1
|
Gulotta A, Polimeni M, Lenton S, Starr CG, Stradner A, Zaccarelli E, Schurtenberger P. Combining Scattering Experiments and Colloid Theory to Characterize Charge Effects in Concentrated Antibody Solutions. Mol Pharm 2024; 21:2250-2271. [PMID: 38661388 PMCID: PMC11080060 DOI: 10.1021/acs.molpharmaceut.3c01023] [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: 10/30/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure factor, the collective diffusion coefficient, or the relative viscosity, and their concentration dependence. Further, charges play an important role in the colloidal stability of mAbs. There exist standard experimental tools to characterize mAb net charges, such as the measurement of the electrophoretic mobility, the second virial coefficient, or the diffusion interaction parameter. However, the resulting values are difficult to directly relate to the actual overall net charge of the antibody and to theoretical predictions based on its known molecular structure. Here, we report the results of a systematic investigation of the solution properties of a charged IgG1 mAb as a function of concentration and ionic strength using a combination of electrophoretic measurements, static and dynamic light scattering, small-angle X-ray scattering, and tracer particle-based microrheology. We analyze and interpret the experimental results using established colloid theory and coarse-grained computer simulations. We discuss the potential and limits of colloidal models for the description of the interaction effects of charged mAbs, in particular pointing out the importance of incorporating shape and charge anisotropy when attempting to predict structural and dynamic solution properties at high concentrations.
Collapse
Affiliation(s)
- Alessandro Gulotta
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
| | - Marco Polimeni
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
| | - Samuel Lenton
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
| | - Charles G. Starr
- Biologics
Drug Product Development and Manufacturing, CMC Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Anna Stradner
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
- LINXS
Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
| | - Emanuela Zaccarelli
- Institute
for Complex Systems, National Research Council (ISC−CNR), Piazzale Aldo Moro 5, Rome 00185, Italy
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Peter Schurtenberger
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
- LINXS
Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
| |
Collapse
|
2
|
Zhang T, Li B, Dong W, Wan Y, Li Y. Acidic pH or salt treatment can convert soluble antibody aggregates in culture harvest into monomers and improve Protein A chromatography step yield. Protein Expr Purif 2024; 215:106391. [PMID: 37939750 DOI: 10.1016/j.pep.2023.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
While purifying a regular monospecific antibody, we found that the Protein A step yield was much lower than expected. Further studies revealed that the antibody formed large-size aggregates that did not bind to the Protein A resin, hence leading to dropped recovery. In an attempt to solve this low yield issue, we found that mildly acidic pH or ammonium sulfate treatment can partially convert the aggregates into monomers. In addition, when acidic pH treated culture harvest was processed by Protein A chromatography, the yield was restored to the normal range, suggesting that the monomers recovered from aggregates regained Protein A binding capability. Thus, low pH treatment of culture harvest can be potentially used as a general approach for improving Protein A step yield in cases where non-binding antibody aggregates are formed through noncovalent interactions.
Collapse
Affiliation(s)
- Ting Zhang
- Downstream Process Development (DSPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Bin Li
- Downstream Process Development (DSPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Wanyuan Dong
- Downstream Process Development (DSPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Yan Wan
- Downstream Process Development (DSPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China.
| | - Yifeng Li
- Downstream Process Development (DSPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China.
| |
Collapse
|
3
|
Duan C, Wang R. A Unified Description of Salt Effects on the Liquid-Liquid Phase Separation of Proteins. ACS CENTRAL SCIENCE 2024; 10:460-468. [PMID: 38435530 PMCID: PMC10906038 DOI: 10.1021/acscentsci.3c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 03/05/2024]
Abstract
Protein aggregation via liquid-liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.
Collapse
Affiliation(s)
- Chao Duan
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Rui Wang
- Department
of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Lab, Berkeley, California 94720, United States
| |
Collapse
|
4
|
Brown SJ, Ryan TM, Drummond CJ, Greaves TL, Han Q. Lysozyme aggregation and unfolding in ionic liquid solvents: Insights from small angle X-ray scattering and high throughput screening. J Colloid Interface Sci 2024; 655:133-144. [PMID: 37931553 DOI: 10.1016/j.jcis.2023.10.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/09/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023]
Abstract
Understanding protein behaviour is crucial for developing functional solvent systems. Ionic liquids (ILs) are designer salts with versatile ion combinations, where some suppress unfavourable protein behaviour. This work utilizes small angle X-ray scattering (SAXS) to investigate the size and shape changes of model protein hen egg white lysozyme (HEWL) in 137 IL and salt solutions. Guinier, Kratky, and pair distance distribution analysis were used to evaluate the protein size, shape, and aggregation changes in these solvents. At low IL and salt concentration (1 mol%), HEWL remained monodispersed and globular. Most ILs increased HEWL size compared to buffer, while the nitrate and mesylate anions induced the most significant size increases. IL cation branching, hydroxyl groups, and longer alkyl chains counteracted this size increase. Common salts exhibited specific ion effects, while the IL effect varied with concentration due to complex ion-pairing. Protein aggregation and unfolding occurred at 10 mol% IL, altering the protein shape, especially for ILs with multiple alkyl chains on the cation, or with a mesylate/nitrate anion. This study highlights the usefulness of adopting a high-throughput SAXS strategy for understanding IL effects on protein behaviour and provides insights on controlling protein aggregation and unfolding with ILs.
Collapse
Affiliation(s)
- Stuart J Brown
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Timothy M Ryan
- SAXS/WAXS Beamline, Australian Synchrotron, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| |
Collapse
|
5
|
Thapa S, Clark F, Schneebeli ST, Li J. Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study. J Chem Theory Comput 2024; 20:375-384. [PMID: 38013425 PMCID: PMC11070933 DOI: 10.1021/acs.jctc.3c00699] [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] [Indexed: 11/29/2023]
Abstract
Peptide self-assembly is critical for biomedical and material discovery and production. While it is costly to experimentally test every possible peptide design, computational assessment provides an affordable solution to evaluate many designs and prioritize synthesis and characterization. Following a theoretical investigation, we present a systematic analysis of all-atom and coarse-grained simulations to predict peptide self-assembly. Benchmarking studies of two model dipeptides allow us to assess the impacts of intrinsic properties (such as amino acids and terminal modifications) and external environment (such as salinity) on the simulated aggregation. Further examination of 20 oligopeptides containing two to five amino acids shows good agreement among our theory, simulations, and prior experimental observations. The success rate of our prediction is 90%. Therefore, our theory, simulation, and analysis can be useful to identify peptide designs that can self-assemble and predict the potential nanostructures. These findings lay the ground for future virtual screening of peptide-assembled nanostructures and computer-aided biologics design.
Collapse
Affiliation(s)
- Subhadra Thapa
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | - Finley Clark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | - Severin. T. Schneebeli
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| |
Collapse
|
6
|
Brudar S, Breydo L, Chung E, Dill KA, Ehterami N, Phadnis K, Senapati S, Shameem M, Tang X, Tayyab M, Hribar-Lee B. Antibody association in solution: cluster distributions and mechanisms. MAbs 2024; 16:2339582. [PMID: 38666507 PMCID: PMC11057677 DOI: 10.1080/19420862.2024.2339582] [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: 12/07/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Understanding factors that affect the clustering and association of antibodies molecules in solution is critical to their development as therapeutics. For 19 different monoclonal antibody (mAb) solutions, we measured the viscosities, the second virial coefficients, the Kirkwood-Buff integrals, and the cluster distributions of the antibody molecules as functions of protein concentration. Solutions were modeled using the statistical-physics Wertheim liquid-solution theory, representing antibodies as Y-shaped molecular structures of seven beads each. We found that high-viscosity solutions result from more antibody molecules per cluster. Multi-body properties such as viscosity are well predicted experimentally by the 2-body Kirkwood-Buff quantity, G22, but not by the second virial coefficient, B22, and well-predicted theoretically from the Wertheim protein-protein sticking energy. Weakly interacting antibodies are rate-limited by nucleation; strongly interacting ones by propagation. This approach gives a way to relate micro to macro properties of solutions of associating proteins.
