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The effect of receptor site nonuniformity on the measurement of rate constants

David A. Edwards, Sumanth Swaminathan
2005 Applied Mathematics Letters  
The BIAcore is an instrument for measuring rate constants in real time by using a surface-volume geometry.  ...  This work accounts for such nonuniformities and establishes that in the limit of small Damköhler number, such effects are negligible due to the averaging characteristics of the instrumentation.  ...  Acknowledgment This work was supported by the National Institute of General Medical Sciences Grant 1R01GM067244-01.  ... 
doi:10.1016/j.aml.2004.10.007 fatcat:xf27yl6ls5ghvhjbuwueb63moy

Organism-Scale Modeling of Early Drosophila Patterning via Bone Morphogenetic Proteins

David M. Umulis, Osamu Shimmi, Michael B. O'Connor, Hans G. Othmer
2010 Developmental Cell  
We found that a model based on positive feedback of a secreted BMP-binding protein, coupled with the experimentally measured embryo geometry, provides the best agreement with population mean image data  ...  To maximize the utility of this information for the study of developmental processes, a new generation of mathematical models is needed for discovery and hypothesis testing.  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge the Rosen Center for Advanced Computing at Purdue University, the Minnesota Supercomputing Institute, National  ... 
doi:10.1016/j.devcel.2010.01.006 pmid:20159596 pmcid:PMC2848394 fatcat:paobd6kshjfopk5b5zpd67gtiy

Correlating the Kinetics of Cytokine-Induced E-Selectin Adhesion and Expression on Endothelial Cells

J. Dora Levin, H. Ping Ting-Beall, Robert M. Hochmuth
2001 Biophysical Journal  
Leukocyte capture depends on specialized characteristics of these receptors, particularly the binding kinetics.  ...  Endothelial cells normally recruit leukocytes to inflamed tissue using cytokine-induced adhesion receptors on the surfaces of interacting cells.  ...  This work was supported by grant RO1-HL23728 from the National Institutes of Health.  ... 
doi:10.1016/s0006-3495(01)76046-8 pmid:11159434 pmcid:PMC1301265 fatcat:52u6gnufkfc6flp4mrems6jqm4

Effects of pituitary adenylate cyclase-activating polypeptide on canine atrial electrophysiology

Masamichi Hirose, Zeng Leatmanoratn, Kenneth R. Laurita, Mark D. Carlson
2001 American Journal of Physiology. Heart and Circulatory Physiology  
Effects of pituitary adenylate cyclase-activating polypeptide on canine atrial electrophysiology. Am J Physiol Heart Circ Physiol 281: H1667-H1674, 2001.  ...  We measured effective refractory period (ERP) and conduction velocity at four atrial sites [high right atrium (HRA), low right atrium (LRA), high left atrium (HLA), and low left atrium (LLA)] and minimum  ...  The authors thank Matthew E. Joseph for skilled technical assistance and Dr. Matthew N. Levy for editorial assistance.  ... 
doi:10.1152/ajpheart.2001.281.4.h1667 pmid:11557557 fatcat:sb5tyzqlhfb7rnncrebdcscqr4

Page 2396 of The Journal of Neuroscience Vol. 10, Issue 7 [page]

1990 The Journal of Neuroscience  
Our analysis of NMDA receptor dose-response curves, using a 2-site model with independent binding, did not include cal- culation of the influence of 8 and a, the rate constants for channel opening and  ...  is negligible for NMDA receptors, but of considerable importance in the study of the peak response to quisqualate-like agonists; (2) a lack of information concerning rate constants for channel opening  ... 

