/fcell.2022.789841] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Viscoelasticity and its alteration in time and space has turned out to act as a key element in fundamental biological processes in living systems, such as morphogenesis and motility. Based on experimental and theoretical findings it can be proposed that viscoelasticity of cells, spheroids and tissues seems to be a collective characteristic that demands macromolecular, intracellular component and intercellular interactions. A major challenge is to couple the alterations in the macroscopic structural or material characteristics of cells, spheroids and tissues, such as cell and tissue phase transitions, to the microscopic interferences of their elements. Therefore, the biophysical technologies need to be improved, advanced and connected to classical biological assays. In this review, the viscoelastic nature of cytoskeletal, extracellular and cellular networks is presented and discussed. Viscoelasticity is conceptualized as a major contributor to cell migration and invasion and it is discussed whether it can serve as a biomarker for the cells’ migratory capacity in several biological contexts. It can be hypothesized that the statistical mechanics of intra- and extracellular networks may be applied in the future as a powerful tool to explore quantitatively the biomechanical foundation of viscoelasticity over a broad range of time and length scales. Finally, the importance of the cellular viscoelasticity is illustrated in identifying and characterizing multiple disorders, such as cancer, tissue injuries, acute or chronic inflammations or fibrotic diseases.
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15
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Dingfelder F, Henriksen A, Wahlund PO, Arosio P, Lorenzen N. Measuring Self-Association of Antibody Lead Candidates with Dynamic Light Scattering. Methods Mol Biol 2022; 2313:241-258. [PMID: 34478142 DOI: 10.1007/978-1-0716-1450-1_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this method chapter, we provide a brief overview of the key methods available to measure self-association of monoclonal antibodies (mAbs) and explain for which experimental throughputs they are usually applied. We then focus on dynamic light scattering (DLS) and describe experimental details on how to measure the diffusion interaction parameter (kD) which is occasionally referred to as the gold standard for measuring self-association of proteins. The kD is a well-established parameter to predict solution viscosity, which is one of the most critical developability parameters of mAbs. Finally, we present a pH and excipient screen that is designed to measure self-association with DLS under conditions that are relevant for bioprocessing and formulation of mAbs. The presented light scattering methods are well suited for lead candidate selections where it is essential to select mAbs with high developability potential for progression toward first human dose.
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Affiliation(s)
- Fabian Dingfelder
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark.
| | - Anette Henriksen
- Department of Modelling and Predictive Technologies, Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Per-Olof Wahlund
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Nikolai Lorenzen
- Department of Biophysics and Injectable Formulation 2, Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark.
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16
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ATP and Tri-Polyphosphate (TPP) Suppress Protein Aggregate Growth by a Supercharging Mechanism. Biomedicines 2021; 9:biomedicines9111646. [PMID: 34829875 PMCID: PMC8616003 DOI: 10.3390/biomedicines9111646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
A common strategy to increase aggregation resistance is through rational mutagenesis to supercharge proteins, which leads to high colloidal stability, but often has the undesirable effect of lowering conformational stability. We show this trade-off can be overcome by using small multivalent polyphosphate ions, adenosine triphosphate (ATP) and tripolyphosphate (TPP) as excipients. These ions are equally effective at suppressing aggregation of ovalbumin and bovine serum albumin (BSA) upon thermal stress as monitored by dynamic and static light scattering. Monomer loss kinetic studies, combined with measurements of native state protein–protein interactions and ζ-potentials, indicate the ions reduce aggregate growth by increasing the protein colloidal stability through binding and overcharging the protein. Out of three additional proteins studied, ribonuclease A (RNaseA), α-chymotrypsinogen (α-Cgn), and lysozyme, we only observed a reduction in aggregate growth for RNaseA, although overcharging by the poly-phosphate ions still occurs for lysozyme and α-Cgn. Because the salts do not alter protein conformational stability, using them as excipients could be a promising strategy for stabilizing biopharmaceuticals once the protein structural factors that determine whether multivalent ion binding will increase colloidal stability are better elucidated. Our findings also have biological implications. Recently, it has been proposed that ATP also plays an important role in maintaining intracellular biological condensates and preventing protein aggregation in densely packed cellular environments. We expect electrostatic interactions are a significant factor in determining the stabilizing ability of ATP towards maintaining proteins in non-dispersed states in vivo.
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17
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Yin F, Khago D, Martin RW, Butts CT. Bayesian analysis of static light scattering data for globular proteins. PLoS One 2021; 16:e0258429. [PMID: 34648536 PMCID: PMC8516215 DOI: 10.1371/journal.pone.0258429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Static light scattering is a popular physical chemistry technique that enables calculation of physical attributes such as the radius of gyration and the second virial coefficient for a macromolecule (e.g., a polymer or a protein) in solution. The second virial coefficient is a physical quantity that characterizes the magnitude and sign of pairwise interactions between particles, and hence is related to aggregation propensity, a property of considerable scientific and practical interest. Estimating the second virial coefficient from experimental data is challenging due both to the degree of precision required and the complexity of the error structure involved. In contrast to conventional approaches based on heuristic ordinary least squares estimates, Bayesian inference for the second virial coefficient allows explicit modeling of error processes, incorporation of prior information, and the ability to directly test competing physical models. Here, we introduce a fully Bayesian model for static light scattering experiments on small-particle systems, with joint inference for concentration, index of refraction, oligomer size, and the second virial coefficient. We apply our proposed model to study the aggregation behavior of hen egg-white lysozyme and human γS-crystallin using in-house experimental data. Based on these observations, we also perform a simulation study on the primary drivers of uncertainty in this family of experiments, showing in particular the potential for improved monitoring and control of concentration to aid inference.
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Affiliation(s)
- Fan Yin
- Department of Statistics, University of California at Irvine, Irvine, CA, United States of America
| | - Domarin Khago
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Rachel W. Martin
- Departments of Chemistry and Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States of America
| | - Carter T. Butts
- Departments of Sociology, Statistics, Computer Science and EECS and Institute for Mathematical Behavioral Sciences, University of California at Irvine, Irvine, CA, United States of America
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18
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Nassar R, Dignon GL, Razban RM, Dill KA. The Protein Folding Problem: The Role of Theory. J Mol Biol 2021; 433:167126. [PMID: 34224747 PMCID: PMC8547331 DOI: 10.1016/j.jmb.2021.167126] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 10/20/2022]
Abstract
The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.