Collapse
Affiliation(s)
- Sandi Brudar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Leonid Breydo
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Elisha Chung
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
- Department of Chemistry and Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA
| | - Nasim Ehterami
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Ketan Phadnis
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Samir Senapati
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Mohammed Shameem
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Xiaolin Tang
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Muhammmad Tayyab
- Formulation Development Group, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
7
|
Vlachy V, Kalyuzhnyi YV, Hribar-Lee B, Dill KA. Protein Association in Solution: Statistical Mechanical Modeling. Biomolecules 2023; 13:1703. [PMID: 38136574 PMCID: PMC10742237 DOI: 10.3390/biom13121703] [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: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics. However, past such approaches, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, were limited to modeling proteins as spheres, and contained no microscopic structure-property relations. Recently, this limitation has been partly overcome by bringing the powerful Wertheim theory of associating molecules to bear on protein association equilibria. Here, we review these developments.
Collapse
Affiliation(s)
- Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | | | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY 11794, USA;
- Department of Chemistry, Physics and Astronomy, Stony Brook University, New York, NY 11790, USA
| |
Collapse
|
8
|
Qin S, Zhou HX. Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence. Commun Biol 2023; 6:886. [PMID: 37644195 PMCID: PMC10465548 DOI: 10.1038/s42003-023-05270-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature (Tc). We obtain a higher Tc for a known high-Tc γ-crystallin, γF, than for a low-Tc paralog, γB. The difference in Tc is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in Tc. This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
Collapse
Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
| |
Collapse
|
9
|
Han Q, El Mohamad M, Brown S, Zhai J, Rosado CJ, Shen Y, Blanch EW, Drummond CJ, Greaves TL. Small angle X-ray scattering investigation of ionic liquid effect on the aggregation behavior of globular proteins. J Colloid Interface Sci 2023; 648:376-388. [PMID: 37302221 DOI: 10.1016/j.jcis.2023.05.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Globular proteins are well-folded model proteins, where ions can substantially influence their structure and aggregation. Ionic liquids (ILs) are salts in the liquid state with versatile ion combinations. Understanding the IL effect on protein behavior remains a major challenge. Here, we employed small angle X-ray scattering to investigate the effect of aqueous ILs on the structure and aggregation of globular proteins, namely, hen egg white lysozyme (Lys), human lysozyme (HLys), myoglobin (Mb), β-lactoglobulin (βLg), trypsin (Tryp) and superfolder green fluorescent protein (sfGFP). The ILs contain ammonium-based cations paired with the mesylate, acetate or nitrate anion. Results showed that only Lys was monomeric, whereas the other proteins formed small or large aggregates in buffer. Solutions with over 17 mol% IL resulted in significant changes in the protein structure and aggregation. The Lys structure was expanded at 1 mol% but compact at 17 mol% with structural changes in loop regions. HLys formed small aggregates, with the IL effect similar to Lys. Mb and βLg mostly had distinct monomer and dimer distributions depending on IL type and IL concentration. Complex aggregation was noted for Tryp and sfGFP. While the anion had the largest ion effect, changing the cation also induced the structural expansion and protein aggregation.
Collapse
Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Mohamad El Mohamad
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Stuart Brown
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Jiali Zhai
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Carlos J Rosado
- Department of Diabetes, Central Clinical School, Monash University, VIC 3004, Australia; Department of Biochemistry, Monash University, VIC 3800, Australia
| | - Yi Shen
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia; The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ewan W Blanch
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| |
Collapse
|
10
|
Qin S, Zhou HX. Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538329. [PMID: 37162827 PMCID: PMC10168431 DOI: 10.1101/2023.04.25.538329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Liquid-liquid phase separation of protein solutions has regained heightened attention for its biological importance and pathogenic relevance. Coarse-grained models are limited when explaining residue-level effects on phase equilibrium. Here we report phase diagrams for γ-crystallins using atomistic modeling. The calculations were made possible by combining our FMAP method for computing chemical potentials and Brownian dynamics simulations for configurational sampling of dense protein solutions, yielding the binodal and critic temperature ( T c ). We obtain a higher T c for a known high- T c γ-crystallin, γF, than for a low- T c paralog, γB. The difference in T c is corroborated by a gap in second virial coefficient. Decomposition of inter-protein interactions reveals one amino-acid substitution between γB and γF, from Ser to Trp at position 130, as the major contributor to the difference in T c . This type of analysis enables us to link phase equilibrium to amino-acid sequence and to design mutations for altering phase equilibrium.
Collapse
Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607, USA
| |
Collapse
|
11
|
Rivera-Rivera LY, Moore TC, Glotzer SC. Inverse design of triblock Janus spheres for self-assembly of complex structures in the crystallization slot via digital alchemy. SOFT MATTER 2023; 19:2726-2736. [PMID: 36974942 DOI: 10.1039/d2sm01593e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The digital alchemy framework is an extended ensemble simulation technique that incorporates particle attributes as thermodynamic variables, enabling the inverse design of colloidal particles for desired behavior. Here, we extend the digital alchemy framework for the inverse design of patchy spheres that self-assemble into target crystal structures. To constrain the potentials to non-trivial solutions, we conduct digital alchemy simulations with constant second virial coefficient. We optimize the size, range, and strength of patchy interactions in model triblock Janus spheres to self-assemble the 2D kagome and snub square lattices and the 3D pyrochlore lattice, and demonstrate self-assembly of all three target structures with the designed models. The particles designed for the kagome and snub square lattices assemble into high quality clusters of their target structures, while competition from similar polymorphs lower the yield of the pyrochlore assemblies. We find that the alchemically designed potentials do not always match physical intuition, illustrating the ability of the method to find nontrivial solutions to the optimization problem. We identify a window of second virial coefficients that result in self-assembly of the target structures, analogous to the crystallization slot in protein crystallization.
Collapse
Affiliation(s)
| | - Timothy C Moore
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Sharon C Glotzer
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
12
|
Larson NR, Wei Y, Cruz TA, Esfandiary R, Kalonia CK, Forrest ML, Middaugh CR. Conformational Changes and Drivers of Monoclonal Antibody Liquid-Liquid Phase Separation. J Pharm Sci 2023; 112:680-690. [PMID: 36306862 PMCID: PMC9974558 DOI: 10.1016/j.xphs.2022.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Liquid-liquid phase separation is a phenomenon within biology whereby proteins can separate into dense and more dilute phases with distinct properties. Three antibodies that undergo liquid-liquid phase separation were characterized in the protein-rich and protein-poor phases. In comparison to the protein-poor phase, the protein-rich phase demonstrates more blue-shift tryptophan emissions and red-shifted amide I absorbances. Large changes involving conformational isomerization around disulfide bonds were observed using Raman spectroscopy. Amide I and protein fluorescence differences between the phases persisted to temperatures above the critical temperature but ceased at the temperature at which aggregation occurred. In addition, large changes occurred in the structural organization of water molecules within the protein-rich phase for all three antibodies. It is hypothesized that as the proteins have the same chemical potential in both phases, the protein viscosity is higher in the protein-rich phase resulting in slowed diffusion dependent protein aggregation in this phase. For all three antibodies we performed accelerated stability studies and found that the protein-rich phase aggregated at the same rate or slower than the protein-poor phase.
