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

International Journal of Molecular Sciences
Xing DuShu-Qun Liu

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/computat...Continue Reading

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Methods Mentioned

BETA
isothermal titration calorimetry
protein folding
NMR
X-ray
nuclear magnetic resonance
differential scanning calorimetry
chip
competition binding

Software Mentioned

ZDOCK
LUDI
FlexX
Glide
LIE
PBSA
GOLD
PB
MM
GBSA

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