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Affiliation(s)
- Roy Nassar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Gregory L Dignon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rostam M Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
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19
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Lanzaro A, Roche A, Sibanda N, Corbett D, Davis P, Shah M, Pathak JA, Uddin S, van der Walle CF, Yuan XF, Pluen A, Curtis R. Cluster Percolation Causes Shear Thinning Behavior in Concentrated Solutions of Monoclonal Antibodies. Mol Pharm 2021; 18:2669-2682. [PMID: 34121411 DOI: 10.1021/acs.molpharmaceut.1c00198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
High-concentration (>100 g/L) solutions of monoclonal antibodies (mAbs) are typically characterized by anomalously large solution viscosity and shear thinning behavior for strain rates ≥103 s-1. Here, the link between protein-protein interactions (PPIs) and the rheology of concentrated solutions of COE-03 and COE-19 mAbs is studied by means of static and dynamic light scattering and microfluidic rheometry. By comparing the experimental data with predictions based on the Baxter sticky hard-sphere model, we surprisingly find a connection between the observed shear thinning and the predicted percolation threshold. The longest shear relaxation time of mAbs was much larger than that of model sticky hard spheres within the same region of the phase diagram, which is attributed to the anisotropy of the mAb PPIs. Our results suggest that not only the strength but also the patchiness of short-range attractive PPIs should be explicitly accounted for by theoretical approaches aimed at predicting the shear rate-dependent viscosity of dense mAb solutions.
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Affiliation(s)
- Alfredo Lanzaro
- Institute for Systems Rheology, Guangzhou University, No. 230 West Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Aisling Roche
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicole Sibanda
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Daniel Corbett
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Davis
- Department of Molecular Biology and Biotechnology, University of Sheffield UK, Sheffield S10 2TN, United Kingdom
| | - Maryam Shah
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Jai A Pathak
- Dosage Form Design and Development, Biopharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, United Kingdom
| | - Shahid Uddin
- Dosage Form Design and Development, Biopharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, United Kingdom
| | - Christopher F van der Walle
- Dosage Form Design and Development, Biopharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, United Kingdom
| | - Xue-Feng Yuan
- Institute for Systems Rheology, Guangzhou University, No. 230 West Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Alain Pluen
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Robin Curtis
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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20
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Pusara S, Yamin P, Wenzel W, Krstić M, Kozlowska M. A coarse-grained xDLVO model for colloidal protein-protein interactions. Phys Chem Chem Phys 2021; 23:12780-12794. [PMID: 34048523 DOI: 10.1039/d1cp01573g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Colloidal protein-protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B22, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion-protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B22 values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins.
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Affiliation(s)
- Srdjan Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Peyman Yamin
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Marjan Krstić
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. and Institute of Theoretical Solid State Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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21
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Rocha MA, Sprague-Piercy MA, Kwok AO, Roskamp KW, Martin RW. Chemical Properties Determine Solubility and Stability in βγ-Crystallins of the Eye Lens. Chembiochem 2021; 22:1329-1346. [PMID: 33569867 PMCID: PMC8052307 DOI: 10.1002/cbic.202000739] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/17/2020] [Indexed: 11/10/2022]
Abstract
βγ-Crystallins are the primary structural and refractive proteins found in the vertebrate eye lens. Because crystallins are not replaced after early eye development, their solubility and stability must be maintained for a lifetime, which is even more remarkable given the high protein concentration in the lens. Aggregation of crystallins caused by mutations or post-translational modifications can reduce crystallin protein stability and alter intermolecular interactions. Common post-translational modifications that can cause age-related cataracts include deamidation, oxidation, and tryptophan derivatization. Metal ion binding can also trigger reduced crystallin solubility through a variety of mechanisms. Interprotein interactions are critical to maintaining lens transparency: crystallins can undergo domain swapping, disulfide bonding, and liquid-liquid phase separation, all of which can cause opacity depending on the context. Important experimental techniques for assessing crystallin conformation in the absence of a high-resolution structure include dye-binding assays, circular dichroism, fluorescence, light scattering, and transition metal FRET.
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Affiliation(s)
- Megan A. Rocha
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
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22
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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: 14] [Impact Index Per Article: 4.7] [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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23
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Pal T, Wessén J, Das S, Chan HS. Subcompartmentalization of polyampholyte species in organelle-like condensates is promoted by charge-pattern mismatch and strong excluded-volume interaction. Phys Rev E 2021; 103:042406. [PMID: 34005864 DOI: 10.1103/physreve.103.042406] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Polyampholyte field theory and explicit-chain molecular dynamics models of sequence-specific phase separation of a system with two intrinsically disordered protein (IDP) species indicate consistently that a substantial polymer excluded volume and a significant mismatch of the IDP sequence charge patterns can act in concert, but not in isolation, to demix the two IDP species upon condensation. This finding reveals an energetic-geometric interplay in a stochastic, "fuzzy" molecular recognition mechanism that may facilitate subcompartmentalization of membraneless organelles.
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Affiliation(s)
- Tanmoy Pal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonas Wessén
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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24
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Dauer K, Kamm W, Wagner KG, Pfeiffer-Marek S. High-Throughput Screening for Colloidal Stability of Peptide Formulations Using Dynamic and Static Light Scattering. Mol Pharm 2021; 18:1939-1955. [PMID: 33789055 DOI: 10.1021/acs.molpharmaceut.0c01028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selection of an appropriate formulation to stabilize therapeutic proteins against aggregation is one of the most challenging tasks in early-stage drug product development. The amount of aggregates is more difficult to quantify in the case of peptides due to their small molecular size. Here, we investigated the suitability of diffusion self-interaction parameters (kD) and osmotic second virial coefficients (B22) for high-throughput (HT) screening of peptide formulations regarding their aggregation risk. These parameters were compared to the effect of thermal stress on colloidal stability. The formulation matrix comprised six buffering systems at two selected pH values, four tonicity agents, and a common preservative. The results revealed that electrostatic interactions are the main driver to control colloidal stability. Preferred formulations consisted of acetate and succinate buffer at pH 4.5 combined with glycerol or mannitol and optional m-cresol. kD proved to be a suitable surrogate for B22 as an indicator of high colloidal stability in the case of peptides as was previously described for globular proteins and antibodies. Formulation assessment solely based on kD obtained by HT methods offers important insights into the optimization of colloidal stability during the early development of peptide-based liquid formulations and can be performed with a limited amount of peptide (∼360 mg).