Collapse
Affiliation(s)
- Nicholas R Larson
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - Yangjie Wei
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - Thayana Araújo Cruz
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Federal University of Rio de Janeiro (UFRJ), IQ, Biochemistry Program, Ilha do Fundao, Rio de Janeiro, 21941-909, Brazil
| | - Reza Esfandiary
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - Cavan K Kalonia
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - M Laird Forrest
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Krevert CS, Gunkel L, Haese C, Hunger J. Ion-specific binding of cations to the carboxylate and of anions to the amide of alanylalanine. Commun Chem 2022; 5:173. [PMID: 36697920 PMCID: PMC9814750 DOI: 10.1038/s42004-022-00789-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Studies of ion-specific effects on oligopeptides have aided our understanding of Hofmeister effects on proteins, yet the use of different model peptides and different experimental sensitivities have led to conflicting conclusions. To resolve these controversies, we study a small model peptide, L-Alanyl-L-alanine (2Ala), carrying all fundamental chemical protein motifs: C-terminus, amide bond, and N-terminus. We elucidate the effect of GdmCl, LiCl, KCl, KI, and KSCN by combining dielectric relaxation, nuclear magnetic resonance (1H-NMR), and (two-dimensional) infrared spectroscopy. Our dielectric results show that all ions reduce the rotational mobility of 2Ala, yet the magnitude of the reduction is larger for denaturing cations than for anions. The NMR chemical shifts of the amide group are particularly sensitive to denaturing anions, indicative of anion-amide interactions. Infrared experiments reveal that LiCl alters the spectral homogeneity and dynamics of the carboxylate, but not the amide group. Interaction of LiCl with the negatively charged pole of 2Ala, the COO- group, can explain the marked cationic effect on dipolar rotation, while interaction of anions between the poles, at the amide, only weakly perturbs dipolar dynamics. As such, our results provide a unifying view on ions' preferential interaction sites at 2Ala and help rationalize Hofmeister effects on proteins.
Collapse
Affiliation(s)
- Carola Sophie Krevert
- grid.419547.a0000 0001 1010 1663Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Lucas Gunkel
- grid.419547.a0000 0001 1010 1663Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Constantin Haese
- grid.419547.a0000 0001 1010 1663Department of Molecular Electronics, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- grid.419547.a0000 0001 1010 1663Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
15
|
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. Int J Mol Sci 2022; 23:ijms232315371. [PMID: 36499696 PMCID: PMC9741033 DOI: 10.3390/ijms232315371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
We present here a freely available web-based database, called BioMThermDB 1.0, of thermophysical and dynamic properties of various proteins and their aqueous solutions. It contains the hydrodynamic radius, electrophoretic mobility, zeta potential, self-diffusion coefficient, solution viscosity, and cloud-point temperature, as well as the conditions for those determinations and details of the experimental method. It can facilitate the meta-analysis and visualization of data, can enable comparisons, and may be useful for comparing theoretical model predictions with experiments.
Collapse
|
16
|
Singla D, Bhattacharya M. Salt-Induced Dissolution of Protein Aggregates. J Phys Chem B 2022; 126:8760-8770. [PMID: 36283072 DOI: 10.1021/acs.jpcb.2c06555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein aggregation is mediated by a complex interplay of noncovalent interactions and is associated with a broad range of aspects from debilitating human diseases to the food industry and therapeutic biotechnology. Deciphering the intricate roles of noncovalent interactions is of paramount importance for the design of effective inhibitory and disaggregation strategies, which remains a formidable challenge. By using a combination of spectroscopic and microscopic tools, here we show that the surfactant-mediated protein aggregation can be modulated by an intriguing interplay of hydrophobic and electrostatic effects. Additionally, our results illuminate the unique role of salt as a potent disaggregation inducer that alters the protein-surfactant electrostatic interactions and triggers the dissolution of preformed protein aggregates resulting in restoring the native protein structure. This unusual salt-induced dissolution and refolding offers a unique approach to regulating the balance between protein self-assembly and disassembly and will offer a potent strategy to design electrostatically targeted inhibitors.
Collapse
Affiliation(s)
- Deepika Singla
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
| | - Mily Bhattacharya
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
| |
Collapse
|
17
|
Kalyuzhnyi YV, Vlachy V. Numerical analysis of the liquid-liquid phase separation in the antibody–human serum albumin mixtures in aqueous buffer solution. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
18
|
Abstract
The aggregation propensity of monoclonal antibodies can be modified by adding different cosolutes into the solution. A simple coarse-grained model in the combination with the thermodynamic perturbation theory was used to predict cluster distribution and viscosity of the solutions of IgG4 monoclonal anibody in the presence of L-Arginine Hydrochloride. The data were analysed using binding polynomial to describe the binding of cosolute (Arginine) to the antibody molecule. The results show that by binding to the antibody molecule the cosolute occupies some of the binding sites of the antibody, and in this way reduces the amount of binding sites available to other antibody molecules. The aggregation propensity of the antibody molecules is therefore reduced.
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Kumari B, Sarkar SK, Bandyopadhyay P. Tests of a generalized Barker-Henderson perturbation theory for the phase coexistence diagram of an anisotropic potential. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
21
|
Hansen J, Pedersen JN, Pedersen JS, Egelhaaf SU, Platten F. Universal effective interactions of globular proteins close to liquid–liquid phase separation: Corresponding-states behavior reflected in the structure factor. J Chem Phys 2022; 156:244903. [DOI: 10.1063/5.0088601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intermolecular interactions in protein solutions, in general, contain many contributions. If short-range attractions dominate, the state diagram exhibits liquid–liquid phase separation (LLPS) that is metastable with respect to crystallization. In this case, the extended law of corresponding states (ELCS) suggests that thermodynamic properties are insensitive to details of the underlying interaction potential. Using lysozyme solutions, we investigate the applicability of the ELCS to the static structure factor and how far effective colloidal interaction models can help to rationalize the phase behavior and interactions of protein solutions in the vicinity of the LLPS binodal. The (effective) structure factor has been determined by small-angle x-ray scattering. It can be described by Baxter’s adhesive hard-sphere model, which implies a single fit parameter from which the normalized second virial coefficient b2 is inferred and found to quantitatively agree with previous results from static light scattering. The b2 values are independent of protein concentration but systematically vary with temperature and solution composition, i.e., salt and additive content. If plotted as a function of temperature normalized by the critical temperature, the values of b2 follow a universal behavior. These findings validate the applicability of the ELCS to globular protein solutions and indicate that the ELCS can also be reflected in the structure factor.
