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Abazari A, Dhadwal HS, Wittpenn J. Observational Clinical Studies of Human Lens Transparency Using the Vision Index Pen. Transl Vis Sci Technol 2019; 8:14. [PMID: 31772825 PMCID: PMC6859888 DOI: 10.1167/tvst.8.6.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022] Open
Affiliation(s)
- Azin Abazari
- Department of Ophthalmology, SUNY Stony Brook, Stony Brook, NY, USA
| | | | - John Wittpenn
- Ophthalmic Consultants of Long Island, East Setauket, NY, USA
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Abstract
Cataract is a major cause of blindness worldwide. It is characterized by lens opacification and is accompanied by extensive posttranslational modifications (PTMs) in various proteins. PTMs play an essential role in lens opacification. Several PTMs have been described in proteins isolated from relatively old human lenses, including phosphorylation, deamidation, racemization, truncation, acetylation, and methylation. An overwhelming majority of previous cataract proteomic studies have exclusively focused on crystallin proteins, which are the most abundant proteome components of the lens. To investigate the proteome of cataract markers, this chapter focuses on the proteomic research on the functional relevance of the major PTMs in crystallins of human cataractous lenses. Elucidating the role of these modifications in cataract formation has been a challenging task because they are among the most difficult PTMs to study analytically. The proteomic status of some amides presents similar properties in normal aged and cataractous lenses, whereas some may undergo greater PTMs in cataract. Therefore, it is of great importance to review the current proteomic research on crystallins, the major protein markers in different types of cataract, to elucidate the pathogenesis of this major human-blinding condition.
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Affiliation(s)
- Keke Zhang
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Department of Ophthalmology, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Myopia, Ministry of Health PR China, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiangjia Zhu
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Department of Ophthalmology, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Myopia, Ministry of Health PR China, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Department of Ophthalmology, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Myopia, Ministry of Health PR China, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai Medical College, Fudan University, Shanghai, China
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3
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Sagar V, Chaturvedi SK, Schuck P, Wistow G. Crystal Structure of Chicken γS-Crystallin Reveals Lattice Contacts with Implications for Function in the Lens and the Evolution of the βγ-Crystallins. Structure 2017. [PMID: 28648607 PMCID: PMC5518705 DOI: 10.1016/j.str.2017.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Previous attempts to crystallize mammalian γS-crystallin were unsuccessful. Native L16 chicken γS crystallized avidly while the Q16 mutant did not. The x-ray structure for chicken γS at 2.3Å resolution shows the canonical structure of the superfamily plus a well-ordered N-arm aligned with a β-sheet of a neighboring N-domain. L16 is also in a lattice contact, partially shielded from solvent. Unexpectedly, the major lattice contact matches a conserved interface (QR) in the multimeric β-crystallins. QR shows little conservation of residue contacts, except for one between symmetry-related tyrosines, but molecular dipoles for the proteins with QR show striking similarities while other γ-crystallins differ. In γS, QR has few hydrophobic contacts and features a thin layer of tightly bound water. The free energy of QR is slightly repulsive and AUC confirms no dimerization in solution. The lattice contacts suggest how γcrystallins allow close packing without aggregation in the crowded environment of the lens.
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Affiliation(s)
- Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Building 6, Room 106, Bethesda, MD 20892, USA
| | - Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, LCIMB, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, LCIMB, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Building 6, Room 106, Bethesda, MD 20892, USA.
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4
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Kolomeisky AB. Staying Together: Protein Molecules in Mesoscopic Clusters. Biophys J 2016; 109:1759-60. [PMID: 26536252 DOI: 10.1016/j.bpj.2015.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/25/2022] Open
Affiliation(s)
- Anatoly B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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5
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Minton AP. Recent applications of light scattering measurement in the biological and biopharmaceutical sciences. Anal Biochem 2016; 501:4-22. [PMID: 26896682 PMCID: PMC5804501 DOI: 10.1016/j.ab.2016.02.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Allen P Minton
- Laboratory of Biochemistry and Genetics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, 20892, USA.
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6
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O'Brien CJ, Blanco MA, Costanzo JA, Enterline M, Fernandez EJ, Robinson AS, Roberts CJ. Modulating non-native aggregation and electrostatic protein-protein interactions with computationally designed single-point mutations. Protein Eng Des Sel 2016; 29:231-243. [PMID: 27160179 DOI: 10.1093/protein/gzw010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/28/2016] [Indexed: 11/14/2022] Open
Abstract
Non-native protein aggregation is a ubiquitous challenge in the production, storage and administration of protein-based biotherapeutics. This study focuses on altering electrostatic protein-protein interactions as a strategy to modulate aggregation propensity in terms of temperature-dependent aggregation rates, using single-charge variants of human γ-D crystallin. Molecular models were combined to predict amino acid substitutions that would modulate protein-protein interactions with minimal effects on conformational stability. Experimental protein-protein interactions were quantified by the Kirkwood-Buff integrals (G22) from laser scattering, and G22 showed semi-quantitative agreement with model predictions. Experimental initial-rates for aggregation showed that increased (decreased) repulsive interactions led to significantly increased (decreased) aggregation resistance, even based solely on single-point mutations. However, in the case of a particular amino acid (E17), the aggregation mechanism was altered by substitution with R or K, and this greatly mitigated improvements in aggregation resistance. The results illustrate that predictions based on native protein-protein interactions can provide a useful design target for engineering aggregation resistance; however, this approach needs to be balanced with consideration of how mutations can impact aggregation mechanisms.