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Affiliation(s)
- Katharina Dauer
- Department of Pharmaceutical Technology and Biopharmaceutics, Institute of Pharmacy, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany.,Pharmaceutical Development Platform, Tides Drug Product Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Walter Kamm
- Pharmaceutical Development Platform, Tides Drug Product Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Karl Gerhard Wagner
- Department of Pharmaceutical Technology and Biopharmaceutics, Institute of Pharmacy, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany
| | - Stefania Pfeiffer-Marek
- Pharmaceutical Development Platform, Tides Drug Product Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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25
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Alrosan M, Tan TC, Easa AM, Gammoh S, Alu'datt MH. Molecular forces governing protein-protein interaction: Structure-function relationship of complexes protein in the food industry. Crit Rev Food Sci Nutr 2021; 62:4036-4052. [PMID: 33455424 DOI: 10.1080/10408398.2021.1871589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The application of protein-protein interaction (PPI) has been widely used in various industries, such as food, nutraceutical, and pharmaceutical. A deeper understanding of PPI is needed, and the molecular forces governing proteins and their interaction must be explained. The design of new structures with improved functional properties, e.g., solubility, emulsion, and gelation, has been fueled by the development of structural and colloidal building blocks. In this review, the molecular forces of protein structures are discussed, followed by the relationship between molecular force and structure, ways of a bind of proteins together in solution or at the interface, and functional properties. A more detailed look is thus taken at the relationship between the various influencing factors on molecular forces involved in PPI. These factors include protein properties, such as types, concentration, and mixing ratio, and solvent conditions, such as ionic strength and pH. This review also summarizes methods tha1t are capable of identifying molecular forces in protein and PPI, as well as characterizing protein structure.
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Affiliation(s)
- Mohammad Alrosan
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia.,Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Thuan-Chew Tan
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
| | - Azhar Mat Easa
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
| | - Sana Gammoh
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Muhammad H Alu'datt
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
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26
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Pham NB, Meng WS. Protein aggregation and immunogenicity of biotherapeutics. Int J Pharm 2020; 585:119523. [PMID: 32531452 DOI: 10.1016/j.ijpharm.2020.119523] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/01/2020] [Accepted: 06/06/2020] [Indexed: 12/19/2022]
Abstract
Recombinant proteins are the mainstay of biopharmaceuticals. A key challenge in the manufacturing and formulation of protein biologic products is the tendency for the active pharmaceutical ingredients to aggregate, resulting in irreversible drug loss, and an increase in immunogenicity risk. While the molecular mechanisms of protein aggregation have been discussed extensively in the literature, knowledge gaps remain in connecting the phenomenon in the context of immunogenicity of biotherapeutics. In this review, we discussed factors that drive aggregation of pharmaceutical recombinant proteins, and highlighted methods of prediction and mitigation that can be deployed through the development stages, from formulation to bioproduction. The purpose is to stimulate new dialogs that would bridge the interface between physical characterizations of protein aggregates in biotherapeutics and the functional attributes of the immune system.
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Affiliation(s)
- Ngoc B Pham
- Graduate School of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, Pittsburgh, PA 15282, United States
| | - Wilson S Meng
- Graduate School of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, Pittsburgh, PA 15282, United States; McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA 15219, United States.
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27
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Jost Lopez A, Quoika PK, Linke M, Hummer G, Köfinger J. Quantifying Protein-Protein Interactions in Molecular Simulations. J Phys Chem B 2020; 124:4673-4685. [PMID: 32379446 PMCID: PMC7294537 DOI: 10.1021/acs.jpcb.9b11802] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Interactions
among proteins, nucleic acids, and other macromolecules
are essential for their biological functions and shape the physicochemcial
properties of the crowded environments inside living cells. Binding
interactions are commonly quantified by dissociation constants Kd, and both binding and nonbinding interactions
are quantified by second osmotic virial coefficients B2. As a measure of nonspecific binding and stickiness, B2 is receiving renewed attention in the context
of so-called liquid–liquid phase separation in protein and
nucleic acid solutions. We show that Kd is fully determined by B2 and the fraction
of the dimer observed in molecular simulations of two proteins in
a box. We derive two methods to calculate B2. From molecular dynamics or Monte Carlo simulations using implicit
solvents, we can determine B2 from insertion
and removal energies by applying Bennett’s acceptance ratio
(BAR) method or the (binless) weighted histogram analysis method (WHAM).
From simulations using implicit or explicit solvents, one can estimate B2 from the probability that the two molecules
are within a volume large enough to cover their range of interactions.
We validate these methods for coarse-grained Monte Carlo simulations
of three weakly binding proteins. Our estimates for Kd and B2 allow us to separate
out the contributions of nonbinding interactions to B2. Comparison of calculated and measured values of Kd and B2 can be
used to (re-)parameterize and improve molecular force fields by calibrating
specific affinities, overall stickiness, and nonbinding interactions.
The accuracy and efficiency of Kd and B2 calculations make them well suited for high-throughput
studies of large interactomes.
