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Int. J. Mol. Sci. 2016, 17(2), 144; doi:10.3390/ijms17020144

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

1,†
,
1,†
,
1
,
1,2
,
1
,
1,3
,
1,4
and
1,4,*
1
Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
2
Department of Applied Mathematics, Yunnan Agricultural University, Kunming 650201, China
3
Laboratory of Molecular Cardiology, Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
4
Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Tatyana Karabencheva-Christova
Received: 9 November 2015 / Revised: 13 January 2016 / Accepted: 18 January 2016 / Published: 26 January 2016
(This article belongs to the Collection Proteins and Protein-Ligand Interactions)
View Full-Text   |   Download PDF [891 KB, uploaded 26 January 2016]   |  

Abstract

Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed. View Full-Text
Keywords: binding mechanisms; thermodynamics; kinetics; binding driving forces; isothermal titration calorimetry (ITC); surface plasmon resonance (SPR); fluorescence polarization (FP); docking; free energy calculations binding mechanisms; thermodynamics; kinetics; binding driving forces; isothermal titration calorimetry (ITC); surface plasmon resonance (SPR); fluorescence polarization (FP); docking; free energy calculations
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Du, X.; Li, Y.; Xia, Y.-L.; Ai, S.-M.; Liang, J.; Sang, P.; Ji, X.-L.; Liu, S.-Q. Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods. Int. J. Mol. Sci. 2016, 17, 144.

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