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Anal Biochem. 2019 Jul 15;577:117-134. doi: 10.1016/j.ab.2019.02.031. Epub 2019 Mar 5.

AFFINImeter: A software to analyze molecular recognition processes from experimental data.

Author information

1
Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain. Electronic address: Angel.Pineiro@usc.es.
2
AFFINImeter Scientific & Development team, Software 4 Science Developments, S. L. Ed. Emprendia, Santiago de Compostela, A Coruña, 15782, Spain.
3
Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City, 04510, Mexico.
4
CIQ-UP, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, P-4169-007, Porto, Portugal.
5
Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain; Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50009, Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), 50009, Zaragoza, Spain; Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), 28029, Madrid, Spain; Fundacion ARAID, Government of Aragon, 50018, Zaragoza, Spain.
6
Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
7
IGBMC, Dept of Integrative Biology, Strasbourg University, F67404, Illkirch CEDEX, France.
8
CNRS, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, UPR 9002, F-67000, Strasbourg, France.
9
Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Física, Universidade de Santiago, 15782, Santiago, Spain.
10
Fundación Pública Galega Centro Tecnolóxico de Supercomputación de Galicia (CESGA), Avda. de Vigo s/n, 15705, Santiago de Compostela, Spain.

Abstract

The comprehension of molecular recognition phenomena demands the understanding of the energetic and kinetic processes involved. General equations valid for the thermodynamic analysis of any observable that is assessed as a function of the concentration of the involved compounds are described, together with their implementation in the AFFINImeter software. Here, a maximum of three different molecular species that can interact with each other to form an enormous variety of supramolecular complexes are considered. The corrections currently employed to take into account the effects of dilution, volume displacement, concentration errors and those due to external factors, especially in the case of ITC measurements, are included. The methods used to fit the model parameters to the experimental data, and to generate the uncertainties are described in detail. A simulation tool and the so called kinITC analysis to get kinetic information from calorimetric experiments are also presented. An example of how to take advantage of the AFFINImeter software for the global multi-temperature analysis of a system exhibiting cooperative 1:2 interactions is presented and the results are compared with data previously published. Some useful recommendations for the analysis of experiments aimed at studying molecular interactions are provided.

KEYWORDS:

Affinity; Analysis software; Isothermal titration calorimetry; Kinetics; Molecular recognition; Thermodynamics

PMID:
30849378
DOI:
10.1016/j.ab.2019.02.031

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