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Affiliation(s)
- Alfredo Jost Lopez
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Patrick K Quoika
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Max Linke
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.,Institute for Biophysics, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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28
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Pantuso E, Mastropietro TF, Briuglia ML, Gerard CJJ, Curcio E, Ter Horst JH, Nicoletta FP, Di Profio G. On the Aggregation and Nucleation Mechanism of the Monoclonal Antibody Anti-CD20 Near Liquid-Liquid Phase Separation (LLPS). Sci Rep 2020; 10:8902. [PMID: 32483267 PMCID: PMC7264149 DOI: 10.1038/s41598-020-65776-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/30/2020] [Indexed: 12/02/2022] Open
Abstract
The crystallization of Anti-CD20, a full-length monoclonal antibody, has been studied in the PEG400/Na2SO4/Water system near Liquid-Liquid Phase Separation (LLPS) conditions by both sitting-drop vapour diffusion and batch methods. In order to understand the Anti-CD20 crystallization propensity in the solvent system of different compositions, we investigated some measurable parameters, normally used to assess protein conformational and colloidal stability in solution, with the aim to understand the aggregation mechanism of this complex biomacromolecule. We propose that under crystallization conditions a minor population of specifically aggregated protein molecules are present. While this minor species hardly contributes to the measured average solution behaviour, it induces and promotes crystal formation. The existence of this minor species is the result of the LLPS occurring concomitantly under crystallization conditions.
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Affiliation(s)
- Elvira Pantuso
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci Edificio Polifunzionale, 87036, Rende, CS, Italy
| | - Teresa F Mastropietro
- National Research Council of Italy (CNR) - Institute on Membrane Technology (ITM), Via P. Bucci Cubo 17/C, 87036, Rende, CS, Italy
| | - Maria L Briuglia
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation (CMAC), Strathclyde Institute of Pharmacy and Biomedical Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Charline J J Gerard
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation (CMAC), Strathclyde Institute of Pharmacy and Biomedical Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Efrem Curcio
- Department of Environmental Engineering (DIAm), University of Calabria, Via P. Bucci Cubo 45/A, 87036, Rende, CS, Italy
- Seligenda Membrane Technologies S.r.l., Via P. Bucci Cubo 45/A, 87036, Rende, CS, Italy
| | - Joop H Ter Horst
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation (CMAC), Strathclyde Institute of Pharmacy and Biomedical Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Fiore P Nicoletta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci Edificio Polifunzionale, 87036, Rende, CS, Italy.
| | - Gianluca Di Profio
- National Research Council of Italy (CNR) - Institute on Membrane Technology (ITM), Via P. Bucci Cubo 17/C, 87036, Rende, CS, Italy.
- Seligenda Membrane Technologies S.r.l., Via P. Bucci Cubo 45/A, 87036, Rende, CS, Italy.
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29
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Schleinitz M, Nolte L, Brandenbusch C. Predicting protein-protein interactions using the ePC-SAFT equation-of-state. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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31
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Singh P, Roche A, van der Walle CF, Uddin S, Du J, Warwicker J, Pluen A, Curtis R. Determination of Protein-Protein Interactions in a Mixture of Two Monoclonal Antibodies. Mol Pharm 2019; 16:4775-4786. [PMID: 31613625 DOI: 10.1021/acs.molpharmaceut.9b00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The coformulation of monoclonal antibody (mAb) mixtures provides an attractive route to achieving therapeutic efficacy where the targeting of multiple epitopes is necessary. Controlling and predicting the behavior of such mixtures requires elucidating the molecular basis for the self- and cross-protein-protein interactions and how they depend on solution variables. While self-interactions are now beginning to be well understood, systematic studies of cross-interactions between mAbs in solution do not exist. Here, we have used static light scattering to measure the set of self- and cross-osmotic second virial coefficients in a solution containing a mixture of two mAbs, mAbA and mAbB, as a function of ionic strength and pH. mAbB exhibits strong association at a low ionic strength, which is attributed to an electrostatic attraction that is enhanced by the presence of a strong short-ranged attraction of nonelectrostatic origin. Under all solution conditions, the measured cross-interactions are intermediate self-interactions and follow similar patterns of behavior. There is a strong electrostatic attraction at higher pH values, reflecting the behavior of mAbB. Protein-protein interactions become more attractive with an increasing pH due to reducing the overall protein net charges, an effect that is attenuated with an increasing ionic strength due to the screening of electrostatic interactions. Under moderate ionic strength conditions, the reduced cross-virial coefficient, which reflects only the energetic contribution to protein-protein interactions, is given by a geometric average of the corresponding self-coefficients. We show the relationship can be rationalized using a patchy sphere model, where the interaction energy between sites i and j is given by the arithmetic mean of the i-i and j-j interactions. The geometric mean does not necessarily apply to all mAb mixtures and is expected to break down at a lower ionic strength due to the nonadditivity of electrostatic interactions.
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Affiliation(s)
- Priyanka Singh
- Manchester Pharmacy School , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Aisling Roche
- School of Chemical Engineering and Analytical Science , University of Manchester , Manchester M1 7DN , United Kingdom
| | - Christopher F van der Walle
- School of Chemical Engineering and Analytical Science , University of Manchester , Manchester M1 7DN , United Kingdom.,Dosage Form Design & Development , AstraZeneca , Granta Park , Cambridge CB21 6GH , United Kingdom
| | - Shahid Uddin
- Formulation Sciences CMC , Immunocore , Milton Park , Abingdon OX14 4RW , United Kingdom
| | - Jiali Du
- Dosage Form Design & Development , AstraZeneca , Gaithersburg MD20878 , United States
| | - Jim Warwicker
- School of Chemistry , University of Manchester , Manchester M1 7DN , United Kingdom
| | - Alain Pluen
- Manchester Pharmacy School , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Robin Curtis
- School of Chemical Engineering and Analytical Science , University of Manchester , Manchester M1 7DN , United Kingdom
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32
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Schleinitz M, Sadowski G, Brandenbusch C. Protein-protein interactions and water activity coefficients can be used to aid a first excipient choice in protein formulations. Int J Pharm 2019; 569:118608. [PMID: 31415881 DOI: 10.1016/j.ijpharm.2019.118608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 10/26/2022]
Abstract
With respect to all biopharmaceuticals marketed to date, monoclonal antibodies represent the largest fraction with more than 48% market share (2012). However, the development of biopharmaceutical formulations is a challenging task, and time-consuming and cost-intensive high-throughput screenings are still state-of-the-art in formulation design. These screening techniques are almost exclusively based on heuristic decisions thus the benefit in terms of mechanistic understanding is often unclear. It requires novel, physical-sound methods to enhance/optimize future formulation development, ideally by understanding molecular interactions in these complex solutions. A suitable and evaluated measure-of-choice to characterize protein-protein interactions in aqueous protein solutions is the second osmotic virial coefficient B22 which can be measured using static light scattering techniques. Furthermore B22 can be modeled/predicted via the extended mxDLVO model for protein-protein interactions in the presence of single excipients and excipient-mixtures. Building up on this approach, giving an additional insight into water-water and water-excipient interactions, the thermodynamic equation-of-state ePC-SAFT is used to calculate water activity coefficients in the presence of excipient-mixtures. Immunoglobulin G (IgG) was chosen as a model protein to predict B22-values for IgG in the presence of model excipient-mixtures (trehalose-NaCl, l-histidine-trehalose, l-histidine-NaCl). The combination of water activity coefficients and B22 allows to quickly identify a first guess on suitable formulation conditions that then can be further evaluated with existing methods/knowledge.