Chemomechanical mapping of ligand-receptor binding kinetics on cells

S. Lee, J. Mandic, K. J. Van Vliet
2007 Proceedings of the National Academy of Sciences of the United States of America  
We quantify the number, distribution, and association/ dissociation rate constants of vascular endothelial growth factor receptor-2 with respect to a monoclonal antibody on both living and fixed human  ...  Modeling and prediction of receptor-mediated cell functions are facilitated by measurement of the binding properties on whole cells, ideally indicating the subcellular locations or cytoskeletal associations  ...  (C and D) Representative profiles at Ͼ400 nonrecognition sites on the cell surface indicate a nonspecific rupture force level of 13 pN. Effective loading rate: 11.7 nN/sec.  ... 
doi:10.1073/pnas.0702668104 pmid:17535923 pmcid:PMC1887608 fatcat:rvoa73mlyrcdtfuzushz7gordq

On spatial periodicity in the formation of cell adhesions to a substrate

Lee A. Segel, Talila Volk, Benjamin Geiger
1983 Cell Biophysics  
A theoretical explanation of the onset of patchiness is given, based on the positively cooperative binding to the substrate of laterally diffusing receptor molecules.  ...  Interference reflection microscopy reveals a fairly regular array of marginal focal contacts in early states of cell spreading.  ...  Locally, formation of complex C restricts membrane motion and enhances further net binding. Fig. 3 . 3 Dependence of "on" rate constant kl and "off" rate constant k I on complex concentration C.  ... 
doi:10.1007/bf02796136 pmid:6197178 fatcat:pet5dr6vgzbzvpeaex7t5becxy

Refining the measurement of rate constants in the BIAcore

David A. Edwards
2004 Journal of Mathematical Biology  
Several models of differing complexity are discussed, including the effective rate constant (ERC) approach.  ...  When estimating rate constants using the BIAcore surface plasmon resonance (SPR) biosensor, one must have an accurate mathematical model to interpret sensogram data.  ...  The author wishes to thank Seth Jackson for contributing numerical code used as a building block for the analysis in section 3. The author wishes to thank Dr.  ... 
doi:10.1007/s00285-004-0270-x pmid:15293014 fatcat:mbkulsdz2fgldds7ba7pdjzv2u

Calcium waves in a model with a random spatially discrete distribution of Ca2+ release sites

A.E. Bugrim, A.M. Zhabotinsky, I.R. Epstein
1997 Biophysical Journal  
We study the propagation of intracellular calcium waves in a model that features Ca2+ release from discrete sites in the endoplasmic reticulum membrane and random spatial distribution of these sites.  ...  The results of our simulations qualitatively reproduce the experimentally observed behavior of the waves.  ...  The more realistic De Young-Keizer scheme allows parallel binding and dissociation at all sites of 'P3R, with rate constants being dependent on the state of the receptor (De Young and Keizer, 1992) .  ... 
doi:10.1016/s0006-3495(97)78318-8 pmid:9414204 pmcid:PMC1181195 fatcat:ajrf3ttebrgshc5zjp5ylfxq5m

Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency

Cihan Kaya, Mary H. Cheng, Ethan R. Block, Tom M. Bartol, Terrence J. Sejnowski, Alexander Sorkin, James R. Faeder, Ivet Bahar
2018 eNeuro  
Simulations show large temporal and spatial variations in the local density of dopamine depending on the morphology of the synaptic/ extrasynaptic region near dopamine release site and on firing pattern  ...  Comparison of the effect of different firing patterns showed that phasic firing would increase the probability of reaching local DA levels sufficiently high to activate low-affinity DA receptors, mainly  ...  This work was supported by the National Institutes of Health awards P41GM103712 and P30DA035778 (IB) and R01DA014204 (AS) and National Science Foundation award number ACI-1548562 (Pittsburgh Supercomputing  ... 
doi:10.1523/eneuro.0298-17.2017 pmid:29430519 pmcid:PMC5804147 fatcat:fjxjeocpzrhwfplkzo3ic5zufy

Lateral motion of fluorescently labeled acetylcholine receptors in membranes of developing muscle fibers