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Affiliation(s)
- C J O'Brien
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - M A Blanco
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - J A Costanzo
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22903, USA
| | - M Enterline
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - E J Fernandez
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22903, USA
| | - A S Robinson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.,Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA
| | - C J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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Wang B, Lou Z, Zhang H, Xu B. Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level. J Chem Phys 2016; 144:114701. [DOI: 10.1063/1.4943878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Bin Wang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
| | - Zhichao Lou
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, People’s Republic of China
| | - Haiqian Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, People’s Republic of China
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
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Morozova S, Hu G, Emrick T, Muthukumar M. Influence of Dipole Orientation on Solution Properties of Polyzwitterions. ACS Macro Lett 2016; 5:118-122. [PMID: 35668586 DOI: 10.1021/acsmacrolett.5b00876] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have studied the influence of segmental dipole orientation on the solution properties of polyzwitterions using dynamic and static light scattering of poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), n-butyl-substituted choline phosphate polymers (PMBP), and their diblock (PMPC-b-PMBP) copolymers in solutions of different salt concentration. We find that these three structures exhibit dramatically different aggregation behaviors. For the conditions in our study, PMPC is a swollen excluded-volume chain without significant presence of dipolar correlations as evident from the lack of sensitivity to the ionic strength of the solution. In contrast, PMBP self-assembles into finite-sized structures in solution, which are stabilized by electrostatic dipole-dipole interactions. Evidence of these interactions is also present in the diblock polymer, PMPB-b-PMPC, which self-assembles into two distinct, stable aggregates in addition to unaggregated chains. These results contribute to the breadth of understanding of polyzwitterions in solution and provide a platform for future simulation and experimental explorations.
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Affiliation(s)
- S. Morozova
- Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - G. Hu
- Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - T. Emrick
- Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - M. Muthukumar
- Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
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9
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Garcia-Manyes S, Giganti D, Badilla CL, Lezamiz A, Perales-Calvo J, Beedle AEM, Fernández JM. Single-molecule Force Spectroscopy Predicts a Misfolded, Domain-swapped Conformation in human γD-Crystallin Protein. J Biol Chem 2015; 291:4226-35. [PMID: 26703476 PMCID: PMC4759196 DOI: 10.1074/jbc.m115.673871] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 12/30/2022] Open
Abstract
Cataract is a protein misfolding disease where the size of the aggregate is directly related to the severity of the disorder. However, the molecular mechanisms that trigger the onset of aggregation remain unknown. Here we use a combination of protein engineering techniques and single-molecule force spectroscopy using atomic force microscopy to study the individual unfolding pathways of the human γD-crystallin, a multidomain protein that must remain correctly folded during the entire lifetime to guarantee lens transparency. When stretching individual polyproteins containing two neighboring HγD-crystallin monomers, we captured an anomalous misfolded conformation in which the β1 and β2 strands of the N terminus domain of two adjacent monomers swap. This experimentally elusive domain-swapped conformation is likely to be responsible for the increase in molecular aggregation that we measure in vitro. Our results demonstrate the power of force spectroscopy at capturing rare misfolded conformations with potential implications for the understanding of the molecular onset of protein aggregation.
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Affiliation(s)
- Sergi Garcia-Manyes
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - David Giganti
- the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Carmen L Badilla
- the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Ainhoa Lezamiz
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - Judit Perales-Calvo
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - Amy E M Beedle
- From the Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, United Kingdom and
| | - Julio M Fernández
- the Department of Biological Sciences, Columbia University, New York, New York 10027
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10
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Vorontsova MA, Chan HY, Lubchenko V, Vekilov PG. Lack of Dependence of the Sizes of the Mesoscopic Protein Clusters on Electrostatics. Biophys J 2015; 109:1959-68. [PMID: 26536272 PMCID: PMC4643268 DOI: 10.1016/j.bpj.2015.09.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Protein-rich clusters of steady submicron size and narrow size distribution exist in protein solutions in apparent violation of the classical laws of phase equilibrium. Even though they contain a minor fraction of the total protein, evidence suggests that they may serve as essential precursors for the nucleation of ordered solids such as crystals, sickle-cell hemoglobin polymers, and amyloid fibrils. The cluster formation mechanism remains elusive. We use the highly basic protein lysozyme at nearly neutral and lower pH as a model and explore the response of the cluster population to the electrostatic forces, which govern numerous biophysical phenomena, including crystallization and fibrillization. We tune the strength of intermolecular electrostatic forces by varying the solution ionic strength I and pH and find that despite the weaker repulsion at higher I and pH, the cluster size remains constant. Cluster responses to the presence of urea and ethanol demonstrate that cluster formation is controlled by hydrophobic interactions between the peptide backbones, exposed to the solvent after partial protein unfolding that may lead to transient protein oligomers. These findings reveal that the mechanism of the mesoscopic clusters is fundamentally different from those underlying the two main classes of ordered protein solid phases, crystals and amyloid fibrils, and partial unfolding of the protein chain may play a significant role.