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Affiliation(s)
- Miko Schleinitz
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Christoph Brandenbusch
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Emil-Figge-Str. 70, 44227 Dortmund, Germany.
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33
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Qin S, Zhou HX. Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform. J Phys Chem B 2019; 123:8203-8215. [PMID: 31490691 DOI: 10.1021/acs.jpcb.9b06808] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The second virial coefficient, B2, measures a protein solution's deviation from ideal behavior. It is widely used to predict or explain solubility, crystallization condition, aggregation propensity, and critical temperature for liquid-liquid phase separation. B2 is determined by the interaction energy between two protein molecules and, specifically, by the integration of the Mayer f-function in the relative configurational space (translation and rotation) of the two molecules. Simple theoretical models, such as one attributed to Derjaguin, Landau, Verwey, and Overbeek (DLVO), can fit the dependence of B2 on salt concentrations. However, model parameters derived often are physically unrealistic and hardly transferable from protein to protein. Previous B2 calculations incorporating atomistic details were done with limited sampling in the configurational space, due to enormous computational cost. Our FMAP method, based on fast Fourier transform, can considerably accelerate such calculations, and here we adapt it to calculate B2 values for proteins represented at the atomic level in implicit solvent. After tuning of a single parameter in the energy function, FMAPB2 predicts well the B2 values for lysozyme and other proteins over wide ranges of solvent conditions (salt concentration, pH, and temperature). The method is available as a web server at http://pipe.rcc.fsu.edu/fmapb2 .
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Affiliation(s)
- Sanbo Qin
- Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States.,Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 32306 , United States
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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34
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Kato A, Katsuki Y, Nishimoto E. Specific monovalent cation effect on protein-protein interactions revealed by protein rotational diffusion analysis. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Kim DM, Yao X, Vanam RP, Marlow MS. Measuring the effects of macromolecular crowding on antibody function with biolayer interferometry. MAbs 2019; 11:1319-1330. [PMID: 31401928 PMCID: PMC6748605 DOI: 10.1080/19420862.2019.1647744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biotherapeutic proteins are commonly dosed at high concentrations into the blood, which is an inherently complex, crowded solution with substantial protein content. The effects of macromolecular crowding may lead to an appreciable level of non-specific hetero-association in this physiological environment. Therefore, developing a method to characterize the diverse consequences of non-specific interactions between proteins under such non-ideal, crowded conditions, which deviate substantially from those commonly employed for in vitro characterization, is vital to achieving a more complete picture of antibody function in a biological context. In this study, we investigated non-specific interactions between human serum albumin (HSA) and two monoclonal antibodies (mAbs) by static light scattering and determined these interactions are both ionic strength-dependent and mAb-dependent. Using biolayer interferometry (BLI), we assessed the effect of HSA on antigen binding by mAbs, demonstrating that these non-specific interactions have a functional impact on mAb:antigen interactions, particularly at low ionic strength. While this effect is mitigated at physiological ionic strength, our in vitro data support the notion that HSA in the blood may lead to non-specific interactions with mAbs in vivo, with a potential impact on their interactions with antigen. Furthermore, the BLI method offers a high-throughput advantage compared to orthogonal techniques such as analytical ultracentrifugation and is amenable to a greater variety of solution conditions compared to nuclear magnetic resonance spectroscopy. Our study demonstrates that BLI is a viable technology for examining the impact of non-specific interactions on specific biologically relevant interactions, providing a direct method to assess binding events in crowded conditions.
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Affiliation(s)
- Dorothy M Kim
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Xiao Yao
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Ram P Vanam
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Michael S Marlow
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA.,Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc ., Ridgefield , CT , USA
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36
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Hale CS, McBride DW, Batarseh R, Hughey J, Vang K, Rodgers VGJ. Development and applications of a concentrating membrane osmometer for colloid solutions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:034102. [PMID: 30927796 DOI: 10.1063/1.5065512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
The membrane concentration osmometer coupled with multiple sample preparations has been used for over a century to determine a number of colloidal properties. At the dilute region, this method has been used to determine solute molecular mass. When the solution is proteinaceous, in the intermediate region, the osmotic pressure profile provides the second virial coefficient, useful for estimating protein crystallization and salting out. At the most crowded concentrations, it provides insight into protein hydration and protein-ion interaction. One of the most critical factors in generating the osmotic pressure profile is minimizing the quantity of protein used and reducing the error in preparing samples. Here, we introduce a membrane concentrating osmometer that allows one to measure osmotic pressure over a wide concentration range from a single sample. A test study was performed using the osmotic pressure profile of self-crowded bovine serum albumin solutions. The resulting profile was in good agreement with previous data in the literature obtained from multiple sample studies. The osmotic pressure profile was further used with a free solvent-based osmotic pressure model to determine protein hydration and ion binding. These results were in excellent agreement with literature values. This concentrating osmometer has several advantages over a conventional concentration osmometer for obtaining the osmotic pressure profile for proteinaceous solutions: (1) the amount of protein required is significantly decreased, (2) the potential for experimental error in sample preparation diminishes, and (3) the time for generating the osmotic pressure profile is substantially reduced.