Collapse
Affiliation(s)
- Jan Hansen
- Heinrich Heine University, Condensed Matter Physics Laboratory, Düsseldorf, Germany
| | - Jannik N. Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stefan U. Egelhaaf
- Heinrich Heine University, Condensed Matter Physics Laboratory, Düsseldorf, Germany
| | - Florian Platten
- Heinrich Heine University, Condensed Matter Physics Laboratory, Düsseldorf, Germany
- Forschungszentrum Jülich, Institute of Biological Information Processing IBI-4, Biomacromolecular Systems and Processes, Jülich, Germany
| |
Collapse
|
22
|
Chaaban H, Vallooran JJ, van de Weert M, Foderà V. Ion-Mediated Morphological Diversity in Protein Amyloid Systems. J Phys Chem Lett 2022; 13:3586-3593. [PMID: 35426676 DOI: 10.1021/acs.jpclett.2c00182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Salt ions are considered among the major determinants ruling protein folding, stability, and self-assembly in the context of amyloid-related diseases, protein drug development, and functional biomaterials. Here, we report that Hofmeister ions not only determine the rate constants of the aggregation reaction for human insulin and hen egg white lysozyme but also control the generation of a plethora of amyloid-like morphologies ranging from the nanoscale to the microscale. We anticipate that the latter is a result of a balance between colloidal and conformational stability combined with an ion-specific effect and highlight the importance of salt ions in controlling the biological functions of protein aggregates.
Collapse
Affiliation(s)
- Hussein Chaaban
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Jijo J Vallooran
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Marco van de Weert
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| |
Collapse
|
23
|
Blanco MA. Computational models for studying physical instabilities in high concentration biotherapeutic formulations. MAbs 2022; 14:2044744. [PMID: 35282775 PMCID: PMC8928847 DOI: 10.1080/19420862.2022.2044744] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.
Collapse
Affiliation(s)
- Marco A. Blanco
- Materials and Biophysical Characterization, Analytical R & D, Merck & Co., Inc, Kenilworth, NJ USA
| |
Collapse
|
24
|
Basak A, Basak S. Protein Aggregation and Self Assembly in Health and Disease. CURR PROTEOMICS 2022. [DOI: 10.2174/1570164618666210223160742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Self-attachment of proteins leading to the formation of highly insoluble protein oligomers and aggregates has become an important focus of research owing to its diverse implications in pathophysiology and diseases. This has become a more frequent phenomenon in most neurological and neurodegenerative diseases as well as in dementia. In recent years such event of protein aggregation has linked to other disease conditions, disorders or adverse health conditions. Interestingly, aggregation of protein also plays role in development, growth or metabolism. Most often physiological proteins are initially bio-synthesised in native or nascent geometrical forms or conformations but later they undergo specific folding pattern and thereby acquire a stable configuration that is biologically relevant and active. It is highly important that these proteins remain in their biologically active configuration in order to exert their functional properties. Any alteration or change to this structural configuration can be detrimental to their specific functions and may cause pathological consequences leading to the onset of diseases or disorders. Several factors such as the action of chaperones, binding partners, physiological metal ions, pH level, temperature, ionic strength, interfacial exposure (solid-liquid, liquid-liquid, gas-liquid), mutation and post translational modification, chemical changes, interaction with small molecules such as lipids, hormones, etc. and solvent environment have been either identified or proposed as important factors in conferring the ultimate status of protein structure and configuration.
Among many misfolding protein conformations, self-assembly or aggregation is the most significant. It leads to the formation of highly oligomeric self-aggregates that precipitate and interfere with many biochemical processes with serious pathological consequences. The most common implication of protein aggregation leading to the formation of deposits / plaques of various morphological types is the onset of neurological and neurodegenerative diseases that include Alzheimer’s, Parkinson’s, Huntington, ALS (Amyotrophic Lateral Sclerosis), CJD (Creutzfeldt Jakob Dementia), Prion diseases, Amyloidosis and other forms of dementia. However increasingly studies revealed that protein aggregation may also be associated with other diseases such as cancer, type 2 diabetes, renal, corneal and cardiovascular diseases. Protein aggregation diseases are now considered as part of “Proteinopathy” which refers to conditions where proteins become structurally abnormal or fail to fold into stable normal configurations. In this review, we reflect on various aspects of protein self-aggregation, potential underlying causes, mechanism, role of secondary structures, pathological consequences and possible intervention strategies as reported in published literatures.
Collapse
Affiliation(s)
- Ajoy Basak
- Pathology and Laboratory Medicine, Faculty of Medicine, U Ottawa, Canada
- Ottawa Hospital Research Institute,
The Ottawa Hospital, U Ottawa, Canada
| | - Sarmistha Basak
- Formerly of Kidney Research Center, Ottawa Hospital Research Institute, U Ottawa, Canada
| |
Collapse
|
25
|
Evidence for a semisolid phase state of aerosols and droplets relevant to the airborne and surface survival of pathogens. Proc Natl Acad Sci U S A 2022; 119:2109750119. [PMID: 35064080 PMCID: PMC8794803 DOI: 10.1073/pnas.2109750119] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 01/25/2023] Open
Abstract
Ambient humidity can influence the survival of pathogens in respiratory aerosols and droplets, although the mechanism and optimum humidity level for public health remain unclear. Here, we present evidence for a humidity-dependent, semisolid state of aerosols and droplets relevant to pathogen survival. These observations indicate that a semisolid state may protect pathogens from inactivation by hindering disinfection reactions at intermediate-to-low humidity levels. The formation of the semisolid state was dependent on the composition of the aerosols, which suggests that the humidity for optimum pathogen destruction will depend on the composition of respiratory particles released from an infected host. These observations can be used to help interpret laboratory studies and inform public health recommendations. The phase state of respiratory aerosols and droplets has been linked to the humidity-dependent survival of pathogens such as SARS-CoV-2. To inform strategies to mitigate the spread of infectious disease, it is thus necessary to understand the humidity-dependent phase changes associated with the particles in which pathogens are suspended. Here, we study phase changes of levitated aerosols and droplets composed of model respiratory compounds (salt and protein) and growth media (organic–inorganic mixtures commonly used in studies of pathogen survival) with decreasing relative humidity (RH). Efflorescence was suppressed in many particle compositions and thus unlikely to fully account for the humidity-dependent survival of viruses. Rather, we identify organic-based, semisolid phase states that form under equilibrium conditions at intermediate RH (45 to 80%). A higher-protein content causes particles to exist in a semisolid state under a wider range of RH conditions. Diffusion and, thus, disinfection kinetics are expected to be inhibited in these semisolid states. These observations suggest that organic-based, semisolid states are an important consideration to account for the recovery of virus viability at low RH observed in previous studies. We propose a mechanism in which the semisolid phase shields pathogens from inactivation by hindering the diffusion of solutes. This suggests that the exogenous lifetime of pathogens will depend, in part, on the organic composition of the carrier respiratory particle and thus its origin in the respiratory tract. Furthermore, this work highlights the importance of accounting for spatial heterogeneities and time-dependent changes in the properties of aerosols and droplets undergoing evaporation in studies of pathogen viability.
Collapse
|
26
|
Batool Z, Hu G, Xinyue H, Wu Y, Fu X, Cai Z, Huang X, Ma M. A comprehensive review on functional properties of preserved eggs as an excellent food ingredient with anti-inflammatory and anti-cancer aspects. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
27
|
Hansen J, Uthayakumar R, Pedersen JS, Egelhaaf SU, Platten F. Interactions in protein solutions close to liquid-liquid phase separation: ethanol reduces attractions via changes of the dielectric solution properties. Phys Chem Chem Phys 2021; 23:22384-22394. [PMID: 34608908 DOI: 10.1039/d1cp03210k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ethanol is a common protein crystallization agent, precipitant, and denaturant, but also alters the dielectric properties of solutions. While ethanol-induced unfolding is largely ascribed to its hydrophobic parts, its effect on protein phase separation and inter-protein interactions remains poorly understood. Here, the effects of ethanol and NaCl on the phase behavior and interactions of protein solutions are studied in terms of the metastable liquid-liquid phase separation (LLPS) and the second virial coefficient B2 using lysozyme solutions. Determination of the phase diagrams shows that the cloud-point temperatures are reduced and raised by the addition of ethanol and salt, respectively. The observed trends can be explained using the extended law of corresponding states as changes of B2. The results for B2 agree quantitatively with those of static light scattering and small-angle X-ray scattering experiments. Furthermore, B2 values calculated based on inter-protein interactions described by the Derjaguin-Landau-Verwey-Overbeek (DLVO) potential and considering the dielectric solution properties and electrostatic screening due to the ethanol and salt content quantitatively agree with the experimentally observed B2 values.