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Affiliation(s)
- Maria A Vorontsova
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas
| | - Ho Yin Chan
- Department of Physics, University of Houston, Houston, Texas
| | - Vassiliy Lubchenko
- Department of Physics, University of Houston, Houston, Texas; Department of Chemistry, University of Houston, Houston, Texas
| | - Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas; Department of Chemistry, University of Houston, Houston, Texas.
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11
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Khago D, Wong EK, Kingsley CN, Freites JA, Tobias DJ, Martin RW. Increased hydrophobic surface exposure in the cataract-related G18V variant of human γS-crystallin. Biochim Biophys Acta Gen Subj 2015; 1860:325-32. [PMID: 26459004 DOI: 10.1016/j.bbagen.2015.09.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/26/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND The objective of this study was to determine whether the cataract-related G18V variant of human γS-crystallin has increased exposure of hydrophobic residues that could explain its aggregation propensity and/or recognition by αB-crystallin. METHODS We used an ANS fluorescence assay and NMR chemical shift perturbation to experimentally probe exposed hydrophobic surfaces. These results were compared to flexible docking simulations of ANS molecules to the proteins, starting with the solution-state NMR structures of γS-WT and γS-G18V. RESULTS γS-G18V exhibits increased ANS fluorescence, suggesting increased exposed hydrophobic surface area. The specific residues involved in ANS binding were mapped by NMR chemical shift perturbation assays, revealing ANS binding sites in γS-G18V that are not present in γS-WT. Molecular docking predicts three binding sites that are specific to γS-G18V corresponding to the exposure of a hydrophobic cavity located at the interdomain interface, as well as two hydrophobic patches near a disordered loop containing solvent-exposed cysteines, all but one of which is buried in γS-WT. CONCLUSIONS Although both proteins display non-specific binding, more residues are involved in ANS binding to γS-G18V, and the affected residues are localized in the N-terminal domain and the nearby interdomain interface, proximal to the mutation site. GENERAL SIGNIFICANCE Characterization of changes in exposed hydrophobic surface area between wild-type and variant proteins can help elucidate the mechanisms of aggregation propensity and chaperone recognition, presented here in the context of cataract formation. Experimental data and simulations provide complementary views of the interactions between proteins and the small molecule probes commonly used to study aggregation. This article is part of a Special Issue entitled Crystallin Biochemistry in Health and Disease.
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Affiliation(s)
- Domarin Khago
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, United States
| | - Eric K Wong
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, United States
| | - Carolyn N Kingsley
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, United States
| | - J Alfredo Freites
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, United States
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, United States.
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, United States.
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12
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Patent Highlights. Pharm Pat Anal 2015. [DOI: 10.4155/ppa.14.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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13
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Vorontsova MA, Maes D, Vekilov PG. Recent advances in the understanding of two-step nucleation of protein crystals. Faraday Discuss 2015; 179:27-40. [DOI: 10.1039/c4fd00217b] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The two-step mechanism of nucleation of crystals in solutions posits that the formation of crystal nuclei occurs within structures of extended lifetimes, in which the nucleating solute is at high concentration. The validity of this mechanism has been demonstrated for proteins, small-molecule organic and inorganic materials, colloids, and polymers. Due to large molecule sizes, proteins are an ideal system to study the details of this nucleation pathway, in particular the formation mechanisms of the nucleation precursors and the associated physico-chemical rules. The precursors of protein crystal nuclei are protein-rich clusters of sizes ∼100 nm that contain 10 000–100 000 molecules and occupy less than 10−3of the total solution volume. Here we demonstrate, using oblique illumination microscopy, the liquid nature of the clusters of the protein lysozyme and reveal their inhomogeneous structure. We test a hypothesis put forth by theory that clusters primarily consist of transient protein oligomers. For this, we explore how varying the strength of the Coulomb interaction affects the cluster characteristics. We find that the cluster’s size is insensitive to variations of pH and ionic strength. In contrast, the addition of urea, a chaotropic agent that leads to protein unfolding, strongly decreases the cluster size. Shear stress, a known protein denaturant, induced by bubbling of the solutions with an inert gas, elicits a similar response. These observations support partial protein unfolding, followed by dimerization, as the mechanism of cluster formation. The amide hydrogen–deuterium exchange, monitored by nuclear magnetic resonance, highlights that lysozyme conformational flexibility is a condition for the formation of the protein-rich clusters and facilitates the nucleation of protein crystals.
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Affiliation(s)
- Maria A. Vorontsova
- Department of Chemical and Biomolecular Engineering
- University of Houston
- Houston
- USA
| | - Dominique Maes
- Structural Biology Brussels
- Vrije Universiteit Brussel
- B-1050 Brussel
- Belgium
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering
- University of Houston
- Houston
- USA
- Department of Chemistry
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