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Affiliation(s)
- Christopher S Hale
- B2K Group (Biotransport and Bioreaction Kinetics Group), Department of Bioengineering, University of California, A127 Bourns Hall, Riverside, California 92521, USA
| | - Devin W McBride
- B2K Group (Biotransport and Bioreaction Kinetics Group), Department of Bioengineering, University of California, A127 Bourns Hall, Riverside, California 92521, USA
| | - Ramsey Batarseh
- B2K Group (Biotransport and Bioreaction Kinetics Group), Department of Bioengineering, University of California, A127 Bourns Hall, Riverside, California 92521, USA
| | - Jordan Hughey
- B2K Group (Biotransport and Bioreaction Kinetics Group), Department of Bioengineering, University of California, A127 Bourns Hall, Riverside, California 92521, USA
| | - Kevin Vang
- B2K Group (Biotransport and Bioreaction Kinetics Group), Department of Bioengineering, University of California, A127 Bourns Hall, Riverside, California 92521, USA
| | - V G J Rodgers
- B2K Group (Biotransport and Bioreaction Kinetics Group), Department of Bioengineering, University of California, A127 Bourns Hall, Riverside, California 92521, USA
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37
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Ferreira GM, Calero-Rubio C, Sathish HA, Remmele RL, Roberts CJ. Electrostatically Mediated Protein-Protein Interactions for Monoclonal Antibodies: A Combined Experimental and Coarse-Grained Molecular Modeling Approach. J Pharm Sci 2019; 108:120-132. [DOI: 10.1016/j.xphs.2018.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/27/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023]
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38
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Woldeyes MA, Qi W, Razinkov VI, Furst EM, Roberts CJ. How Well Do Low- and High-Concentration Protein Interactions Predict Solution Viscosities of Monoclonal Antibodies? J Pharm Sci 2019; 108:142-154. [DOI: 10.1016/j.xphs.2018.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/10/2018] [Accepted: 07/03/2018] [Indexed: 11/26/2022]
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39
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Steric Repulsion Forces Contributed by PEGylation of Interleukin-1 Receptor Antagonist Reduce Gelation and Aggregation at the Silicone Oil-Water Interface. J Pharm Sci 2018; 108:162-172. [PMID: 30395835 DOI: 10.1016/j.xphs.2018.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
Abstract
Silicone oil, used as a lubricating coating in pharmaceutical containers, has been implicated as a cause of therapeutic protein aggregation. After adsorbing to silicone oil-water interfaces, proteins may form interfacial gels, which can be transported into solution as insoluble aggregates if the interfaces are perturbed. Mechanical interfacial perturbation of both monomeric recombinant human interleukin-1 receptor antagonist (rhIL-1ra) and PEGylated rhIL-1ra (PEG rhIL-1ra) in siliconized syringes resulted in losses of soluble monomeric protein. However, the loss of rhIL-1ra was twice that for PEG rhIL-1ra; even though in solution, PEG rhIL-1ra had a lower ΔGunf and exhibited a more perturbed tertiary structure at the interface. Net protein-protein interactions in solution for rhIL-1ra were attractive but increased steric repulsion because of PEGylation led to net repulsive interactions for PEG rhIL-1ra. Attractive interactions for rhIL-1ra were associated with increases in intermolecular β-sheet content at the interface, whereas no intermolecular β-sheet structures were observed for adsorbed PEG rhIL-1ra. rhIL-1ra formed interfacial gels that were 5 times stronger than those formed by PEG rhIL-1ra. Thus, the steric repulsion contributed by the PEGylation resulted in decreased interfacial gelation and in the reduction of aggregation, in spite of the destabilizing effects of PEGylation on the protein's conformational stability.
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40
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Dignon GL, Zheng W, Best RB, Kim YC, Mittal J. Relation between single-molecule properties and phase behavior of intrinsically disordered proteins. Proc Natl Acad Sci U S A 2018; 115:9929-9934. [PMID: 30217894 PMCID: PMC6176625 DOI: 10.1073/pnas.1804177115] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Proteins that undergo liquid-liquid phase separation (LLPS) have been shown to play a critical role in many physiological functions through formation of condensed liquid-like assemblies that function as membraneless organelles within biological systems. To understand how different proteins may contribute differently to these assemblies and their functions, it is important to understand the molecular driving forces of phase separation and characterize their phase boundaries and material properties. Experimental studies have shown that intrinsically disordered regions of these proteins are a major driving force, as many of them undergo LLPS in isolation. Previous work on polymer solution phase behavior suggests a potential correspondence between intramolecular and intermolecular interactions that can be leveraged to discover relationships between single-molecule properties and phase boundaries. Here, we take advantage of a recently developed coarse-grained framework to calculate the θ temperature [Formula: see text], the Boyle temperature [Formula: see text], and the critical temperature [Formula: see text] for 20 diverse protein sequences, and we show that these three properties are highly correlated. We also highlight that these correlations are not specific to our model or simulation methodology by comparing between different pairwise potentials and with data from other work. We, therefore, suggest that smaller simulations or experiments to determine [Formula: see text] or [Formula: see text] can provide useful insights into the corresponding phase behavior.
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Affiliation(s)
- Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015;
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41
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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O'Brien CJ, Calero-Rubio C, Razinkov VI, Robinson AS, Roberts CJ. Biophysical characterization and molecular simulation of electrostatically driven self-association of a single-chain antibody. Protein Sci 2018; 27:1275-1285. [PMID: 29637646 DOI: 10.1002/pro.3415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022]
Abstract
Colloidal protein-protein interactions (PPI) are often expected to impact key behaviors of proteins in solution, such as aggregation rates and mechanisms, aggregate structure, protein solubility, and solution viscosity. PPI of an anti-fluorescein single chain antibody variable fragment (scFv) were characterized experimentally at low to intermediate ionic strength using a combination of static light scattering and sedimentation equilibrium ultracentrifugation. Surprisingly, the results indicated that interactions were strongly net-attractive and electrostatics promoted self-association. Only repulsive interactions were expected based on prior work and calculations based a homology model of a related scFv crystal structure. However, the crystal structure lacks the charged, net-neutral linker sequence. PyRosetta was used to generate a set of scFv structures with different linker conformations, and coarse-grained Monte Carlo simulations were used to evaluate the effect of different linker configurations via second osmotic virial coefficient (B22 ) simulations. The results show that the configuration of the linker has a significant effect on the calculated B22 values, and can result in strong electrostatic attractions between oppositely charged residues on the protein surface. This is particularly relevant for development of non-natural antibody products, where charged linkers and other loop regions may be prevalent. The results also provide a preliminary computational framework to evaluate the effect of unstructured linkers on experimental protein-protein interaction parameters such as B22 .
