Accounting for unintended binding events in the analysis of quartz crystal microbalance kinetic data.
Previous methods for analyzing protein-ligand binding events using the quartz crystal microbalance with dissipation monitoring (QCM-D) fail to account for unintended binding that inevitably occurs during surface measurements and obscure kinetic information. In this article, we present a system of differential equations that accounts for both reversible and irreversible unintended interactions. This model is tested on three protein-ligand systems, each of which has different features, to establish the feasibility of using the QCM-D for protein binding analysis. Based on this analysis, we were able to obtain kinetic information for the intended interaction that is consistent with those obtained in literature via bulk-phase methods. In the appendix, we include a method for decoupling these from the intended binding events and extracting relevant affinity information.
Chemistry Department, Pomona College, 645 North College Avenue, Claremont, CA 91711, United States.
Gabriella T
GT
Heller
Chemistry Department, Pomona College, 645 North College Avenue, Claremont, CA 91711, United States.
Theodore J
TJ
Zwang
Mathematics Department, Pomona College, 610 North College Avenue, Claremont, CA 91711, United States.
Elizabeth A
EA
Sarapata
Chemistry Department, Pomona College, 645 North College Avenue, Claremont, CA 91711, United States.
Michael A
MA
Haber
Chemistry Department, Pomona College, 645 North College Avenue, Claremont, CA 91711, United States.
Matthew H
MH
Sazinsky
Mathematics Department, Pomona College, 610 North College Avenue, Claremont, CA 91711, United States.
Ami E
AE
Radunskaya
Chemistry Department, Pomona College, 645 North College Avenue, Claremont, CA 91711, United States. Electronic address: malkiat.johal@pomona.edu.
Malkiat S
MS
Johal
D000818:Animals; D002110:Caffeine / Q000378:metabolism; D002417:Cattle; D005841:Gentisates / Q000378:metabolism; D006427:Hemin / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008024:Ligands; D054834:Lipocalins / Q000378:metabolism; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D011506:Proteins / Q000378:metabolism*; D058525:Quartz Crystal Microbalance Techniques; D012709:Serum Albumin / Q000378:metabolism; D012710:Serum Albumin, Bovine / Q000378:metabolism
D005841:Gentisates; D008024:Ligands; D054834:Lipocalins; D011506:Proteins; D012709:Serum Albumin; D012710:Serum Albumin, Bovine; D002110:Caffeine; D006427:Hemin; C010925:2,5-dihydroxybenzoic acid
Dissociation constant; Kinetics; Nonspecific interactions; QCM-D; Unintended interactions