Collapse
Affiliation(s)
- Jan Hansen
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Rajeevann Uthayakumar
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Jan Skov Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stefan U Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany. .,Institute of Biological Information Processing (IBI-4: Biomacromolecular Systems and Processes), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| |
Collapse
|
28
|
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: 41] [Impact Index Per Article: 13.7] [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.
Collapse
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.
| |
Collapse
|
29
|
Cui J, Peuke AD, Limami AM, Tcherkez G. Why is phloem sap nitrate kept low? PLANT, CELL & ENVIRONMENT 2021; 44:2838-2843. [PMID: 34075592 DOI: 10.1111/pce.14116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/10/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Jing Cui
- Research School of Biology, ANU College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Andreas D Peuke
- ADP International Plant Science Consulting, Gundelfingen-Wildtal, Germany
| | - Anis M Limami
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé, France
| | - Guillaume Tcherkez
- Research School of Biology, ANU College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé, France
| |
Collapse
|
30
|
Janc T, Korb JP, Lukšič M, Vlachy V, Bryant RG, Mériguet G, Malikova N, Rollet AL. Multiscale Water Dynamics on Protein Surfaces: Protein-Specific Response to Surface Ions. J Phys Chem B 2021; 125:8673-8681. [PMID: 34342225 DOI: 10.1021/acs.jpcb.1c02513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins function in crowded aqueous environments, interacting with a diverse range of compounds, and among them, dissolved ions. These interactions are water-mediated. In the present study, we combine field-dependent NMR relaxation (NMRD) and theory to probe water dynamics on the surface of proteins in concentrated aqueous solutions of hen egg-white lysozyme (LZM) and bovine serum albumin (BSA). The experiments reveal that the presence of salts (NaCl or NaI) leads to an opposite ion-specific response for the two proteins: an addition of salt to LZM solutions increases water relaxation rates with respect to the salt-free case, while for BSA solutions, a decrease is observed. The magnitude of the change depends on the ion identity. The developed model accounts for the non-Lorentzian shape of the NMRD profiles and reproduces the experimental data over four decades in Larmor frequency (10 kHz to 110 MHz). It is applicable up to high protein concentrations. The model incorporates the observed ion-specific effects via changes in the protein surface roughness, represented by the surface fractal dimension, and the accompanying changes in the surface water residence times. The response is protein-specific, linked to geometrical aspects of the individual protein surfaces, and goes beyond protein-independent Hofmeister-style ordering of ions.
Collapse
Affiliation(s)
- Tadeja Janc
- Laboratoire PHENIX, CNRS, Sorbonne Université, Paris 75252, France.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jean-Pierre Korb
- Laboratoire PHENIX, CNRS, Sorbonne Université, Paris 75252, France
| | - Miha Lukšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Robert G Bryant
- Chemistry Department, University of Virginia, Charlottesville, Virginia 22904, United States
| | | | - Natalie Malikova
- Laboratoire PHENIX, CNRS, Sorbonne Université, Paris 75252, France
| | | |
Collapse
|
31
|
Hidayat AS, Horino H, Rzeznicka II. Smartphone-Enabled Quantification of Potassium in Blood Plasma. SENSORS 2021; 21:s21144751. [PMID: 34300494 PMCID: PMC8309773 DOI: 10.3390/s21144751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
This work describes a new method for determining K+ concentration, [K+], in blood plasma using a smartphone with a custom-built optical attachment. The method is based on turbidity measurement of blood plasma solutions in the presence of sodium tetraphenylborate, a known potassium precipitating reagent. The images obtained by a smartphone camera are analyzed by a custom image-processing algorithm which enables the transformation of the image data from RGB to HSV color space and calculation of a mean value of the light-intensity component (V). Analysis of images of blood plasma containing different amounts of K+ reveal a correlation between V and [K+]. The accuracy of the method was confirmed by comparing the results with the results obtained using commercial ion-selective electrode device (ISE) and atomic absorption spectroscopy (AAS). The accuracy of the method was within ± 0.18 mM and precision ± 0.27 mM in the [K+] range of 1.5–7.5 mM when using treated blood plasma calibration. Spike tests on a fresh blood plasma show good correlation of the data obtained by the smartphone method with ISE and AAS. The advantage of the method is low cost and integration with a smartphone which offers possibility to measure [K+] on demand and in remote areas where access to hospitals is limited.
Collapse
Affiliation(s)
- Achmad Syarif Hidayat
- Shibaura Institute of Technology, Graduate School of Engineering and Science, 3-7-5 Koto-ku, Tokyo 135-8548, Japan;
| | - Hideyuki Horino
- Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 982-8577, Japan;
| | - Izabela I. Rzeznicka
- Shibaura Institute of Technology, Graduate School of Engineering and Science, 3-7-5 Koto-ku, Tokyo 135-8548, Japan;
- Correspondence:
| |
Collapse
|
32
|
Fahim A, Annunziata O. Effect of a Good buffer on the fate of metastable protein-rich droplets near physiological composition. Int J Biol Macromol 2021; 186:519-527. [PMID: 34265335 DOI: 10.1016/j.ijbiomac.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Metastable protein-rich microdroplets are produced from liquid-liquid phase separation (LLPS) of protein aqueous solutions. These globules can be intermediates for the formation of other protein-rich phases. Lysozyme aqueous solutions undergo LLPS around 0 °C in the presence of NaCl near physiological conditions. Here, it is shown that insertion of small amounts of 4-(2-hydroxyethyl)-1-piperazineethanesulfonate (HEPES, 0.1 M) as a second additive to lysozyme-NaCl-water solutions near physiological ionic strength (0.2 M) is an essential step for triggering conversion of protein-rich droplets into another phase. Specifically, LLPS induced by cooling reproducibly leads to a rapid and high-yield formation of compact tetragonal crystalline microparticles only in the presence of HEPES. These microcrystals exhibit small size (1-3 μm), narrow size distribution and guest-binding properties. The temperature-concentration phase diagram shows a characteristic topology with LLPS boundary metastable with respect to tetragonal microcrystals, which in turn become less stable than rod-shaped orthorhombic crystals above 40 °C. Interestingly, dynamic light scattering, hydrogen-ion titrations and isothermal titration calorimetry reveal that lysozyme-HEPES interactions were found to be weakly attractive and exothermic. Our findings indicate that additives of salting-in type can represent an important factor controlling the fate of metastable protein-rich microdroplets relevant to drug formulations, femtosecond crystallography, and potential implications in protein-driven cytoplasmic compartmentalization.
Collapse
Affiliation(s)
- Aisha Fahim
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie St., Sid Richardson Bldg. #438, Fort Worth, TX 76129, USA
| | - Onofrio Annunziata
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie St., Sid Richardson Bldg. #438, Fort Worth, TX 76129, USA..
| |
Collapse
|
33
|
Identifying hydrophobic protein patches to inform protein interaction interfaces. Proc Natl Acad Sci U S A 2021; 118:2018234118. [PMID: 33526682 DOI: 10.1073/pnas.2018234118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.