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Affiliation(s)
- Christopher J O'Brien
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716
| | - Cesar Calero-Rubio
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716
| | | | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716.,Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Los Angeles, 70118
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716
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Islam S, Inglefield DL, Velev OD. Revisiting the colloidal fundamentals of water-dispersible polyesters: interactions and self-assembly of polymer nanoaggregates in water. SOFT MATTER 2018; 14:2118-2130. [PMID: 29488992 DOI: 10.1039/c7sm02536j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Water-dispersible sulfopolyesters are a major class of film-forming and solution-modifying polymers, which are routinely used in applications such as inks, adhesives, coatings, and personal care products. Since these polyesters are designed to be used as waterborne dispersions, understanding their colloidal interactions in dispersions is critical for their application. By using a range of commercially available water-dispersible sulfopolyesters as a model system, we investigated the relationship between their molecular composition, colloidal interactions, and phase equilibria. We established how these polyesters undergo different molecular configurations and nanoaggregated states, depending on the nature of the liquid medium. For example, the polyesters are in a solvated molecular form in certain organic solvents, whereas they self-assemble into compact nanoaggregates in water. We found that the interactions of these nanoaggregates follow the classical DLVO theory of critical colloidal coagulation where the stability of these nanoparticles is extremely sensitive to multivalent electrolytes (i.e., Ccrit ∝ z-6). By using static, dynamic, and electrophoretic light scattering, we correlate their nanoscale intermolecular and interparticle interactions with corresponding macroscale phase behavior in both organic medium and water, based on the theoretical framework of second virial coefficients. We present a model for nanoaggregate formation in water based on the critical surface charge density of these nanoparticles. Such fundamental understanding of colloidal interactions could be used to efficiently control and improve the colloidal stability and film-formation ability of these polyesters and may enable the design of novel high-performance surfactant-free waterborne dispersion systems.
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Affiliation(s)
- Sabina Islam
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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Sorret LL, DeWinter MA, Schwartz DK, Randolph TW. Protein-protein interactions controlling interfacial aggregation of rhIL-1ra are not described by simple colloid models. Protein Sci 2018; 27:1191-1204. [PMID: 29388282 DOI: 10.1002/pro.3382] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 01/21/2023]
Abstract
We investigated the effects of protein-protein interaction strength on interfacial viscoelastic properties and aggregation of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) at silicone oil-water interfaces. Osmotic second virial coefficients determined by static light scattering were used to quantify protein-protein interactions in bulk solution. Attractive protein-protein interactions dominated at low ionic strengths and their magnitude decreased with increasing ionic strength, in contrast to repulsive interactions that would be expected based on uniformly charged sphere models. Interfacial shear rheometry was used to characterize rhIL-1ra interfacial layers. More attractive protein-protein interactions in bulk solution correlated with stronger interfacial gels. Thioflavin-T fluorescence measurements indicated that the intermolecular β-sheet content of rhIL-1ra incubated in the presence of silicone oil-water interfaces correlated with gel strength. Siliconized syringes were used to probe the effects of mechanical perturbation of the interfacial gel layers. When rhIL-1ra solutions in siliconized glass syringes were subjected to end-over-end rotation, monomeric rhIL-1ra was lost from solution, and particles containing aggregated protein were released into the bulk aqueous phase. The loss of monomeric rhIL-1ra in response to mechanical perturbation was highest under the conditions where the strongest gels were observed. Aggregation of rhIL-1ra was strictly interface-induced and growth of aggregates in the bulk solution was not observed, even in the presence of particles released from silicone oil-water interfaces.
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Affiliation(s)
- Lea L Sorret
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Madison A DeWinter
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Theodore W Randolph
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309
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Fujii S, Takahashi R, Ha LJ, Sakurai K. A tetramer micelle: the smallest aggregation number corresponding to the vertex number of regular polyhedra in platonic micelles. SOFT MATTER 2018; 14:875-878. [PMID: 29303521 DOI: 10.1039/c7sm02028g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, we describe the construction of tetramer micelles based on the idea of "Platonic micelles" whose aggregation number (Nagg) matches the vertex number of regular polyhedra and exhibits the monodispersity and discreteness in the Nagg.
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Affiliation(s)
- Shota Fujii
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Kitakyushu, Fukuoka 808-0135, Japan.
| | - Rintaro Takahashi
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Kitakyushu, Fukuoka 808-0135, Japan.
| | - Lee Ji Ha
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Kitakyushu, Fukuoka 808-0135, Japan.
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Kitakyushu, Fukuoka 808-0135, Japan.
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Dudukovic NA, Hudson BC, Paravastu AK, Zukoski CF. Self-assembly pathways and polymorphism in peptide-based nanostructures. NANOSCALE 2018; 10:1508-1516. [PMID: 29303206 DOI: 10.1039/c7nr06724k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dipeptide derivative molecules can self-assemble into space-filling nanofiber networks at low volume fractions (<1%), allowing the formation of molecular gels with tunable mechanical properties. The self-assembly of dipeptide-based molecules is reminiscent of pathological amyloid fibril formation by naturally occurring polypeptides. Fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) is the most widely studied such molecule, but the thermodynamic and kinetic phenomena giving rise to Fmoc-FF gel formation remain poorly understood. We have previously presented evidence that the gelation process is a first order phase transition characterized by low energy barriers to nucleation, short induction times, and rapid quasi-one-dimensional crystal growth, stemming from solvent-solute interactions and highly specific molecular packing. Here, we discuss the phase behavior of Fmoc-FF in different solvents. We find that Fmoc-FF gel formation can be induced in apolar solvents, in addition to previously established pathways in aqueous systems. We further show that in certain solvent systems anisotropic crystals (nanofibers) are an initial metastable state, after which macroscopic crystal aggregates with no preferred axis of growth are formed. The molecular conformation is sensitive to solvent composition during assembly, indicating that Fmoc-FF may be a simple model system to study complex thermodynamic and kinetic phenomena involved in peptide self-assembly.
