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Related Concept Videos

Enzyme Inhibition01:30

Enzyme Inhibition

Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.
Enzymes02:34

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Structural features of the interfaces in enzyme-inhibitor complexes.

A N Nekrasov1, A A Zinchenko

  • 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences ul. Miklukho-Maklaya, 16/10, Moscow, 117997 Russia. alexei_nekrasov@mail.ru

Journal of Biomolecular Structure & Dynamics
|May 19, 2010
PubMed
Summary

Protein-protein interactions are vital for life. Informational structure analysis reveals three site types (ADD+, NORMAL, ADD-) in enzyme-inhibitor complexes, with ADD- sites crucial for adaptive binding.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Structural Biology

Background:

  • Specific protein-protein interactions are fundamental to biological processes.
  • Computational methods are increasingly used to study these interactions and binding sites.
  • Understanding enzyme-inhibitor complexes is key to drug discovery and biological mechanism elucidation.

Purpose of the Study:

  • To investigate protein-protein interaction interfaces in enzyme-inhibitor complexes using the informational structure analysis method.
  • To identify and characterize different types of interaction sites based on informational structure.
  • To explore the role of adaptive conformational reorganization in protein-protein interactions.

Main Methods:

  • Application of the informational structure analysis method to amino acid sequences.
  • Analysis of enzyme-inhibitor complexes to identify interaction interface sites.
  • Classification of interaction sites into ADD+, NORMAL, and ADD- types based on informational structure properties.

Main Results:

  • The informational structure analysis method identified three distinct site types: ADD+, NORMAL, and ADD-.
  • These site types differ in the density of first-rank elements within their informational structure.
  • ADD+, NORMAL, and ADD- sites exhibit varying capacities for adaptive conformational reorganization.
  • In hydrolytic enzyme-inhibitor complexes, at least one interaction interface site was consistently of the ADD- type.

Conclusions:

  • ADD- sites possess enhanced capabilities for adaptive conformational changes.
  • This increased adaptability of ADD- sites facilitates effective protein-protein interactions, particularly in enzyme-inhibitor complexes.
  • The informational structure analysis provides a novel framework for understanding the dynamics of protein-protein binding interfaces.