Collapse
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
|
36
|
Brudar S, Hribar-Lee B. Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model. J Phys Chem B 2021; 125:2504-2512. [PMID: 33656887 PMCID: PMC8041305 DOI: 10.1021/acs.jpcb.0c10339] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins has recently been associated with the onset of numerous diseases. Despite several studies in this area of protein aggregation, buffer-specific effects always seem to be overlooked. In this study we investigated the influence of buffers on the phase stability of hen egg-white lysozyme (HEWL) and its respective protein-protein interactions by measuring the cloud point temperature, second virial coefficient, and interaction diffusion coefficient of several HEWL-buffer solutions (MOPS, phosphate, HEPES, cacodylate) at pH 7.0. The results indicate that the buffer molecules, depending on their hydration, adsorb on the protein surface, and modulate their electrostatic stability. The obtained information was used to extend the recently developed coarse-grained protein model to incorporate buffer-specific effects. Treated by Wertheim's perturbation theory the model qualitatively correctly predicted the experimentally observed phase separation of all investigated HEWL-buffer solutions, and further allowed us to predict the phase stability of protein formulations even in experimentally unattainable conditions. Since the theory can be straightforwardly extended to include multiple components it presents a useful tool to study protein aggregation in crowded cell-like systems.
Collapse
Affiliation(s)
- Sandi Brudar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
37
|
Frataxins Emerge as New Players of the Intracellular Antioxidant Machinery. Antioxidants (Basel) 2021; 10:antiox10020315. [PMID: 33672495 PMCID: PMC7923443 DOI: 10.3390/antiox10020315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/30/2022] Open
Abstract
Frataxin is a mitochondrial protein which deficiency causes Friedreich's ataxia, a cardio-neurodegenerative disease. The lack of frataxin induces the dysregulation of mitochondrial iron homeostasis and oxidative stress, which finally causes the neuronal death. The mechanism through which frataxin regulates the oxidative stress balance is rather complex and poorly understood. While the absence of human (Hfra) and yeast (Yfh1) frataxins turn out cells sensitive to oxidative stress, this does not occur when the frataxin gene is knocked-out in E. coli. To better understand the biological roles of Hfra and Yfh1 as endogenous antioxidants, we have studied their ability to inhibit the formation of reactive oxygen species (ROS) from Cu2+- and Fe3+-catalyzed degradation of ascorbic acid. Both proteins drastically reduce the formation of ROS, and during this process they are not oxidized. In addition, we have also demonstrated that merely the presence of Yfh1 or Hfra is enough to protect a highly oxidation-prone protein such as α-synuclein. This unspecific intervention (without a direct binding) suggests that frataxins could act as a shield to prevent the oxidation of a broad set of intracellular proteins, and reinforces that idea that frataxin can be used to prevent neurological pathologies linked to an enhanced oxidative stress.
Collapse
|
38
|
Han Q, Ryan TM, Rosado CJ, Drummond CJ, Greaves TL. Effect of ionic liquids on the fluorescence properties and aggregation of superfolder green fluorescence protein. J Colloid Interface Sci 2021; 591:96-105. [PMID: 33596505 DOI: 10.1016/j.jcis.2021.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 10/22/2022]
Abstract
Proteins generally tend to aggregate with less desirable properties in numerous solvents, which is one of the major challenges in the development of solvents for functional proteins. This work aims to utilize fluorescence spectroscopy and small angle X-ray scattering (SAXS) to understand the effects of ionic liquids (ILs) on the fluorescence and aggregation behavior of superfolder green fluorescent protein (sfGFP). The studied ILs consisted of four different anions coupled with primary, tertiary and quaternary ammonium cations. The results show that the chromophore fluorescence was generally maintained in 1 mol% IL-water mixtures, then decreased with increasing IL concentration. We primarily employed the pseudo-radius of gyration (pseudo-Rg) to evaluate sfGFP aggregation. The sfGFP was less aggregated with nitrate-based ILs compared to in buffer, and more aggregated in the mesylate-based ILs. Further, we show that the polyol additives of glycerol and glucose in IL-water mixtures slightly decreased the sfGFP propensity to aggregate. Size-exclusion chromatography (SEC)-SAXS was used to characterize the monomeric sfGFP in ethylammonium nitrate (EAN) and triethylammonium mesylate (TEAMs)-water mixtures. The presence of 1 mol% TEAMs maintained the sfGFP fluorescence, promoted the compact structure, but slightly increased the amount of large aggregates, which contrasted with that of EAN.
Collapse
Affiliation(s)
- Qi Han
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Timothy M Ryan
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Carlos J Rosado
- Department of Diabetes, Central Clinical School, Monash University, VIC 3004, Australia
| | - Calum J Drummond
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
| |
Collapse
|
39
|
Pathak JA, Nugent S, Bender MF, Roberts CJ, Curtis RJ, Douglas JF. Comparison of Huggins Coefficients and Osmotic Second Virial Coefficients of Buffered Solutions of Monoclonal Antibodies. Polymers (Basel) 2021; 13:601. [PMID: 33671342 PMCID: PMC7922252 DOI: 10.3390/polym13040601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 01/08/2023] Open
Abstract
The Huggins coefficient kH is a well-known metric for quantifying the increase in solution viscosity arising from intermolecular interactions in relatively dilute macromolecular solutions, and there has been much interest in this solution property in connection with developing improved antibody therapeutics. While numerous kH measurements have been reported for select monoclonal antibodies (mAbs) solutions, there has been limited study of kH in terms of the fundamental molecular interactions that determine this property. In this paper, we compare measurements of the osmotic second virial coefficient B22, a common metric of intermolecular and interparticle interaction strength, to measurements of kH for model antibody solutions. This comparison is motivated by the seminal work of Russel for hard sphere particles having a short-range "sticky" interparticle interaction, and we also compare our data with known results for uncharged flexible polymers having variable excluded volume interactions because proteins are polypeptide chains. Our observations indicate that neither the adhesive hard sphere model, a common colloidal model of globular proteins, nor the familiar uncharged flexible polymer model, an excellent model of intrinsically disordered proteins, describes the dependence of kH of these antibodies on B22. Clearly, an improved understanding of protein and ion solvation by water as well as dipole-dipole and charge-dipole effects is required to understand the significance of kH from the standpoint of fundamental protein-protein interactions. Despite shortcomings in our theoretical understanding of kH for antibody solutions, this quantity provides a useful practical measure of the strength of interprotein interactions at elevated protein concentrations that is of direct significance for the development of antibody formulations that minimize the solution viscosity.