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Affiliation(s)
- Nikola A Dudukovic
- Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551, USA.
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Manning MC, Liu J, Li T, Holcomb RE. Rational Design of Liquid Formulations of Proteins. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:1-59. [DOI: 10.1016/bs.apcsb.2018.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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48
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Calero-Rubio C, Ghosh R, Saluja A, Roberts CJ. Predicting Protein-Protein Interactions of Concentrated Antibody Solutions Using Dilute Solution Data and Coarse-Grained Molecular Models. J Pharm Sci 2017; 107:1269-1281. [PMID: 29274822 DOI: 10.1016/j.xphs.2017.12.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions for solutions of an IgG1 molecule were quantified using static light scattering (SLS) measurements from low to high protein concentrations (c2). SLS was used to determine second osmotic virial coefficients (B22) at low c2, and excess Rayleigh profiles (Rex/K vs. c2) and zero-q structure factors (Sq=0) as a function of c2 at higher c2 for a series of conditions (pH, sucrose concentration, and total ionic strength [TIS]). Repulsive (attractive) interactions were observed at low TIS (high TIS) for pH 5 and 6.5, with increasing repulsions when 5% w/w sucrose was also present. Previously developed and refined coarse-grained antibody models were used to fit model parameters from B22 versus TIS data. The resulting parameters from low-c2 conditions were used as the sole input to multiprotein Monte Carlo simulations to predict high-c2Rex/K and Sq=0 behavior up to 150 g/L. Experimental results at high-c2 conditions were quantitatively predicted by the simulations for the coarse-grained models that treated antibody molecules as either 6 or 12 (sub) domains, which preserved the basic shape of a monoclonal antibody. Finally, preferential accumulation of sucrose around the protein surface was identified via high-precision density measurements, which self-consistently explained the simulation and experimental SLS results.
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Affiliation(s)
- Cesar Calero-Rubio
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Ranendu Ghosh
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Atul Saluja
- Department of Drug Product Science and Technology, Bristol-Myers Squibb, New Brunswick, New Jersey 08901
| | - Christopher J Roberts
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716.
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49
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Vogtt K, Beaucage G, Weaver M, Jiang H. Thermodynamic stability of worm-like micelle solutions. SOFT MATTER 2017; 13:6068-6078. [PMID: 28782782 DOI: 10.1039/c7sm01132f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Worm-like micelles (WLMs) are nano-scale self-assemblies widely used for viscosity enhancement, for drug delivery, and in personal care products. The stability of WLMs under variable ionic and surfactant concentrations is important to applications of these fascinating materials. In this work it is demonstrated that a virial approach can be used to understand and predict WLM stability. A mixed surfactant system consisting of sodium laureth sulfate and cocoamidopropyl betaine was examined using small-angle neutron scattering. A linear relationship between the second virial coefficient, A2, and the salt to surfactant ratio, Θs-s, is derived and demonstrated. The Θs-s-dependent term is described via association/dissociation kinetics of salt ions between the bulk and an ion cloud surrounding the WLMs yielding, , where Keq is the association/dissociation constant, nsurf is the molar surfactant concentration, b is the molar excluded volume, M the WLM molar mass, Θs-s is the salt-surfactant ratio and Θ is the salt-surfactant ratio where the interactions are solely determined by the excluded volume. The ratio b/M2 is independent of WLM contour length. The exponent ϑ is found to be approximately 5/4 in agreement with polymer scaling laws for the semi-dilute regime in good solvents.
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Affiliation(s)
- Karsten Vogtt
- Chemical and Materials Engineering, University of Cincinnati, Cincinnati, OH 45221, USA.
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50
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Lin Y, Currie SL, Rosen MK. Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs. J Biol Chem 2017; 292:19110-19120. [PMID: 28924037 PMCID: PMC5704491 DOI: 10.1074/jbc.m117.800466] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 09/12/2017] [Indexed: 01/04/2023] Open
Abstract
Liquid–liquid phase separation (LLPS) is thought to contribute to the establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane. RNA granules control RNA metabolism and comprise a large class of condensates that are enriched in RNA-binding proteins and RNA molecules. Many RNA granule proteins are composed of both modular domains and intrinsically disordered regions (IDRs) having low amino acid sequence complexity. Phase separation of these molecules likely plays an important role in the generation and stability of RNA granules. To understand how folded domains and IDRs can cooperate to modulate LLPS, we generated a series of engineered proteins. These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline–rich-motif (polyPRM) ligand. We found that the wild-type IDR promotes LLPS of the polySH3–polyPRM system, decreasing the phase separation threshold concentration by 8-fold. Systematic mutation of tyrosine residues in Gly/Ser-Tyr-Gly/Ser motifs of the IDR reduced this effect, depending on the number but not on the position of these substitutions. Mutating all tyrosines to non-aromatic residues or phosphorylating the IDR raised the phase separation threshold above that of the unmodified polySH3–polyPRM pair. These results show that low-complexity IDRs can modulate LLPS both positively and negatively, depending on the degree of aromaticity and phosphorylation status. Our findings provide plausible mechanisms by which these sequences could alter RNA granule properties on evolutionary and cellular timescales.
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Affiliation(s)
- Yuan Lin
- From the Department of Biophysics, University of Texas Southwestern Medical Center and.,the Howard Hughes Medical Institute, Dallas, Texas 75390
| | - Simon L Currie
- From the Department of Biophysics, University of Texas Southwestern Medical Center and.,the Howard Hughes Medical Institute, Dallas, Texas 75390
| | - Michael K Rosen
- From the Department of Biophysics, University of Texas Southwestern Medical Center and .,the Howard Hughes Medical Institute, Dallas, Texas 75390
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