D. Axelrod, P. Ravdin, D. E. Koppel, J. Schlessinger, W. W. Webb, E. L. Elson, T. R. Podleski
1976 Proceedings of the National Academy of Sciences of the United States of America  
We have made direct, quantitative measurements of the lateral motion and age-dependent distribution of acetylcholine receptors (AChR) on the surface of rat myotubes in primary culture.  ...  The relevance of these results to an understanding of the membrane dynamics and localization of muscle AChR is discussed.  ...  We are pleased to acknowledge the support of NIH Grants GM-21661 (W.W.W. and E.L.E.) and NS-10638 (T.R.P.), the NSF Division of Condensed Matter no.  ... 
doi:10.1073/pnas.73.12.4594 pmid:1070010 pmcid:PMC431558 fatcat:6jiwoawhwnamzphy4bgtd5hicy

GABAB-Mediated Presynaptic Inhibition of Excitatory Transmission and Synaptic Vesicle Dynamics in Cultured Hippocampal Neurons

Jeffry S. Isaacson, Bertil Hille
1997 Neuron  
In this study, we have examined the actions GABA B receptors do not alter the rate or extent of of the GABA B receptor agonist, baclofen, on exo-and endocytosis. endocytosis in hippocampal neurons grown  ...  To what extent are the dynamics of portant effect on transmitter release at a step downvesicle recycling subject to modulation? We examined stream of calcium influx.  ...  We studied the initial rates of FM1-43 destaining at individual release sites as a measure of the rate of release of synaptic vesicles to determine more directly the range of Pr from sites arising from  ... 
doi:10.1016/s0896-6273(01)80053-2 pmid:9010212 fatcat:vb2m6dmn2nfkdimxyyqlkfqhsi

Steric hindrance effects on surface reactions: applications to BIAcore

David A. Edwards
2007 Journal of Mathematical Biology  
The BIAcore surface plasmon resonance (SPR) biosensor for measuring rate constants has such a geometry.  ...  Though several models of the BIAcore have been presented, few take into account that large ligand molecules can block multiple receptor sites, thus skewing the sensogram data.  ...  Effective rate constant solution Instead, we restate our results in the effective rate constant (ERC) context, which presents a simple ODE model for the actual sensogram dataB.  ... 
doi:10.1007/s00285-007-0093-7 pmid:17530254 fatcat:6bnvfzk62fdbnoegv7fbjgxirq

Social Ultrasonic Vocalization in Awake Head-Restrained Mouse

Benjamin Weiner, Stav Hertz, Nisim Perets, Michael London
2016 Frontiers in Behavioral Neuroscience  
By analyzing the vocalizations of NRMM, we established criteria to predict which individuals are likely to vocalize while head fixed based on the USV rate and average syllable duration.  ...  The USVs emitted by HRMM are similar to the USVs of NRMM in the presence of a female mouse in their spectral structure, inter-syllable interval distribution, and USV sequence length, and therefore are  ...  The effect of membrane nonuniformity on signal transfer in reconstructed dendritic trees and on the I/f relation of the neuron is also considered, and experimental methods for assessing membrane nonuniformity  ... 
doi:10.3389/fnbeh.2016.00236 pmid:28066202 pmcid:PMC5165246 fatcat:ko43equycrgezgtjofxibgk37q

Tonic inhibition sets the state of excitability in olfactory bulb granule cells

Christina Labarrera, Michael London, Kamilla Angelo
2013 Journal of Physiology  
By analyzing the vocalizations of NRMM, we established criteria to predict which individuals are likely to vocalize while head fixed based on the USV rate and average syllable duration.  ...  The USVs emitted by HRMM are similar to the USVs of NRMM in the presence of a female mouse in their spectral structure, inter-syllable interval distribution, and USV sequence length, and therefore are  ...  The effect of membrane nonuniformity on signal transfer in reconstructed dendritic trees and on the I/f relation of the neuron is also considered, and experimental methods for assessing membrane nonuniformity  ... 
doi:10.1113/jphysiol.2012.241851 pmid:23318869 fatcat:h3pxvv5x6feibjq4bzfswk6njy
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