Collapse
Affiliation(s)
- Jai A. Pathak
- Vaccine Production Program (VPP), Vaccine Research Center (VRC), Formulation and Stabilization Sciences Department, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), 9 W. Watkins Mill Rd., Gaithersburg, MD 20878, USA; (J.A.P.); (S.N.); (M.B.)
| | - Sean Nugent
- Vaccine Production Program (VPP), Vaccine Research Center (VRC), Formulation and Stabilization Sciences Department, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), 9 W. Watkins Mill Rd., Gaithersburg, MD 20878, USA; (J.A.P.); (S.N.); (M.B.)
| | - Michael F. Bender
- Vaccine Production Program (VPP), Vaccine Research Center (VRC), Formulation and Stabilization Sciences Department, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), 9 W. Watkins Mill Rd., Gaithersburg, MD 20878, USA; (J.A.P.); (S.N.); (M.B.)
| | - Christopher J. Roberts
- Colburn Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA;
| | - Robin J. Curtis
- Department of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK;
| | - Jack F. Douglas
- Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-8544, USA
| |
Collapse
|
40
|
Johnson EC, Gresham IJ, Prescott SW, Nelson A, Wanless EJ, Webber GB. The direction of influence of specific ion effects on a pH and temperature responsive copolymer brush is dependent on polymer charge. POLYMER 2021. [DOI: 10.1016/j.polymer.2020.123287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
41
|
Zhao H, Guo M, Ding T, Ye X, Liu D. Exploring the mechanism of hollow microcapsule formation by self-assembly of soy 11s protein upon heating. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.105379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
42
|
Hvozd T, Kalyuzhnyi YV, Vlachy V. Aggregation, liquid-liquid phase separation, and percolation behaviour of a model antibody fluid constrained by hard-sphere obstacles. SOFT MATTER 2020; 16:8432-8443. [PMID: 32812624 DOI: 10.1039/d0sm01014f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study is concerned with the behaviour of proteins within confinement created by hard-sphere obstacles. An individual antibody molecule is depicted as an assembly of seven hard spheres, organized to resemble a Y-shaped (on average) antibody (7-bead model) protein. For comparison with other studies we, in one case, model the protein as a hard sphere decorated by three short-range attractive sites. The antibody has two Fab and one Fc domains located in the corners of the letter Y. In this calculation, only the Fab-Fab and Fab-Fc attractive pair interactions are possible. The confinement is formed by the randomly distributed hard-sphere obstacles fixed in space. Aside from size exclusion, the obstacles do not interact with antibodies, but they affect the protein-protein correlation. We used a combination of the scaled-particle theory, Wertheim's thermodynamic perturbation theory and the Flory-Stockmayer theory to calculate: (i) the second virial coefficient of the protein fluid, (ii) the percolation threshold, (iii) cluster size distributions, and (iv) the liquid-liquid phase separation as a function of the strength of the various pair interactions of the protein and the model parameters, such as protein concentration and the packing fraction of obstacles. The conclusion is that hard-sphere obstacles strongly decrease the critical density and also, but to a much lesser extent, the critical temperature. Also, the confinement enhances clustering, making the percolating region broader. The effect depends on the model parameters, such as the packing fraction of obstacles η0, the inter-site interaction strength εIJ, and the ratio between the size of the obstacle σ0 and the size of one bead of the model antibody σhs; the value of this ratio is varied here from 2 to 5. Interestingly, at low to moderate packing fractions of obstacles, the second virial coefficient first slightly decreases (destabilization), and the slope depends on the observation temperature, but then at higher values of η0 it increases. The calculated values of the second virial coefficient also depend on the size of the obstacles.
Collapse
Affiliation(s)
- Taras Hvozd
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine. and Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|
43
|
Ashkarran AA, Mahmoudi M. Magnetic Levitation Systems for Disease Diagnostics. Trends Biotechnol 2020; 39:311-321. [PMID: 32861547 DOI: 10.1016/j.tibtech.2020.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022]
Abstract
Magnetic levitation (MagLev) is a well-documented, robust technique for density measurements and separations. Although the potential of MagLev as an emerging tool in biotechnology has been recently investigated, the practical use of MagLev in diagnosis and disease detection merits further attention. This review highlights the diagnostic capacity of a simple and portable MagLev system and the possibilities and limitations of the MagLev technique for density-based separation, classification, and manipulation of soft matter and biological systems (e.g., cells, proteins), which in turn may pave the way for the discovery of disease-specific biomarkers.
Collapse
Affiliation(s)
- Ali Akbar Ashkarran
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI, USA
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
44
|
Pathak B, Christy J, Sefiane K, Gozuacik D. Complex Pattern Formation in Solutions of Protein and Mixed Salts Using Dehydrating Sessile Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9728-9737. [PMID: 32787115 DOI: 10.1021/acs.langmuir.0c01122] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A sessile droplet of a complex fluid exhibits several stages of drying leading to the formation of a final pattern on the substrate. We report such pattern formation in dehydrating droplets of protein (BSA) and salts (MgCl2 and KCl) at various concentrations of the two components (protein and salts) as part of a parametric study for the understanding of complex patterns of dehydrating biofluid droplets (blood and urine), which will eventually be used for diagnosis of bladder cancer. The exact analysis of the biofluid patterns will require a rigorous parametric study; however, the current work provides an initial understanding of the effect of the basic components present in a biofluid droplet. Arrangement of the protein and the salts, due to evaporation, leads to the formation of some very distinctive final structures at the end of the droplet lifetime. Furthermore, these structures can be manipulated by varying the initial ratio of the two components in the solution. MgCl2 forms chains of crystals beyond a threshold initial concentration of protein (>3 wt %). However, the formation of such a crystal is also limited by the maximum concentration of the salt initially present in the droplet (≤1 wt %). On the other hand, KCl forms dendritic and rectangular crystals in the presence of BSA. The formation of these crystals also depends on the relative concentration of salt and protein in the droplet. We also investigated the dried-out patterns in dehydrating droplets of mixed salts (MgCl2 + KCl) and protein. The patterns can be tuned from a continuous dendritic structure to a snow-flake type structure just by altering the initial ratio of the two salts in the mixture, keeping all other parameters constant.
Collapse
Affiliation(s)
- Binita Pathak
- Department of Mechanical Engineering, Indian Institute of Technology, BHU, Varanasi 221005, India
| | - John Christy
- School of Engineering, The University of Edinburgh, Kings Buildings, Edinburgh EH9 3JL, United Kingdom
| | - Khellil Sefiane
- School of Engineering, The University of Edinburgh, Kings Buildings, Edinburgh EH9 3JL, United Kingdom
- Tianjin Key Lab of Refrigeration Technology, Tianjin University of Commerce, Tianjin City 300134, PR China
| | - Devrim Gozuacik
- Koç University, School of Medicine, KUTTAM Research Center for Translational Medicine, Topkapı-Zeytinburnu, 34010 Istanbul, Turkey
| |
Collapse
|
45
|
Kozawa D, Cho SY, Gong X, Nguyen FT, Jin X, Lee MA, Lee H, Zeng A, Xue G, Schacherl J, Gibson S, Vega L, Strano MS. A Fiber Optic Interface Coupled to Nanosensors: Applications to Protein Aggregation and Organic Molecule Quantification. ACS NANO 2020; 14:10141-10152. [PMID: 32667777 DOI: 10.1021/acsnano.0c03417] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fluorescent nanosensors hold promise to address analytical challenges in the biopharmaceutical industry. The monitoring of therapeutic protein critical quality attributes such as aggregation is a long-standing challenge requiring low detection limits and multiplexing of different product parameters. However, general approaches for interfacing nanosensors to the biopharmaceutical process remain minimally explored to date. Herein, we design and fabricate a integrated fiber optic nanosensor element, measuring sensitivity, response time, and stability for applications to the rapid process monitoring. The fiber optic-nanosensor interface, or optode, consists of label-free nIR fluorescent single-walled carbon nanotube transducers embedded within a protective yet porous hydrogel attached to the end of the fiber waveguide. The optode platform is shown to be capable of differentiating the aggregation status of human immunoglobulin G, reporting the relative fraction of monomers and dimer aggregates with sizes 5.6 and 9.6 nm, respectively, in under 5 min of analysis time. We introduce a lab-on-fiber design with potential for at-line monitoring with integration of 3D-printed miniaturized sensor tips having high mechanical flexibility. A parallel measurement of fluctuations in laser excitation allows for intensity normalization and significantly lower noise level (3.7 times improved) when using lower quality lasers, improving the cost effectiveness of the platform. As an application, we demonstrate the capability of the fully integrated lab-on-fiber system to rapidly monitor various bioanalytes including serotonin, norepinephrine, adrenaline, and hydrogen peroxide, in addition to proteins and their aggregation states. These results in total constitute an effective form factor for nanosensor-based transducers for applications in industrial process monitoring.
