title: Internal Structure and Preferential Protein Binding of Colloidal Aggregates.
abstract: Colloidal aggregates of small molecules are the most common artifact in early drug discovery, sequestering and inhibiting target proteins without specificity. Understanding their structure and mechanism has been crucial to developing tools to control for, and occasionally even exploit, these particles. Unfortunately, their polydispersity and transient stability have prevented exploration of certain elementary properties, such as how they pack. Dye-stabilized colloidal aggregates exhibit enhanced homogeneity and stability when compared to conventional colloidal aggregates, enabling investigation of some of these properties. By small-angle X-ray scattering and multiangle light scattering, pair distance distribution functions suggest that the dye-stabilized colloids are filled, not hollow, spheres. Stability of the coformulated colloids enabled investigation of their preference for binding DNA, peptides, or folded proteins, and their ability to purify one from the other. The coformulated colloids showed little ability to bind DNA. Correspondingly, the colloids preferentially sequestered protein from even a 1600-fold excess of peptides that are themselves the result of a digest of the same protein. This may reflect the avidity advantage that a protein has in a surface-to-surface interaction with the colloids. For the first time, colloids could be shown to have preferences of up to 90-fold for particular proteins over others. Loaded onto the colloids, bound enzyme could be spun down, resuspended, and released back into buffer, regaining most of its activity. Implications of these observations for colloid mechanisms and utility will be considered.
authors.affiliation: Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco , 1700 Fourth Street, San Francisco, California 94158-2550, United States.
authors.forename: Da
authors.initials: D
authors.lastname: Duan
authors.affiliation: Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco , 1700 Fourth Street, San Francisco, California 94158-2550, United States.
authors.forename: Hayarpi
authors.initials: H
authors.lastname: Torosyan
authors.affiliation: Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco , San Francisco, California 94158, United States.
authors.forename: Daniel
authors.initials: D
authors.lastname: Elnatan
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.|Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9.
authors.forename: Christopher K
authors.initials: CK
authors.lastname: McLaughlin
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.|Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Logie
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.|Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9.
authors.forename: Molly S
authors.identifier: 0000-0003-1830-3475
authors.initials: MS
authors.lastname: Shoichet
authors.affiliation: Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco , San Francisco, California 94158, United States.
authors.forename: David A
authors.initials: DA
authors.lastname: Agard
authors.affiliation: Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco , 1700 Fourth Street, San Francisco, California 94158-2550, United States.
authors.forename: Brian K
authors.identifier: 0000-0002-6098-7367
authors.initials: BK
authors.lastname: Shoichet
mesh_terms: D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D003102:Colloids; D004396:Coloring Agents / Q000737:chemistry; D003224:Congo Red / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D000067493:Dynamic Light Scattering; D004958:Estradiol / Q000031:analogs & derivatives / Q000737:chemistry; D005452:Fluoresceins / Q000737:chemistry; D000077267:Fulvestrant; D009536:Niacinamide / Q000031:analogs & derivatives / Q000737:chemistry; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D010671:Phenylurea Compounds / Q000737:chemistry; D011485:Protein Binding; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry / Q000378:metabolism; D053838:Scattering, Small Angle; D000077157:Sorafenib; D014357:Trypsin / Q000737:chemistry / Q000378:metabolism; D014361:Trypsin Inhibitors / Q000737:chemistry / Q000378:metabolism; D014961:X-Ray Diffraction; D001618:beta-Lactamases / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D003102:Colloids; D004396:Coloring Agents; D005452:Fluoresceins; D010455:Peptides; D010671:Phenylurea Compounds; D011506:Proteins; D012269:Ribosomal Proteins; D014361:Trypsin Inhibitors; C029466:ribosomal protein L2; D000077267:Fulvestrant; D009536:Niacinamide; D003224:Congo Red; D004958:Estradiol; D004247:DNA; D000077157:Sorafenib; D014357:Trypsin; C048795:AmpC beta-lactamases; D001618:beta-Lactamases