Collapse
Affiliation(s)
- Daichi Kozawa
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Soo-Yeon Cho
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xun Gong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Freddy T Nguyen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiaojia Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael A Lee
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heejin Lee
- Process Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Alicia Zeng
- Process Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Gang Xue
- Process Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jeff Schacherl
- Process Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Scott Gibson
- Process Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Leonela Vega
- Process Development, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
46
|
Fujimura D, Inagaki F, Okada R, Rosenberg A, Furusawa A, Choyke PL, Kobayashi H. Conjugation Ratio, Light Dose, and pH Affect the Stability of Panitumumab-IR700 for Near-Infrared Photoimmunotherapy. ACS Med Chem Lett 2020; 11:1598-1604. [PMID: 32832029 DOI: 10.1021/acsmedchemlett.0c00262] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/06/2020] [Indexed: 01/09/2023] Open
Abstract
Near-infrared photoimmunotherapy (NIR-PIT), a newly developed cancer-cell-specific therapy, relies on a monoclonal antibody-photoabsorber conjugate (APC) and is based on a photoinduced ligand release reaction. Local exposure of the tumor to NIR light induces rapid immunogenic necrotic cell death. The molecular properties of APCs, including their stability and aggregation properties, have important implications for the long-term stability and shelf life. In this study, panitumumab was conjugated with IRDye700DX (IR700) as a model for other NIR-PIT agents. Higher IR700-to-mAb conjugation ratios correlated with increased in vitro cell death up to a ratio of 2.5 dye molecules per antibody. Conjugation ratios higher than 2.5 did not improve cell killing activity. APC aggregation was induced in a light-dose-dependent manner. A near-room-level light dose was sufficient to induce aggregation of APCs. Solvent pH lower than 4 induced aggregation, but higher pH did not induce aggregation. The IR700-to-mAb conjugation ratio, light irradiation dose, and solvent pH affect the APC stability and efficacy.
Collapse
Affiliation(s)
- Daiki Fujimura
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fuyuki Inagaki
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ryuhei Okada
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Adrian Rosenberg
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aki Furusawa
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Peter L. Choyke
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hisataka Kobayashi
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
47
|
Kalyuzhnyi YV, Nezbeda I, Cummings PT. Integral equation theory for a mixture of spherical and patchy colloids: analytical description. SOFT MATTER 2020; 16:3456-3465. [PMID: 32201867 DOI: 10.1039/c9sm02309g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An analytic theory for the structure and thermodynamics of two-component mixtures of patchy and spherical colloids is developed. The theory is based on an analytical solution of the multidensity Ornstein-Zernike equation supplemented by the associative Percus-Yevick closure relations. We derive closed-form analytic expressions for the partial structure factors and thermodynamic properties using the energy route for the model with arbitrary number of patches and any hard-sphere size ratio of the particles. To assess the accuracy of the theoretical predictions we compare them against existing and newly generated set of computer simulation data. In our numerical calculations we consider the model with equal hard-sphere sizes and one patch. Very good agreement between results of the theory and simulation for the pair correlation functions, excess internal energy and pressure is observed for almost all values of the system density, temperature and composition studied. Only in the region of low concentrations of spherical colloids the theoretical results become less accurate.
Collapse
Affiliation(s)
- Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii St., Lviv 79011, Ukraine.
| | | | | |
Collapse
|
48
|
Zakariya SM, Furkan M, Zaman M, Chandel TI, Ali SM, Uversky VN, Khan RH. An in-vitro elucidation of inhibitory potential of carminic acid: Possible therapeutic approach for neurodegenerative diseases. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
49
|
Khatun S, Singh A, Maji S, Maiti TK, Pawar N, Gupta AN. Fractal self-assembly and aggregation of human amylin. SOFT MATTER 2020; 16:3143-3153. [PMID: 32159545 DOI: 10.1039/c9sm02463h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Human amylin is an intrinsically disordered protein believed to have a central role in Type-II diabetes mellitus (T2DM). The formation of intermediate oligomers is a seminal event in the eventual self-assembled fibril structures of amylin. However, the recent experimental investigations have shown the presence of different self-assembled (oligomers, protofilaments, and fibrils) and aggregated structures (amorphous aggregates) of amylin formed during its aggregation. Here, we show that amylin under diffusion-limited conditions leads to fractal self-assembly. The pH and solvent sensitive fractal self-assemblies of amylin were observed using an optical microscope. Confocal microscopy and scanning electron microscopy (SEM) with energy dispersion X-ray analysis (EDAX) were used to confirm the fractal self-assembly of amylin in water and PBS buffer, respectively. The fractal characteristics of the self-assemblies and the aggregates formed during the aggregation of amylin under different pH conditions were investigated using laser light scattering. The hydropathy and the docking study indicated the interactions between the anisotropically distributed hydrophobic residues and polar/ionic residues on the solvent-accessible surface of the protein as the crucial interaction hot-spots for driving the self-assembly and aggregation of human amylin. The simultaneous presence of various self-assemblies of human amylin was observed through different microscopy techniques. The present study may help in designing different fractal-like nanomaterials with potential applications in drug delivery, sensing, and tissue engineering.
Collapse
Affiliation(s)
- Suparna Khatun
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology, Kharagpur-721302, India.
| | | | | | | | | | | |
Collapse
|
50
|
Stradner A, Schurtenberger P. Potential and limits of a colloid approach to protein solutions. SOFT MATTER 2020; 16:307-323. [PMID: 31830196 DOI: 10.1039/c9sm01953g] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Looking at globular proteins with the eyes of a colloid scientist has a long tradition, in fact a significant part of the early colloid literature was focused on protein solutions. However, it has also been recognized that proteins are much more complex than the typical hard sphere-like synthetic model colloids. Proteins are not perfect spheres, their interaction potentials are in general not isotropic, and using theories developed for such particles are thus clearly inadequate in many cases. In this perspective article, we now take a closer look at the field. In particular, we reflect on the fact that modern colloid science has been undergoing a tremendous development, where a multitude of novel systems have been developed in the lab and in silico. During the last decade we have seen a rapidly increasing number of reports on the synthesis of anisotropic, patchy and/or responsive synthetic colloids, that start to resemble their complex biological counterparts. This experimental development is also reflected in a corresponding theoretical and simulation effort. The experimental and theoretical toolbox of colloid science has thus rapidly expanded, and there is obviously an enormous potential for an application of these new concepts to protein solutions, which has already been realized and harvested in recent years. In this perspective article we make an attempt to critically discuss the exploitation of colloid science concepts to better understand protein solutions. We not only consider classical applications such as the attempt to understand and predict solution stability and phase behaviour, but also discuss new challenges related to the dynamics, flow behaviour and liquid-solid transitions found in concentrated or crowded protein solutions. It not only aims to provide an overview on the progress in experimental and theoretical (bio)colloid science, but also discusses current shortcomings in our ability to correctly reproduce and predict the structural and dynamic properties of protein solutions based on such a colloid approach.
Collapse
Affiliation(s)
- Anna Stradner
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-221 00 Lund, Sweden.
| | | |
Collapse
|